P2RP: a Web-based framework for the identification and analysis of regulatory proteins in prokaryotic genomes.

PubMed

Barakat, Mohamed; Ortet, Philippe; Whitworth, David E

2013-04-20

Regulatory proteins (RPs) such as transcription factors (TFs) and two-component system (TCS) proteins control how prokaryotic cells respond to changes in their external and/or internal state. Identification and annotation of TFs and TCSs is non-trivial, and between-genome comparisons are often confounded by different standards in annotation. There is a need for user-friendly, fast and convenient tools to allow researchers to overcome the inherent variability in annotation between genome sequences. We have developed the web-server P2RP (Predicted Prokaryotic Regulatory Proteins), which enables users to identify and annotate TFs and TCS proteins within their sequences of interest. Users can input amino acid or genomic DNA sequences, and predicted proteins therein are scanned for the possession of DNA-binding domains and/or TCS domains. RPs identified in this manner are categorised into families, unambiguously annotated, and a detailed description of their features generated, using an integrated software pipeline. P2RP results can then be outputted in user-specified formats. Biologists have an increasing need for fast and intuitively usable tools, which is why P2RP has been developed as an interactive system. As well as assisting experimental biologists to interrogate novel sequence data, it is hoped that P2RP will be built into genome annotation pipelines and re-annotation processes, to increase the consistency of RP annotation in public genomic sequences. P2RP is the first publicly available tool for predicting and analysing RP proteins in users' sequences. The server is freely available and can be accessed along with documentation at http://www.p2rp.org.

Initiation of arcing on tungsten surface exposed to steady state He plasmas

NASA Astrophysics Data System (ADS)

Kajita, Shin; Noiri, Yasuyuki; Ohno, Noriyasu

2015-09-01

Arcing was initiated in steady state helium plasmas by negatively biasing a tungsten electrode to around -500 V. On the tungsten electrode, nanostructures were grown by the plasma irradiation. In this study, we characterized the property of the initiated arcing by measuring the temporal evolutions of the electrode potential and the arc current. The ignition frequency and duration of arcing were presented from the potential measurements; the arc duration was in the range of <10 ms and the distribution altered when changing the biasing voltage. The behavior of arc spots was observed with a fast framing camera. It was shown that the spots split frequently, and sometimes, they run on the surface independently. From the fluctuation of the arc current, the fractal feature of arcing was revealed.

PANNZER2: a rapid functional annotation web server.

PubMed

Törönen, Petri; Medlar, Alan; Holm, Liisa

2018-05-08

The unprecedented growth of high-throughput sequencing has led to an ever-widening annotation gap in protein databases. While computational prediction methods are available to make up the shortfall, a majority of public web servers are hindered by practical limitations and poor performance. Here, we introduce PANNZER2 (Protein ANNotation with Z-scoRE), a fast functional annotation web server that provides both Gene Ontology (GO) annotations and free text description predictions. PANNZER2 uses SANSparallel to perform high-performance homology searches, making bulk annotation based on sequence similarity practical. PANNZER2 can output GO annotations from multiple scoring functions, enabling users to see which predictions are robust across predictors. Finally, PANNZER2 predictions scored within the top 10 methods for molecular function and biological process in the CAFA2 NK-full benchmark. The PANNZER2 web server is updated on a monthly schedule and is accessible at http://ekhidna2.biocenter.helsinki.fi/sanspanz/. The source code is available under the GNU Public Licence v3.

Mitochondrial-related proteomic changes during obesity and fasting in mice are greater in the liver than skeletal muscles.

PubMed

Nesteruk, Monika; Hennig, Ewa E; Mikula, Michal; Karczmarski, Jakub; Dzwonek, Artur; Goryca, Krzysztof; Rubel, Tymon; Paziewska, Agnieszka; Woszczynski, Marek; Ledwon, Joanna; Dabrowska, Michalina; Dadlez, Michal; Ostrowski, Jerzy

2014-03-01

Although mitochondrial dysfunction is implicated in the pathogenesis of obesity, the molecular mechanisms underlying obesity-related metabolic abnormalities are not well established. We performed mitochondrial quantitative proteomic and whole transcriptome analysis followed by functional annotations within liver and skeletal muscles, using fasted and non-fasted 16- and 48-week-old high-fat diet (HFD)-fed and normal diet-fed (control group) wild-type C56BL/6J mice, and hyperphagic ob/ob and db/db obese mice. Our study identified 1,675 and 704 mitochondria-associated proteins with at least two peptides in liver and muscle, respectively. Of these, 221 liver and 44 muscle proteins were differentially expressed (adjusted p values ≤ 0.05) between control and all obese mice, while overnight fasting altered expression of 107 liver and 35 muscle proteins. In the liver, we distinguished a network of 27 proteins exhibiting opposite direction of expression changes in HFD-fed and hyperphagic mice when compared to control. The network centered on cytochromes P450 3a11 (Cyp3a11) and 4a14 (Cyp4a14), and fructose-bisphosphate aldolase B (Aldob) proteins which bridged proteins cluster involved in Metabolism of xenobiotics with proteins engaged in Fatty acid metabolism and PPAR signaling pathways. Functional annotations revealed that most of the hepatic molecular alterations, which characterized both obesity and fasting, related to different aspects of energy metabolism (such as Fatty acid metabolism, Peroxisome, and PPAR signaling); however, only a limited number of functional annotations could be selected from skeletal muscle data sets. Thus, our comprehensive molecular overview revealed that both obesity and fasting states induce more pronounced mitochondrial proteome changes in the liver than in the muscles.

Vacuum Deposition From A Welding Torch

NASA Technical Reports Server (NTRS)

Poorman, R. M.

1993-01-01

Process derived from arc welding produces films of high quality. Modified gas/tungsten-arc welding process developed for use in outer space. Welding apparatus in process includes hollow tungsten electrode through which inert gas flows so arc struck between electrode and workpiece in vacuum of space. Offers advantages of fast deposition, possibility of applying directional impetus to flow of materials, very low pressure at surface being coated, and inert environment.

Automated Update, Revision, and Quality Control of the Maize Genome Annotations Using MAKER-P Improves the B73 RefGen_v3 Gene Models and Identifies New Genes1[OPEN

PubMed Central

Law, MeiYee; Childs, Kevin L.; Campbell, Michael S.; Stein, Joshua C.; Olson, Andrew J.; Holt, Carson; Panchy, Nicholas; Lei, Jikai; Jiao, Dian; Andorf, Carson M.; Lawrence, Carolyn J.; Ware, Doreen; Shiu, Shin-Han; Sun, Yanni; Jiang, Ning; Yandell, Mark

2015-01-01

The large size and relative complexity of many plant genomes make creation, quality control, and dissemination of high-quality gene structure annotations challenging. In response, we have developed MAKER-P, a fast and easy-to-use genome annotation engine for plants. Here, we report the use of MAKER-P to update and revise the maize (Zea mays) B73 RefGen_v3 annotation build (5b+) in less than 3 h using the iPlant Cyberinfrastructure. MAKER-P identified and annotated 4,466 additional, well-supported protein-coding genes not present in the 5b+ annotation build, added additional untranslated regions to 1,393 5b+ gene models, identified 2,647 5b+ gene models that lack any supporting evidence (despite the use of large and diverse evidence data sets), identified 104,215 pseudogene fragments, and created an additional 2,522 noncoding gene annotations. We also describe a method for de novo training of MAKER-P for the annotation of newly sequenced grass genomes. Collectively, these results lead to the 6a maize genome annotation and demonstrate the utility of MAKER-P for rapid annotation, management, and quality control of grasses and other difficult-to-annotate plant genomes. PMID:25384563

Volumetric modulated arc therapy of head-and-neck cancer on a fast-rotating O-ring linac: Plan quality and delivery time comparison with a C-arm linac.

PubMed

Michiels, Steven; Poels, Kenneth; Crijns, Wouter; Delombaerde, Laurence; De Roover, Robin; Vanstraelen, Bianca; Haustermans, Karin; Nuyts, Sandra; Depuydt, Tom

2018-05-05

Linac improvements in gantry speed, leaf speed and dose rate may increase the time-efficiency of volumetric modulated arc therapy (VMAT) delivery. The plan quality achievable with faster VMAT however remains to be investigated. In this study, a fast-rotating O-ring linac with fast-moving leaves is compared with a C-arm linac in terms of plan quality and delivery time for VMAT of head-and-neck cancer (HNC). For 30 patients with HNC, treatment planning was performed using dual-arc (HA2) and triple-arc (HA3) VMAT on a Halcyon fast-rotating O-ring linac and using dual-arc VMAT on a TrueBeam C-arm linac (TB2). Target coverage metrics and complication probabilities were compared. Plan delivery was verified using 3%/3 mm gamma-index analysis of helical diode array measurements. Volumetric image acquisition and plan delivery times were compared. All studied VMAT-techniques fulfilled the target coverage objectives. D 2% to the boost volume was higher for HA2 (median 103.7%, 1st-3rd quartile [103.5%;104.0%]) and HA3 (103.2% [103.0%;103.7%)] than for TB2 (102.6% [102.3%;103.0%)], resulting in an increased boost target dose heterogeneity for HA2 and HA3. Complication probabilities were comparable between HA2 and TB2, while HA3 showed a xerostomia probability reduction (0.8% [0.2%;1.8%]) and dysphagia probability reduction (1.0% [0.2%;1.8%]) compared with TB2. Gamma-index agreement scores were never below 93.0% for HA2, HA3 and TB2. Volumetric imaging and plan delivery time was shorter for HA2 (1 m 24 s ± 1 s) and HA3 (1 m 54 s ± 1 s) than for TB2 (2 m 47 s ± 1 s). For VMAT of HNC, the fast-rotating O-ring linac at least maintains the plan quality of two arcs on a C-arm linac while reducing the image acquisition and plan delivery time. Copyright © 2018 Elsevier B.V. All rights reserved.

Forearc structure in the Lesser Antilles inferred from depth to the Curie temperature and thermo-mechanical simulations

NASA Astrophysics Data System (ADS)

Gailler, Lydie; Arcay, Diane; Münch, Philippe; Martelet, Guillaume; Thinon, Isabelle; Lebrun, Jean-Frédéric

2017-06-01

Imaging deep active volcanic areas remains a challenge in our understanding of their activity and evolution, especially in subduction zones. Study of magnetic anomalies is appropriate to access such dynamics in depth. The magnetic anomaly pattern of the Lesser Antilles Arc (LAA) subduction is studied through Curie Point Depth (CPD), interpreted as the depth of the 580 °C isotherm, and developed to better assess the deep thermal structure of the arc. The depth of the estimated CPD exhibits a complex topography. Keeping in mind the overall uncertainty associated with this method, a main doming is evidenced below the Guadeloupe archipelago. Its apex is shifted towards the ancient arc, suggesting a very hot state of the fore-arc/arc domain. To better understand the LAA thermal state, we perform 2D thermo-mechanical simulations of the subduction zone. Recalling that magnetite is a serpentinization by-product, we simulate water transfer triggered by slab dehydration to test the assumption of fore-arc serpentinization suggested by the positive magnetic anomaly in the vicinity of the Guadeloupe archipelago. In this area, the subduction-induced arc lithosphere hydration and related weakening trigger a fast heating of the upper plate by basal convective removal. This process of fast arc lithosphere thinning may apply where simultaneously the volcanic arc is split in two and normal convergence is high enough. As serpentinization strongly decreases P-wave velocity, we propose a new interpretation of a published seismic profile below Guadeloupe. The seismic layer previously interpreted as the arc lower crust may rather be a layer of serpentinized mantle, as supported by spatial correlations between gravimetric and magnetic anomalies. Consequently, at the scale of Guadeloupe Island, the fore-arc Moho would be shallower than initially assumed, with a dome shape more consistent with both the extensive deformation active since the Oligocene in the inner fore-arc and the CPD doming.

BEACON: automated tool for Bacterial GEnome Annotation ComparisON.

PubMed

Kalkatawi, Manal; Alam, Intikhab; Bajic, Vladimir B

2015-08-18

Genome annotation is one way of summarizing the existing knowledge about genomic characteristics of an organism. There has been an increased interest during the last several decades in computer-based structural and functional genome annotation. Many methods for this purpose have been developed for eukaryotes and prokaryotes. Our study focuses on comparison of functional annotations of prokaryotic genomes. To the best of our knowledge there is no fully automated system for detailed comparison of functional genome annotations generated by different annotation methods (AMs). The presence of many AMs and development of new ones introduce needs to: a/ compare different annotations for a single genome, and b/ generate annotation by combining individual ones. To address these issues we developed an Automated Tool for Bacterial GEnome Annotation ComparisON (BEACON) that benefits both AM developers and annotation analysers. BEACON provides detailed comparison of gene function annotations of prokaryotic genomes obtained by different AMs and generates extended annotations through combination of individual ones. For the illustration of BEACON's utility, we provide a comparison analysis of multiple different annotations generated for four genomes and show on these examples that the extended annotation can increase the number of genes annotated by putative functions up to 27%, while the number of genes without any function assignment is reduced. We developed BEACON, a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/ .

FAST: FAST Analysis of Sequences Toolbox

PubMed Central

Lawrence, Travis J.; Kauffman, Kyle T.; Amrine, Katherine C. H.; Carper, Dana L.; Lee, Raymond S.; Becich, Peter J.; Canales, Claudia J.; Ardell, David H.

2015-01-01

FAST (FAST Analysis of Sequences Toolbox) provides simple, powerful open source command-line tools to filter, transform, annotate and analyze biological sequence data. Modeled after the GNU (GNU's Not Unix) Textutils such as grep, cut, and tr, FAST tools such as fasgrep, fascut, and fastr make it easy to rapidly prototype expressive bioinformatic workflows in a compact and generic command vocabulary. Compact combinatorial encoding of data workflows with FAST commands can simplify the documentation and reproducibility of bioinformatic protocols, supporting better transparency in biological data science. Interface self-consistency and conformity with conventions of GNU, Matlab, Perl, BioPerl, R, and GenBank help make FAST easy and rewarding to learn. FAST automates numerical, taxonomic, and text-based sorting, selection and transformation of sequence records and alignment sites based on content, index ranges, descriptive tags, annotated features, and in-line calculated analytics, including composition and codon usage. Automated content- and feature-based extraction of sites and support for molecular population genetic statistics make FAST useful for molecular evolutionary analysis. FAST is portable, easy to install and secure thanks to the relative maturity of its Perl and BioPerl foundations, with stable releases posted to CPAN. Development as well as a publicly accessible Cookbook and Wiki are available on the FAST GitHub repository at https://github.com/tlawrence3/FAST. The default data exchange format in FAST is Multi-FastA (specifically, a restriction of BioPerl FastA format). Sanger and Illumina 1.8+ FastQ formatted files are also supported. FAST makes it easier for non-programmer biologists to interactively investigate and control biological data at the speed of thought. PMID:26042145

Effect of Cut Quality on Hybrid Laser Arc Welding of Thick Section Steels

NASA Astrophysics Data System (ADS)

Farrokhi, F.; Nielsen, S. E.; Schmidt, R. H.; Pedersen, S. S.; Kristiansen, M.

From an industrial point of view, in a laser cutting-welding production chain, it is of great importance to know the influence of the attainable laser cut quality on the subsequent hybrid laser arc welding process. Many studies have been carried out in the literature to obtain lower surface roughness values on the laser cut edge. However, in practice, the cost and reliability of the cutting process is crucial and it does not always comply with obtaining the highest surface quality. In this study, a number of experiments on 25 mm steel plates were carried out to evaluate the influence of cut surface quality on the final quality of the subsequent hybrid laser welded joints. The different cut surfaces were obtained by different industrial cutting methods including laser cutting, abrasive water cutting, plasma cutting, and milling. It was found that the mentioned cutting methods could be used as preparation processes for the subsequent hybrid laser arc welding. However, cut quality could determine the choice of process parameters of the following hybrid laser arc welding.

Expression of the Arginine Deiminase Pathway Genes in Lactobacillus sakei Is Strain Dependent and Is Affected by the Environmental pH

PubMed Central

Rimaux, T.; Rivière, A.; Illeghems, K.; Weckx, S.; De Vuyst, L.

2012-01-01

The adaptation of Lactobacillus sakei to a meat environment is reflected in its metabolic potential. For instance, the ability to utilize arginine through the arginine deiminase (ADI) pathway, resulting in additional ATP, represents a competitive benefit. In L. sakei CTC 494, the arc operon (arcABCTDR) shows the same gene order and organization as that in L. sakei 23K, the genome sequence of which is known. However, differences in relative gene expression were found, and these seemed to be optimal in different growth phases, namely, the highest relative gene expression level was in the end exponential growth phase in the case of L. sakei CTC 494 and in the mid-exponential growth phase of L. sakei 23K. Also, the environmental pH influenced the relative expression level of the arc operon, as shown for L. sakei CTC 494, with the highest relative expression level occurring at the optimal pH for growth (pH 6.0). Deviations from this optimal pH (pH 5.0 and pH 7.0) resulted in an overall decline of the relative expression level of all genes of the arc operon. Furthermore, a differential relative expression of the individual genes of the arc operon was found, with the highest relative gene expression occurring for the first two genes of the arc operon (arcA and arcB). Finally, it was shown that some L. sakei strains were able to convert agmatine into putrescine, suggesting an operational agmatine deiminase pathway in these strains, a metabolic trait that is undesirable in meat fermentations. This study shows that this metabolic trait is most probably encoded by a previously erroneously annotated second putative arc operon. PMID:22544250

Assisted annotation of medical free text using RapTAT

PubMed Central

Gobbel, Glenn T; Garvin, Jennifer; Reeves, Ruth; Cronin, Robert M; Heavirland, Julia; Williams, Jenifer; Weaver, Allison; Jayaramaraja, Shrimalini; Giuse, Dario; Speroff, Theodore; Brown, Steven H; Xu, Hua; Matheny, Michael E

2014-01-01

Objective To determine whether assisted annotation using interactive training can reduce the time required to annotate a clinical document corpus without introducing bias. Materials and methods A tool, RapTAT, was designed to assist annotation by iteratively pre-annotating probable phrases of interest within a document, presenting the annotations to a reviewer for correction, and then using the corrected annotations for further machine learning-based training before pre-annotating subsequent documents. Annotators reviewed 404 clinical notes either manually or using RapTAT assistance for concepts related to quality of care during heart failure treatment. Notes were divided into 20 batches of 19–21 documents for iterative annotation and training. Results The number of correct RapTAT pre-annotations increased significantly and annotation time per batch decreased by ∼50% over the course of annotation. Annotation rate increased from batch to batch for assisted but not manual reviewers. Pre-annotation F-measure increased from 0.5 to 0.6 to >0.80 (relative to both assisted reviewer and reference annotations) over the first three batches and more slowly thereafter. Overall inter-annotator agreement was significantly higher between RapTAT-assisted reviewers (0.89) than between manual reviewers (0.85). Discussion The tool reduced workload by decreasing the number of annotations needing to be added and helping reviewers to annotate at an increased rate. Agreement between the pre-annotations and reference standard, and agreement between the pre-annotations and assisted annotations, were similar throughout the annotation process, which suggests that pre-annotation did not introduce bias. Conclusions Pre-annotations generated by a tool capable of interactive training can reduce the time required to create an annotated document corpus by up to 50%. PMID:24431336

Fast gene ontology based clustering for microarray experiments.

PubMed

Ovaska, Kristian; Laakso, Marko; Hautaniemi, Sampsa

2008-11-21

Analysis of a microarray experiment often results in a list of hundreds of disease-associated genes. In order to suggest common biological processes and functions for these genes, Gene Ontology annotations with statistical testing are widely used. However, these analyses can produce a very large number of significantly altered biological processes. Thus, it is often challenging to interpret GO results and identify novel testable biological hypotheses. We present fast software for advanced gene annotation using semantic similarity for Gene Ontology terms combined with clustering and heat map visualisation. The methodology allows rapid identification of genes sharing the same Gene Ontology cluster. Our R based semantic similarity open-source package has a speed advantage of over 2000-fold compared to existing implementations. From the resulting hierarchical clustering dendrogram genes sharing a GO term can be identified, and their differences in the gene expression patterns can be seen from the heat map. These methods facilitate advanced annotation of genes resulting from data analysis.

Leptin-sensitive neurons in the arcuate nucleus integrate activity and temperature circadian rhythms and anticipatory responses to food restriction

PubMed Central

Li, Ai-Jun; Dinh, Thu T.; Jansen, Heiko T.; Ritter, Sue

2013-01-01

Previously, we investigated the role of neuropeptide Y and leptin-sensitive networks in the mediobasal hypothalamus in sleep and feeding and found profound homeostatic and circadian deficits with an intact suprachiasmatic nucleus. We propose that the arcuate nuclei (Arc) are required for the integration of homeostatic circadian systems, including temperature and activity. We tested this hypothesis using saporin toxin conjugated to leptin (Lep-SAP) injected into Arc in rats. Lep-SAP rats became obese and hyperphagic and progressed through a dynamic phase to a static phase of growth. Circadian rhythms were examined over 49 days during the static phase. Rats were maintained on a 12:12-h light-dark (LD) schedule for 13 days and, thereafter, maintained in continuous dark (DD). After the first 13 days of DD, food was restricted to 4 h/day for 10 days. We found that the activity of Lep-SAP rats was arrhythmic in DD, but that food anticipatory activity was, nevertheless, entrainable to the restricted feeding schedule, and the entrained rhythm persisted during the subsequent 3-day fast in DD. Thus, for activity, the circuitry for the light-entrainable oscillator, but not for the food-entrainable oscillator, was disabled by the Arc lesion. In contrast, temperature remained rhythmic in DD in the Lep-SAP rats and did not entrain to restricted feeding. We conclude that the leptin-sensitive network that includes the Arc is required for entrainment of activity by photic cues and entrainment of temperature by food, but is not required for entrainment of activity by food or temperature by photic cues. PMID:23986359

Automated update, revision, and quality control of the maize genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes.

PubMed

Law, MeiYee; Childs, Kevin L; Campbell, Michael S; Stein, Joshua C; Olson, Andrew J; Holt, Carson; Panchy, Nicholas; Lei, Jikai; Jiao, Dian; Andorf, Carson M; Lawrence, Carolyn J; Ware, Doreen; Shiu, Shin-Han; Sun, Yanni; Jiang, Ning; Yandell, Mark

2015-01-01

The large size and relative complexity of many plant genomes make creation, quality control, and dissemination of high-quality gene structure annotations challenging. In response, we have developed MAKER-P, a fast and easy-to-use genome annotation engine for plants. Here, we report the use of MAKER-P to update and revise the maize (Zea mays) B73 RefGen_v3 annotation build (5b+) in less than 3 h using the iPlant Cyberinfrastructure. MAKER-P identified and annotated 4,466 additional, well-supported protein-coding genes not present in the 5b+ annotation build, added additional untranslated regions to 1,393 5b+ gene models, identified 2,647 5b+ gene models that lack any supporting evidence (despite the use of large and diverse evidence data sets), identified 104,215 pseudogene fragments, and created an additional 2,522 noncoding gene annotations. We also describe a method for de novo training of MAKER-P for the annotation of newly sequenced grass genomes. Collectively, these results lead to the 6a maize genome annotation and demonstrate the utility of MAKER-P for rapid annotation, management, and quality control of grasses and other difficult-to-annotate plant genomes. © 2015 American Society of Plant Biologists. All Rights Reserved.

Final Technical Report - Use of Systems Biology Approaches to Develop Advanced Biofuel-Synthesizing Cyanobacterial Strains

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

Pakrasi, Himadri

The overall objective of this project was to use a systems biology approach to evaluate the potentials of a number of cyanobacterial strains for photobiological production of advanced biofuels and/or their chemical precursors. Cyanobacteria are oxygen evolving photosynthetic prokaryotes. Among them, certain unicellular species such as Cyanothece can also fix N 2, a process that is exquisitely sensitive to oxygen. To accommodate such incompatible processes in a single cell, Cyanothece produces oxygen during the day, and creates an O 2-limited intracellular environment during the night to perform O 2-sensitive processes such as N 2-fixation. Thus, Cyanothece cells are natural bioreactorsmore » for the storage of captured solar energy with subsequent utilization at a different time during a diurnal cycle. Our studies include the identification of a novel, fast-growing, mixotrophic, transformable cyanobacterium. This strain has been sequenced and will be made available to the community. In addition, we have developed genome-scale models for a family of cyanobacteria to assess their metabolic repertoire. Furthermore, we developed a method for rapid construction of metabolic models using multiple annotation sources and a metabolic model of a related organism. This method will allow rapid annotation and screening of potential phenotypes based on the newly available genome sequences of many organisms.« less

A Hybrid Ant Colony Optimization Algorithm for the Extended Capacitated Arc Routing Problem.

PubMed

Li-Ning Xing; Rohlfshagen, P; Ying-Wu Chen; Xin Yao

2011-08-01

The capacitated arc routing problem (CARP) is representative of numerous practical applications, and in order to widen its scope, we consider an extended version of this problem that entails both total service time and fixed investment costs. We subsequently propose a hybrid ant colony optimization (ACO) algorithm (HACOA) to solve instances of the extended CARP. This approach is characterized by the exploitation of heuristic information, adaptive parameters, and local optimization techniques: Two kinds of heuristic information, arc cluster information and arc priority information, are obtained continuously from the solutions sampled to guide the subsequent optimization process. The adaptive parameters ease the burden of choosing initial values and facilitate improved and more robust results. Finally, local optimization, based on the two-opt heuristic, is employed to improve the overall performance of the proposed algorithm. The resulting HACOA is tested on four sets of benchmark problems containing a total of 87 instances with up to 140 nodes and 380 arcs. In order to evaluate the effectiveness of the proposed method, some existing capacitated arc routing heuristics are extended to cope with the extended version of this problem; the experimental results indicate that the proposed ACO method outperforms these heuristics.

USI: a fast and accurate approach for conceptual document annotation.

PubMed

Fiorini, Nicolas; Ranwez, Sylvie; Montmain, Jacky; Ranwez, Vincent

2015-03-14

Semantic approaches such as concept-based information retrieval rely on a corpus in which resources are indexed by concepts belonging to a domain ontology. In order to keep such applications up-to-date, new entities need to be frequently annotated to enrich the corpus. However, this task is time-consuming and requires a high-level of expertise in both the domain and the related ontology. Different strategies have thus been proposed to ease this indexing process, each one taking advantage from the features of the document. In this paper we present USI (User-oriented Semantic Indexer), a fast and intuitive method for indexing tasks. We introduce a solution to suggest a conceptual annotation for new entities based on related already indexed documents. Our results, compared to those obtained by previous authors using the MeSH thesaurus and a dataset of biomedical papers, show that the method surpasses text-specific methods in terms of both quality and speed. Evaluations are done via usual metrics and semantic similarity. By only relying on neighbor documents, the User-oriented Semantic Indexer does not need a representative learning set. Yet, it provides better results than the other approaches by giving a consistent annotation scored with a global criterion - instead of one score per concept.

Implementation of a long leg X-point target divertor in the ARC fusion pilot plant

NASA Astrophysics Data System (ADS)

Kuang, A. Q.; Cao, N. M.; Creely, A. J.; Dennett, C. A.; Hecla, J.; Hoffman, H.; Major, M.; Ruiz Ruiz, J.; Tinguely, R. A.; Tolman, E. A.; Brunner, D.; Labombard, B.; Sorbom, B. N.; Whyte, D. G.; Grover, P.; Laughman, C.

2017-10-01

A long leg X-point target divertor geometry in a double null geometry has been implemented in the ARC pilot plant design, exploiting ARC's demountable toroidal field (TF) coils and FLiBe immersion blanket, which allow superconducting poloidal field coils to be located inside the TF coils, adequately shielded from neutrons. This new design maintains the original TF coil size, core plasma shape, and attains a tritium breedin ratio 1.08. The long leg divertor geometry provides significant advantages. Neutron transport computations indicate a factor of 10 reduction in divertor material neutron damage rate compared to the first wall, easing requirements for high heat flux components. Simulations have shown that long legged divertors are able to maintain a passively stable detachment front that stays in the divertor leg over a wide power window, in principle, responding immediately to fast changes in power exhaust. The ARC design exploits this new paradigm for divertor heat flux control: fewer concerns about coping with fast transients and a focus on neutron-tolerant diagnostics to measure and adjust detachment front locations in the outer divertor legs over long timescales.

Activation of anorexigenic pro-opiomelanocortin neurones during refeeding is independent of vagal and brainstem inputs.

PubMed

Fekete, C; Zséli, G; Singru, P S; Kádár, A; Wittmann, G; Füzesi, T; El-Bermani, W; Lechan, R M

2012-11-01

After fasting, satiety is observed within 2 h after reintroducing food, accompanied by activation of anorexigenic, pro-opiomelanocortin (POMC)-synthesising neurones in the arcuate nucleus (ARC), indicative of the critical role that α-melanocyte-stimulating hormone has in the regulation of meal size during refeeding. To determine whether refeeding-induced activation of POMC neurones in the arcuate is dependent upon the vagus nerve and/or ascending brainstem pathways, bilateral subdiaphragmatic vagotomy or transection of the afferent brainstem input to one side of the ARC was performed. One day after vagotomy or 2 weeks after brain surgery, animals were fasted and then refed for 2 h. Sections containing the ARC from vagotomised animals or animals with effective transection were immunostained for c-Fos and POMC to detect refeeding-induced activation of POMC neurones. Quantitative analyses of double-labelled preparations demonstrated that sham-operated and vagotomised animals markedly increased the number of c-Fos-immunoreactive (-IR) POMC neurones with refeeding. Furthermore, transection of the ascending brainstem pathway had no effect on diminishing c-Fos-immunoreactivity in POMC neurones on either side of the ARC, although it did diminish activation in a separate, subpopulation of neurones in the dorsomedial posterior ARC (dmpARC) on the transected side. We conclude that inputs mediated via the vagus nerve and/or arising from the brainstem do not have a primary role in refeeding-induced activation of POMC neurones in the ARC, and propose that these neurones may be activated solely by direct effects of circulating hormones/metabolites during refeeding. Activation of the dmpARC by refeeding indicates a previously unrecognised role for these neurones in appetite regulation in the rat. © 2012 The Authors. Journal of Neuroendocrinology © 2012 British Society for Neuroendocrinology.

Seafloor Spreading in the Lau-Havre Backarc Basins: From Fast to Ultra Slow

NASA Astrophysics Data System (ADS)

Martinez, F.; Dunn, R. A.; Sleeper, J. D.

2013-12-01

Seafloor spreading in the Lau Basin occurs along the well-organized Eastern Lau Spreading Center (ELSC) and Valu Fa Ridges (VFR) opening at 97-39 mm/yr. The ELSC/VFR produce two distinct crustal types sub-parallel to the ridge as a function of their separation from the arc volcanic front. Arc-proximal spreading forms a shallow, thick crust with arc-like lavas that abruptly changes to a deeper, thinner crust with backarc basin basalt (BABB)-like lavas as the ridges separate from the arc volcanic front. Southward in the Havre Trough opening rates decrease to 15 mm/yr and a well-organized spreading axis is largely absent. Instead, active volcanism appears to be distributed across a broad zone located asymmetrically near the arc side of the basin. Further, crustal accretion appears to have two distinct styles forming a shallower terrain floored by arc-like lavas and deeper rifted basins floored by more BABB-like lavas [Wysoczanski et al., 2010, G-cubed]. Although these crustal terrains broadly resemble those flanking the ELSC/VFR, in the Havre Trough they are organized into bands that trend across the basin with the shallower arc-like terrains typically trailing from Kermadec arc front volcanoes. We hypothesize that the variation in style of crustal accretion along the Lau-Havre backarc system is controlled by the southward decreasing rate of plate extension superimposed on a compositionally variable mantle wedge. Distinct hydrous and less-hydrous mantle domains have been proposed for the mantle wedge [Martinez & Taylor, 2002; Dunn & Martinez, 2011; Nature]. Within the hydrous domain (< about 50 km from the arc volcanic front) further compositional 'fingers' trailing basinward from arc front volcanoes have been interpreted in the Lau Basin based on ridge axis morphology and chemistry [Sleeper & Martinez, submitted]. In the Lau Basin, intermediate to fast spreading rates impose a 2D plate-driven advective regime in the mantle wedge constraining volcanic accretion to the 2D narrow ridge axis. Effects of the cross trending compositional 'fingers' are minimized and only expressed as second-order geological and geochemical features at the ridge. As opening rates decrease to ultra-slow in the Havre Trough, 2D plate-driven components of mantle advection and melting are minimized. The inherent buoyancy of melts dominate advection and volcanic emplacement allowing a clearer expression of intrinsic 3D compositional and melt generation patterns in the mantle wedge. These observations suggest that mantle wedge structure fundamentally consists of arc-like mantle source compositional fingers trailing basinward from arc front volcanoes within a hydrous but more MORB source-like mantle. Spreading rate controls the degree of expression of these compositional fingers in back-arc volcanic crustal accretion. Fast to intermediate rate spreading imposes a 2D ridge-parallel distribution to crustal domains whereas slow to ultra slow spreading rates allow 3D mantle wedge compositional and melt generation patterns to be expressed.

Slab Roll-Back and Trench Retreat As Controlling Factor for Island-Arc Related Basin Evolution: A Case Study from Southern Central America

NASA Astrophysics Data System (ADS)

Brandes, C.; Winsemann, J.

2014-12-01

Slab roll-back and trench retreat are important factors for basin subsidence, magma generation and volcanism in arc-trench systems. From the sedimentary and tectonic record of the Central American island-arc it is evident that repeated slab roll-back and trench retreats occurred since the Late Cretaceous. These trench retreats were most probably related to the subduction of oceanic plateaus and seamounts. Evidence for trench retreats is given by pulses of uplift in the outer-arc area, followed by subsidence in both the fore-arc and back-arc basins. The first slab roll-back probably occurred during the Early Paleocene indicated by the collapse of carbonate platforms, and the re-deposition of large carbonate blocks into deep-water turbidites. At this time the island-arc was transformed from an incipient non-extensional stage into an extensional stage. A new pulse of uplift or decreased subsidence, respectively during the Late Eocene is attributed to subduction of rough crust, a subsequent slab detachment and the establishment of a new subduction zone further westward. Strong uplift especially affected the outer arc of the North Costa Rican arc segment. In the Sandino Fore-arc basin very coarse-grained deep-water channel-levee complexes were deposited. These deposits contain large well-rounded andesitic boulders and are rich in reworked shallow-water carbonates pointing to uplift of the inner fore-arc. Evidence for the subsequent trench retreat is given by an increased subsidence during the early Oligocene in the Sandino Fore-arc Basin and the collapse of the Barra Honda platform in North Costa Rica. Another trench retreat might have occurred in Miocene times. A phase of higher subsidence from 18 to 13 Ma is documented in the geohistory curve of the North Limon Back-arc Basin. After a short pulse of uplift the subsidence increased to approx. 300 m/myr.

xHMMER3x2: Utilizing HMMER3's speed and HMMER2's sensitivity and specificity in the glocal alignment mode for improved large-scale protein domain annotation.

PubMed

Yap, Choon-Kong; Eisenhaber, Birgit; Eisenhaber, Frank; Wong, Wing-Cheong

2016-11-29

While the local-mode HMMER3 is notable for its massive speed improvement, the slower glocal-mode HMMER2 is more exact for domain annotation by enforcing full domain-to-sequence alignments. Since a unit of domain necessarily implies a unit of function, local-mode HMMER3 alone remains insufficient for precise function annotation tasks. In addition, the incomparable E-values for the same domain model by different HMMER builds create difficulty when checking for domain annotation consistency on a large-scale basis. In this work, both the speed of HMMER3 and glocal-mode alignment of HMMER2 are combined within the xHMMER3x2 framework for tackling the large-scale domain annotation task. Briefly, HMMER3 is utilized for initial domain detection so that HMMER2 can subsequently perform the glocal-mode, sequence-to-full-domain alignments for the detected HMMER3 hits. An E-value calibration procedure is required to ensure that the search space by HMMER2 is sufficiently replicated by HMMER3. We find that the latter is straightforwardly possible for ~80% of the models in the Pfam domain library (release 29). However in the case of the remaining ~20% of HMMER3 domain models, the respective HMMER2 counterparts are more sensitive. Thus, HMMER3 searches alone are insufficient to ensure sensitivity and a HMMER2-based search needs to be initiated. When tested on the set of UniProt human sequences, xHMMER3x2 can be configured to be between 7× and 201× faster than HMMER2, but with descending domain detection sensitivity from 99.8 to 95.7% with respect to HMMER2 alone; HMMER3's sensitivity was 95.7%. At extremes, xHMMER3x2 is either the slow glocal-mode HMMER2 or the fast HMMER3 with glocal-mode. Finally, the E-values to false-positive rates (FPR) mapping by xHMMER3x2 allows E-values of different model builds to be compared, so that any annotation discrepancies in a large-scale annotation exercise can be flagged for further examination by dissectHMMER. The xHMMER3x2 workflow allows large-scale domain annotation speed to be drastically improved over HMMER2 without compromising for domain-detection with regard to sensitivity and sequence-to-domain alignment incompleteness. The xHMMER3x2 code and its webserver (for Pfam release 27, 28 and 29) are freely available at http://xhmmer3x2.bii.a-star.edu.sg/ . Reviewed by Thomas Dandekar, L. Aravind, Oliviero Carugo and Shamil Sunyaev. For the full reviews, please go to the Reviewers' comments section.

Document image retrieval through word shape coding.

PubMed

Lu, Shijian; Li, Linlin; Tan, Chew Lim

2008-11-01

This paper presents a document retrieval technique that is capable of searching document images without OCR (optical character recognition). The proposed technique retrieves document images by a new word shape coding scheme, which captures the document content through annotating each word image by a word shape code. In particular, we annotate word images by using a set of topological shape features including character ascenders/descenders, character holes, and character water reservoirs. With the annotated word shape codes, document images can be retrieved by either query keywords or a query document image. Experimental results show that the proposed document image retrieval technique is fast, efficient, and tolerant to various types of document degradation.

Vacuum arc plasma thrusters with inductive energy storage driver

NASA Technical Reports Server (NTRS)

Schein, Jochen (Inventor); Gerhan, Andrew N. (Inventor); Woo, Robyn L. (Inventor); Au, Michael Y. (Inventor); Krishnan, Mahadevan (Inventor)

2004-01-01

An apparatus for producing a vacuum arc plasma source device using a low mass, compact inductive energy storage circuit powered by a low voltage DC supply acts as a vacuum arc plasma thruster. An inductor is charged through a switch, subsequently the switch is opened and a voltage spike of Ldi/dt is produced initiating plasma across a resistive path separating anode and cathode. The plasma is subsequently maintained by energy stored in the inductor. Plasma is produced from cathode material, which allows for any electrically conductive material to be used. A planar structure, a tubular structure, and a coaxial structure allow for consumption of cathode material feed and thereby long lifetime of the thruster for long durations of time.

Hippocampal Arc (Arg3.1) expression is induced by memory recall and required for memory reconsolidation in trace fear conditioning.

PubMed

Chia, Chester; Otto, Tim

2013-11-01

Mounting evidence suggests that long-lasting, protein synthesis-dependent changes in synaptic strength accompany both the initial acquisition and subsequent recall of specific memories. Within brain areas thought to be important for learning and memory, including the hippocampus, learning-related plasticity is likely mediated in part by NMDA receptor activation and experience-dependent changes in gene expression. In the present study, we examined the role of activity-regulated cytoskeletal-associated protein (Arc/Arg3.1) expression in the acquisition, recall, and reconsolidation of memory in a trace fear conditioning paradigm. First, we show that the expression of Arc protein in ventral hippocampus (VH) is dramatically enhanced by memory recall 24h after the acquisition of trace fear conditioning, and that both memory recall and the associated recall-induced enhancement of Arc expression are blocked by pre-training administration of 2-amino-5-phosphonovaleric acid (APV). Next, we show that while infusion of Arc antisense oligodeoxynucleotides (ODNs) into VH prior to testing had little effect on memory recall, it significantly reduced both Arc protein expression and freezing behavior during subsequent testing sessions. Collectively, these results suggest that Arc/Arg3.1 protein plays an important functional role in both the initial acquisition of hippocampal-dependent memory and the reconsolidation of these memories after recall. Copyright © 2013 Elsevier Inc. All rights reserved.

ISEScan: automated identification of insertion sequence elements in prokaryotic genomes.

PubMed

Xie, Zhiqun; Tang, Haixu

2017-11-01

The insertion sequence (IS) elements are the smallest but most abundant autonomous transposable elements in prokaryotic genomes, which play a key role in prokaryotic genome organization and evolution. With the fast growing genomic data, it is becoming increasingly critical for biology researchers to be able to accurately and automatically annotate ISs in prokaryotic genome sequences. The available automatic IS annotation systems are either providing only incomplete IS annotation or relying on the availability of existing genome annotations. Here, we present a new IS elements annotation pipeline to address these issues. ISEScan is a highly sensitive software pipeline based on profile hidden Markov models constructed from manually curated IS elements. ISEScan performs better than existing IS annotation systems when tested on prokaryotic genomes with curated annotations of IS elements. Applying it to 2784 prokaryotic genomes, we report the global distribution of IS families across taxonomic clades in Archaea and Bacteria. ISEScan is implemented in Python and released as an open source software at https://github.com/xiezhq/ISEScan. hatang@indiana.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

The interaction of fasting, caloric restriction, and diet-induced obesity with 17β-estradiol on the expression of KNDy neuropeptides and their receptors in the female mouse

PubMed Central

Yang, Jennifer A.; Yasrebi, Ali; Snyder, Marisa; Roepke, Troy A.

2016-01-01

Arcuate neurons that coexpress kisspeptin (Kiss1), neurokinin B (Tac2), and dynorphin (Pdyn) mediate negative feedback of 17β-estradiol (E2) on the HPG axis. Previous studies report that fasting and caloric restriction reduce Kiss1 expression. The objective of this study was to determine the interactions of E2 with fasting, caloric restriction, and diet-induced obesity on KNDy gene and receptor expression. Ovariectomized female mice were separated into control and estradiol benzoate (E2B)-treated groups. E2B decreased Kiss1 and the tachykinin 2 receptor, Tac3r, in ARC tissue and Tac2 in Tac2 neurons. Diet-induced obesity decreased Kiss1 in oil-treated animals and the kisspeptin receptor, Kiss1r and Tac3r in the ARC of E2B-treated animals. Chronic caloric (30%) restriction reduced all three neuropeptides in oil-treated females and Kiss1r by E2B in CR animals. Taken together, our experiments suggest that steroidal environment and energy state negatively regulate KNDy gene expression in both ARC and Tac2 neurons. PMID:27507595

AGORA : Organellar genome annotation from the amino acid and nucleotide references.

PubMed

Jung, Jaehee; Kim, Jong Im; Jeong, Young-Sik; Yi, Gangman

2018-03-29

Next-generation sequencing (NGS) technologies have led to the accumulation of highthroughput sequence data from various organisms in biology. To apply gene annotation of organellar genomes for various organisms, more optimized tools for functional gene annotation are required. Almost all gene annotation tools are mainly focused on the chloroplast genome of land plants or the mitochondrial genome of animals.We have developed a web application AGORA for the fast, user-friendly, and improved annotations of organellar genomes. AGORA annotates genes based on a BLAST-based homology search and clustering with selected reference sequences from the NCBI database or user-defined uploaded data. AGORA can annotate the functional genes in almost all mitochondrion and plastid genomes of eukaryotes. The gene annotation of a genome with an exon-intron structure within a gene or inverted repeat region is also available. It provides information of start and end positions of each gene, BLAST results compared with the reference sequence, and visualization of gene map by OGDRAW. Users can freely use the software, and the accessible URL is https://bigdata.dongguk.edu/gene_project/AGORA/.The main module of the tool is implemented by the python and php, and the web page is built by the HTML and CSS to support all browsers. gangman@dongguk.edu.

Towards Automated Annotation of Benthic Survey Images: Variability of Human Experts and Operational Modes of Automation

PubMed Central

Beijbom, Oscar; Edmunds, Peter J.; Roelfsema, Chris; Smith, Jennifer; Kline, David I.; Neal, Benjamin P.; Dunlap, Matthew J.; Moriarty, Vincent; Fan, Tung-Yung; Tan, Chih-Jui; Chan, Stephen; Treibitz, Tali; Gamst, Anthony; Mitchell, B. Greg; Kriegman, David

2015-01-01

Global climate change and other anthropogenic stressors have heightened the need to rapidly characterize ecological changes in marine benthic communities across large scales. Digital photography enables rapid collection of survey images to meet this need, but the subsequent image annotation is typically a time consuming, manual task. We investigated the feasibility of using automated point-annotation to expedite cover estimation of the 17 dominant benthic categories from survey-images captured at four Pacific coral reefs. Inter- and intra- annotator variability among six human experts was quantified and compared to semi- and fully- automated annotation methods, which are made available at coralnet.ucsd.edu. Our results indicate high expert agreement for identification of coral genera, but lower agreement for algal functional groups, in particular between turf algae and crustose coralline algae. This indicates the need for unequivocal definitions of algal groups, careful training of multiple annotators, and enhanced imaging technology. Semi-automated annotation, where 50% of the annotation decisions were performed automatically, yielded cover estimate errors comparable to those of the human experts. Furthermore, fully-automated annotation yielded rapid, unbiased cover estimates but with increased variance. These results show that automated annotation can increase spatial coverage and decrease time and financial outlay for image-based reef surveys. PMID:26154157

FAST TRACK COMMUNICATION: Metal vapour causes a central minimum in arc temperature in gas-metal arc welding through increased radiative emission

NASA Astrophysics Data System (ADS)

Schnick, M.; Füssel, U.; Hertel, M.; Spille-Kohoff, A.; Murphy, A. B.

2010-01-01

A computational model of the argon arc plasma in gas-metal arc welding (GMAW) that includes the influence of metal vapour from the electrode is presented. The occurrence of a central minimum in the radial distributions of temperature and current density is demonstrated. This is in agreement with some recent measurements of arc temperatures in GMAW, but contradicts other measurements and also the predictions of previous models, which do not take metal vapour into account. It is shown that the central minimum is a consequence of the strong radiative emission from the metal vapour. Other effects of the metal vapour, such as the flux of relatively cold vapour from the electrode and the increased electrical conductivity, are found to be less significant. The different effects of metal vapour in gas-tungsten arc welding and GMAW are explained.

Optical diagnostics of the arc plasma using fast intensified CCD-spectrograph system

NASA Astrophysics Data System (ADS)

Pavelescu, Gabriela; Guillot, Stephane; Braic, Mariana T.; Hong, Dunpin; Pavelescu, D.; Fleurier, Claude; Braic, Viorel; Gherendi, F.; Dumitrescu, G.; Anghelita, P.; Bauchire, J. M.

2004-10-01

Spectroscopic diagnostics, using intensified high speed CCD camera, was applied to study the arc dynamics in low voltage circuit breakers, in vacuum and in air. Time-resolved emission spectroscopy of the vacuum arc plasma, generated during electrode separation, provided information about the interruption process. The investigations were focused on the partial unsuccessful interruption around current zero. Absorption spectroscopy, in a peculiar setup, was used in order to determine the metallic atoms densities in the interelectrode space of a low voltage circuit breaker, working in ambient air.

Seismic anisotropy along the Cyprean arc and northeast Mediterranean Sea inferred from shear wave splitting analysis

NASA Astrophysics Data System (ADS)

Yolsal-Çevikbilen, Seda

2014-08-01

The Cyprean arc is considered to be a convergent boundary in the Eastern Mediterranean where the African plate is being subducted beneath the Anatolian plate. Mapping the lateral variations of seismic anisotropy parameters can provide essential hints to mantle dynamics and flow patterns in relation to the geometry and style of deformation developed under different pressure, temperature conditions around the subducting African lithosphere. In this study, seismic anisotropy parameters, fast polarization directions (ϕ) and delay times (δt) beneath the Cyprean arc and NE Mediterranean Sea are inferred from the shear wave splitting analysis performed on core-mantle refracted teleseismic shear waves (SKS phases). Earthquake data used in the present work are extracted from the continuous recordings of 8 broad-band seismic stations located in the study region for a time period during 1999 and 2012. The overall results exhibits clear evidences of mantle anisotropy with relatively uniform NE-SW aligned fast polarization directions. No abrupt changes in fast polarization directions (ϕ) are observed. However, near the Dead Sea Transform Fault, ϕ values tend to rotate from NE-SW to N-S and NW-SE in accordance with Pn anisotropy observations. Delay times (δt) vary between 0.61 s ± 0.10 s and 1.90 s ± 0.13 s. The range of delay times are generally consistent with those observed in the mantle rather than implying a crustal anisotropy. A predominant pattern of NNE-SSW fast polarization directions that is coherent with earlier SKS splitting measurements observed beneath north, central and East Anatolia suggests a SW directed asthenospheric flow caused by slab rollback process along the Hellenic and Cyprean arcs. Furthermore, apparent splitting parameters did not exhibit any significant directional dependence which may imply possibility of the presence of anisotropic models with two-layer anisotropy or dipping axis of symmetry beneath the northeast Mediterranean Sea and Cyprean arc. Consequently, a simple, single-layered and sub-horizontal anisotropy model is tentatively suggested for the study region.

Method of center localization for objects containing concentric arcs

NASA Astrophysics Data System (ADS)

Kuznetsova, Elena G.; Shvets, Evgeny A.; Nikolaev, Dmitry P.

2015-02-01

This paper proposes a method for automatic center location of objects containing concentric arcs. The method utilizes structure tensor analysis and voting scheme optimized with Fast Hough Transform. Two applications of the proposed method are considered: (i) wheel tracking in video-based system for automatic vehicle classification and (ii) tree growth rings analysis on a tree cross cut image.

An arc control and protection system for the JET lower hybrid antenna based on an imaging system.

PubMed

Figueiredo, J; Mailloux, J; Kirov, K; Kinna, D; Stamp, M; Devaux, S; Arnoux, G; Edwards, J S; Stephen, A V; McCullen, P; Hogben, C

2014-11-01

Arcs are the potentially most dangerous events related to Lower Hybrid (LH) antenna operation. If left uncontrolled they can produce damage and cause plasma disruption by impurity influx. To address this issue an arc real time control and protection imaging system for the Joint European Torus (JET) LH antenna has been implemented. The LH system is one of the additional heating systems at JET. It comprises 24 microwave generators (klystrons, operating at 3.7 GHz) providing up to 5 MW of heating and current drive to the JET plasma. This is done through an antenna composed of an array of waveguides facing the plasma. The protection system presented here is based primarily on an imaging arc detection and real time control system. It has adapted the ITER like wall hotspot protection system using an identical CCD camera and real time image processing unit. A filter has been installed to avoid saturation and spurious system triggers caused by ionization light. The antenna is divided in 24 Regions Of Interest (ROIs) each one corresponding to one klystron. If an arc precursor is detected in a ROI, power is reduced locally with subsequent potential damage and plasma disruption avoided. The power is subsequently reinstated if, during a defined interval of time, arcing is confirmed not to be present by image analysis. This system was successfully commissioned during the restart phase and beginning of the 2013 scientific campaign. Since its installation and commissioning, arcs and related phenomena have been prevented. In this contribution we briefly describe the camera, image processing, and real time control systems. Most importantly, we demonstrate that an LH antenna arc protection system based on CCD camera imaging systems works. Examples of both controlled and uncontrolled LH arc events and their consequences are shown.

MitoFish and MiFish Pipeline: A Mitochondrial Genome Database of Fish with an Analysis Pipeline for Environmental DNA Metabarcoding.

PubMed

Sato, Yukuto; Miya, Masaki; Fukunaga, Tsukasa; Sado, Tetsuya; Iwasaki, Wataru

2018-06-01

Fish mitochondrial genome (mitogenome) data form a fundamental basis for revealing vertebrate evolution and hydrosphere ecology. Here, we report recent functional updates of MitoFish, which is a database of fish mitogenomes with a precise annotation pipeline MitoAnnotator. Most importantly, we describe implementation of MiFish pipeline for metabarcoding analysis of fish mitochondrial environmental DNA, which is a fast-emerging and powerful technology in fish studies. MitoFish, MitoAnnotator, and MiFish pipeline constitute a key platform for studies of fish evolution, ecology, and conservation, and are freely available at http://mitofish.aori.u-tokyo.ac.jp/ (last accessed April 7th, 2018).

CAMERA: An integrated strategy for compound spectra extraction and annotation of LC/MS data sets

PubMed Central

Kuhl, Carsten; Tautenhahn, Ralf; Böttcher, Christoph; Larson, Tony R.; Neumann, Steffen

2013-01-01

Liquid chromatography coupled to mass spectrometry is routinely used for metabolomics experiments. In contrast to the fairly routine and automated data acquisition steps, subsequent compound annotation and identification require extensive manual analysis and thus form a major bottle neck in data interpretation. Here we present CAMERA, a Bioconductor package integrating algorithms to extract compound spectra, annotate isotope and adduct peaks, and propose the accurate compound mass even in highly complex data. To evaluate the algorithms, we compared the annotation of CAMERA against a manually defined annotation for a mixture of known compounds spiked into a complex matrix at different concentrations. CAMERA successfully extracted accurate masses for 89.7% and 90.3% of the annotatable compounds in positive and negative ion mode, respectively. Furthermore, we present a novel annotation approach that combines spectral information of data acquired in opposite ion modes to further improve the annotation rate. We demonstrate the utility of CAMERA in two different, easily adoptable plant metabolomics experiments, where the application of CAMERA drastically reduced the amount of manual analysis. PMID:22111785

The effectiveness of annotated (vs. non-annotated) digital pathology slides as a teaching tool during dermatology and pathology residencies.

PubMed

Marsch, Amanda F; Espiritu, Baltazar; Groth, John; Hutchens, Kelli A

2014-06-01

With today's technology, paraffin-embedded, hematoxylin & eosin-stained pathology slides can be scanned to generate high quality virtual slides. Using proprietary software, digital images can also be annotated with arrows, circles and boxes to highlight certain diagnostic features. Previous studies assessing digital microscopy as a teaching tool did not involve the annotation of digital images. The objective of this study was to compare the effectiveness of annotated digital pathology slides versus non-annotated digital pathology slides as a teaching tool during dermatology and pathology residencies. A study group composed of 31 dermatology and pathology residents was asked to complete an online pre-quiz consisting of 20 multiple choice style questions, each associated with a static digital pathology image. After completion, participants were given access to an online tutorial composed of digitally annotated pathology slides and subsequently asked to complete a post-quiz. A control group of 12 residents completed a non-annotated version of the tutorial. Nearly all participants in the study group improved their quiz score, with an average improvement of 17%, versus only 3% (P = 0.005) in the control group. These results support the notion that annotated digital pathology slides are superior to non-annotated slides for the purpose of resident education. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Crowdtruth validation: a new paradigm for validating algorithms that rely on image correspondences.

PubMed

Maier-Hein, Lena; Kondermann, Daniel; Roß, Tobias; Mersmann, Sven; Heim, Eric; Bodenstedt, Sebastian; Kenngott, Hannes Götz; Sanchez, Alexandro; Wagner, Martin; Preukschas, Anas; Wekerle, Anna-Laura; Helfert, Stefanie; März, Keno; Mehrabi, Arianeb; Speidel, Stefanie; Stock, Christian

2015-08-01

Feature tracking and 3D surface reconstruction are key enabling techniques to computer-assisted minimally invasive surgery. One of the major bottlenecks related to training and validation of new algorithms is the lack of large amounts of annotated images that fully capture the wide range of anatomical/scene variance in clinical practice. To address this issue, we propose a novel approach to obtaining large numbers of high-quality reference image annotations at low cost in an extremely short period of time. The concept is based on outsourcing the correspondence search to a crowd of anonymous users from an online community (crowdsourcing) and comprises four stages: (1) feature detection, (2) correspondence search via crowdsourcing, (3) merging multiple annotations per feature by fitting Gaussian finite mixture models, (4) outlier removal using the result of the clustering as input for a second annotation task. On average, 10,000 annotations were obtained within 24 h at a cost of $100. The annotation of the crowd after clustering and before outlier removal was of expert quality with a median distance of about 1 pixel to a publically available reference annotation. The threshold for the outlier removal task directly determines the maximum annotation error, but also the number of points removed. Our concept is a novel and effective method for fast, low-cost and highly accurate correspondence generation that could be adapted to various other applications related to large-scale data annotation in medical image computing and computer-assisted interventions.

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

PubMed

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

1997-01-01

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

The interaction of fasting, caloric restriction, and diet-induced obesity with 17β-estradiol on the expression of KNDy neuropeptides and their receptors in the female mouse.

PubMed

Yang, Jennifer A; Yasrebi, Ali; Snyder, Marisa; Roepke, Troy A

2016-12-05

Arcuate neurons that coexpress kisspeptin (Kiss1), neurokinin B (Tac2), and dynorphin (Pdyn) mediate negative feedback of 17β-estradiol (E2) on the HPG axis. Previous studies report that fasting and caloric restriction reduce arcuate Kiss1 expression. The objective of this study was to determine the interactions of E2 with fasting, caloric restriction, and diet-induced obesity on KNDy gene and receptor expression. Ovariectomized female mice were separated into control and estradiol benzoate (E2B)-treated groups. E2B decreased Kiss1 and the tachykinin 2 receptor, Tac3r, in ARC tissue and Tac2 in Tac2 neurons. Diet-induced obesity decreased Kiss1 in oil-treated animals and the kisspeptin receptor, Kiss1r and Tac3r in the ARC of E2B-treated animals. Chronic caloric (30%) restriction reduced all three neuropeptides in oil-treated females and Kiss1r by E2B in CR animals. Taken together, our experiments suggest that steroidal environment and energy state negatively regulate KNDy gene expression in both ARC and Tac2 neurons. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Field guide to the Mesozoic arc and accretionary complex of South-Central Alaska, Indian to Hatcher Pass

USGS Publications Warehouse

Karl, Susan M.; Oswald, P.J.; Hults, Chad P.

2015-01-01

This field trip traverses exposures of a multi-generation Mesozoic magmatic arc and subduction-accretion complex that had a complicated history of magmatic activity and experienced variations in composition and deformational style in response to changes in the tectonic environment. This Mesozoic arc formed at an unknown latitude to the south, was accreted to North America, and was subsequently transported along faults to its present location (Plafker and others, 1989; Hillhouse and Coe, 1994). Some of these faults are still active. Similar tectonic, igneous, and sedimentary processes to those that formed the Mesozoic arc complex persist today in southern Alaska, building on, and deforming the Mesozoic arc. The rocks we will see on this field trip provide insights on the three-dimensional composition of the modern arc, and the processes involved in the evolution of an arc and its companion accretionary complex.

Paleomagnetic tests for tectonic reconstructions of the Late Jurassic-Early Cretaceous Woyla Group, Sumatra

NASA Astrophysics Data System (ADS)

Advokaat, Eldert; Bongers, Mayke; van Hinsbergen, Douwe; Rudyawan, Alfend; Marshal, Edo

2017-04-01

SE Asia consists of multiple continental blocks, volcanic arcs and suture zones representing remnants of closing ocean basins. The core of this mainland is called Sundaland, and was formed by accretion of continental and arc fragments during the Paleozoic and Mesozoic. The former positions of these blocks are still uncertain but reconstructions based on tectonostratigraphic, palaeobiogeographic, geological and palaeomagnetic studies indicate the continental terranes separated from the eastern margin of Gondwana. During the mid-Cretaceous, more continental and arc fragments accreted to Sundaland, including the intra-oceanic Woyla Arc now exposed on Sumatra. These continental fragments were derived from Australia, but the former position of the Woyla Arc is unconstrained. Interpretations on the former position of the Woyla Arc fall in two end-member groups. The first group interprets the Woyla Arc to be separated from West Sumatra by a small back-arc basin. This back arc basin opened in the Late Jurassic, and closed mid-Cretaceous, when the Woyla Arc collided with West Sumatra. The other group interprets the Woyla Arc to be derived from Gondwana, at a position close to the northern margin of Greater India in the Late Jurassic. Subsequently the Woyla Arc moved northwards and collided with West Sumatra in the mid-Cretaceous. Since these scenarios predict very different plate kinematic evolutions for the Neotethyan realm, we here aim to place paleomagnetic constraints on paleolatitudinal evolution of the Woyla Arc. The Woyla Arc consists mainly of basaltic to andesitic volcanics and dykes, and volcaniclastic shales and sandstones. Associated limestones with volcanic debris are interpreted as fringing reefs. This assemblage is interpreted as remnants of an Early Cretaceous intra-oceanic arc. West Sumatra exposes granites, surrounded by quartz sandstones, shales and volcanic tuffs. These sediments are in part metamorphosed. This assemblage is interpreted as a Jurassic-Early Cretaceous Andean margin above a NE dipping subduction zone. We sampled limestones of the Woyla Group, and sediments of the West Sumatra margin for paleomagnetic analyses. Here we present new paleomagnetic data from Upper Jurassic-Lower Cretaceous limestones of the Woyla Arc. Preliminary results suggest that the Woyla Arc was formed near equatorial latitudes. This precludes interpretations that the Woyla arc was derived from Gondwana, near the northern Indian margin. To account for (1) synchronous magmatism at the Woyla Arc and the West Sumatra continental margin, and (2) the juxtaposition of unmetamorphosed units of the Woyla Arc to highly metamorphosed units of the West Sumatra margin, we interpret the Woyla Group to be intra-oceanic arc formed above a SW dipping subduction zone in the Early Cretaceous, which was subsequently thrusted over the West Sumatra margin during the mid-Cretaceous.

Experimental investigation on the initial expansion stage of vacuum arc on cup-shaped TMF contacts

NASA Astrophysics Data System (ADS)

Wang, Ting; Xiu, Shixin; Liu, Zixi; Zhang, Yanzhe; Feng, Dingyu

2018-02-01

Arc behavior and measures to control it directly affect the properties of vacuum circuit breakers. Nowadays, transverse magnetic field (TMF) contacts are widely used for medium voltages. A magnetic field perpendicular to the current direction between the TMF contacts makes the arc move, transmitting its energy to the whole contact and avoiding excessive local ablation. Previous research on TMF arc behavior concentrated mainly on the arc movement and less on the initial stage (from arc ignition to an unstable arc column). A significant amount of experiment results suggest that there is a short period of arc stagnation after ignition. The duration of this arc stagnation and the arc characteristics during this stage affect the subsequent arc motion and even the breaking property of interrupters. The present study is of the arc characteristics in the initial stage. Experiments were carried out in a demountable vacuum chamber with cup-shaped TMF contacts. Using a high-speed camera, both single-point arc ignition mode and multiple-point arc ignition (MPAI) mode were observed. The experimental data show that the probability of MPAI mode occurring is related to the arc current. The influences of arc-ignition mode, arc current, and contact diameter on the initial expansion process were investigated. In addition, simulations were performed to analyze the multiple arc expansion process mechanically. Based on the experimental phenomena and simulation results, the mechanism of the arc expansion motion was analyzed.

Trans-ethnic Meta-analysis and Functional Annotation Illuminates the Genetic Architecture of Fasting Glucose and Insulin.

PubMed

Liu, Ching-Ti; Raghavan, Sridharan; Maruthur, Nisa; Kabagambe, Edmond Kato; Hong, Jaeyoung; Ng, Maggie C Y; Hivert, Marie-France; Lu, Yingchang; An, Ping; Bentley, Amy R; Drolet, Anne M; Gaulton, Kyle J; Guo, Xiuqing; Armstrong, Loren L; Irvin, Marguerite R; Li, Man; Lipovich, Leonard; Rybin, Denis V; Taylor, Kent D; Agyemang, Charles; Palmer, Nicholette D; Cade, Brian E; Chen, Wei-Min; Dauriz, Marco; Delaney, Joseph A C; Edwards, Todd L; Evans, Daniel S; Evans, Michele K; Lange, Leslie A; Leong, Aaron; Liu, Jingmin; Liu, Yongmei; Nayak, Uma; Patel, Sanjay R; Porneala, Bianca C; Rasmussen-Torvik, Laura J; Snijder, Marieke B; Stallings, Sarah C; Tanaka, Toshiko; Yanek, Lisa R; Zhao, Wei; Becker, Diane M; Bielak, Lawrence F; Biggs, Mary L; Bottinger, Erwin P; Bowden, Donald W; Chen, Guanjie; Correa, Adolfo; Couper, David J; Crawford, Dana C; Cushman, Mary; Eicher, John D; Fornage, Myriam; Franceschini, Nora; Fu, Yi-Ping; Goodarzi, Mark O; Gottesman, Omri; Hara, Kazuo; Harris, Tamara B; Jensen, Richard A; Johnson, Andrew D; Jhun, Min A; Karter, Andrew J; Keller, Margaux F; Kho, Abel N; Kizer, Jorge R; Krauss, Ronald M; Langefeld, Carl D; Li, Xiaohui; Liang, Jingling; Liu, Simin; Lowe, William L; Mosley, Thomas H; North, Kari E; Pacheco, Jennifer A; Peyser, Patricia A; Patrick, Alan L; Rice, Kenneth M; Selvin, Elizabeth; Sims, Mario; Smith, Jennifer A; Tajuddin, Salman M; Vaidya, Dhananjay; Wren, Mary P; Yao, Jie; Zhu, Xiaofeng; Ziegler, Julie T; Zmuda, Joseph M; Zonderman, Alan B; Zwinderman, Aeilko H; Adeyemo, Adebowale; Boerwinkle, Eric; Ferrucci, Luigi; Hayes, M Geoffrey; Kardia, Sharon L R; Miljkovic, Iva; Pankow, James S; Rotimi, Charles N; Sale, Michele M; Wagenknecht, Lynne E; Arnett, Donna K; Chen, Yii-Der Ida; Nalls, Michael A; Province, Michael A; Kao, W H Linda; Siscovick, David S; Psaty, Bruce M; Wilson, James G; Loos, Ruth J F; Dupuis, Josée; Rich, Stephen S; Florez, Jose C; Rotter, Jerome I; Morris, Andrew P; Meigs, James B

2016-07-07

Knowledge of the genetic basis of the type 2 diabetes (T2D)-related quantitative traits fasting glucose (FG) and insulin (FI) in African ancestry (AA) individuals has been limited. In non-diabetic subjects of AA (n = 20,209) and European ancestry (EA; n = 57,292), we performed trans-ethnic (AA+EA) fine-mapping of 54 established EA FG or FI loci with detailed functional annotation, assessed their relevance in AA individuals, and sought previously undescribed loci through trans-ethnic (AA+EA) meta-analysis. We narrowed credible sets of variants driving association signals for 22/54 EA-associated loci; 18/22 credible sets overlapped with active islet-specific enhancers or transcription factor (TF) binding sites, and 21/22 contained at least one TF motif. Of the 54 EA-associated loci, 23 were shared between EA and AA. Replication with an additional 10,096 AA individuals identified two previously undescribed FI loci, chrX FAM133A (rs213676) and chr5 PELO (rs6450057). Trans-ethnic analyses with regulatory annotation illuminate the genetic architecture of glycemic traits and suggest gene regulation as a target to advance precision medicine for T2D. Our approach to utilize state-of-the-art functional annotation and implement trans-ethnic association analysis for discovery and fine-mapping offers a framework for further follow-up and characterization of GWAS signals of complex trait loci. Copyright © 2016 American Society of Human Genetics. All rights reserved.

Contribution for Iron Vapor and Radiation Distribution Affected by Current Frequency of Pulsed Arc

NASA Astrophysics Data System (ADS)

Shimokura, Takuya; Mori, Yusuke; Iwao, Toru; Yumoto, Motoshige

Pulsed GTA welding has been used for improvement of stability, weld speed, and heat input control. However, the temperature and radiation power of the pulsed arc have not been elucidated. Furthermore, arc contamination by metal vapor changes the arc characteristics, e.g. by increasing radiation power. In this case, the metal vapor in pulsed GTA welding changes the distribution of temperature and radiation power as a function of time. This paper presents the relation between metal vapor and radiation power at different pulse frequencies. We calculate the Fe vapor distribution of the pulsed current. Results show that the Fe vapor is transported at fast arc velocity during the peak current period. During the base current period, the Fe vapor concentration is low and distribution is diffuse. The transition of Fe vapor distribution does not follow the pulsed current; the radiation power density distribution differs for high frequencies and low frequencies. In addition, the Fe vapor and radiation distribution are affected by the pulsed arc current frequency.

Observation of a high-quality quasi-periodic rapidly propagating wave train using SDO/AIA

NASA Astrophysics Data System (ADS)

Nisticò, G.; Pascoe, D. J.; Nakariakov, V. M.

2014-09-01

Context. We present a new event of quasi-periodic wave trains observed in EUV wavebands that rapidly propagate away from an active region after a flare. Aims: We measured the parameters of a wave train observed on 7 December 2013 after an M1.2 flare, such as the phase speeds, periods and wavelengths, in relationship to the local coronal environment and the energy sources. Methods: We compared our observations with a numerical simulation of fast magnetoacoustic waves that undergo dispersive evolution and leakage in a coronal loop embedded in a potential magnetic field. Results: The wave train is observed to propagate as several arc-shaped intensity disturbances for almost half an hour, with a speed greater than 1000 km s-1 and a period of about 1 min. The wave train followed two different patterns of propagation, in accordance with the magnetic structure of the active region. The oscillatory signal is found to be of high-quality, i.e. there is a large number (10 or more) of subsequent wave fronts observed. The observations are found to be consistent with the numerical simulation of a fast wave train generated by a localised impulsive energy release. Conclusions: Transverse structuring in the corona can efficiently create and guide high-quality quasi-periodic propagating fast wave trains. The movies are available in electronic form at http://www.aanda.org

Unique variable polarity plasma arc welding for space shuttle

NASA Technical Reports Server (NTRS)

Schwinghamer, R. J.

1985-01-01

Since the introduction of the Plasma Arc Torch in 1955 and subsequent to the work at Boeing in the 1960's, significant improvements crucial to success have been made in the Variable Polarity Plasma Arc (VPPA) Process at the Marshall Space Flight Center. Several very important advantages to this process are given, and the genesis of PA welding, the genesis of VPPA welding, special equiment requirements, weld property development, results with other aluminum alloys, and the eventual successful VPPA transition to production operations are discussed.

Tailoring the response of Autonomous Reactivity Control (ARC) systems

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

Qvist, Staffan A.; Hellesen, Carl; Gradecka, Malwina

The Autonomous Reactivity Control (ARC) system was developed to ensure inherent safety of Generation IV reactors while having a minimal impact on reactor performance and economic viability. In this study we present the transient response of fast reactor cores to postulated accident scenarios with and without ARC systems installed. Using a combination of analytical methods and numerical simulation, the principles of ARC system design that assure stability and avoids oscillatory behavior have been identified. A comprehensive transient analysis study for ARC-equipped cores, including a series of Unprotected Loss of Flow (ULOF) and Unprotected Loss of Heat Sink (ULOHS) simulations, weremore » performed for Argonne National Laboratory (ANL) Advanced Burner Reactor (ABR) designs. With carefully designed ARC-systems installed in the fuel assemblies, the cores exhibit a smooth non-oscillatory transition to stabilization at acceptable temperatures following all postulated transients. To avoid oscillations in power and temperature, the reactivity introduced per degree of temperature change in the ARC system needs to be kept below a certain threshold the value of which is system dependent, the temperature span of actuation needs to be as large as possible.« less

Database of the Geology and Thermal Activity of Norris Geyser Basin, Yellowstone National Park

USGS Publications Warehouse

Flynn, Kathryn; Graham Wall, Brita; White, Donald E.; Hutchinson, Roderick A.; Keith, Terry E.C.; Clor, Laura; Robinson, Joel E.

2008-01-01

This dataset contains contacts, geologic units and map boundaries from Plate 1 of USGS Professional Paper 1456, 'The Geology and Remarkable Thermal Activity of Norris Geyser Basin, Yellowstone National Park, Wyoming.' The features are contained in the Annotation, basins_poly, contours, geology_arc, geology_poly, point_features, and stream_arc feature classes as well as a table of geologic units and their descriptions. This dataset was constructed to produce a digital geologic map as a basis for studying hydrothermal processes in Norris Geyser Basin. The original map does not contain registration tic marks. To create the geodatabase, the original scanned map was georegistered to USGS aerial photographs of the Norris Junction quadrangle collected in 1994. Manmade objects, i.e. roads, parking lots, and the visitor center, along with stream junctions and other hydrographic features, were used for registration.

An arc control and protection system for the JET lower hybrid antenna based on an imaging system

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

Figueiredo, J., E-mail: joao.figueiredo@jet.efda.org; Mailloux, J.; Kirov, K.

Arcs are the potentially most dangerous events related to Lower Hybrid (LH) antenna operation. If left uncontrolled they can produce damage and cause plasma disruption by impurity influx. To address this issue an arc real time control and protection imaging system for the Joint European Torus (JET) LH antenna has been implemented. The LH system is one of the additional heating systems at JET. It comprises 24 microwave generators (klystrons, operating at 3.7 GHz) providing up to 5 MW of heating and current drive to the JET plasma. This is done through an antenna composed of an array of waveguidesmore » facing the plasma. The protection system presented here is based primarily on an imaging arc detection and real time control system. It has adapted the ITER like wall hotspot protection system using an identical CCD camera and real time image processing unit. A filter has been installed to avoid saturation and spurious system triggers caused by ionization light. The antenna is divided in 24 Regions Of Interest (ROIs) each one corresponding to one klystron. If an arc precursor is detected in a ROI, power is reduced locally with subsequent potential damage and plasma disruption avoided. The power is subsequently reinstated if, during a defined interval of time, arcing is confirmed not to be present by image analysis. This system was successfully commissioned during the restart phase and beginning of the 2013 scientific campaign. Since its installation and commissioning, arcs and related phenomena have been prevented. In this contribution we briefly describe the camera, image processing, and real time control systems. Most importantly, we demonstrate that an LH antenna arc protection system based on CCD camera imaging systems works. Examples of both controlled and uncontrolled LH arc events and their consequences are shown.« less

Pronounced zonation of seismic anisotropy in the Western Hellenic subduction zone and its geodynamic significance

NASA Astrophysics Data System (ADS)

Olive, Jean-Arthur; Pearce, Frederick; Rondenay, Stéphane; Behn, Mark D.

2014-04-01

Many subduction zones exhibit significant retrograde motion of their arc and trench. The observation of fast shear-wave velocities parallel to the trench in such settings has been inferred to represent trench-parallel mantle flow beneath a retreating slab. Here, we investigate this process by measuring seismic anisotropy in the shallow Aegean mantle. We carry out shear-wave splitting analysis on a dense array of seismometers across the Western Hellenic Subduction Zone, and find a pronounced zonation of anisotropy at the scale of the subduction zone. Fast SKS splitting directions subparallel to the trench-retreat direction dominate the region nearest to the trench. Fast splitting directions abruptly transition to trench-parallel above the corner of the mantle wedge, and rotate back to trench-normal over the back-arc. We argue that the trench-normal anisotropy near the trench is explained by entrainment of an asthenospheric layer beneath the shallow-dipping portion of the slab. Toward the volcanic arc this signature is overprinted by trench-parallel anisotropy in the mantle wedge, likely caused by a layer of strained serpentine immediately above the slab. Arcward steepening of the slab and horizontal divergence of mantle flow due to rollback may generate an additional component of sub-slab trench-parallel anisotropy in this region. Poloidal flow above the retreating slab is likely the dominant source of back-arc trench-normal anisotropy. We hypothesize that trench-normal anisotropy associated with significant entrainment of the asthenospheric mantle near the trench may be widespread but only observable at shallow-dipping subduction zones where stations nearest the trench do not overlie the mantle wedge.

Topological nature of the node-arc semimetal PtSn4 probed by de Haas-van Alphen quantum oscillations

NASA Astrophysics Data System (ADS)

Wang, Y. J.; Liang, D. D.; Ge, M.; Yang, J.; Gong, J. X.; Luo, L.; Pi, L.; Zhu, W. K.; Zhang, C. J.; Zhang, Y. H.

2018-04-01

Dirac node arc semimetal state is a new topological quantum state which is proposed to exist in PtSn4 (Wu et al 2016 Dirac node arcs in PtSn4 Nat. Phys. 12 667–71). We present a systematic de Haas-van Alphen quantum oscillation study on this compound. Two intriguing oscillation branches, i.e. F 1 and F 2, are detected in the fast Fourier transformation spectra, both of which are characterized to possess tiny effective mass and ultrahigh quantum mobility. And the F 2 branch exhibits an angle-dependent nontrivial Berry phase. The features are consistent with the existence of the node arc semimetal state and shed new light on its complicated Fermi surfaces and topological nature.

Verdant: automated annotation, alignment and phylogenetic analysis of whole chloroplast genomes.

PubMed

McKain, Michael R; Hartsock, Ryan H; Wohl, Molly M; Kellogg, Elizabeth A

2017-01-01

Chloroplast genomes are now produced in the hundreds for angiosperm phylogenetics projects, but current methods for annotation, alignment and tree estimation still require some manual intervention reducing throughput and increasing analysis time for large chloroplast systematics projects. Verdant is a web-based software suite and database built to take advantage a novel annotation program, annoBTD. Using annoBTD, Verdant provides accurate annotation of chloroplast genomes without manual intervention. Subsequent alignment and tree estimation can incorporate newly annotated and publically available plastomes and can accommodate a large number of taxa. Verdant sharply reduces the time required for analysis of assembled chloroplast genomes and removes the need for pipelines and software on personal hardware. Verdant is available at: http://verdant.iplantcollaborative.org/plastidDB/ It is implemented in PHP, Perl, MySQL, Javascript, HTML and CSS with all major browsers supported. mrmckain@gmail.comSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

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

Gonzalez-Esquer, C. Raul; Twary, Scott N.; Hovde, Blake T.

Picochlorum soloecismus is a halotolerant, fast-growing, and moderate-lipid-producing microalga that is being evaluated as a renewable feedstock for biofuel production. Herein, we report on an improved high-quality draft assembly and annotation for the nuclear, chloroplast, and mitochondrial genomes of P. soloecismus DOE 101.

A curated catalog of canine and equine keratin genes

PubMed Central

Pujar, Shashikant; McGarvey, Kelly M.; Welle, Monika; Galichet, Arnaud; Müller, Eliane J.; Pruitt, Kim D.; Leeb, Tosso

2017-01-01

Keratins represent a large protein family with essential structural and functional roles in epithelial cells of skin, hair follicles, and other organs. During evolution the genes encoding keratins have undergone multiple rounds of duplication and humans have two clusters with a total of 55 functional keratin genes in their genomes. Due to the high similarity between different keratin paralogs and species-specific differences in gene content, the currently available keratin gene annotation in species with draft genome assemblies such as dog and horse is still imperfect. We compared the National Center for Biotechnology Information (NCBI) (dog annotation release 103, horse annotation release 101) and Ensembl (release 87) gene predictions for the canine and equine keratin gene clusters to RNA-seq data that were generated from adult skin of five dogs and two horses and from adult hair follicle tissue of one dog. Taking into consideration the knowledge on the conserved exon/intron structure of keratin genes, we annotated 61 putatively functional keratin genes in both the dog and horse, respectively. Subsequently, curators in the RefSeq group at NCBI reviewed their annotation of keratin genes in the dog and horse genomes (Annotation Release 104 and Annotation Release 102, respectively) and updated annotation and gene nomenclature of several keratin genes. The updates are now available in the NCBI Gene database (https://www.ncbi.nlm.nih.gov/gene). PMID:28846680

Ontology modularization to improve semantic medical image annotation.

PubMed

Wennerberg, Pinar; Schulz, Klaus; Buitelaar, Paul

2011-02-01

Searching for medical images and patient reports is a significant challenge in a clinical setting. The contents of such documents are often not described in sufficient detail thus making it difficult to utilize the inherent wealth of information contained within them. Semantic image annotation addresses this problem by describing the contents of images and reports using medical ontologies. Medical images and patient reports are then linked to each other through common annotations. Subsequently, search algorithms can more effectively find related sets of documents on the basis of these semantic descriptions. A prerequisite to realizing such a semantic search engine is that the data contained within should have been previously annotated with concepts from medical ontologies. One major challenge in this regard is the size and complexity of medical ontologies as annotation sources. Manual annotation is particularly time consuming labor intensive in a clinical environment. In this article we propose an approach to reducing the size of clinical ontologies for more efficient manual image and text annotation. More precisely, our goal is to identify smaller fragments of a large anatomy ontology that are relevant for annotating medical images from patients suffering from lymphoma. Our work is in the area of ontology modularization, which is a recent and active field of research. We describe our approach, methods and data set in detail and we discuss our results. Copyright © 2010 Elsevier Inc. All rights reserved.

Sandstone provenance and U-Pb ages of detrital zircons from Permian-Triassic forearc sediments within the Sukhothai Arc, northern Thailand: Record of volcanic-arc evolution in response to Paleo-Tethys subduction

NASA Astrophysics Data System (ADS)

Hara, Hidetoshi; Kunii, Miyuki; Miyake, Yoshihiro; Hisada, Ken-ichiro; Kamata, Yoshihito; Ueno, Katsumi; Kon, Yoshiaki; Kurihara, Toshiyuki; Ueda, Hayato; Assavapatchara, San; Treerotchananon, Anuwat; Charoentitirat, Thasinee; Charusiri, Punya

2017-09-01

Provenance analysis and U-Pb dating of detrital zircons in Permian-Triassic forearc sediments from the Sukhothai Arc in northern Thailand clarify the evolution of a missing arc system associated with Paleo-Tethys subduction. The turbidite-dominant formations within the forearc sediments include the Permian Ngao Group (Kiu Lom, Pha Huat, and Huai Thak formations), the Early to earliest Late Triassic Lampang Group (Phra That and Hong Hoi formations), and the Late Triassic Song Group (Pha Daeng and Wang Chin formations). The sandstones are quartzose in the Pha Huat, Huai Thak, and Wang Chin formations, and lithic wacke in the Kiu Lom, Phra That, Hong Hoi and Pha Daeng formations. The quartzose sandstones contain abundant quartz, felsic volcanic and plutonic fragments, whereas the lithic sandstones contain mainly basaltic to felsic volcanic fragments. The youngest single-grain (YSG) zircon U-Pb age generally approximates the depositional age in the study area, but in the case of the limestone-dominant Pha Huat Formation the YSG age is clearly older. On the other hand, the youngest cluster U-Pb age (YC1σ) represents the peak of igneous activity in the source area. Geological evidence, geochemical signatures, and the YC1σ ages of the sandstones have allowed us to reconstruct the Sukhothai arc evolution. The initial Sukhothai Arc (Late Carboniferous-Early Permian) developed as a continental island arc. Subsequently, there was general magmatic quiescence with minor I-type granitic activity during the Middle to early Late Permian. In the latest Permian to early Late Triassic, the Sukhothai Arc developed in tandem with Early to Middle Triassic I-type granitic activity, Middle to Late Triassic volcanism, evolution of an accretionary complex, and an abundant supply of sediments from the volcanic rocks to the trench through a forearc basin. Subsequently, the Sukhothai Arc became quiescent as the Paleo-Tethys closed after the Late Triassic. In addition, parts of sediments of supposed Devonian-Carboniferous age within the Sukhothai Arc were revised as the Triassic Lampang Group, and the Early Cretaceous Khorat Group.

GFam: a platform for automatic annotation of gene families.

PubMed

Sasidharan, Rajkumar; Nepusz, Tamás; Swarbreck, David; Huala, Eva; Paccanaro, Alberto

2012-10-01

We have developed GFam, a platform for automatic annotation of gene/protein families. GFam provides a framework for genome initiatives and model organism resources to build domain-based families, derive meaningful functional labels and offers a seamless approach to propagate functional annotation across periodic genome updates. GFam is a hybrid approach that uses a greedy algorithm to chain component domains from InterPro annotation provided by its 12 member resources followed by a sequence-based connected component analysis of un-annotated sequence regions to derive consensus domain architecture for each sequence and subsequently generate families based on common architectures. Our integrated approach increases sequence coverage by 7.2 percentage points and residue coverage by 14.6 percentage points higher than the coverage relative to the best single-constituent database within InterPro for the proteome of Arabidopsis. The true power of GFam lies in maximizing annotation provided by the different InterPro data sources that offer resource-specific coverage for different regions of a sequence. GFam's capability to capture higher sequence and residue coverage can be useful for genome annotation, comparative genomics and functional studies. GFam is a general-purpose software and can be used for any collection of protein sequences. The software is open source and can be obtained from http://www.paccanarolab.org/software/gfam/.

ARC Researchers at ASME 2015 Internal Combustion Engine Division Fall

Science.gov Websites

-sense. Therefore, the focus of this paper is on the various methods of computing CA50 for analysing and classifying cycle-to-cycle variability. The assumptions made to establish fast and possibly on-line methods SI engine. Then the various fast methods for computing CA50 feed the two statistical methods

Fluorescent Protein Voltage Probes Derived from ArcLight that Respond to Membrane Voltage Changes with Fast Kinetics

PubMed Central

Han, Zhou; Jin, Lei; Platisa, Jelena; Cohen, Lawrence B.; Baker, Bradley J.; Pieribone, Vincent A.

2013-01-01

We previously reported the discovery of a fluorescent protein voltage probe, ArcLight, and its derivatives that exhibit large changes in fluorescence intensity in response to changes of plasma membrane voltage. ArcLight allows the reliable detection of single action potentials and sub-threshold activities in individual neurons and dendrites. The response kinetics of ArcLight (τ1-on ~10 ms, τ2-on ~ 50 ms) are comparable with most published genetically-encoded voltage probes. However, probes using voltage-sensing domains other than that from the Ciona intestinalis voltage sensitive phosphatase exhibit faster kinetics. Here we report new versions of ArcLight, in which the Ciona voltage-sensing domain was replaced with those from chicken, zebrafish, frog, mouse or human. We found that the chicken and zebrafish-based ArcLight exhibit faster kinetics, with a time constant (τ) less than 6ms for a 100 mV depolarization. Although the response amplitude of these two probes (8-9%) is not as large as the Ciona-based ArcLight (~35%), they are better at reporting action potentials from cultured neurons at higher frequency. In contrast, probes based on frog, mouse and human voltage sensing domains were either slower than the Ciona-based ArcLight or had very small signals. PMID:24312287

Defiant: (DMRs: easy, fast, identification and ANnoTation) identifies differentially Methylated regions from iron-deficient rat hippocampus.

PubMed

Condon, David E; Tran, Phu V; Lien, Yu-Chin; Schug, Jonathan; Georgieff, Michael K; Simmons, Rebecca A; Won, Kyoung-Jae

2018-02-05

Identification of differentially methylated regions (DMRs) is the initial step towards the study of DNA methylation-mediated gene regulation. Previous approaches to call DMRs suffer from false prediction, use extreme resources, and/or require library installation and input conversion. We developed a new approach called Defiant to identify DMRs. Employing Weighted Welch Expansion (WWE), Defiant showed superior performance to other predictors in the series of benchmarking tests on artificial and real data. Defiant was subsequently used to investigate DNA methylation changes in iron-deficient rat hippocampus. Defiant identified DMRs close to genes associated with neuronal development and plasticity, which were not identified by its competitor. Importantly, Defiant runs between 5 to 479 times faster than currently available software packages. Also, Defiant accepts 10 different input formats widely used for DNA methylation data. Defiant effectively identifies DMRs for whole-genome bisulfite sequencing (WGBS), reduced-representation bisulfite sequencing (RRBS), Tet-assisted bisulfite sequencing (TAB-seq), and HpaII tiny fragment enrichment by ligation-mediated PCR-tag (HELP) assays.

Necklace: combining reference and assembled transcriptomes for more comprehensive RNA-Seq analysis.

PubMed

Davidson, Nadia M; Oshlack, Alicia

2018-05-01

RNA sequencing (RNA-seq) analyses can benefit from performing a genome-guided and de novo assembly, in particular for species where the reference genome or the annotation is incomplete. However, tools for integrating an assembled transcriptome with reference annotation are lacking. Necklace is a software pipeline that runs genome-guided and de novo assembly and combines the resulting transcriptomes with reference genome annotations. Necklace constructs a compact but comprehensive superTranscriptome out of the assembled and reference data. Reads are subsequently aligned and counted in preparation for differential expression testing. Necklace allows a comprehensive transcriptome to be built from a combination of assembled and annotated transcripts, which results in a more comprehensive transcriptome for the majority of organisms. In addition RNA-seq data are mapped back to this newly created superTranscript reference to enable differential expression testing with standard methods.

Global Dynamics of Dayside Auroral Precipitation in Conjunction with Solar Wind Pressure Pulses

NASA Technical Reports Server (NTRS)

Brittnacher, M.; Chua, D.; Fillingim, M.; Parks, G. K.; Spann, James F., Jr.; Germany, G. A.; Carlson, C. W.; Greenwald, R. A.

1999-01-01

Global observation of the dayside auroral region by the Ultraviolet Imager (UVI) during transient solar wind pressure pulse events on October 1, 1997 has revealed unusual features in the auroral precipitation. The auroral arc structure on the dayside, possibly connected with the LLBL, split into 2 arc structures; one moving poleward and fading over a 5 min period, and the other stationary or slightly shifted equatorward (by changes in the x component). The y component was large and positive, and the z component was small and negative. The splitting of the arc structure extended from 9 to 15 MLT and was concurrent with an enhancement of the convection in the cusp region identified by SuperDARN observations. The convection reversal on the morningside was adjacent to and poleward of the weak lower latitude band of precipitation. The sensitivity of the UVI instrument enabled observation of arc structures down to about 0.2 erg electron energy flux, as confirmed by comparison with particle measurements from the FAST satellite for other dayside events. Removal of the spacecraft wobble by PIXON image reconstruction restored the original resolution of the UVI of about 40 km from apogee. This event is being analyzed in connection with a larger study of global dynamics of dayside energy and momentum transfer related to changes in IMF conditions using UVI images in conjunction with observations from FAST and SuperDARN.

Incorporating geometric ray tracing to generate initial conditions for intensity modulated arc therapy optimization

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

Oliver, Mike; Gladwish, Adam; Craig, Jeff

2008-07-15

Purpose and background: Intensity modulated arc therapy (IMAT) is a rotational variant of Intensity modulated radiation therapy (IMRT) that is achieved by allowing the multileaf collimator (MLC) positions to vary as the gantry rotates around the patient. This work describes a method to generate an IMAT plan through the use of a fast ray tracing technique based on dosimetric and geometric information for setting initial MLC leaf positions prior to final IMAT optimization. Methods and materials: Three steps were used to generate an IMAT plan. The first step was to generate arcs based on anatomical contours. The second step wasmore » to generate ray importance factor (RIF) maps by ray tracing the dose distribution inside the planning target volume (PTV) to modify the MLC leaf positions of the anatomical arcs to reduce the maximum dose inside the PTV. The RIF maps were also segmented to create a new set of arcs to improve the dose to low dose voxels within the PTV. In the third step, the MLC leaf positions from all arcs were put through a leaf position optimization (LPO) algorithm and brought into a fast Monte Carlo dose calculation engine for a final dose calculation. The method was applied to two phantom cases, a clinical prostate case and the Radiological Physics Center (RPC)'s head and neck phantom. The authors assessed the plan improvements achieved by each step and compared plans with and without using RIF. They also compared the IMAT plan with an IMRT plan for the RPC phantom. Results: All plans that incorporated RIF and LPO had lower objective function values than those that incorporated LPO only. The objective function value was reduced by about 15% after the generation of RIF arcs and 52% after generation of RIF arcs and leaf position optimization. The IMAT plan for the RPC phantom had similar dose coverage for PTV1 and PTV2 (the same dose volume histogram curves), however, slightly lower dose to the normal tissues compared to a six-field IMRT plan. Conclusion: The use of a ray importance factor can generate initial IMAT arcs efficiently for further MLC leaf position optimization to obtain more favorable IMAT plan.« less

Method for defect free keyhole plasma arc welding

NASA Technical Reports Server (NTRS)

Harwig, Dennis D. (Inventor); Hunt, James F. (Inventor); Ryan, Patrick M. (Inventor); Fisher, Walter J. (Inventor)

1993-01-01

A plasma arc welding process for welding metal of increased thickness with one pass includes operating the plasma arc welding apparatus at a selected plasma gas flow rate, travel speed and arc current, to form a weld having a penetration ratio to weld height to weld width, and maintaining the penetration ratio at less than 0.74. Parameters for the plasma gas flow rate, travel speed and arc current are adjusted to a steady state condition during a start up period and maintained during the steady state condition to complete a weld. During a terminal stopping period, the travel speed is stopped and instantaneously replaced by filler wire which adds material to fill the keyhole that had been formed by the welding process. Parameters are subsequently adjusted during the stopping period to terminate the weld in a sound manner.

Shear-wave polarization anisotropy in the mantle wedge beneath the southern part of Tohoku, Japan

NASA Astrophysics Data System (ADS)

Shimizu, J.; Nakajima, J.; Hasegawa, A.

2003-12-01

We investigated shear-wave polarization anisotropy in the mantle wedge beneath the southern part of Tohoku, Japan, by using waveform data of intermediate depth earthquakes with M>2.5 recorded by the seismic networks of Tohoku University and Japan Meteorological Agency (JMA). We selected waveform data with ray paths whose incident angles to the surface are 35 degrees or less to avoid contamination of particle motions by converted phases. All the seismograms thus selected were filtered with bandpassed ranges of 2-8 Hz. Cross-correlation method [Ando et al., 1983] was used for determining delay time between the leading and following shear-waves (delay time) and the leading shear-wave polarization direction (fast direction). Two horizontal components of observed seismograms were rotated with the direction from 0 to 180 degrees with an interval of 5 degrees, and shifted one horizontal component by a time lag. The time lag varied from 0 to 1 s with an interval of 0.01 s. The length of time window used to calculate correlation coefficient was set to be nearly equal to one cycle of the shear-wave. We do not use the data whose maximum correlation coefficient is less than 0.8. Obtained results show that most of the fast directions at stations in the back-arc side are nearly E-W, whereas those at stations in the fore-arc side are N-S. We infer that the anisotropy caused by lattice-preferred orientation of olivine, which is probably produced by flow in the mantle wedge, is a likely candidate for the observed shear-wave splitting with E-W trend fast directions in the back-arc side. Although it is not certain what causes the N-S trend fast directions in the for-arc side, the same trend is seen in the previous studies of other areas in Tohoku [Okada et al.,1995; Nakajima, 2002]. Observed delay times are mostly 0.1-0.3 s, which is consistent with the results of Okada et al. [1995] and Nakajima [2002]. Acknowledgments: We are grateful to the staff of the JMA for allowing us to use their data.

The future of transposable element annotation and their classification in the light of functional genomics - what we can learn from the fables of Jean de la Fontaine?

PubMed

Arensburger, Peter; Piégu, Benoît; Bigot, Yves

2016-01-01

Transposable element (TE) science has been significantly influenced by the pioneering ideas of David Finnegan near the end of the last century, as well as by the classification systems that were subsequently developed. Today, whole genome TE annotation is mostly done using tools that were developed to aid gene annotation rather than to specifically study TEs. We argue that further progress in the TE field is impeded both by current TE classification schemes and by a failure to recognize that TE biology is fundamentally different from that of multicellular organisms. Novel genome wide TE annotation methods are helping to redefine our understanding of TE sequence origins and evolution. We briefly discuss some of these new methods as well as ideas for possible alternative classification schemes. Our hope is to encourage the formation of a society to organize a larger debate on these questions and to promote the adoption of standards for annotation and an improved TE classification.

Enabling comparative modeling of closely related genomes: Example genus Brucella

DOE PAGES

Faria, José P.; Edirisinghe, Janaka N.; Davis, James J.; ...

2014-03-08

For many scientific applications, it is highly desirable to be able to compare metabolic models of closely related genomes. In this study, we attempt to raise awareness to the fact that taking annotated genomes from public repositories and using them for metabolic model reconstructions is far from being trivial due to annotation inconsistencies. We are proposing a protocol for comparative analysis of metabolic models on closely related genomes, using fifteen strains of genus Brucella, which contains pathogens of both humans and livestock. This study lead to the identification and subsequent correction of inconsistent annotations in the SEED database, as wellmore » as the identification of 31 biochemical reactions that are common to Brucella, which are not originally identified by automated metabolic reconstructions. We are currently implementing this protocol for improving automated annotations within the SEED database and these improvements have been propagated into PATRIC, Model-SEED, KBase and RAST. This method is an enabling step for the future creation of consistent annotation systems and high-quality model reconstructions that will support in predicting accurate phenotypes such as pathogenicity, media requirements or type of respiration.« less

Enabling comparative modeling of closely related genomes: Example genus Brucella

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

Faria, José P.; Edirisinghe, Janaka N.; Davis, James J.

For many scientific applications, it is highly desirable to be able to compare metabolic models of closely related genomes. In this study, we attempt to raise awareness to the fact that taking annotated genomes from public repositories and using them for metabolic model reconstructions is far from being trivial due to annotation inconsistencies. We are proposing a protocol for comparative analysis of metabolic models on closely related genomes, using fifteen strains of genus Brucella, which contains pathogens of both humans and livestock. This study lead to the identification and subsequent correction of inconsistent annotations in the SEED database, as wellmore » as the identification of 31 biochemical reactions that are common to Brucella, which are not originally identified by automated metabolic reconstructions. We are currently implementing this protocol for improving automated annotations within the SEED database and these improvements have been propagated into PATRIC, Model-SEED, KBase and RAST. This method is an enabling step for the future creation of consistent annotation systems and high-quality model reconstructions that will support in predicting accurate phenotypes such as pathogenicity, media requirements or type of respiration.« less

Improved Annotation of 3′ Untranslated Regions and Complex Loci by Combination of Strand-Specific Direct RNA Sequencing, RNA-Seq and ESTs

PubMed Central

Song, Junfang; Duc, Céline; Storey, Kate G.; McLean, W. H. Irwin; Brown, Sara J.; Simpson, Gordon G.; Barton, Geoffrey J.

2014-01-01

The reference annotations made for a genome sequence provide the framework for all subsequent analyses of the genome. Correct and complete annotation in addition to the underlying genomic sequence is particularly important when interpreting the results of RNA-seq experiments where short sequence reads are mapped against the genome and assigned to genes according to the annotation. Inconsistencies in annotations between the reference and the experimental system can lead to incorrect interpretation of the effect on RNA expression of an experimental treatment or mutation in the system under study. Until recently, the genome-wide annotation of 3′ untranslated regions received less attention than coding regions and the delineation of intron/exon boundaries. In this paper, data produced for samples in Human, Chicken and A. thaliana by the novel single-molecule, strand-specific, Direct RNA Sequencing technology from Helicos Biosciences which locates 3′ polyadenylation sites to within +/− 2 nt, were combined with archival EST and RNA-Seq data. Nine examples are illustrated where this combination of data allowed: (1) gene and 3′ UTR re-annotation (including extension of one 3′ UTR by 5.9 kb); (2) disentangling of gene expression in complex regions; (3) clearer interpretation of small RNA expression and (4) identification of novel genes. While the specific examples displayed here may become obsolete as genome sequences and their annotations are refined, the principles laid out in this paper will be of general use both to those annotating genomes and those seeking to interpret existing publically available annotations in the context of their own experimental data. PMID:24722185

An efficient annotation and gene-expression derivation tool for Illumina Solexa datasets.

PubMed

Hosseini, Parsa; Tremblay, Arianne; Matthews, Benjamin F; Alkharouf, Nadim W

2010-07-02

The data produced by an Illumina flow cell with all eight lanes occupied, produces well over a terabyte worth of images with gigabytes of reads following sequence alignment. The ability to translate such reads into meaningful annotation is therefore of great concern and importance. Very easily, one can get flooded with such a great volume of textual, unannotated data irrespective of read quality or size. CASAVA, a optional analysis tool for Illumina sequencing experiments, enables the ability to understand INDEL detection, SNP information, and allele calling. To not only extract from such analysis, a measure of gene expression in the form of tag-counts, but furthermore to annotate such reads is therefore of significant value. We developed TASE (Tag counting and Analysis of Solexa Experiments), a rapid tag-counting and annotation software tool specifically designed for Illumina CASAVA sequencing datasets. Developed in Java and deployed using jTDS JDBC driver and a SQL Server backend, TASE provides an extremely fast means of calculating gene expression through tag-counts while annotating sequenced reads with the gene's presumed function, from any given CASAVA-build. Such a build is generated for both DNA and RNA sequencing. Analysis is broken into two distinct components: DNA sequence or read concatenation, followed by tag-counting and annotation. The end result produces output containing the homology-based functional annotation and respective gene expression measure signifying how many times sequenced reads were found within the genomic ranges of functional annotations. TASE is a powerful tool to facilitate the process of annotating a given Illumina Solexa sequencing dataset. Our results indicate that both homology-based annotation and tag-count analysis are achieved in very efficient times, providing researchers to delve deep in a given CASAVA-build and maximize information extraction from a sequencing dataset. TASE is specially designed to translate sequence data in a CASAVA-build into functional annotations while producing corresponding gene expression measurements. Achieving such analysis is executed in an ultrafast and highly efficient manner, whether the analysis be a single-read or paired-end sequencing experiment. TASE is a user-friendly and freely available application, allowing rapid analysis and annotation of any given Illumina Solexa sequencing dataset with ease.

A study on crustal shear wave splitting in the western part of the Banda arc-continent collision

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

Syuhada, E-mail: hadda9@gmail.com; Research Centre for Physics - Indonesian Institute of Sciences; Hananto, Nugroho D.

2016-03-11

We analyzed shear wave splitting parameters from local shallow (< 30 km) earthquakes recorded at six seismic stations in the western part of the Banda arc-continent collision. We determined fast polarization and delay time for 195 event-stations pairs calculated from good signal-to-noise ratio waveforms. We observed that there is evidence for shear wave splitting at all stations with dominant fast polarization directions oriented about NE-SW, which are parallel to the collision direction of the Australian plate. However, minor fast polarization directions are oriented around NW-SE being perpendicular to the strike of Timor through. Furthermore, the changes in fast azimuths with themore » earthquake-station back azimuth suggest that the crustal anisotropy in the study area is not uniform. Splitting delay times are within the range of 0.05 s to 0.8 s, with a mean value of 0.29±0.18 s. Major seismic stations exhibit a weak tendency increasing of delay times with increasing hypocentral distance suggesting the main anisotropy contribution of the shallow crust. In addition, these variations in fast azimuths and delay times indicate that the crustal anisotropy in this region might not only be caused by extensive dilatancy anisotropy (EDA), but also by heterogeneity shallow structure such as the presence of foliations in the rock fabric and the fracture zones associated with active faults.« less

Slab roll-back and trench retreat as controlling factor for basin subsidence in southern Central America

NASA Astrophysics Data System (ADS)

Brandes, Christian; Winsemann, Jutta

2015-04-01

Slab roll-back and trench retreat are important factors for basin subsidence, magma generation and volcanism in arc-trench systems. Based on the sedimentary and tectonic record of the southern Central American island-arc we conclude that repeated phases of slab roll-back and trench retreats occurred the arc-trench system since the Late Cretaceous. These trench retreats were most probably related to the subduction of oceanic plateaus and seamounts and effected both the fore-arc and back-arc evolution. We used numerical basin modelling techniques to analyse the burial history of fore-arc and back-arc basins in Central America and combined the results with field data of the sedimentological evolution of the basin-fills. From the basin models, geohistory curves were extracted for the fore-arc and back-arc basins to derive the subsidence evolution. The Sandino Fore-arc Basin is characterized by low subsidence during the first 40 Myr. Since the Late Cretaceous the basin has a linear moderate subsidence with a phase of accelerated subsidence in the Oligocene. In the North and South Limón Back-arc Basin, subsidence started at approximately the same time as in the Sandino Fore-arc Basin. The North and South Limón Basins show a linear subsidence trend in the Paleocene and Eocene. Evidence for trench retreats is given by pulses of uplift in the outer-arc area, followed by subsidence in both the fore-arc and back-arc basins. The first slab roll-back probably occurred during the Early Paleocene. This is indicated by the collapse of carbonate platforms, and the re-deposition of large carbonate blocks into deep-water turbidites. A new pulse of uplift or decreased subsidence, respectively during the Late Eocene is attributed to subduction of rough crust. A subsequent slab detachment and the establishment of a new subduction zone further westward was described by Walther et al. (2000). Strong uplift affected the entire fore-arc area, which led to the deposition of very coarse-grained deepwater channel-levee complexes in the Sandino Fore-arc Basin. The channel-fills are rich in reworked shallow-water carbonates that points to strong uplift of the inner fore-arc. A subsequent trench retreat is indicated by an increased subsidence during the Early Oligocene in the Sandino Fore-arc Basin and the collapse of the Barra Honda carbonate platform in North Costa Rica. Another trench retreat might have occurred in Miocene times (Cailleau and Oncken, 2008). A phase of higher subsidence from 18 to 13 Ma is documented in the geohistory curve of the North Limon Back-arc Basin. After a short pulse of uplift the subsidence increased to approx. 300 m/myr (Brandes et al., 2008). References: Brandes C., Astorga A., Littke R. and Winsemann J. (2008) Basin modelling of the Limón Back-arc Basin (Costa Rica): burial history and temperature evolution of an island-arc related basin system. Basin Research 20, 1, 119-142. Cailleau, B. and Oncken, O. (2008) Past forearc deformation in Nicaragua and coupling at the megathrust interface: Evidence for subduction retreat. Geochemistry, Geophysics, Geosystems 9, Q07S24, doi:10.1029/2007GC001754. Walther, C.H.E., Flueh, E.R., Ranero, C.R., von Huene, R. and Strauch, W. (2000) Crustal structure across the Pacific margin of Nicaragua: evidence for ophiolithic basement and a shallow mantle sliver. Geophysical Journal International 141, 759-777.

The Cambrian Ross Orogeny in northern Victoria Land (Antarctica) and New Zealand: A synthesis

USGS Publications Warehouse

Federico, L.; Capponi, G.; Crispini, L.; Bradshaw, J.D.

2007-01-01

In the Cambrian, the paleo-Pacific margin of the Gondwana supercontinent included East Antarctica, Australia, Tasmania and New Zealand and was affected by themajor Ross-Delamerian Orogeny. In Antarctica, evidence suggests that this resulted from oblique subduction and that in northern Victoria Land it was accompanied by the opening and subsequent closure of a back-arc basin. Comparison of the type and timing of sedimentary, magmatic and metamorphic events in areas noted above shows strong similarities between northern Victoria Land and New Zealand. In both regions Middle Cambrian volcanites are interpreted as arc/back-arc assemblages produced by west-directed subduction; sediments interbedded with the volcanites show provenance both from the arc and from the Gondwana margin and therefore place the basin close to the continent. Back-arc closure in the Late Cambrian was likely accomplished through a second subduction system

Automated tumor analysis for molecular profiling in lung cancer

PubMed Central

Boyd, Clinton; James, Jacqueline A.; Loughrey, Maurice B.; Hougton, Joseph P.; Boyle, David P.; Kelly, Paul; Maxwell, Perry; McCleary, David; Diamond, James; McArt, Darragh G.; Tunstall, Jonathon; Bankhead, Peter; Salto-Tellez, Manuel

2015-01-01

The discovery and clinical application of molecular biomarkers in solid tumors, increasingly relies on nucleic acid extraction from FFPE tissue sections and subsequent molecular profiling. This in turn requires the pathological review of haematoxylin & eosin (H&E) stained slides, to ensure sample quality, tumor DNA sufficiency by visually estimating the percentage tumor nuclei and tumor annotation for manual macrodissection. In this study on NSCLC, we demonstrate considerable variation in tumor nuclei percentage between pathologists, potentially undermining the precision of NSCLC molecular evaluation and emphasising the need for quantitative tumor evaluation. We subsequently describe the development and validation of a system called TissueMark for automated tumor annotation and percentage tumor nuclei measurement in NSCLC using computerized image analysis. Evaluation of 245 NSCLC slides showed precise automated tumor annotation of cases using Tissuemark, strong concordance with manually drawn boundaries and identical EGFR mutational status, following manual macrodissection from the image analysis generated tumor boundaries. Automated analysis of cell counts for % tumor measurements by Tissuemark showed reduced variability and significant correlation (p < 0.001) with benchmark tumor cell counts. This study demonstrates a robust image analysis technology that can facilitate the automated quantitative analysis of tissue samples for molecular profiling in discovery and diagnostics. PMID:26317646

Virus-Clip: a fast and memory-efficient viral integration site detection tool at single-base resolution with annotation capability.

PubMed

Ho, Daniel W H; Sze, Karen M F; Ng, Irene O L

2015-08-28

Viral integration into the human genome upon infection is an important risk factor for various human malignancies. We developed viral integration site detection tool called Virus-Clip, which makes use of information extracted from soft-clipped sequencing reads to identify exact positions of human and virus breakpoints of integration events. With initial read alignment to virus reference genome and streamlined procedures, Virus-Clip delivers a simple, fast and memory-efficient solution to viral integration site detection. Moreover, it can also automatically annotate the integration events with the corresponding affected human genes. Virus-Clip has been verified using whole-transcriptome sequencing data and its detection was validated to have satisfactory sensitivity and specificity. Marked advancement in performance was detected, compared to existing tools. It is applicable to versatile types of data including whole-genome sequencing, whole-transcriptome sequencing, and targeted sequencing. Virus-Clip is available at http://web.hku.hk/~dwhho/Virus-Clip.zip.

The effects of prosthetic foot roll-over shape arc length on the gait of trans-tibial prosthesis users.

PubMed

Hansen, Andrew H; Meier, Margrit R; Sessoms, Pinata H; Childress, Dudley S

2006-12-01

The Shape&Roll prosthetic foot was used to examine the effect of roll-over shape arc length on the gait of 14 unilateral trans-tibial prosthesis users. Simple modifications to the prosthetic foot were used to alter the effective forefoot rocker length, leaving factors such as alignment, limb length, and heel and mid-foot characteristics unchanged. Shortening the roll-over shape arc length caused a significant reduction in the maximum external dorsiflexion moment on the prosthetic side at all walking speeds (p < 0.001 for main effect of arc length), due to a reduction in forefoot leverage (moment arm) about the ankle. Roll-over shape arc length significantly affected the initial loading on the sound limb at normal and fast speeds (p = 0.001 for the main effect of arc length), with participants experiencing larger first peaks of vertical ground reaction forces on their sound limbs when using the foot with the shortest effective forefoot rocker arc length. Additionally, the difference between step lengths on the sound and prosthetic limbs was larger with the shortest arc length condition, although this difference was not statistically significant (p = 0.06 for main effect). It appears that prosthesis users may experience a drop-off effect at the end of single limb stance on prosthetic feet with short roll-over shape arc lengths, leading to increased loading and/or a shortened step on the contralateral limb.

Homology to peptide pattern for annotation of carbohydrate-active enzymes and prediction of function.

PubMed

Busk, P K; Pilgaard, B; Lezyk, M J; Meyer, A S; Lange, L

2017-04-12

Carbohydrate-active enzymes are found in all organisms and participate in key biological processes. These enzymes are classified in 274 families in the CAZy database but the sequence diversity within each family makes it a major task to identify new family members and to provide basis for prediction of enzyme function. A fast and reliable method for de novo annotation of genes encoding carbohydrate-active enzymes is to identify conserved peptides in the curated enzyme families followed by matching of the conserved peptides to the sequence of interest as demonstrated for the glycosyl hydrolase and the lytic polysaccharide monooxygenase families. This approach not only assigns the enzymes to families but also provides functional prediction of the enzymes with high accuracy. We identified conserved peptides for all enzyme families in the CAZy database with Peptide Pattern Recognition. The conserved peptides were matched to protein sequence for de novo annotation and functional prediction of carbohydrate-active enzymes with the Hotpep method. Annotation of protein sequences from 12 bacterial and 16 fungal genomes to families with Hotpep had an accuracy of 0.84 (measured as F1-score) compared to semiautomatic annotation by the CAZy database whereas the dbCAN HMM-based method had an accuracy of 0.77 with optimized parameters. Furthermore, Hotpep provided a functional prediction with 86% accuracy for the annotated genes. Hotpep is available as a stand-alone application for MS Windows. Hotpep is a state-of-the-art method for automatic annotation and functional prediction of carbohydrate-active enzymes.

Arc/Arg3.1 governs inflammatory dendritic cell migration from the skin and thereby controls T cell activation.

PubMed

Ufer, Friederike; Vargas, Pablo; Engler, Jan Broder; Tintelnot, Joseph; Schattling, Benjamin; Winkler, Hana; Bauer, Simone; Kursawe, Nina; Willing, Anne; Keminer, Oliver; Ohana, Ora; Salinas-Riester, Gabriela; Pless, Ole; Kuhl, Dietmar; Friese, Manuel A

2016-09-23

Skin-migratory dendritic cells (migDCs) are pivotal antigen-presenting cells that continuously transport antigens to draining lymph nodes and regulate immune responses. However, identification of migDCs is complicated by the lack of distinguishing markers, and it remains unclear which molecules determine their migratory capacity during inflammation. We show that, in the skin, the neuronal plasticity molecule activity-regulated cytoskeleton-associated protein/activity-regulated gene 3.1 (Arc/Arg3.1) was strictly confined to migDCs. Mechanistically, Arc/Arg3.1 was required for accelerated DC migration during inflammation because it regulated actin dynamics through nonmuscle myosin II. Accordingly, Arc/Arg3.1-dependent DC migration was critical for mounting T cell responses in experimental autoimmune encephalomyelitis and allergic contact dermatitis. Thus, Arc/Arg3.1 was restricted to migDCs in the skin and drove fast DC migration by exclusively coordinating cytoskeletal changes in response to inflammatory challenges. These findings commend Arc/Arg3.1 as a universal switch in migDCs that may be exploited to selectively modify immune responses. Copyright © 2016, American Association for the Advancement of Science.

Laser-induced incandescence (LII) diagnostic for in situ monitoring of nanoparticle synthesis in a high-pressure arc discharge

NASA Astrophysics Data System (ADS)

Yatom, Shurik; Vekselman, Vladislav; Mitrani, James; Stratton, Brentley; Raitses, Yevgeny; LaboratoryPlasma Nanosynthesis Team

2016-10-01

A DC arc discharge is commonly used for synthesis of carbon nanoparticles, including buckyballs, carbon nanotubes, and graphene flakes. In this work we show the first results of nanoparticles monitored during the arc discharge. The graphite electrode is vaporized by high current (60 A) in a buffer Helium gas leading to nanoparticle synthesis in a low temperature plasma. The arc was shown to oscillate, which can possibly influence the nano-synthesis. To visualize the nanoparticles in-situ we employ the LII technique. The nanoparticles with radii >50 nm, emerging from the arc area are heated with a short laser pulse and incandesce. The resulting radiation is captured with an ICCD camera, showing the location of the generated nanoparticles. The images of incandescence are studied together with temporally synchronized fast-framing imaging of C2 emission, to connect the dynamics of arc instabilities, C2 molecules concentration and nanoparticles. The time-resolved incandescence signal is analyzed with combination of ex-situ measurements of the synthesized nanoparticles and LII modeling, to provide the size distribution of produced nanoparticles. This work was supported by US Department of Energy, Office of Science, Basic Energy Sciences, Materials Sciences and Engineering Division.

CycADS: an annotation database system to ease the development and update of BioCyc databases

PubMed Central

Vellozo, Augusto F.; Véron, Amélie S.; Baa-Puyoulet, Patrice; Huerta-Cepas, Jaime; Cottret, Ludovic; Febvay, Gérard; Calevro, Federica; Rahbé, Yvan; Douglas, Angela E.; Gabaldón, Toni; Sagot, Marie-France; Charles, Hubert; Colella, Stefano

2011-01-01

In recent years, genomes from an increasing number of organisms have been sequenced, but their annotation remains a time-consuming process. The BioCyc databases offer a framework for the integrated analysis of metabolic networks. The Pathway tool software suite allows the automated construction of a database starting from an annotated genome, but it requires prior integration of all annotations into a specific summary file or into a GenBank file. To allow the easy creation and update of a BioCyc database starting from the multiple genome annotation resources available over time, we have developed an ad hoc data management system that we called Cyc Annotation Database System (CycADS). CycADS is centred on a specific database model and on a set of Java programs to import, filter and export relevant information. Data from GenBank and other annotation sources (including for example: KAAS, PRIAM, Blast2GO and PhylomeDB) are collected into a database to be subsequently filtered and extracted to generate a complete annotation file. This file is then used to build an enriched BioCyc database using the PathoLogic program of Pathway Tools. The CycADS pipeline for annotation management was used to build the AcypiCyc database for the pea aphid (Acyrthosiphon pisum) whose genome was recently sequenced. The AcypiCyc database webpage includes also, for comparative analyses, two other metabolic reconstruction BioCyc databases generated using CycADS: TricaCyc for Tribolium castaneum and DromeCyc for Drosophila melanogaster. Linked to its flexible design, CycADS offers a powerful software tool for the generation and regular updating of enriched BioCyc databases. The CycADS system is particularly suited for metabolic gene annotation and network reconstruction in newly sequenced genomes. Because of the uniform annotation used for metabolic network reconstruction, CycADS is particularly useful for comparative analysis of the metabolism of different organisms. Database URL: http://www.cycadsys.org PMID:21474551

BG7: A New Approach for Bacterial Genome Annotation Designed for Next Generation Sequencing Data

PubMed Central

Pareja-Tobes, Pablo; Manrique, Marina; Pareja-Tobes, Eduardo; Pareja, Eduardo; Tobes, Raquel

2012-01-01

BG7 is a new system for de novo bacterial, archaeal and viral genome annotation based on a new approach specifically designed for annotating genomes sequenced with next generation sequencing technologies. The system is versatile and able to annotate genes even in the step of preliminary assembly of the genome. It is especially efficient detecting unexpected genes horizontally acquired from bacterial or archaeal distant genomes, phages, plasmids, and mobile elements. From the initial phases of the gene annotation process, BG7 exploits the massive availability of annotated protein sequences in databases. BG7 predicts ORFs and infers their function based on protein similarity with a wide set of reference proteins, integrating ORF prediction and functional annotation phases in just one step. BG7 is especially tolerant to sequencing errors in start and stop codons, to frameshifts, and to assembly or scaffolding errors. The system is also tolerant to the high level of gene fragmentation which is frequently found in not fully assembled genomes. BG7 current version – which is developed in Java, takes advantage of Amazon Web Services (AWS) cloud computing features, but it can also be run locally in any operating system. BG7 is a fast, automated and scalable system that can cope with the challenge of analyzing the huge amount of genomes that are being sequenced with NGS technologies. Its capabilities and efficiency were demonstrated in the 2011 EHEC Germany outbreak in which BG7 was used to get the first annotations right the next day after the first entero-hemorrhagic E. coli genome sequences were made publicly available. The suitability of BG7 for genome annotation has been proved for Illumina, 454, Ion Torrent, and PacBio sequencing technologies. Besides, thanks to its plasticity, our system could be very easily adapted to work with new technologies in the future. PMID:23185310

Interplay between stiffness and degradation of architectured gelatin hydrogels leads to differential modulation of chondrogenesis in vitro and in vivo.

PubMed

Sarem, Melika; Arya, Neha; Heizmann, Miriam; Neffe, Axel T; Barbero, Andrea; Gebauer, Tim P; Martin, Ivan; Lendlein, Andreas; Shastri, V Prasad

2018-03-15

The limited capacity of cartilage to heal large lesions through endogenous mechanisms has led to extensive effort to develop materials to facilitate chondrogenesis. Although physical-chemical properties of biomaterials have been shown to impact in vitro chondrogenesis, whether these findings are translatable in vivo is subject of debate. Herein, architectured 3D hydrogel scaffolds (ArcGel) (produced by crosslinking gelatin with ethyl lysine diisocyanate (LDI)) were used as a model system to investigate the interplay between scaffold mechanical properties and degradation on matrix deposition by human articular chondrocytes (HAC) from healthy donors in vitro and in vivo. Using ArcGel scaffolds of different tensile and shear modulus, and degradation behavior; in this study, we compared the fate of ex vivo engineered ArcGels-chondrocytes constructs, i.e. the traditional tissue engineering approach, with thede novoformation of cartilaginous tissue in HAC laden ArcGels in an ectopic nude mouse model. While the softer and fast degrading ArcGel (LNCO3) was more efficient at promoting chondrogenic differentiation in vitro, upon ectopic implantation, the stiffer and slow degrading ArcGel (LNCO8) was superior in maintaining chondrogenic phenotype in HAC and retention of cartilaginous matrix. Furthermore, surprisingly the de novo formation of cartilage tissue was promoted only in LNCO8. Since HAC cultured for only three days in the LNCO8 environment showed upregulation of hypoxia-associated genes, this suggests a potential role for hypoxia in the observed in vivo outcomes. In summary, this study sheds light on how immediate environment (in vivo versus in vitro) can significantly impact the outcomes of cell-laden biomaterials. In this study, 3D architectured hydrogels (ArcGels) with different mechanical and biodegradation properties were investigated for their potential to promote formation of cartilaginous matrix by human articular chondrocytes in vitro and in vivo. Two paradigms were explored (i) ex vivo engineering followed by in vivo implantation in ectopic site of nude mice and (ii) short in vitro culture (3 days) followed by implantation to induce de novo cartilage formation. Softer and fast degrading ArcGel were better at promoting chondrogenesis in vitro, while stiffer and slow degrading ArcGel were strikingly superior in both maintaining chondrogenesis in vivo and inducing de novo formation of cartilage. Our findings highlight the importance of the interplay between scaffold mechanics and degradation in chondrogenesis. Copyright © 2018 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Singular-Arc Time-Optimal Trajectory of Aircraft in Two-Dimensional Wind Field

NASA Technical Reports Server (NTRS)

Nguyen, Nhan

2006-01-01

This paper presents a study of a minimum time-to-climb trajectory analysis for aircraft flying in a two-dimensional altitude dependent wind field. The time optimal control problem possesses a singular control structure when the lift coefficient is taken as a control variable. A singular arc analysis is performed to obtain an optimal control solution on the singular arc. Using a time-scale separation with the flight path angle treated as a fast state, the dimensionality of the optimal control solution is reduced by eliminating the lift coefficient control. A further singular arc analysis is used to decompose the original optimal control solution into the flight path angle solution and a trajectory solution as a function of the airspeed and altitude. The optimal control solutions for the initial and final climb segments are computed using a shooting method with known starting values on the singular arc The numerical results of the shooting method show that the optimal flight path angle on the initial and final climb segments are constant. The analytical approach provides a rapid means for analyzing a time optimal trajectory for aircraft performance.

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

PubMed Central

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

2013-01-01

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

Distinguishing friends, foes, and freeloaders in giant genomes.

PubMed

Bennetzen, Jeffrey L; Park, Minkyu

2018-04-01

Most annotations of large eukaryotic genomes initially find transposable elements (TEs) and other repeats, then mask them so that subsequent efforts can be concentrated on the annotation and study of non-TE genes. However, TEs often contribute to host biology, and their community biologies are of intrinsic interest. This review discusses the challenges, rationale and technologies for comprehensive TE annotation in the commonly giant genomes of animals and plants. Complete discovery of the TEs in a fully sequenced genome is laborious, but feasible, with current strategies in the hands of a careful researcher. These deep TE studies have begun to provide important perspectives on how genomes evolve and the degree to which genome changes do and do not affect eukaryotic biology. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Magma addition rates in continental arcs: New methods of calculation and global implications

NASA Astrophysics Data System (ADS)

Ratschbacher, B. C.; Paterson, S. R.

2017-12-01

The transport of mass, heat and geochemical constituents (elements and volatiles) from the mantle to the atmosphere occurs via magma addition to the lithosphere. Calculation of magma addition rates (MARs) in continental arcs based on exposed proportions of igneous arc rocks is complex and rarely consistently determined. Multiple factors influence MAR calculations such as crust versus mantle contributions to magmas, a change in MARs across the arc and with depths throughout the arc crustal column, `arc tempos' with periods of high and low magmatic activity, the loss of previous emplaced arc rocks by subsequent magmatism and return to the mantle, arc migration, variations in the intrusive versus extrusive additions and evolving arc widths and thicknesses during tectonism. All of these factors need to be considered when calculating MARs.This study makes a new attempt to calculate MARs in continental arcs by studying three arc sections: the Famatinian arc, Argentina, the Sierra Nevada batholith, California and the Coast Mountain batholith, Washington and British Columbia. Arcs are divided into fore-arc, main arc and back arc sections and `boxes' with a defined width, length and thickness spanning upper middle and lower crustal levels are assigned to each section. Representative exposed crustal slices for each depth are then used to calculate MARs based on outcrop proportions for each box. Geochemical data is used to infer crustal recycling percentages and total thickness of the arc. Preliminary results show a correlation between MARs, crustal thicknesses and magmatic flare-up durations. For instance, the Famatinian arc shows a strong decrease in MARs between the main arc section (9.4 km3/Ma/arc-km) and the fore-arc (0.61 km3/Ma/arc-km) and back-arc (1.52 km3/Ma/arc-km) regions and an increase in the amount of magmatism with depth.Global MARs over geologic timescales have the potential to investigate mantle melt generation rates and the volatile outgassing contribution of unerupted arc magmas to the balance of volatile element cycling from the mantle to the surface. We address this question by using exposed arc length estimates from 760 Ma until present (Cao et al. 2017, EPSL) and scale to MARs based on constrains from the detailed study of the three arc sections and a further division into magma-rich and magma-poor arcs.

Mining the Temporal Dimension of the Information Propagation

NASA Astrophysics Data System (ADS)

Berlingerio, Michele; Coscia, Michele; Giannotti, Fosca

In the last decade, Social Network Analysis has been a field in which the effort devoted from several researchers in the Data Mining area has increased very fast. Among the possible related topics, the study of the information propagation in a network attracted the interest of many researchers, also from the industrial world. However, only a few answers to the questions “How does the information propagates over a network, why and how fast?” have been discovered so far. On the other hand, these answers are of large interest, since they help in the tasks of finding experts in a network, assessing viral marketing strategies, identifying fast or slow paths of the information inside a collaborative network. In this paper we study the problem of finding frequent patterns in a network with the help of two different techniques: TAS (Temporally Annotated Sequences) mining, aimed at extracting sequential patterns where each transition between two events is annotated with a typical transition time that emerges from input data, and Graph Mining, which is helpful for locally analyzing the nodes of the networks with their properties. Finally we show preliminary results done in the direction of mining the information propagation over a network, performed on two well known email datasets, that show the power of the combination of these two approaches.

Video Salient Object Detection via Fully Convolutional Networks.

PubMed

Wang, Wenguan; Shen, Jianbing; Shao, Ling

This paper proposes a deep learning model to efficiently detect salient regions in videos. It addresses two important issues: 1) deep video saliency model training with the absence of sufficiently large and pixel-wise annotated video data and 2) fast video saliency training and detection. The proposed deep video saliency network consists of two modules, for capturing the spatial and temporal saliency information, respectively. The dynamic saliency model, explicitly incorporating saliency estimates from the static saliency model, directly produces spatiotemporal saliency inference without time-consuming optical flow computation. We further propose a novel data augmentation technique that simulates video training data from existing annotated image data sets, which enables our network to learn diverse saliency information and prevents overfitting with the limited number of training videos. Leveraging our synthetic video data (150K video sequences) and real videos, our deep video saliency model successfully learns both spatial and temporal saliency cues, thus producing accurate spatiotemporal saliency estimate. We advance the state-of-the-art on the densely annotated video segmentation data set (MAE of .06) and the Freiburg-Berkeley Motion Segmentation data set (MAE of .07), and do so with much improved speed (2 fps with all steps).This paper proposes a deep learning model to efficiently detect salient regions in videos. It addresses two important issues: 1) deep video saliency model training with the absence of sufficiently large and pixel-wise annotated video data and 2) fast video saliency training and detection. The proposed deep video saliency network consists of two modules, for capturing the spatial and temporal saliency information, respectively. The dynamic saliency model, explicitly incorporating saliency estimates from the static saliency model, directly produces spatiotemporal saliency inference without time-consuming optical flow computation. We further propose a novel data augmentation technique that simulates video training data from existing annotated image data sets, which enables our network to learn diverse saliency information and prevents overfitting with the limited number of training videos. Leveraging our synthetic video data (150K video sequences) and real videos, our deep video saliency model successfully learns both spatial and temporal saliency cues, thus producing accurate spatiotemporal saliency estimate. We advance the state-of-the-art on the densely annotated video segmentation data set (MAE of .06) and the Freiburg-Berkeley Motion Segmentation data set (MAE of .07), and do so with much improved speed (2 fps with all steps).

Magnetotail energy dissipation during an auroral substorm

PubMed Central

Panov, E.V.; Baumjohann, W.; Wolf, R.A.; Nakamura, R.; Angelopoulos, V.; Weygand, J. M.; Kubyshkina, M.V.

2016-01-01

Violent releases of space plasma energy from the Earth’s magnetotail during substorms produce strong electric currents and bright aurora. But what modulates these currents and aurora and controls dissipation of the energy released in the ionosphere? Using data from the THEMIS fleet of satellites and ground-based imagers and magnetometers, we show that plasma energy dissipation is controlled by field-aligned currents (FACs) produced and modulated during magnetotail topology change and oscillatory braking of fast plasma jets at 10-14 Earth radii in the nightside magnetosphere. FACs appear in regions where plasma sheet pressure and flux tube volume gradients are non-collinear. Faster tailward expansion of magnetotail dipolarization and subsequent slower inner plasma sheet restretching during substorm expansion and recovery phases cause faster poleward then slower equatorward movement of the substorm aurora. Anharmonic radial plasma oscillations build up displaced current filaments and are responsible for discrete longitudinal auroral arcs that move equatorward at a velocity of about 1km/s. This observed auroral activity appears sufficient to dissipate the released energy. PMID:27917231

Communication Apprehension. Focused Access to Selected Topics (FAST) Bibliography No. 15.

ERIC Educational Resources Information Center

Shermis, Michael

This annotated bibliography contains 31 references of articles and papers in the ERIC database that deal with communication apprehension (CA). The first section provides strategies for instructors and students to alleviate communication apprehension, speech anxiety, stage fright, and other problems people have with public speaking. The second…

Fast, Nonspattering Inert-Gas Welding

NASA Technical Reports Server (NTRS)

Gilbert, Jeffrey L.

1991-01-01

Proposed welding technique combines best features of metal (other than tungsten)/inert-gas welding, plasma arc welding, and tungsten/inert-gas welding. Advantages include: wire fed to weld joint preheated, therefore fed at high speed without spattering; high-frequency energy does not have to be supplied to workpiece to initiate welding; size of arc gap not critical, power-supply control circuit adjusts voltage across gap to compensate for changes; only low gas-flow rate needed; welding electrode replaced easily as prefabricated assembly; external wire-feeding manipulator not needed; and welding process relatively forgiving of operator error.

Global Identification and Characterization of Transcriptionally Active Regions in the Rice Genome

PubMed Central

Stolc, Viktor; Deng, Wei; He, Hang; Korbel, Jan; Chen, Xuewei; Tongprasit, Waraporn; Ronald, Pamela; Chen, Runsheng; Gerstein, Mark; Wang Deng, Xing

2007-01-01

Genome tiling microarray studies have consistently documented rich transcriptional activity beyond the annotated genes. However, systematic characterization and transcriptional profiling of the putative novel transcripts on the genome scale are still lacking. We report here the identification of 25,352 and 27,744 transcriptionally active regions (TARs) not encoded by annotated exons in the rice (Oryza. sativa) subspecies japonica and indica, respectively. The non-exonic TARs account for approximately two thirds of the total TARs detected by tiling arrays and represent transcripts likely conserved between japonica and indica. Transcription of 21,018 (83%) japonica non-exonic TARs was verified through expression profiling in 10 tissue types using a re-array in which annotated genes and TARs were each represented by five independent probes. Subsequent analyses indicate that about 80% of the japonica TARs that were not assigned to annotated exons can be assigned to various putatively functional or structural elements of the rice genome, including splice variants, uncharacterized portions of incompletely annotated genes, antisense transcripts, duplicated gene fragments, and potential non-coding RNAs. These results provide a systematic characterization of non-exonic transcripts in rice and thus expand the current view of the complexity and dynamics of the rice transcriptome. PMID:17372628

IODP Expedition 351 Izu-Bonin-Mariana Arc Origins: Preliminary Results

NASA Astrophysics Data System (ADS)

Ishizuka, O.; Arculus, R. J.; Bogus, K.

2014-12-01

Understanding how subduction zones initiate and continental crust forms in intraoceanic arcs requires knowledge of the inception and evolution of a representative intraoceanic arc, such as the Izu-Bonin-Mariana (IBM) Arc system. This can be obtained by exploring regions adjacent to an arc, where unequivocal pre-arc crust overlain by undisturbed arc-derived materials exists. IODP Exp. 351 (June-July 2014) specifically targeted evidence for the earliest evolution of the IBM system following inception. Site U1438 (4711 m water depth) is located in the Amami Sankaku Basin (ASB), west of the Kyushu-Palau Ridge (KPR), a paleo-IBM arc. Primary objectives of Exp. 351 were: 1) determine the nature of the crust and mantle pre-existing the IBM arc; 2) identify and model the process of subduction initiation and initial arc crust formation; 3) determine the compositional evolution of the IBM arc during the Paleogene; 4) establish geophysical properties of the ASB. Seismic reflection profiles indicate a ~1.3 km thick sediment layer overlying ~5.5 km thick igneous crust, presumed to be oceanic. This igneous crust seemed likely to be the basement of the IBM arc. Four holes were cored at Site U1438 spanning the entire sediment section and into basement. The cored interval comprises 5 units: uppermost Unit I is hemipelagic sediment with intercalated ash layers, presumably recording explosive volcanism mainly from the Ryukyu and Kyushu arcs; Units II and III host a series of volcaniclastic gravity-flow deposits, likely recording the magmatic history of the IBM Arc from arc initiation until 25 Ma; Siliceous pelagic sediment (Unit IV) underlies these deposits with minimal coarse-grained sediment input and may pre-date arc initiation. Sediment-basement contact occurs at 1461 mbsf. A basaltic lava flow section dominantly composed of plagioclase and clinopyroxene with rare chilled margins continues to the bottom of the Site (1611 mbsf). The expedition successfully recovered pre-IBM Arc basement, a volcanic and geologic record spanning pre-Arc, Arc initiation to remnant Arc stages, which permits testing for subduction initiation and subsequent Arc evolution.

Impurity Radiation From The LHCD Launcher During Operation In JET And Investigation Of Launcher Damage

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

Kirov, K.K.; Mailloux, J.; Ekedahl, A.

2005-09-26

In this study, the most likely causes of the enhanced radiation in front of the LHCD launcher are investigated: fast ions from the warm plasma, fast electrons parasitically accelerated in front of the grill and arcs. Evidence for the presence of each of these mechanisms is discussed. The experimental conditions favouring the appearance of these phenomena and their impact on the launcher have also been highlighted.

Structure and seismicity of the upper mantle using deployments of broadband seismographs in Antarctica and the Mariana Islands

NASA Astrophysics Data System (ADS)

Barklage, Mitchell

We determine shear wave splitting parameters of teleseismic SKS and SKKS phases recorded at 43 broadband seismometers deployed in South Victoria Land as part of the Transantarctic Mountains seismic experiment (TAMSEIS) from 2000-2003. We use an eigenvalue technique to linearize the rotated and shifted shear wave particle motions and determine the best splitting parameters. The data show a fairly consistent fast direction of azimuthal anisotropy oriented approximately N60°E with splitting times of about 1 second. Based on a previous study of the azimuthal variations of Rayleigh wave phase velocities which show a similar fast direction, we suggest the anisotropy is localized in the uppermost mantle, with a best estimate of 3% anisotropy in a layer of about 150 km thickness. We suggest that the observed anisotropy near the Ross Sea coast, a region underlain by thin lithosphere, results either from upper mantle flow related to Cenozoic Ross Sea extension or to edge-driven convection associated with a sharp change in lithospheric thickness between East and West Antarctica. Both hypotheses are consistent with the more E-W fast axis orientation for stations on Ross Island and along the coast, sub-parallel to the extension direction and the lithospheric boundary. Anisotropy in East Antarctica, which is underlain by cold thick continental lithosphere, must be localized within the lithospheric upper mantle and reflect a relict tectonic fabric from past deformation events. Fast axes for the most remote stations in the Vostok Highlands are rotated by 20° and are parallel to splitting measurements at South Pole. These observations seem to delineate a distinct domain of lithospheric fabric, which may represent the extension of the Darling Mobile Belt or Pinjarra Orogen into the interior of East Antarctica. Seismic tomography imaging provides an opportunity to constrain mantle wedge processes associated with subduction, volatile transport, arc volcanism, and back-arc spreading. We investigate seismic velocity structure of the upper mantle across the Central Mariana subduction system using data from the 2003-2004 Mariana Subduction Factory Imaging Experiment. This 11-month experiment consisted of 20 broadband seismic stations deployed on islands and 58 semi-broadband ocean bottom seismographs deployed across the forearc, island arc, and back-arc spreading center. We determine Vp and Vp/Vs structure on a three dimensional grid using over 25,000 local travel time observations as well as over 2000 teleseismic arrival times determined by waveform cross correlation. The mantle wedge is characterized by a region of low velocity and high Vp/Vs beneath the forearc, an inclined zone of low velocity underlying the volcanic front, and a broad region of low velocity beneath the back-arc spreading center. The slow velocity anomalies are strongest at roughly 20-30 km depth in the forearc, 60-70 km depth beneath the volcanic arc, and 20-30 km beneath the back-arc spreading center. The slow velocity anomalies beneath the arc and back-arc appear as separate and distinct features in our images, with a small channel of connectivity occurring at approximately 75 km depth. The subducting Pacific plate is characterized by high seismic velocities. An exception occurs in the forearc beneath the big blue seamount and at the top of the slab at roughly 80 km depth where slow velocities are observed. We interpret the forearc anomalies to represent a region of large scale serpentinization of the mantle whereas the arc and back-arc anomalies represent regions of high temperature with a small amount of increased water content and/or melt and constrain the source regions in the mantle for arc and back-arc lavas. We investigate the double seismic zone (dsz) beneath the Central Mariana Arc using data from a land-sea array of 58 ocean bottom seismographs and 20 land seismographs deployed during 2003-2004. Nearly 600 well-recorded earthquakes were located using a P and S wave arrival times and a double difference relocation technique. The double seismic zone is well imaged from the forearc region to a depth of nearly 200 km. The width of the dsz is approximately 30 km at shallow depths and gradually becomes narrower with depth until it is now longer resolvable at depths greater than 180-200 km. Focal mechanisms determined from P and S wave polarities and amplitudes indicate that events from 70-150 km depth show along strike extension, whereas events greater than 150 km show downdip extension. Both the upper and lower zones of the dsz show similar focal mechanisms, demonstrating that the dsz is not caused by bending or unbending stresses. Along-strike tension may result from stresses related to the increasing curvature of the Mariana slab over the past few million years, as indicated by plate reconstructions. Downdip extension may result from slab pull forces consistent with the strong density anomaly of an old, cold plate relative to the surrounding mantle.

An efficient annotation and gene-expression derivation tool for Illumina Solexa datasets

PubMed Central

2010-01-01

Background The data produced by an Illumina flow cell with all eight lanes occupied, produces well over a terabyte worth of images with gigabytes of reads following sequence alignment. The ability to translate such reads into meaningful annotation is therefore of great concern and importance. Very easily, one can get flooded with such a great volume of textual, unannotated data irrespective of read quality or size. CASAVA, a optional analysis tool for Illumina sequencing experiments, enables the ability to understand INDEL detection, SNP information, and allele calling. To not only extract from such analysis, a measure of gene expression in the form of tag-counts, but furthermore to annotate such reads is therefore of significant value. Findings We developed TASE (Tag counting and Analysis of Solexa Experiments), a rapid tag-counting and annotation software tool specifically designed for Illumina CASAVA sequencing datasets. Developed in Java and deployed using jTDS JDBC driver and a SQL Server backend, TASE provides an extremely fast means of calculating gene expression through tag-counts while annotating sequenced reads with the gene's presumed function, from any given CASAVA-build. Such a build is generated for both DNA and RNA sequencing. Analysis is broken into two distinct components: DNA sequence or read concatenation, followed by tag-counting and annotation. The end result produces output containing the homology-based functional annotation and respective gene expression measure signifying how many times sequenced reads were found within the genomic ranges of functional annotations. Conclusions TASE is a powerful tool to facilitate the process of annotating a given Illumina Solexa sequencing dataset. Our results indicate that both homology-based annotation and tag-count analysis are achieved in very efficient times, providing researchers to delve deep in a given CASAVA-build and maximize information extraction from a sequencing dataset. TASE is specially designed to translate sequence data in a CASAVA-build into functional annotations while producing corresponding gene expression measurements. Achieving such analysis is executed in an ultrafast and highly efficient manner, whether the analysis be a single-read or paired-end sequencing experiment. TASE is a user-friendly and freely available application, allowing rapid analysis and annotation of any given Illumina Solexa sequencing dataset with ease. PMID:20598141

Differential expression of appetite-regulating genes in avian models of anorexia and obesity.

PubMed

Yi, J; Yuan, J; Gilbert, E R; Siegel, P B; Cline, M A

2017-08-01

Chickens from lines that have been selected for low (LWS) or high (HWS) juvenile body weight for more than 57 generations provide a unique model by which to research appetite regulation. The LWS display different severities of anorexia, whereas all HWS become obese. In the present study, we measured mRNA abundance of various factors in appetite-associated nuclei in the hypothalamus. The lateral hypothalamus (LHA), paraventricular nucleus (PVN), ventromedial hypothalamus (VMH), dorsomedial nucleus (DMN) and arcuate nucleus (ARC) were collected from 5 day-old chicks that were fasted for 180 minutes or provided with continuous access to food. Fasting increased neuropeptide Y receptor subtype 1 (NPYR1) mRNA in the LHA and c-Fos in the VMH, at the same time as decreasing c-Fos in the LHA, neuropeptide Y receptor subtype 5 and ghrelin in the PVN, and neuropeptide Y receptor subtype 2 in the ARC. Fasting increased melanocortin receptor subtype 3 (MC3R) expression in the DMN and NPY in the ARC of LWS but not HWS chicks. Expression of NPY was greater in LWS than HWS in the DMN. neuropeptide Y receptor subtype 5 mRNA was greater in LWS than HWS in the LHA, PVN and ARC. Expression of orexin was greater in LWS than HWS in the LHA. There was greater expression of NPYR1, melanocortin receptor subtype 4 and cocaine- and amphetamine-regulated transcript in HWS than LWS and mesotocin in LWS than HWS in the PVN. In the ARC, agouti-related peptide and MC3R were greater in LWS than HWS and, in the VMH, orexin receptor 2 and leptin receptor were greater in LWS than HWS. Greater mesotocin in the PVN, orexin in the LHA and ORXR2 in the VMH of LWS may contribute to their increased sympathetic tone and anorexic phenotype. The results of the present study also suggest that an increased hypothalamic anorexigenic tone in the LWS over-rides orexigenic factors such as NPY and AgRP that were more highly expressed in LWS than HWS in several nuclei. Published 2017. This article is a U.S. Government work and is in the public domain in the USA.

The sensitivity in the IR spectrum of the intact and pathological tissues by laser biophotometry.

PubMed

Ravariu, Cristian; Bondarciuc, Ala

2014-03-01

In this paper, we use the laser biophotometry for in vivo investigations, searching the most sensitive interactions of the near-infrared spectrum with different tissues. The experimental methods are based on the average reflection coefficient (ARC) measurements. For healthy persons, ARC is the average of five values provided by the biophotometer. The probe is applied on dry skin with minimum pilosity, in five regions: left-right shank, left-right forearm, and epigastrium. For the pathological tissues, the emitting terminal is moved over the suspected area, controlling the reflection coefficient level, till a minimum value occurs, as ARC-Pathological. Then, the probe is moved on the symmetrical healthy region of the body to read the complementary coefficient from intact tissue, ARC-Intact, from the same patient. The experimental results show an ARC range between 67 and 59 mW for intact tissues and a lower range, up to 58-42 mW, for pathological tissues. The method is efficient only in those pathological processes accompanied by variable skin depigmentation, water retention, inflammation, thrombosis, or swelling. Frequently, the ARC ranges are overlapping for some diseases. This induces uncertain diagnosis. Therefore, a statistical algorithm is adopted for a differential diagnosis. The laser biophotometry provides a quantitative biometric parameter, ARC, suitable for fast diagnosis in the internal and emergency medicine. These laser biophotometry measurements are representatives for the Romanian clinical trials.

Stability of Alfvén eigenmodes in the vicinity of auroral arc

NASA Astrophysics Data System (ADS)

Hiraki, Yasutaka

2013-08-01

The purpose of this study is to give a theoretical suggestion to the essential question why east-west elongated auroral arc can keep its anisotropic structure for a long time. It could be related to the stability of east-westward traveling modes in the vicinity of arc, which may develop into wavy or spiral structures, whereas north-southward modes are related to splitting of arcs. Taking into account the arc-inducing field-aligned current and magnetic shears, we examine changes in the stability of Alfvén eigenmodes that are coupled to perpendicular modes in the presence of convection electric field. It is demonstrated that the poleward current shear suppresses growth of the westward mode in case of the westward convection electric field. Only the poleward mode is still unstable because of the properties of feedback shear waves. It is suggested that this tends to promote (poleward) arc splitting as often observed during quiet times. We further draw a diagram of the westward mode growth rate as a function of convection electric field and current shear, evaluating critical fields for instabilities of lower Alfvén harmonics. It is discovered that a switching phenomenon of fast-growing mode from fundamental to the first harmonic occurs for a high electric field regime. Our stability criterion is applied to some observed situations of auroral arc current system during pre-breakup active times.

A micro-computed tomography study of the negotiation and anatomical feature in apical root canal of mandibular molars.

PubMed

Min, Yi; Ma, Jing-Zhi; Shen, Ya; Cheung, Gary Shun-Pan; Gao, Yuan

2016-11-01

The aim of this study was to investigate the clinical negotiation of various apical anatomic features of the mandibular first molars in a Chinese population using micro-computed tomography (micro-CT). A total of 152 mandibular first molars were scanned with micro-CT at 30 µm resolution. The apical 5 mm of root canal (ARC) was reconstructed three dimensionally and classified. Subsequently, the access cavity was prepared with the ARC anatomy blinded to the operator. The ARC was negotiated with a size 10 K file with or without precurve. Information on the ability to obtain a reproducible glide path was recorded. The anatomical classification of ARC was Type I with 68.45% in mandibular first molars. The negotiation result of ARC with Category i was 387 canals (74.00%). With a bent negotiating file, 96 canals were negotiated, including 88 reproducible glide paths (Category ii) and 8 irregular glide paths (Category iii). About 7.65% canals could not be negotiated with patency successfully (Category iv). The statistical analyze shown the anatomic feature of ARC had effect on the negotiation of ARC (p < 0.05). In conclusion, ARC anatomic variations had a strong potential impact on the negotiation. The category of negotiation in ARC would be helpful in the using of NiTi rotary instruments. Negotiation of ARC to the working length with patency should be careful and skillful because of the complexities of ARC. SCANNING 38:819-824, 2016. © 2016 Wiley Periodicals, Inc. © Wiley Periodicals, Inc.

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

PubMed Central

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

2007-01-01

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

Characterization of the transcriptome of fast and slow muscle myotomal fibres in the pacu (Piaractus mesopotamicus).

PubMed

Mareco, Edson A; Garcia de la Serrana, Daniel; Johnston, Ian A; Dal-Pai-Silva, Maeli

2015-03-14

The Pacu (Piaractus mesopotamicus) is a member of the Characiform family native to the Prata Basin (South America) and a target for the aquaculture industry. A limitation for the development of a selective breeding program for this species is a lack of available genetic information. The primary objectives of the present study were 1) to increase the genetic resources available for the species, 2) to exploit the anatomical separation of myotomal fibres types to compare the transcriptomes of slow and fast muscle phenotypes and 3) to systematically investigate the expression of Ubiquitin Specific Protease (USP) family members in fast and slow muscle in response to fasting and refeeding. We generated 0.6 Tb of pair-end reads from slow and fast skeletal muscle libraries. Over 665 million reads were assembled into 504,065 contigs with an average length of 1,334 bp and N50 = 2,772 bp. We successfully annotated nearly 47% of the transcriptome and identified around 15,000 unique genes and over 8000 complete coding sequences. 319 KEGG metabolic pathways were also annotated and 380 putative microsatellites were identified. 956 and 604 genes were differentially expressed between slow and fast skeletal muscle, respectively. 442 paralogues pairs arising from the teleost-specific whole genome duplication were identified, with the majority showing different expression patterns between fibres types (301 in slow and 245 in fast skeletal muscle). 45 members of the USP family were identified in the transcriptome. Transcript levels were quantified by qPCR in a separate fasting and refeeding experiment. USP genes in fast muscle showed a similar transient increase in expression with fasting as the better characterized E3 ubiquitin ligases. We have generated a 53-fold coverage transcriptome for fast and slow myotomal muscle in the pacu (Piaractus mesopotamicus) significantly increasing the genetic resources available for this important aquaculture species. We describe significant differences in gene expression between muscle fibre types for fundamental components of general metabolism, the Pi3k/Akt/mTor network and myogenesis, including detailed analysis of paralogue expression. We also provide a comprehensive description of USP family member expression between muscle fibre types and with changing nutritional status.

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

Ryan, Philip Michael; Ahn, Joonwook; Bell, R. E.

High-harmonic fast wave (HHFW) heating and current drive is being developed in NSTX to provide bulk electron heating and q(0) control during non-inductively sustained Hmode plasmas fuelled by deuterium neutral-beam injection (NBI). In addition, it is used to assist the plasma current ramp-up. A major modification to increase the RF power limit was made in 2009; the original end-grounded, single end-powered current straps of the 12- element array were replaced with center-grounded, double end-powered straps. Greater than 3 MW have been coupled into NBI-driven, ELMy H-mode plasmas with this upgraded antenna. Improved core HHFW heating, particularly at longer wavelengths andmore » during low-density start-up and plasma current ramp-up, has been obtained by lowering the edge density with lithium wall conditioning, thereby moving the critical density for fast-wave propagation away from the vessel wall [1]. Significant core electron heating of NBI-fuelled H-modes has been observed for the first time over a range of launched wavelengths and H-modes can be accessed by HHFW alone. Visible and IR camera images of the antenna and divertor indicate that fast wave interactions can deposit considerable RF energy on the outboard divertor plate, especially at longer wavelengths that begin to propagate closer to the vessel walls. Edge power loss can also arise from HHFWgenerated parametric decay instabilities; edge ion heating is observed that is wavelength dependent. During plasmas where HHFW is combined with NBI, there is a significant enhancement in neutron rate, and fast-ion D-alpha (FIDA) emission measurements clearly show broadening of the fast-ion profile in the plasma core. Large edge localized modes (ELMs) have been observed immediately following the termination of RF power, whether the power turn off is programmed or due to antenna arcing. Causality has not been established but new experiments are planned and will be reported. Fast digitization of the reflected power signal indicates a much faster rise time for arcs than for ELMs. Based on this observation, an ELM/arc discrimination system is being implemented to maintain RF power during ELMs even when the reflection coefficient becomes large. This work is supported by US DOE contracts DE-AC-05-00OR22725 and DE-AC02- 09CH11466. References [1] C. K. Phillips, et al, Nuclear Fusion 10, 075015 (2009)« less

Single-molecule fluorimetry and gating currents inspire an improved optical voltage indicator

PubMed Central

Treger, Jeremy S; Priest, Michael F; Bezanilla, Francisco

2015-01-01

Voltage-sensing domains (VSDs) underlie the movement of voltage-gated ion channels, as well as the voltage-sensitive fluorescent responses observed from a common class of genetically encoded voltage indicators (GEVIs). Despite the widespread use and potential utility of these GEVIs, the biophysical underpinnings of the relationship between VSD movement and fluorophore response remain unclear. We investigated the recently developed GEVI ArcLight, and its close variant Arclight', at both the single-molecule and macroscopic levels to better understand their characteristics and mechanisms of activity. These studies revealed a number of previously unobserved features of ArcLight's behavior, including millisecond-scale fluorescence fluctuations in single molecules as well as a previously unreported delay prior to macroscopic fluorescence onset. Finally, these mechanistic insights allowed us to improve the optical response of ArcLight to fast or repetitive pulses with the development of ArcLightning, a novel GEVI with improved kinetics. DOI: http://dx.doi.org/10.7554/eLife.10482.001 PMID:26599732

Flow Shears at the Poleward Boundary of Omega Bands Observed During Conjunctions of Swarm and THEMIS ASI

NASA Astrophysics Data System (ADS)

Liu, Jiang; Lyons, L. R.; Archer, W. E.; Gallardo-Lacourt, B.; Nishimura, Y.; Zou, Ying; Gabrielse, C.; Weygand, J. M.

2018-02-01

Omega bands are curved aurora forms that evolve from a quiet arc located along the poleward edge of a diffuse auroral band within the midnight to morningside auroral oval. They usually propagate eastward. Because omega bands are a significant contributor to an active magnetotail, knowledge about their generation is important for understanding tail dynamics. Previous studies have shown that auroral streamers, footprints of fast flows in the tail, can propagate into omega bands. Such events, however, are limited, and it is still unclear whether and how the flows trigger the bands. The ionospheric flows associated with omega bands may provide valuable information on the driving mechanisms of the bands. We examine these flows taking advantage of the conjunctions between the Swarm spacecraft and Time History of Events and Macroscale Interactions during Substorms all-sky imagers, which allow us to demonstrate the relative location of the flows to the omega bands' bright arcs for the first time. We find that a strong eastward ionospheric flow is consistently present immediately poleward of the omega band's bright arc, resulting in a sharp flow shear near the poleward boundary of the band. This ionospheric flow shear should correspond to a flow shear near the inner edge of the plasma sheet. This plasma sheet shear may drive a Kelvin-Helmholz instability which then distorts the quiet arc to form omega bands. It seems plausible that the strong eastward flows are driven by streamer-related fast flows or enhanced convection in the magnetotail.

Petrological, geochemical, isotopic, and geochronological constraints for the Late Devonian-Early Carboniferous magmatism in SW Gondwana (27-32°LS): an example of geodynamic switching

NASA Astrophysics Data System (ADS)

Dahlquist, Juan A.; Alasino, Pablo H.; Basei, Miguel A. S.; Morales Cámera, Matías M.; Macchioli Grande, Marcos; da Costa Campos Neto, Mario

2018-04-01

We report a study integrating 13 new U-Pb LA-MC-ICP-MS zircon ages and Hf-isotope data from dated magmatic zircons together with complete petrological and whole-rock geochemistry data for the dated granitic rocks. Sample selection was strongly based on knowledge reported in previous investigations. Latest Devonian-Early Carboniferous granite samples were collected along a transect of 900 km, from the inner continental region (present-day Eastern Sierras Pampeanas) to the magmatic arc (now Western Sierras Pampeanas and Frontal Cordillera). Based on these data together with ca. 100 published whole-rock geochemical analyses we conclude that Late Devonian-Early Carboniferous magmatism at this latitude represents continuous activity (ranging from 322 to 379 Ma) on the pre-Andean margin of SW Gondwana, although important whole-rock and isotopic compositional variations occurred through time and space. Combined whole-rock chemistry and isotope data reveal that peraluminous A-type magmatism started in the intracontinental region during the Late Devonian, with subsequent development of synchronous Carboniferous peraluminous and metaluminous A-type magmatism in the retro-arc region and calc-alkaline magmatism in the western paleomargin. We envisage that magmatic evolution was mainly controlled by episodic fluctuations in the angle of subduction of the oceanic plate (between flat-slab and normal subduction), supporting a geodynamic switching model. Subduction fluctuations were relatively fast (ca. 7 Ma) during the Late Devonian and Early Carboniferous, and the complete magmatic switch-off and switch-on process lasted for 57 Ma. Hf T DM values of zircon (igneous and inherited) from some Carboniferous peraluminous A-type granites in the retro-arc suggest that Gondwana continental lithosphere formed during previous orogenies was partly the source of the Devonian-Carboniferous granitic magmas, thus precluding the generation of the parental magmas from exotic terranes.

Fast T Wave Detection Calibrated by Clinical Knowledge with Annotation of P and T Waves.

PubMed

Elgendi, Mohamed; Eskofier, Bjoern; Abbott, Derek

2015-07-21

There are limited studies on the automatic detection of T waves in arrhythmic electrocardiogram (ECG) signals. This is perhaps because there is no available arrhythmia dataset with annotated T waves. There is a growing need to develop numerically-efficient algorithms that can accommodate the new trend of battery-driven ECG devices. Moreover, there is also a need to analyze long-term recorded signals in a reliable and time-efficient manner, therefore improving the diagnostic ability of mobile devices and point-of-care technologies. Here, the T wave annotation of the well-known MIT-BIH arrhythmia database is discussed and provided. Moreover, a simple fast method for detecting T waves is introduced. A typical T wave detection method has been reduced to a basic approach consisting of two moving averages and dynamic thresholds. The dynamic thresholds were calibrated using four clinically known types of sinus node response to atrial premature depolarization (compensation, reset, interpolation, and reentry). The determination of T wave peaks is performed and the proposed algorithm is evaluated on two well-known databases, the QT and MIT-BIH Arrhythmia databases. The detector obtained a sensitivity of 97.14% and a positive predictivity of 99.29% over the first lead of the validation databases (total of 221,186 beats). We present a simple yet very reliable T wave detection algorithm that can be potentially implemented on mobile battery-driven devices. In contrast to complex methods, it can be easily implemented in a digital filter design.

Interplay effect on a 6-MV flattening-filter-free linear accelerator with high dose rate and fast multi-leaf collimator motion treating breast and lung phantoms.

PubMed

Netherton, Tucker; Li, Yuting; Nitsch, Paige; Shaitelman, Simona; Balter, Peter; Gao, Song; Klopp, Ann; Muruganandham, Manickam; Court, Laurence

2018-06-01

Using a new linear accelerator with high dose rate (800 MU/min), fast MLC motions (5.0 cm/s), fast gantry rotation (15 s/rotation), and 1 cm wide MLCs, we aimed to quantify the effects of complexity, arc number, and fractionation on interplay for breast and lung treatments under target motion. To study lung interplay, eight VMAT plans (1-6 arcs) and four-nine-field sliding-window IMRT plans varying in complexity were created. For the breast plans, four-four-field sliding-window IMRT plans were created. Using the Halcyon 1.0 linear accelerator, each plan was delivered five times each under sinusoidal breathing motion to a phantom with 20 implanted MOSFET detectors; MOSFET dose (cGy), delivery time, and MU/cGy values were recorded. Maximum and mean dose deviations were calculated from MOSFET data. The number of MOSFETs with at least 19 of 20 detectors agreeing with their expected dose within 5% per fraction was calculated across 10 6 iterations to model dose deviation as function of fraction number for all plan variants. To put interplay plans into clinical context, additional IMRT and VMAT plans were created and delivered for the sites of head and neck, prostate, whole brain, breast, pelvis, and lung. Average modulation and interplay effect were compared to those from conventional linear accelerators, as reported from previous studies. The mean beam modulation for plans created for the Halcyon 1.0 linear accelerator was 2.9 MU/cGy (two- to four-field IMRT breast plans), 6.2 MU/cGy (at least five-field IMRT), and 3.6 MU/cGy (four-arc VMAT). To achieve treatment plan objectives, Halcyon 1.0 VMAT plans require more arcs and modulation than VMAT on conventional linear accelerators. Maximum and mean dose deviations increased with increasing plan complexity under tumor motion for breast and lung treatments. Concerning VMAT plans under motion, maximum, and mean dose deviations were higher for one arc than for two arcs regardless of plan complexity. For plan variants with maximum dose deviations greater than 3.7%, dose deviation as a function of fraction number was protracted. For treatments on the Halcyon 1.0 linear accelerator, the convergence of dose deviation with fraction number happened more slowly than reported for conventional linear accelerators. However, if plan complexity is reduced for IMRT and if tumor motion is less than ~10-mm, interplay is greatly reduced. To minimize dose deviations across multiple fractions for dynamic targets, we recommend limiting treatment plan complexity and avoiding one-arc VMAT on the Halcyon 1.0 linear accelerator when interplay is a concern. © 2018 American Association of Physicists in Medicine.

Teenage Television Viewing. Focused Access to Selected Topics (FAST) Bibliography No. 8.

ERIC Educational Resources Information Center

Shermis, Michael

Surveying the television habits of teenagers, this annotated bibliography contains 30 references of articles and papers in the ERIC database. The first section, "Impact on Health, Sexual Behavior, Use of Alcohol," addresses such issues as the relationship of viewing sexual content to sexual activity and sex role acquisition, and relationships…

The News about High School Journalism: Focused Access to Selected Topics (FAST) Bibliography No. 4.

ERIC Educational Resources Information Center

Cowles, Margaret Haining

This annotated bibliography contains 33 items from the ERIC database on high school journalism topics of interest to student writers and editors, journalism instructors, publications advisers, and school administrators. The first section contains overviews. Ensuing sections address how journalism benefits students; legal issues in high school…

Nuclear, Chloroplast, and Mitochondrial Genome Sequences of the Prospective Microalgal Biofuel Strain Picochlorum soloecismus

DOE PAGES

Gonzalez-Esquer, C. Raul; Twary, Scott N.; Hovde, Blake T.; ...

2018-01-25

Picochlorum soloecismus is a halotolerant, fast-growing, and moderate-lipid-producing microalga that is being evaluated as a renewable feedstock for biofuel production. Herein, we report on an improved high-quality draft assembly and annotation for the nuclear, chloroplast, and mitochondrial genomes of P. soloecismus DOE 101.

Business Ethics. Focused Access to Selected Topics (FAST) Bibliography No. 17.

ERIC Educational Resources Information Center

Shermis, Michael

Addressing the needs of students who choose careers in business, this annotated bibliography contains 30 references of articles and papers in the ERIC database dealing with ethics in business. Sources cited in the first section, "Business Instruction," deal with teaching ethics in business communication, business literature, and other areas of the…

Wave-particle interactions on the FAST satellite

NASA Technical Reports Server (NTRS)

Temerin, M. A.; Carlson, C. W.; Cattell, C. A.; Ergun, R. E.; Mcfadden, J. P.

1990-01-01

NASA's Fast Auroral Snapshot, or 'FAST' satellite, scheduled for launch in 1993, will investigate the plasma physics of the low altitude auroral zone from a 3500-km apogee polar orbit. FAST will give attention to wave, double-layer, and soliton production processes due to electrons and ions, as well as to wave-wave interactions, and the acceleration of electrons and ions by waves and electric fields. FAST will employ an intelligent data-handling system capacle of data acquisition at rates of up to 1 Mb/sec, in addition to a 1-Gbit solid-state memory. The data need be gathered for only a few minutes during passes through the auroral zone, since the most interesting auroral phenomena occur in such narrow regions as auroral arcs, electrostatic shocks, and superthermal electron bursts.

Integrated genome browser: visual analytics platform for genomics.

PubMed

Freese, Nowlan H; Norris, David C; Loraine, Ann E

2016-07-15

Genome browsers that support fast navigation through vast datasets and provide interactive visual analytics functions can help scientists achieve deeper insight into biological systems. Toward this end, we developed Integrated Genome Browser (IGB), a highly configurable, interactive and fast open source desktop genome browser. Here we describe multiple updates to IGB, including all-new capabilities to display and interact with data from high-throughput sequencing experiments. To demonstrate, we describe example visualizations and analyses of datasets from RNA-Seq, ChIP-Seq and bisulfite sequencing experiments. Understanding results from genome-scale experiments requires viewing the data in the context of reference genome annotations and other related datasets. To facilitate this, we enhanced IGB's ability to consume data from diverse sources, including Galaxy, Distributed Annotation and IGB-specific Quickload servers. To support future visualization needs as new genome-scale assays enter wide use, we transformed the IGB codebase into a modular, extensible platform for developers to create and deploy all-new visualizations of genomic data. IGB is open source and is freely available from http://bioviz.org/igb aloraine@uncc.edu. © The Author 2016. Published by Oxford University Press.

New Caledonia a classic example of an arc continent collision

NASA Astrophysics Data System (ADS)

Aitchison, J.

2011-12-01

The SW Pacific island of New Caledonia presents a classic example of an arc-continent collision. This event occurred in the Late Eocene when elements of an intra-oceanic island arc system, the Loyalty-D'Entrecasteaux arc, which stretched SSE from near Papua New Guinea east of New Caledonia to offshore New Zealand, collided with micro-continental fragments that had rifted off eastern Gondwana (Australia) in the late Cretaceous. Intervening Late Cretaceous to Paleogene oceanic crust of the South Loyalty Basin was eliminated through eastward subduction beneath this west-facing intra-oceanic island arc. As with many arc-continent collisions elsewhere collision was accompanied by ophiolite emplacement. The erosional remnants of which are extensive in New Caledonia. Collision led to subduction flip, followed by extensive rollback in front of the newly established east-facing Vitiaz arc. Post-collisional magmatism occurred after slab break-off and is represented by small-scale granitoid intrusions. Additional important features of New Caledonia include the presence of a regionally extensive UHP metamorphic terrain consisting of blueschists and eclogites that formed during the subduction process and were rapidly exhumed as a result of the collision Not only was collision and associated orogeny short-lived this collision system has not been overprinted by any major subsequent collision. New Caledonia thus provides an exceptional location for the study of processes related to arc-continent collision in general.

Crustal thickness control on Sr/Y signatures of recent arc magmas: an Earth scale perspective

PubMed Central

Chiaradia, Massimo

2015-01-01

Arc magmas originate in subduction zones as partial melts of the mantle, induced by aqueous fluids/melts liberated by the subducted slab. Subsequently, they rise through and evolve within the overriding plate crust. Aside from broadly similar features that distinguish them from magmas of other geodynamic settings (e.g., mid-ocean ridges, intraplate), arc magmas display variably high Sr/Y values. Elucidating the debated origin of high Sr/Y signatures in arc magmas, whether due to mantle-source, slab melting or intracrustal processes, is instrumental for models of crustal growth and ore genesis. Here, using a statistical treatment of >23000 whole rock geochemical data, I show that average Sr/Y values and degree of maturation (MgO depletion at peak Sr/Y values) of 19 out of 22 Pliocene-Quaternary arcs correlate positively with arc thickness. This suggests that crustal thickness exerts a first order control on the Sr/Y variability of arc magmas through the stabilization or destabilization of mineral phases that fractionate Sr (plagioclase) and Y (amphibole ± garnet). In fact, the stability of these mineral phases is function of the pressure at which magma evolves, which depends on crustal thickness. The data presented show also that high Sr/Y Pliocene-Quaternary intermediate-felsic arc rocks have a distinct origin from their Archean counterparts. PMID:25631193

The Association Between Obesity and Cognitive Function in Older Persons: How Much Is Mediated by Inflammation, Fasting Plasma Glucose, and Hypertriglyceridemia?

PubMed

Gunathilake, Roshan; Oldmeadow, Christopher; McEvoy, Mark; Inder, Kerry J; Schofield, Peter W; Nair, Balakrishnan R; Attia, John

2016-12-01

The aim of the study was to determine how much of the association between obesity, measured by body mass index (BMI), and cognition in older persons is mediated through inflammation, fasting plasma glucose, and hypertriglyceridemia. Anthropometrics, high-sensitivity C-reactive protein (CRP), fasting plasma glucose, and serum triglycerides were measured in 3,256 community-dwelling individuals aged 55-85 years residing in Newcastle, New South Wales, Australia. Audio recorded cognitive screen (ARCS) was used to assess multiple cognitive domains. Mediation analyses showed very modest but significant direct mediation effects, whereby obesity was associated with better cognitive function after adjusting for potential confounders (controlled direct effect ≈ 1/500 point increase in the total ARCS score per 1.0-kg/m 2 increase in BMI). There were significant indirect negative mediation effects from BMI to cognition mediated through CRP, that is, increased BMI was associated with increased CRP which was associated with decreased cognition (natural indirect effect -0.20 unit; 95% confidence interval [CI] -0.39, -0.02), and through fasting plasma glucose, that is, increased BMI was associated with increased fasting plasma glucose which was associated with decreased cognition (natural indirect effect -0.12 unit; 95% CI -0.24, -0.01], but not through serum triglycerides. There is a weak positive association between obesity and cognitive performance in older persons, which is partially antagonized by inflammation and elevated fasting plasma glucose, but not hypertriglyceridemia. Further studies are needed to elucidate whether this is due to selection bias, or truly reflects biologically complex and counter balancing pathways involved in obesity. © The Author 2016. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Arctigenin protects against neuronal hearing loss by promoting neural stem cell survival and differentiation.

PubMed

Huang, Xinghua; Chen, Mo; Ding, Yan; Wang, Qin

2017-03-01

Neuronal hearing loss has become a prevalent health problem. This study focused on the function of arctigenin (ARC) in promoting survival and neuronal differentiation of mouse cochlear neural stem cells (NSCs), and its protection against gentamicin (GMC) induced neuronal hearing loss. Mouse cochlea was used to isolate NSCs, which were subsequently cultured in vitro. The effects of ARC on NSC survival, neurosphere formation, differentiation of NSCs, neurite outgrowth, and neural excitability in neuronal network in vitro were examined. Mechanotransduction ability demonstrated by intact cochlea, auditory brainstem response (ABR), and distortion product optoacoustic emissions (DPOAE) amplitude in mice were measured to evaluate effects of ARC on GMC-induced neuronal hearing loss. ARC increased survival, neurosphere formation, neuron differentiation of NSCs in mouse cochlear in vitro. ARC also promoted the outgrowth of neurites, as well as neural excitability of the NSC-differentiated neuron culture. Additionally, ARC rescued mechanotransduction capacity, restored the threshold shifts of ABR and DPOAE in our GMC ototoxicity murine model. This study supports the potential therapeutic role of ARC in promoting both NSCs proliferation and differentiation in vitro to functional neurons, thus supporting its protective function in the therapeutic treatment of neuropathic hearing loss in vivo. © 2017 Wiley Periodicals, Inc.

Structural Determinants at the Interface of the ARC2 and Leucine-Rich Repeat Domains Control the Activation of the Plant Immune Receptors Rx1 and Gpa21[C][W][OA

PubMed Central

Slootweg, Erik J.; Spiridon, Laurentiu N.; Roosien, Jan; Butterbach, Patrick; Pomp, Rikus; Westerhof, Lotte; Wilbers, Ruud; Bakker, Erin; Bakker, Jaap; Petrescu, Andrei-José; Smant, Geert; Goverse, Aska

2013-01-01

Many plant and animal immune receptors have a modular nucleotide-binding-leucine-rich repeat (NB-LRR) architecture in which a nucleotide-binding switch domain, NB-ARC, is tethered to a LRR sensor domain. The cooperation between the switch and sensor domains, which regulates the activation of these proteins, is poorly understood. Here, we report structural determinants governing the interaction between the NB-ARC and LRR in the highly homologous plant immune receptors Gpa2 and Rx1, which recognize the potato cyst nematode Globodera pallida and Potato virus X, respectively. Systematic shuffling of polymorphic sites between Gpa2 and Rx1 showed that a minimal region in the ARC2 and N-terminal repeats of the LRR domain coordinate the activation state of the protein. We identified two closely spaced amino acid residues in this region of the ARC2 (positions 401 and 403) that distinguish between autoactivation and effector-triggered activation. Furthermore, a highly acidic loop region in the ARC2 domain and basic patches in the N-terminal end of the LRR domain were demonstrated to be required for the physical interaction between the ARC2 and LRR. The NB-ARC and LRR domains dissociate upon effector-dependent activation, and the complementary-charged regions are predicted to mediate a fast reassociation, enabling multiple rounds of activation. Finally, we present a mechanistic model showing how the ARC2, NB, and N-terminal half of the LRR form a clamp, which regulates the dissociation and reassociation of the switch and sensor domains in NB-LRR proteins. PMID:23660837

Structural determinants at the interface of the ARC2 and leucine-rich repeat domains control the activation of the plant immune receptors Rx1 and Gpa2.

PubMed

Slootweg, Erik J; Spiridon, Laurentiu N; Roosien, Jan; Butterbach, Patrick; Pomp, Rikus; Westerhof, Lotte; Wilbers, Ruud; Bakker, Erin; Bakker, Jaap; Petrescu, Andrei-José; Smant, Geert; Goverse, Aska

2013-07-01

Many plant and animal immune receptors have a modular nucleotide-binding-leucine-rich repeat (NB-LRR) architecture in which a nucleotide-binding switch domain, NB-ARC, is tethered to a LRR sensor domain. The cooperation between the switch and sensor domains, which regulates the activation of these proteins, is poorly understood. Here, we report structural determinants governing the interaction between the NB-ARC and LRR in the highly homologous plant immune receptors Gpa2 and Rx1, which recognize the potato cyst nematode Globodera pallida and Potato virus X, respectively. Systematic shuffling of polymorphic sites between Gpa2 and Rx1 showed that a minimal region in the ARC2 and N-terminal repeats of the LRR domain coordinate the activation state of the protein. We identified two closely spaced amino acid residues in this region of the ARC2 (positions 401 and 403) that distinguish between autoactivation and effector-triggered activation. Furthermore, a highly acidic loop region in the ARC2 domain and basic patches in the N-terminal end of the LRR domain were demonstrated to be required for the physical interaction between the ARC2 and LRR. The NB-ARC and LRR domains dissociate upon effector-dependent activation, and the complementary-charged regions are predicted to mediate a fast reassociation, enabling multiple rounds of activation. Finally, we present a mechanistic model showing how the ARC2, NB, and N-terminal half of the LRR form a clamp, which regulates the dissociation and reassociation of the switch and sensor domains in NB-LRR proteins.

TissueWikiMobile: an Integrative Protein Expression Image Browser for Pathological Knowledge Sharing and Annotation on a Mobile Device

PubMed Central

Cheng, Chihwen; Stokes, Todd H.; Hang, Sovandy; Wang, May D.

2016-01-01

Doctors need fast and convenient access to medical data. This motivates the use of mobile devices for knowledge retrieval and sharing. We have developed TissueWikiMobile on the Apple iPhone and iPad to seamlessly access TissueWiki, an enormous repository of medical histology images. TissueWiki is a three terabyte database of antibody information and histology images from the Human Protein Atlas (HPA). Using TissueWikiMobile, users are capable of extracting knowledge from protein expression, adding annotations to highlight regions of interest on images, and sharing their professional insight. By providing an intuitive human computer interface, users can efficiently operate TissueWikiMobile to access important biomedical data without losing mobility. TissueWikiMobile furnishes the health community a ubiquitous way to collaborate and share their expert opinions not only on the performance of various antibodies stains but also on histology image annotation. PMID:27532057

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

Jeong, K; Basavatia, A; Mynampati, D

Purpose: To compare VMAT SRS plans, dynamic conformal arc (DCA) plans, and Brainlab iPlan’s capability of planning and delivering brain SRS plans by employing HybridArc. HybridArc utilizes both DCA and IMRT. Using HybridArc, the amount of DCA versus IMRT needs to be optimized. Methods: Four SRS patients with the aim of reducing brainstem dose were selected for this study. All patients were contoured in iPlan and transferred to Eclipse for VMAT planning. In iPlan, DCA plans were created for each case. Moreover, nine HybridArc plans with DCA-IMRT ratios between 9:1 through 1:9 were created with a single ring structure generatedmore » by subtracting 3 mm expansion of target from a 10 mm expansion of the target. Two static IMRT beams were used in each of the five DCA arcs for HybridArc. The dose was prescribed to DCA only and HybridArc plans and normalized so that the target volume (TV) receives 100% dose to 99.5% of the TV to achieve 120% ∼ 130% max dose within targets. Following metrics were compared: PITV, V12Gy, CGIc, CGIg, CGI, brainstem max dose, and total monitor units (MUs). Results: A brainstem max dose comparable with VMAT from 30% IMRT and less with 50% or more IMRT could be achieved. PITV decreased with increasing IMRT portion and begins to saturate past an IMRT portion of 30%. The CGIg index, which represents how fast the dose falls off, was better with HybridArc in all HybridArc plans. Total MUs increased with increasing IMRT but less than VMAT in all cases. Conclusion: Overall, a lower brainstem max dose and a lower V12Gy with fewer MUs can be achieved with HybridArc. Considering all factors, it would be best to use a DCA-IMRT ratio of either 7:3 or 6:4.« less

Laser geodynamic satellite thermal/optical/vibrational analysis and testing, volume 2, book 2. [cubes and far fields

NASA Technical Reports Server (NTRS)

1975-01-01

The main tasks described involved an interferometric evaluation of several cubes, a prediction of their dihedral angles, a comparison of these predictions with independent measurements, a prediction and comparison of far field performance, recommendations as to revised dihedral angles and a subsequent analysis of cubes which were reworked to confirm the recommendations. A tolerance study and theoretical evaluation of several cubes was also performed to aid in understanding the results. The far field characteristics evaluated included polarization effects and treated both intensity distribution and encircled energy data. The energy in the 13.2 - 16.9 arc-sec annular region was tabulated as an indicator of performance sensitivity. The results are provided in viewgraph form, and show the average dihedral angle of an original set of test cubes to have been 1.8 arc-sec with an average far field annulus diameter of 18 arc-sec. Since the peak energy in the 13.2 - 16.9 arc-sec annulus was found to occur for a 1.35 arc-sec cube, and since cube tolerances were shown to increase the annulus diameter slightly, a nominal dihedral angle of 1.25 arc-sec was recommended.

ARC Software and Models

Science.gov Websites

produce software code and methodologies that are transferred to TARDEC and industry partners. These constraints", ASME Dynamic Systems and Control Conference, 2013, DOI:10.1115/DSCC2013-3935 Software Monitoring",IEEE Transactions on Control Systems Technology, DOI:10.1109/TCST.2012.2217143 Fast

Intracortical pathways mediate nonlinear fast oscillation (>200 Hz) interactions within rat barrel cortex.

PubMed

Staba, Richard J; Ard, Tyler D; Benison, Alexander M; Barth, Daniel S

2005-05-01

Whisker evoked fast oscillations (FOs; >200 Hz) within the rodent posteromedial barrel subfield are thought to reflect very rapid integration of multiwhisker stimuli, yet the pathways mediating FO interactions remain unclear and may involve interactions within thalamus and/or cortex. In the present study using anesthetized rats, a cortical incision was made between sites representing the stimulated whiskers to determine how intracortical networks contributed to patterns of FOs. With cortex intact, simultaneous stimulation of a pair of whiskers aligned in a row evoked supralinear responses between sites separated by several millimeters. In contrast, stimulation of a nonadjacent pair of whiskers within an arc evoked FOs with no evidence for nonlinear interactions. However, stimulation of an adjacent pair of whiskers in an arc did evoke supralinear responses. After a cortical cut, supralinear interactions associated with FOs within a row were lost. These data indicate a distinct bias for stronger long-range connectivity that extends along barrel rows and that horizontal intracortical pathways exclusively mediate FO-related integration of tactile information.

Back-arc basin development: Constraints on geochronology and geochemistry of arc-like and OIB-like basalts in the Central Qilian block (Northwest China)

NASA Astrophysics Data System (ADS)

Gao, Zhong; Zhang, Hong-Fei; Yang, He; Pan, Fa-Bin; Luo, Bi-Ji; Guo, Liang; Xu, Wang-Chun; Tao, Lu; Zhang, Li-Qi; Wu, Jing

2018-06-01

The Lajishan belt of the Central Qilian block was a back-arc basin during Early Paleozoic. The basaltic magmatism and temporal evolution in this basin provide an opportunity to study the development of back-arc basin in an active continental margin. In this study, we carry out an integrated study of geochronological, geochemical and Sr-Nd isotopic compositions for the Early Paleozoic arc-like and OIB-like basalts. The Lajishan arc-like basalts are enriched in large ion lithophile element (LILE) and show negative Nb and Ta anomalies whereas the OIB-like basalts have high LILE abundances and show positive Nb and Ta anomalies. The arc-like basalts have initial 87Sr/86Sr values of 0.7050-0.7054 and εNd(t) values of +0.51-+2.63, and the OIB-like basalts have initial 87Sr/86Sr values of 0.7049-0.7050 and εNd(t) values of +0.66-+1.57. The geochemical and Sr-Nd isotopic compositions suggest that the arc-like basalts are derived from partial melting of a depleted mantle source metasomatized by slab-derived components at shallow depth levels, and the OIB-like basalts also originated from a metasomatized mantle wedge source. U-Pb zircon dating yielded the ages of 494 ± 4 Ma for the arc-like basalts and 468 ± 6 Ma for the OIB-like basalts. We argue that the arc-like basalts are products of back-arc extension before the back-arc rifting initiated in earlier stage, resulting from the northward subduction of the Qaidam-West Qinling oceanic slab, while the OIB-like basalts represent products of further back-arc spreading in response to rollback of the Qaidam-West Qinling oceanic lithospheric slab. The association of arc-like and OIB-like basalts in the Lajishan belt records the development of back-arc basin from initial rifting to subsequent spreading, offering insight into how basaltic magmatism generates in the formation of back-arc basin in subduction zone setting.

Across and along arc geochemical variations in altered volcanic rocks: Evidence from mineral chemistry of Jurassic lavas in northern Chile, and tectonic implications

NASA Astrophysics Data System (ADS)

Rossel, Pablo; Oliveros, Verónica; Ducea, Mihai N.; Hernandez, Laura

2015-12-01

Postmagmatic processes mask the original whole-rock chemistry of most Mesozoic igneous rocks from the Andean arc and back-arc units preserved in Chile. Mineral assemblages corresponding to subgreenschist metamorphic facies and/or propylitic hydrothermal alteration are ubiquitous in volcanic and plutonic rocks, suggesting element mobility at macroscopic and microscopic scale. However, fresh primary phenocrysts of clinopyroxene and plagioclase do occur in some of the altered rocks. We use major and trace element chemistry of such mineral phases to infer the geochemical variations of four Jurassic arc and four back-arc units from northern Chile. Clinopyroxene belonging to rocks of the main arc and two units of the bark-arc are augites with low contents of HFSE and REE; they originated from melting of an asthenospheric mantle source. Clinopyroxenes from a third back-arc unit show typical OIB affinities, with high Ti and trace element contents and low Si. Trace elemental variations in clinopyroxenes from these arc and back-arc units suggest that olivine and clinopyroxene were the main fractionating phases during early stages of magma evolution. The last back-arc unit shows a broad spectrum of clinopyroxene compositions that includes depleted arc-like augite, high Al and high Sr-Ca diopside (adakite-like signature). The origin of these lavas is the result of melting of a mixture of depleted mantle plus Sr-rich sediments and subsequent high pressure fractionation of garnet. Thermobarometric calculations suggest that the Jurassic arc and back-arc magmatism had at least one crustal stagnation level where crystallization and fractionation took place, located at ca. ~ 8-15 km. The depth of this stagnation level is consistent with lower-middle crust boundary in extensional settings. Crystallization conditions calculated for high Al diopsides suggest a deeper stagnation level that is not consistent with a thinned back-arc continental crust. Thus minor garnet fractionation occurred before these magmas reached the base of the crust. The presented data support the existence of a heterogeneous sub arc mantle and complex magmatic processes in the early stages of the Andean subduction.

GRN2SBML: automated encoding and annotation of inferred gene regulatory networks complying with SBML.

PubMed

Vlaic, Sebastian; Hoffmann, Bianca; Kupfer, Peter; Weber, Michael; Dräger, Andreas

2013-09-01

GRN2SBML automatically encodes gene regulatory networks derived from several inference tools in systems biology markup language. Providing a graphical user interface, the networks can be annotated via the simple object access protocol (SOAP)-based application programming interface of BioMart Central Portal and minimum information required in the annotation of models registry. Additionally, we provide an R-package, which processes the output of supported inference algorithms and automatically passes all required parameters to GRN2SBML. Therefore, GRN2SBML closes a gap in the processing pipeline between the inference of gene regulatory networks and their subsequent analysis, visualization and storage. GRN2SBML is freely available under the GNU Public License version 3 and can be downloaded from http://www.hki-jena.de/index.php/0/2/490. General information on GRN2SBML, examples and tutorials are available at the tool's web page.

Protannotator: a semiautomated pipeline for chromosome-wise functional annotation of the "missing" human proteome.

PubMed

Islam, Mohammad T; Garg, Gagan; Hancock, William S; Risk, Brian A; Baker, Mark S; Ranganathan, Shoba

2014-01-03

The chromosome-centric human proteome project (C-HPP) aims to define the complete set of proteins encoded in each human chromosome. The neXtProt database (September 2013) lists 20,128 proteins for the human proteome, of which 3831 human proteins (∼19%) are considered "missing" according to the standard metrics table (released September 27, 2013). In support of the C-HPP initiative, we have extended the annotation strategy developed for human chromosome 7 "missing" proteins into a semiautomated pipeline to functionally annotate the "missing" human proteome. This pipeline integrates a suite of bioinformatics analysis and annotation software tools to identify homologues and map putative functional signatures, gene ontology, and biochemical pathways. From sequential BLAST searches, we have primarily identified homologues from reviewed nonhuman mammalian proteins with protein evidence for 1271 (33.2%) "missing" proteins, followed by 703 (18.4%) homologues from reviewed nonhuman mammalian proteins and subsequently 564 (14.7%) homologues from reviewed human proteins. Functional annotations for 1945 (50.8%) "missing" proteins were also determined. To accelerate the identification of "missing" proteins from proteomics studies, we generated proteotypic peptides in silico. Matching these proteotypic peptides to ENCODE proteogenomic data resulted in proteomic evidence for 107 (2.8%) of the 3831 "missing proteins, while evidence from a recent membrane proteomic study supported the existence for another 15 "missing" proteins. The chromosome-wise functional annotation of all "missing" proteins is freely available to the scientific community through our web server (http://biolinfo.org/protannotator).

fLPS: Fast discovery of compositional biases for the protein universe.

PubMed

Harrison, Paul M

2017-11-13

Proteins often contain regions that are compositionally biased (CB), i.e., they are made from a small subset of amino-acid residue types. These CB regions can be functionally important, e.g., the prion-forming and prion-like regions that are rich in asparagine and glutamine residues. Here I report a new program fLPS that can rapidly annotate CB regions. It discovers both single-residue and multiple-residue biases. It works through a process of probability minimization. First, contigs are constructed for each amino-acid type out of sequence windows with a low degree of bias; second, these contigs are searched exhaustively for low-probability subsequences (LPSs); third, such LPSs are iteratively assessed for merger into possible multiple-residue biases. At each of these stages, efficiency measures are taken to avoid or delay probability calculations unless/until they are necessary. On a current desktop workstation, the fLPS algorithm can annotate the biased regions of the yeast proteome (>5700 sequences) in <1 s, and of the whole current TrEMBL database (>65 million sequences) in as little as ~1 h, which is >2 times faster than the commonly used program SEG, using default parameters. fLPS discovers both shorter CB regions (of the sort that are often termed 'low-complexity sequence'), and milder biases that may only be detectable over long tracts of sequence. fLPS can readily handle very large protein data sets, such as might come from metagenomics projects. It is useful in searching for proteins with similar CB regions, and for making functional inferences about CB regions for a protein of interest. The fLPS package is available from: http://biology.mcgill.ca/faculty/harrison/flps.html , or https://github.com/pmharrison/flps , or is a supplement to this article.

Listening Skills in Business. Focused Access to Selected Topics (FAST) Bibliography No. 19.

ERIC Educational Resources Information Center

Shermis, Michael

Addressing the increasing importance of listening skills in the business world, this annotated bibliography contains 22 items from the ERIC database from 1979 to 1988. The sources cited in the first section of the bibliography are primarily concerned with teaching techniques and strategies for teachers of secondary and higher education business…

The determination of micro-arc plasma composition and properties of nanoparticles formed during cathodic plasma electrolysis of 304 stainless steel

NASA Astrophysics Data System (ADS)

Jovović, Jovica; Stojadinović, Stevan; Vasilić, Rastko; Tadić, Nenad; Šišović, Nikola M.

2017-05-01

This paper presents the research focused on the determination of micro-arc plasma composition during cathodic plasma electrolysis of AISI304 stainless steel in water solution of sodium hydroxide. The complex line shape of several Fe I spectral lines was observed and, by means of a dedicated fitting procedure based on the spectral line broadening theory and H2O thermal decomposition data, the mole fraction of micro-arc plasma constituents (H2, Fe, O, H, H2O, and OH) was determined. Subsequent characterization of the cathodic plasma electrolysis product formed during the process revealed that it consists of Fe-nanoparticles with median diameter of approximately 60 nm.

The Studies of a Vacuum Gap Breakdown after High-Current Arc Interruption with Increasing the Voltage

NASA Astrophysics Data System (ADS)

Schneider, A. V.; Popov, S. A.; Batrakov, A. V.; Dubrovskaya, E. L.; Lavrinovich, V. A.

2017-12-01

Vacuum-gap breakdown has been studied after high-current arc interruption with a subsequent increase in the transient recovery voltage across a gap. The effects of factors, such as the rate of the rise in the transient voltage, the potential of the shield that surrounds a discharge gap, and the arc burning time, have been determined. It has been revealed that opening the contacts earlier leads to the formation of an anode spot, which is the source of electrode material vapors into the discharge gap after current zero moment. Under the conditions of increasing voltage, this fact results in the breakdown. Too late opening leads to the breakdown of a short gap due to the high electric fields.

LGR4 and Its Ligands, R-Spondin 1 and R-Spondin 3, Regulate Food Intake in the Hypothalamus of Male Rats

PubMed Central

Li, Ji-Yao; Chai, Biaoxin; Zhang, Weizhen; Fritze, Danielle M.; Zhang, Chao

2014-01-01

The hypothalamus plays a key role in the regulation of feeding behavior. Several hypothalamic nuclei, including the arcuate nucleus (ARC), paraventricular nucleus, and ventromedial nucleus of the hypothalamus (VMH), are involved in energy homeostasis. Analysis of microarray data derived from ARC revealed that leucine-rich repeat-containing G protein-coupled receptor 4 (LGR4) is highly expressed. LGR4, LGR5, and LGR6 form a subfamily of closely related receptors. Recently, R-spondin (Rspo) family proteins were identified as ligands of the LGR4 subfamily. In the present study, we investigated the distribution and function of LGR4–LGR6 and Rspos (1–4) in the brain of male rat. In situ hybridization showed that LGR4 is expressed in the ARC, VMH, and median eminence of the hypothalamus. LGR4 colocalizes with neuropeptide Y, proopiomelanocortin, and brain-derived neurotrophic factor neurons. LGR5 is not detectable with in situ hybridization; LGR6 is only expressed in the epithelial lining of the lower portion of the third ventricle and median eminence. Rspo1 is expressed in the VMH and down-regulated with fasting. Rspo3 is expressed in the paraventricular nucleus and also down-regulated with fasting. Rspos 1 and 3 colocalize with the neuronal marker HuD, indicating that they are expressed by neurons. Injection of Rspo1 or Rspo3 into the third brain ventricle inhibited food intake. Rspo1 decreased neuropeptide Y and increased proopiomelanocortin expression in the ARC. Rspo1 and Rspo3 mRNA is up-regulated by insulin. These data indicate that Rspo1 and Rspo3 and their receptor LGR4 form novel circuits in the brain to regulate energy homeostasis. PMID:24280058

LGR4 and its ligands, R-spondin 1 and R-spondin 3, regulate food intake in the hypothalamus of male rats.

PubMed

Li, Ji-Yao; Chai, Biaoxin; Zhang, Weizhen; Fritze, Danielle M; Zhang, Chao; Mulholland, Michael W

2014-02-01

The hypothalamus plays a key role in the regulation of feeding behavior. Several hypothalamic nuclei, including the arcuate nucleus (ARC), paraventricular nucleus, and ventromedial nucleus of the hypothalamus (VMH), are involved in energy homeostasis. Analysis of microarray data derived from ARC revealed that leucine-rich repeat-containing G protein-coupled receptor 4 (LGR4) is highly expressed. LGR4, LGR5, and LGR6 form a subfamily of closely related receptors. Recently, R-spondin (Rspo) family proteins were identified as ligands of the LGR4 subfamily. In the present study, we investigated the distribution and function of LGR4-LGR6 and Rspos (1-4) in the brain of male rat. In situ hybridization showed that LGR4 is expressed in the ARC, VMH, and median eminence of the hypothalamus. LGR4 colocalizes with neuropeptide Y, proopiomelanocortin, and brain-derived neurotrophic factor neurons. LGR5 is not detectable with in situ hybridization; LGR6 is only expressed in the epithelial lining of the lower portion of the third ventricle and median eminence. Rspo1 is expressed in the VMH and down-regulated with fasting. Rspo3 is expressed in the paraventricular nucleus and also down-regulated with fasting. Rspos 1 and 3 colocalize with the neuronal marker HuD, indicating that they are expressed by neurons. Injection of Rspo1 or Rspo3 into the third brain ventricle inhibited food intake. Rspo1 decreased neuropeptide Y and increased proopiomelanocortin expression in the ARC. Rspo1 and Rspo3 mRNA is up-regulated by insulin. These data indicate that Rspo1 and Rspo3 and their receptor LGR4 form novel circuits in the brain to regulate energy homeostasis.

The receptive function of hypothalamic and brainstem centres to hormonal and nutrient signals affecting energy balance.

PubMed

Riediger, Thomas

2012-11-01

The hypothalamic arcuate nucleus (ARC) and the area postrema (AP) represent targets for hormonal and metabolic signals involved in energy homoeostasis, e.g. glucose, amylin, insulin, leptin, peptide YY (PYY), glucagon-like peptide 1 (GLP-1) and ghrelin. Orexigenic neuropeptide Y expressing ARC neurons are activated by food deprivation and inhibited by feeding in a nutrient-dependent manner. PYY and leptin also reverse or prevent fasting-induced activation of the ARC. Interestingly, hypothalamic responses to fasting are blunted in different models of obesity (e.g. diet-induced obesity (DIO) or late-onset obesity). The AP also responds to feeding-related signals. The pancreatic hormone amylin acts via the AP to control energy intake. Amylin-sensitive AP neurons are also glucose-responsive. Furthermore, diet-derived protein attenuates amylin responsiveness suggesting a modulation of AP sensitivity by macronutrient supply. This review gives an overview of the receptive function of the ARC and the AP to hormonal and nutritional stimuli involved in the control of energy balance and the possible implications in the context of obesity. Collectively, there is consistency between the neurophysiological actions of these stimuli and their effects on energy homoeostasis under experimental conditions. However, surprisingly little progress has been made in the development of effective pharmacological approaches against obesity. A promising way to improve effectiveness involves combination treatments (e.g. amylin/leptin agonists). Hormonal alterations (e.g. GLP-1 and PYY) are also considered to mediate body weight loss observed in obese patients receiving bariatric surgery. The effects of hormonal and nutritional signals and their interactions might hold the potential to develop poly-mechanistic therapeutic strategies against obesity.

Imaging the seismic structure beneath oceanic spreading centers using ocean bottom geophysical techniques

NASA Astrophysics Data System (ADS)

Zha, Yang

This dissertation focuses on imaging the crustal and upper mantle seismic velocity structure beneath oceanic spreading centers. The goals are to provide a better understanding of the crustal magmatic system and the relationship between mantle melting processes, crustal architecture and ridge characteristics. To address these questions I have analyzed ocean bottom geophysical data collected from the fast-spreading East Pacific Rise and the back-arc Eastern Lau Spreading Center using a combination of ambient noise tomography and seafloor compliance analysis. To characterize the crustal melt distribution at fast spreading ridges, I analyze seafloor compliance - the deformation under long period ocean wave forcing - measured during multiple expeditions between 1994 and 2007 at the East Pacific Rise 9º - 10ºN segment. A 3D numerical modeling technique is developed and used to estimate the effects of low shear velocity zones on compliance measurements. The forward modeling suggests strong variations of lower crustal shear velocity along the ridge axis, with zones of possible high melt fractions beneath certain segments. Analysis of repeated compliance measurements at 9º48'N indicates a decrease of crustal melt fraction following the 2005 - 2006 eruption. This temporal variability provides direct evidence for short-term variations of the magmatic system at a fast spreading ridge. To understand the relationship between mantle melting processes and crustal properties, I apply ambient noise tomography of ocean bottom seismograph (OBS) data to image the upper mantle seismic structure beneath the Eastern Lau Spreading Center (ELSC). The seismic images reveal an asymmetric upper mantle low velocity zone (LVZ) beneath the ELSC, representing a zone of partial melt. As the ridge migrates away from the volcanic arc, the LVZ becomes increasingly offset and separated from the sub-arc low velocity zone. The separation of the ridge and arc low velocity zones is spatially coincident with the abrupt transition in crustal composition and ridge morphology. Therefore these results confirm a previous prediction that the changing interaction between the arc and back-arc magmatic systems is responsible for the abrupt change in crustal properties along the ELSC. I further investigate the crustal structure along and across the ELSC using seafloor compliance. Compliance measurements are inverted for local crustal shear velocity structure as well as sediment thickness at 30 OBS locations using a Monte Carlo method. Sediment increases asymmetrically with seafloor age, with much a higher rate to the east of the ridge. Along the ELSC, upper crustal velocities increase from south to north as the ridge migrates away from the volcanic arc front, consistent with a less porous upper crust with possibly less subduction input. Furthermore, average upper crust shear velocities for crust produced at past ELSC when it was near the volcanic arc are considerably slower than crust produced at present day northern ELSC. I show that the implications of previous active seismic studies in the axial ELSC can be extended much farther off-axis and back in time. I also address a challenge of ocean bottom seismology and develop a new method for determining OBS horizontal orientations using multi-component ambient noise correlation. I demonstrate that the OBS orientations can be robustly estimated through maximizing the correlation between the diagonal and cross terms of the noise correlation function. This method is applied to the ELSC OBS experiment dataset and the obtained orientations are consistent with results from a conventional teleseismic method. The new method is promising for a wide range of applications.

Predicting RNA-protein binding sites and motifs through combining local and global deep convolutional neural networks.

PubMed

Pan, Xiaoyong; Shen, Hong-Bin

2018-05-02

RNA-binding proteins (RBPs) take over 5∼10% of the eukaryotic proteome and play key roles in many biological processes, e.g. gene regulation. Experimental detection of RBP binding sites is still time-intensive and high-costly. Instead, computational prediction of the RBP binding sites using pattern learned from existing annotation knowledge is a fast approach. From the biological point of view, the local structure context derived from local sequences will be recognized by specific RBPs. However, in computational modeling using deep learning, to our best knowledge, only global representations of entire RNA sequences are employed. So far, the local sequence information is ignored in the deep model construction process. In this study, we present a computational method iDeepE to predict RNA-protein binding sites from RNA sequences by combining global and local convolutional neural networks (CNNs). For the global CNN, we pad the RNA sequences into the same length. For the local CNN, we split a RNA sequence into multiple overlapping fixed-length subsequences, where each subsequence is a signal channel of the whole sequence. Next, we train deep CNNs for multiple subsequences and the padded sequences to learn high-level features, respectively. Finally, the outputs from local and global CNNs are combined to improve the prediction. iDeepE demonstrates a better performance over state-of-the-art methods on two large-scale datasets derived from CLIP-seq. We also find that the local CNN run 1.8 times faster than the global CNN with comparable performance when using GPUs. Our results show that iDeepE has captured experimentally verified binding motifs. https://github.com/xypan1232/iDeepE. xypan172436@gmail.com or hbshen@sjtu.edu.cn. Supplementary data are available at Bioinformatics online.

A review of vacuum ARC ion source research at ANSTO

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

Evans, P.J.; Noorman, J.T.; Watt, G.C.

1996-08-01

The authors talk briefly describes the history and current status of vacuum arc ion source research at the Australian Nuclear Science and Technology Organization (ANSTO). In addition, the author makes some mention of the important role of previous Vacuum Arc Ion Source Workshops in fostering the development of this research field internationally. During the period 1986 - 89, a type of plasma centrifuge known as a vacuum arc centrifuge was developed at ANSTO as part of a research project on stable isotope separation. In this device, a high current vacuum arc discharge was used to produce a metal plasma whichmore » was subsequently rotated in an axial magnetic field. The high rotational speeds (10{sup 5} - 10{sup 6} rad sec{sup {minus}1}) achievable with this method produce centrifugal separation of ions with different mass:charge ratios such as isotopic species. The first portent of things to come occurred in 1985 when Dr. Ian Brown visited ANSTO`s Lucas Heights Research Laboratories and presented a talk on the metal vapour vacuum arc (MEVVA) ion source which had only recently been invented by Brown and co-workers, J. Galvin and R. MacGill, at Lawrence Berkeley Laboratory. For those of us involved in vacuum arc centrifuge research, this was an exciting development primarily because the metal vapour vacuum arc plasma source was common to both devices. Thus, a type of arc, which had since the 1930`s been extensively investigated as a means of switching high current loads, had found wider application as a useful plasma source.« less

Analysing the connectivity and communication of suicidal users on twitter

PubMed Central

Colombo, Gualtiero B.; Burnap, Pete; Hodorog, Andrei; Scourfield, Jonathan

2016-01-01

In this paper we aim to understand the connectivity and communication characteristics of Twitter users who post content subsequently classified by human annotators as containing possible suicidal intent or thinking, commonly referred to as suicidal ideation. We achieve this understanding by analysing the characteristics of their social networks. Starting from a set of human annotated Tweets we retrieved the authors’ followers and friends lists, and identified users who retweeted the suicidal content. We subsequently built the social network graphs. Our results show a high degree of reciprocal connectivity between the authors of suicidal content when compared to other studies of Twitter users, suggesting a tightly-coupled virtual community. In addition, an analysis of the retweet graph has identified bridge nodes and hub nodes connecting users posting suicidal ideation with users who were not, thus suggesting a potential for information cascade and risk of a possible contagion effect. This is particularly emphasised by considering the combined graph merging friendship and retweeting links. PMID:26973360

Variation in forearc basin development along the Sunda Arc, Indonesia

NASA Astrophysics Data System (ADS)

van der Werff, W.

The present forearc basin configuration along the Sunda Arc initially appears to have been controlled by extension and differential subsidence of basement blocks in response to the late Eocene collision of India with Asia. The late Oligocene increase in convergence between the South-east Asian and Indian Plates associated with a new pulse of subduction, resulted in basement uplift and the formation of a regional unconformity that can be recognized along the entire Sunda Arc. From the early to late Miocene, the Sumba and Savu forearc sectors along the eastern Sunda Arc may have been characterized by forearc extension. Submarine fan deposition on the arcward side of the evolving accretionary prism represents the first phase in forearc basin deposition. These fans were subsequently covered by basin and slope sediments derived from the evolving magmatic arc. Structural response to increased late Miocene compression varied along strike of the Sunda Arc. North of Bali, Lombok and Sumbawa, the incipient collision between Australia and the western Banda Arc caused back-arc thrusting and basin inversion. Towards the south of Java, an increase in both the size of the accretionary prism and convergence rates resulted in uplift and large scale folding of the outer forearc basin strata. Along the west coast of Sumatra, increased compression resulted in uplift along the inner side of the forearc along older transcurrent faults. Uplift of West Sumatra was followed by the deposition of a westward prograding sequence of terrigenous sediments that resulted in the development of a broad shelf. Initial forearc basin subsidence relates to the age of the subducting oceanic lithosphere, on top of which the basin is situated. Along the western Sunda Arc, both fexural loading of the evolving accretionary prism, and across arc strike-slip faulting represent additional factors that result in forearc subsidence.

Log file-based patient dose calculations of double-arc VMAT for head-and-neck radiotherapy.

PubMed

Katsuta, Yoshiyuki; Kadoya, Noriyuki; Fujita, Yukio; Shimizu, Eiji; Majima, Kazuhiro; Matsushita, Haruo; Takeda, Ken; Jingu, Keiichi

2018-04-01

The log file-based method cannot display dosimetric changes due to linac component miscalibration because of the insensitivity of log files to linac component miscalibration. The purpose of this study was to supply dosimetric changes in log file-based patient dose calculations for double-arc volumetric-modulated arc therapy (VMAT) in head-and-neck cases. Fifteen head-and-neck cases participated in this study. For each case, treatment planning system (TPS) doses were produced by double-arc and single-arc VMAT. Miscalibration-simulated log files were generated by inducing a leaf miscalibration of ±0.5 mm into the log files that were acquired during VMAT irradiation. Subsequently, patient doses were estimated using the miscalibration-simulated log files. For double-arc VMAT, regarding planning target volume (PTV), the change from TPS dose to miscalibration-simulated log file dose in D mean was 0.9 Gy and that for tumor control probability was 1.4%. As for organ-at-risks (OARs), the change in D mean was <0.7 Gy and normal tissue complication probability was <1.8%. A comparison between double-arc and single-arc VMAT for PTV showed statistically significant differences in the changes evaluated by D mean and radiobiological metrics (P < 0.01), even though the magnitude of these differences was small. Similarly, for OARs, the magnitude of these changes was found to be small. Using the log file-based method for PTV and OARs, the log file-based method estimate of patient dose using the double-arc VMAT has accuracy comparable to that obtained using the single-arc VMAT. Copyright © 2018 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56 419 completely sequenced and manually annotated full-length cDNAs

PubMed Central

Takeda, Jun-ichi; Suzuki, Yutaka; Nakao, Mitsuteru; Barrero, Roberto A.; Koyanagi, Kanako O.; Jin, Lihua; Motono, Chie; Hata, Hiroko; Isogai, Takao; Nagai, Keiichi; Otsuki, Tetsuji; Kuryshev, Vladimir; Shionyu, Masafumi; Yura, Kei; Go, Mitiko; Thierry-Mieg, Jean; Thierry-Mieg, Danielle; Wiemann, Stefan; Nomura, Nobuo; Sugano, Sumio; Gojobori, Takashi; Imanishi, Tadashi

2006-01-01

We report the first genome-wide identification and characterization of alternative splicing in human gene transcripts based on analysis of the full-length cDNAs. Applying both manual and computational analyses for 56 419 completely sequenced and precisely annotated full-length cDNAs selected for the H-Invitational human transcriptome annotation meetings, we identified 6877 alternative splicing genes with 18 297 different alternative splicing variants. A total of 37 670 exons were involved in these alternative splicing events. The encoded protein sequences were affected in 6005 of the 6877 genes. Notably, alternative splicing affected protein motifs in 3015 genes, subcellular localizations in 2982 genes and transmembrane domains in 1348 genes. We also identified interesting patterns of alternative splicing, in which two distinct genes seemed to be bridged, nested or having overlapping protein coding sequences (CDSs) of different reading frames (multiple CDS). In these cases, completely unrelated proteins are encoded by a single locus. Genome-wide annotations of alternative splicing, relying on full-length cDNAs, should lay firm groundwork for exploring in detail the diversification of protein function, which is mediated by the fast expanding universe of alternative splicing variants. PMID:16914452

Fast T Wave Detection Calibrated by Clinical Knowledge with Annotation of P and T Waves

PubMed Central

Elgendi, Mohamed; Eskofier, Bjoern; Abbott, Derek

2015-01-01

Background There are limited studies on the automatic detection of T waves in arrhythmic electrocardiogram (ECG) signals. This is perhaps because there is no available arrhythmia dataset with annotated T waves. There is a growing need to develop numerically-efficient algorithms that can accommodate the new trend of battery-driven ECG devices. Moreover, there is also a need to analyze long-term recorded signals in a reliable and time-efficient manner, therefore improving the diagnostic ability of mobile devices and point-of-care technologies. Methods Here, the T wave annotation of the well-known MIT-BIH arrhythmia database is discussed and provided. Moreover, a simple fast method for detecting T waves is introduced. A typical T wave detection method has been reduced to a basic approach consisting of two moving averages and dynamic thresholds. The dynamic thresholds were calibrated using four clinically known types of sinus node response to atrial premature depolarization (compensation, reset, interpolation, and reentry). Results The determination of T wave peaks is performed and the proposed algorithm is evaluated on two well-known databases, the QT and MIT-BIH Arrhythmia databases. The detector obtained a sensitivity of 97.14% and a positive predictivity of 99.29% over the first lead of the validation databases (total of 221,186 beats). Conclusions We present a simple yet very reliable T wave detection algorithm that can be potentially implemented on mobile battery-driven devices. In contrast to complex methods, it can be easily implemented in a digital filter design. PMID:26197321

The Relationship of Magnetotail Flow Bursts and Ground Onset Signatures

NASA Technical Reports Server (NTRS)

Kepko, Larry; Spanswick, Emma; Angelopoulos, Vassilis; Donovan, Eric

2010-01-01

It has been known for decades that auroral substorm onset occurs on (or at least near) the most equatorward auroral arc, which is thought to map to the near geosynchronous region. The lack of auroral signatures poleward of this arc prior to onset has been a major criticism of flow-burst driven models of substorm onset. The combined THEMIS 5 spacecraft in-situ and ground array measurements provide an unprecedented opportunity to examine the causal relationship between midtail plasma flows, aurora, and ground magnetic signatures. I first present an event from 2008 using multi-spectral all sky imager data from Gillam and in-situ data from THEMIS. The multispectral data indicate an equatorward moving auroral form prior to substorm onset. When this forms reaches the most equatorward arc, the arc brightens and an auroral substorm begins. The THEMIS data show fast Earthward flows prior to onset as well. I discuss further the association of flow bursts and Pi2 pulsations, in the con text of the directly-driven Pi2 model. This model directly links flows and Pi2 pulsations, providing an important constraint on substorm onset theories.

Testing the Auroral Current-Voltage Relation in Multiple Arcs

NASA Astrophysics Data System (ADS)

Cameron, T. G.; Knudsen, D. J.; Cully, C. M.

2013-12-01

The well-known current-voltage relation within auroral inverted-V regions [Knight, Planet. Space Sci., 21, 741, 1973] predicts current carried by an auroral flux tube given the total potential drop between a plasma-sheet source region and the ionosphere. Numerous previous studies have tested this relation using spacecraft that traverse auroral arcs at low (ionospheric) or mid altitudes. Typically, the potential drop is estimated at the peak of the inverted-V, and field-aligned current is estimated from magnetometer data; statistical information is then gathered over many arc crossings that occur over a wide range of source conditions. In this study we use electron data from the FAST satellite to examine the current-voltage relation in multiple arc sets, in which the key source parameters (plasma sheet density and temperature) are presumed to be identical. We argue that this approach provides a more sensitive test of the Knight relation, and we seek to explain remaining variability with factors other than source variability. This study is supported by a grant from the Natural Sciences and Engineering Research Council of Canada.

Study of the ionization rate of the released deuterium in vacuum arc discharges with metal deuteride cathodes

NASA Astrophysics Data System (ADS)

Liu, Fei-Xiang; Long, Ji-Dong; Zheng, Le; Dong, Pan; Li, Chen; Chen, Wei

2018-02-01

The ionization rate of the released deuterium from a metal deuteride cathode in vacuum arc discharges is investigated by both experiments and modeling analysis. Experimental results show that the deuterium ionization rate increases from 2% to 30% with the increasing arc current in the range of 2-100 A. Thus the full ionization assumption, as is widely used in arc plasma simulations, is not satisfied for the released deuterium at low discharge current. According to the modeling results, the neutral-to-ion conversion efficiency for the deuterium traveling across the cathodic spot region can be significantly less than one, due to the fast plasma expansion and rarefaction in the vacuum. In addition, the model also reveals that, unlike the metal atoms which are mainly ionized in the sheath region and flow back to the cathode, the deuterium ionization primarily occurs in the quasi-neutral region and moves towards the anode. Consequently, the cathodic sheath layer acts like a filter that increases the deuterium fraction beyond the sheath region.

Origin of the oceanic basalt basement of the Solomon Islands arc and its relationship to the Ontong Java Plateau-insights from Cenozoic plate motion models

USGS Publications Warehouse

Wells, R.E.

1989-01-01

Cenozoic global plate motion models based on a hotspot reference frame may provide a useful framework for analyzing the tectonic evolution of the Solomon Islands convergent margin. A postulated late Miocene collision of the Ontong Java Plateau (OJP) with a NE-facing arc is consistent with the predicted path of the OJP across the Pacific Basin and its Miocene arrival at the trench. Late-stage igneous activity (65-30 Ma) predicted for the OJP as it rode over the Samoan hotspot occurred in correlative stratigraphic sections on Malaita, the supposed accreted flake of OJP in the Solomon Islands arc. Convergence similar to the present velocities between Australia and the Pacific plates was characteristic of the last 43 million years. Prior to 43 Ma Pacific-Australia plate motions were divergent, seemingly at odds with geologic evidence for early Tertiary convergence, particularly in Papua New Guinea. A postulated South Pacific plate may have existed between Australia and the Pacific plate and would have allowed implied northward subduction along the northeastern Australia plate boundary that lasted into the early Eocene. Subsequent reorganization of plate motions in the middle Eocene correlates with middle Eocene marginal basin formation along ridges oblique to the main plate boundary. Cessation of spreading on the Pacific-South Pacific Ridge and its subsequent subduction beneath Asia followed the change in Pacific plate motion at 43 Ma. A trapped remnant of the extinct, NW-trending ridge may still lie beneath the western Philippine Sea. The terminal deformation, metamorphism and ophiolite obduction in the Eocene orogen of the southwest Pacific also correlates with the major change in Pacific plate motion at 43 Ma and the subsequent compression of the dying Eocene arc against outlying continental and oceanic crustal blocks of the Australian plate. The Solomon Islands oceanic basement may represent juxtaposition of oceanic plateaus of the Australian plate beneath overthrust, dismembered ophiolite derived from adjacent marginal basin crust. ?? 1989.

Seismic anisotropy and slab dynamics from SKS splitting recorded in Colombia

NASA Astrophysics Data System (ADS)

Porritt, Robert W.; Becker, Thorsten W.; Monsalve, Gaspar

2014-12-01

The Nazca, Caribbean, and South America plates meet in northwestern South America where the northern end of the Andean volcanic arc and Wadati-Benioff zone seismicity indicate ongoing subduction. However, the termination of Quaternary volcanism at ~5.5°N and eastward offset in seismicity underneath Colombia suggest the presence of complex slab geometry. To help link geometry to dynamics, we analyze SKS splitting for 38 broadband stations of the Colombian national network. Measurements of fast polarization axes in western Colombia close to the trench show dominantly trench-perpendicular orientations. Orientations measured at stations in the back arc, farther to the east, however, abruptly change to roughly trench parallel anisotropy. This may indicate along-arc mantle flow, possibly related to the suggested "Caldas" slab tear, or a lithospheric signature, but smaller-scale variations in anisotropy remain to be explained. Our observations are atypical globally and challenge our understanding of the complexities of subduction zone seismic anisotropy.

DynGO: a tool for visualizing and mining of Gene Ontology and its associations

PubMed Central

Liu, Hongfang; Hu, Zhang-Zhi; Wu, Cathy H

2005-01-01

Background A large volume of data and information about genes and gene products has been stored in various molecular biology databases. A major challenge for knowledge discovery using these databases is to identify related genes and gene products in disparate databases. The development of Gene Ontology (GO) as a common vocabulary for annotation allows integrated queries across multiple databases and identification of semantically related genes and gene products (i.e., genes and gene products that have similar GO annotations). Meanwhile, dozens of tools have been developed for browsing, mining or editing GO terms, their hierarchical relationships, or their "associated" genes and gene products (i.e., genes and gene products annotated with GO terms). Tools that allow users to directly search and inspect relations among all GO terms and their associated genes and gene products from multiple databases are needed. Results We present a standalone package called DynGO, which provides several advanced functionalities in addition to the standard browsing capability of the official GO browsing tool (AmiGO). DynGO allows users to conduct batch retrieval of GO annotations for a list of genes and gene products, and semantic retrieval of genes and gene products sharing similar GO annotations. The result are shown in an association tree organized according to GO hierarchies and supported with many dynamic display options such as sorting tree nodes or changing orientation of the tree. For GO curators and frequent GO users, DynGO provides fast and convenient access to GO annotation data. DynGO is generally applicable to any data set where the records are annotated with GO terms, as illustrated by two examples. Conclusion We have presented a standalone package DynGO that provides functionalities to search and browse GO and its association databases as well as several additional functions such as batch retrieval and semantic retrieval. The complete documentation and software are freely available for download from the website . PMID:16091147

Two-dimensional proteome reference maps for the soybean cyst nematode Heterodera glycines

USDA-ARS?s Scientific Manuscript database

Two-dimensional electrophoresis (2-DE) reference maps of Heterodera glycines were constructed. After in-gel digestion with trypsin, 803 spots representing 426 proteins were subsequently identified by LC-MS/MS. Proteins with annotated function were further categorized by Gene Ontology. Results showed...

Self-healing fuse development.

NASA Technical Reports Server (NTRS)

Jones, N. D.

1972-01-01

The self-healing fuse is a very fast acting current overload protective device which opens and recloses in a few milliseconds. The fuse confines a mercury column in an insulated channel and returns the mercury to the channel after firing. Ratings 5 to 50 A at 600 peak volts are possible with a life of hundreds of cycles. Compared to conventional fuses, much less fault current energy fires the fuse by heating the mercury to boiling temperature. Next an arc discharge develops while explosive forces expel the liquid mercury from the channel. Then the high impedance arc either extinguishes immediately, or operates for a few milliseconds, until a switch opens the circuit.

The fractal nature of vacuum arc cathode spots

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

Anders, Andre

2005-05-27

Cathode spot phenomena show many features of fractals, for example self-similar patterns in the emitted light and arc erosion traces. Although there have been hints on the fractal nature of cathode spots in the literature, the fractal approach to spot interpretation is underutilized. In this work, a brief review of spot properties is given, touching the differences between spot type 1 (on cathodes surfaces with dielectric layers) and spot type 2 (on metallic, clean surfaces) as well as the known spot fragment or cell structure. The basic properties of self-similarity, power laws, random colored noise, and fractals are introduced. Severalmore » points of evidence for the fractal nature of spots are provided. Specifically power laws are identified as signature of fractal properties, such as spectral power of noisy arc parameters (ion current, arc voltage, etc) obtained by fast Fourier transform. It is shown that fractal properties can be observed down to the cutoff by measurement resolution or occurrence of elementary steps in physical processes. Random walk models of cathode spot motion are well established: they go asymptotically to Brownian motion for infinitesimal step width. The power spectrum of the arc voltage noise falls as 1/f {sup 2}, where f is frequency, supporting a fractal spot model associated with Brownian motion.« less

Crustal shear velocity structure in the Southern Lau Basin constrained by seafloor compliance

NASA Astrophysics Data System (ADS)

Zha, Yang; Webb, Spahr C.

2016-05-01

Seafloor morphology and crustal structure vary significantly in the Lau back-arc basin, which contains regions of island arc formation, rifting, and seafloor spreading. We analyze seafloor compliance: deformation under long period ocean wave forcing, at 30 ocean bottom seismometers to constrain crustal shear wave velocity structure along and across the Eastern Lau Spreading Center (ELSC). Velocity models obtained through Monte Carlo inversion of compliance data show systematic variation of crustal structure in the basin. Sediment thicknesses range from zero thickness at the ridge axis to 1400 m near the volcanic arc. Sediment thickness increases faster to the east than to the west of the ELSC, suggesting a more abundant source of sediment near the active arc volcanoes. Along the ELSC, upper crustal velocities increase from the south to the north where the ridge has migrated farther away from the volcanic arc front. Along the axial ELSC, compliance analysis did not detect a crustal low-velocity body, indicating less melt in the ELSC crustal accretion zone compared to the fast spreading East Pacific Rise. Average upper crust shear velocities for the older ELSC crust produced when the ridge was near the volcanic arc are 0.5-0.8 km/s slower than crust produced at the present-day northern ELSC, consistent with a more porous extrusive layer. Crust in the western Lau Basin, which although thought to have been produced through extension and rifting of old arc crust, is found to have upper crustal velocities similar to older oceanic crust produced at the ELSC.

Extreme Magnetosphere-Ionosphere Coupling at the Plasmapause: a - In-A Bright SAR Arc

NASA Astrophysics Data System (ADS)

Baumgardner, J.; Wroten, J.; Semeter, J.; Mendillo, M.; Kozyra, J.

2007-05-01

Heat conduction from the ring current - plasmapause interaction region generates high electron temperature within the ionosphere that drive stable auroral red (SAR) arc emission at 6300 A. On the night of 29 October 1991, a SAR arc was observed using an all-sky imager and meridional imaging spectrograph at Millstone Hill. At xxxx UT, the SAR arc was south of Millstone at approximate L = 2 and reached emission levels of 13,000 rayleighs (R). Over two solar cycle of imaging observations have been made at Millstone Hill, and SAR arc brightness levels (excluding this event) averaged ~ 500 R. Simultaneous observations using the incoherent scatter radar (ISR), a DMSP satellite pass, the MSIS neutral atmosphere and SAR arc modeling using the Rees and Roble formalism succeeded in simulations of the observed emission. The reason for the unusual brightness was not the extreme temperatures achieved (and therefore heat conduction input), but the fact that the end of the plasmapause field line where the elevated Te values were measured did not occur in the ionospheric trough, but equatorward of it, thereby having far more ambient electrons to heat and subsequently collide with atomic oxygen. This unusual spatial geometry probably resulted from unusual convection patterns early in a superstorm scenario.

Segtor: Rapid Annotation of Genomic Coordinates and Single Nucleotide Variations Using Segment Trees

PubMed Central

Renaud, Gabriel; Neves, Pedro; Folador, Edson Luiz; Ferreira, Carlos Gil; Passetti, Fabio

2011-01-01

Various research projects often involve determining the relative position of genomic coordinates, intervals, single nucleotide variations (SNVs), insertions, deletions and translocations with respect to genes and their potential impact on protein translation. Due to the tremendous increase in throughput brought by the use of next-generation sequencing, investigators are routinely faced with the need to annotate very large datasets. We present Segtor, a tool to annotate large sets of genomic coordinates, intervals, SNVs, indels and translocations. Our tool uses segment trees built using the start and end coordinates of the genomic features the user wishes to use instead of storing them in a database management system. The software also produces annotation statistics to allow users to visualize how many coordinates were found within various portions of genes. Our system currently can be made to work with any species available on the UCSC Genome Browser. Segtor is a suitable tool for groups, especially those with limited access to programmers or with interest to analyze large amounts of individual genomes, who wish to determine the relative position of very large sets of mapped reads and subsequently annotate observed mutations between the reads and the reference. Segtor (http://lbbc.inca.gov.br/segtor/) is an open-source tool that can be freely downloaded for non-profit use. We also provide a web interface for testing purposes. PMID:22069465

Studies on the Parametric Effects of Plasma Arc Welding of 2205 Duplex Stainless Steel

NASA Astrophysics Data System (ADS)

Selva Bharathi, R.; Siva Shanmugam, N.; Murali Kannan, R.; Arungalai Vendan, S.

2018-03-01

This research study attempts to create an optimized parametric window by employing Taguchi algorithm for Plasma Arc Welding (PAW) of 2 mm thick 2205 duplex stainless steel. The parameters considered for experimentation and optimization are the welding current, welding speed and pilot arc length respectively. The experimentation involves the parameters variation and subsequently recording the depth of penetration and bead width. Welding current of 60-70 A, welding speed of 250-300 mm/min and pilot arc length of 1-2 mm are the range between which the parameters are varied. Design of experiments is used for the experimental trials. Back propagation neural network, Genetic algorithm and Taguchi techniques are used for predicting the bead width, depth of penetration and validated with experimentally achieved results which were in good agreement. Additionally, micro-structural characterizations are carried out to examine the weld quality. The extrapolation of these optimized parametric values yield enhanced weld strength with cost and time reduction.

High-tension electrical-arc-induced thermal burns caused by railway overhead cables.

PubMed

Koller, J

1991-10-01

Eleven patients with high-tension electrical-arc-induced thermal burns due to railway overhead cables were treated at the Bratislava Burn Department during a relatively short period of 18 months. All the injuries occurred by the same mechanism, that is persons climbing on top of railway carriages and approaching the 25,000 V a.c. overhead cables. All the burns were the result of an electrical arc passing externally to the body, with subsequent ignition of the victim's clothes. The cutaneous burns, ranging from 24 to 79 per cent of the BSA, were mostly deep partial to full skin thickness injuries. One patient died on day 5 postburn, the other survived. In spite of high-tension aetiology, no true electrical injuries appear to have occurred and no amputations were necessary. The pathophysiology and possible preventive measures are discussed. It must be stressed that arcing can be induced by an earthed object approaching, but not touching, a cable carrying a high voltage.

Lessons learned from the initial sequencing of the pig genome: comparative analysis of an 8 Mb region of pig chromosome 17

PubMed Central

Hart, Elizabeth A; Caccamo, Mario; Harrow, Jennifer L; Humphray, Sean J; Gilbert, James GR; Trevanion, Steve; Hubbard, Tim; Rogers, Jane; Rothschild, Max F

2007-01-01

Background We describe here the sequencing, annotation and comparative analysis of an 8 Mb region of pig chromosome 17, which provides a useful test region to assess coverage and quality for the pig genome sequencing project. We report our findings comparing the annotation of draft sequence assembled at different depths of coverage. Results Within this region we annotated 71 loci, of which 53 are orthologous to human known coding genes. When compared to the syntenic regions in human (20q13.13-q13.33) and mouse (chromosome 2, 167.5 Mb-178.3 Mb), this region was found to be highly conserved with respect to gene order. The most notable difference between the three species is the presence of a large expansion of zinc finger coding genes and pseudogenes on mouse chromosome 2 between Edn3 and Phactr3 that is absent from pig and human. All of our annotation has been made publicly available in the Vertebrate Genome Annotation browser, VEGA. We assessed the impact of coverage on sequence assembly across this region and found, as expected, that increased sequence depth resulted in fewer, longer contigs. One-third of our annotated loci could not be fully re-aligned back to the low coverage version of the sequence, principally because the transcripts are fragmented over several contigs. Conclusion We have demonstrated the considerable advantages of sequencing at increased read depths and discuss the implications that lower coverage sequence may have on subsequent comparative and functional studies, particularly those involving complex loci such as GNAS. PMID:17705864

Comprehensive annotation of secondary metabolite biosynthetic genes and gene clusters of Aspergillus nidulans, A. fumigatus, A. niger and A. oryzae

PubMed Central

2013-01-01

Background Secondary metabolite production, a hallmark of filamentous fungi, is an expanding area of research for the Aspergilli. These compounds are potent chemicals, ranging from deadly toxins to therapeutic antibiotics to potential anti-cancer drugs. The genome sequences for multiple Aspergilli have been determined, and provide a wealth of predictive information about secondary metabolite production. Sequence analysis and gene overexpression strategies have enabled the discovery of novel secondary metabolites and the genes involved in their biosynthesis. The Aspergillus Genome Database (AspGD) provides a central repository for gene annotation and protein information for Aspergillus species. These annotations include Gene Ontology (GO) terms, phenotype data, gene names and descriptions and they are crucial for interpreting both small- and large-scale data and for aiding in the design of new experiments that further Aspergillus research. Results We have manually curated Biological Process GO annotations for all genes in AspGD with recorded functions in secondary metabolite production, adding new GO terms that specifically describe each secondary metabolite. We then leveraged these new annotations to predict roles in secondary metabolism for genes lacking experimental characterization. As a starting point for manually annotating Aspergillus secondary metabolite gene clusters, we used antiSMASH (antibiotics and Secondary Metabolite Analysis SHell) and SMURF (Secondary Metabolite Unknown Regions Finder) algorithms to identify potential clusters in A. nidulans, A. fumigatus, A. niger and A. oryzae, which we subsequently refined through manual curation. Conclusions This set of 266 manually curated secondary metabolite gene clusters will facilitate the investigation of novel Aspergillus secondary metabolites. PMID:23617571

GAMOLA2, a Comprehensive Software Package for the Annotation and Curation of Draft and Complete Microbial Genomes

PubMed Central

Altermann, Eric; Lu, Jingli; McCulloch, Alan

2017-01-01

Expert curated annotation remains one of the critical steps in achieving a reliable biological relevant annotation. Here we announce the release of GAMOLA2, a user friendly and comprehensive software package to process, annotate and curate draft and complete bacterial, archaeal, and viral genomes. GAMOLA2 represents a wrapping tool to combine gene model determination, functional Blast, COG, Pfam, and TIGRfam analyses with structural predictions including detection of tRNAs, rRNA genes, non-coding RNAs, signal protein cleavage sites, transmembrane helices, CRISPR repeats and vector sequence contaminations. GAMOLA2 has already been validated in a wide range of bacterial and archaeal genomes, and its modular concept allows easy addition of further functionality in future releases. A modified and adapted version of the Artemis Genome Viewer (Sanger Institute) has been developed to leverage the additional features and underlying information provided by the GAMOLA2 analysis, and is part of the software distribution. In addition to genome annotations, GAMOLA2 features, among others, supplemental modules that assist in the creation of custom Blast databases, annotation transfers between genome versions, and the preparation of Genbank files for submission via the NCBI Sequin tool. GAMOLA2 is intended to be run under a Linux environment, whereas the subsequent visualization and manual curation in Artemis is mobile and platform independent. The development of GAMOLA2 is ongoing and community driven. New functionality can easily be added upon user requests, ensuring that GAMOLA2 provides information relevant to microbiologists. The software is available free of charge for academic use. PMID:28386247

GAMOLA2, a Comprehensive Software Package for the Annotation and Curation of Draft and Complete Microbial Genomes.

PubMed

Altermann, Eric; Lu, Jingli; McCulloch, Alan

2017-01-01

Expert curated annotation remains one of the critical steps in achieving a reliable biological relevant annotation. Here we announce the release of GAMOLA2, a user friendly and comprehensive software package to process, annotate and curate draft and complete bacterial, archaeal, and viral genomes. GAMOLA2 represents a wrapping tool to combine gene model determination, functional Blast, COG, Pfam, and TIGRfam analyses with structural predictions including detection of tRNAs, rRNA genes, non-coding RNAs, signal protein cleavage sites, transmembrane helices, CRISPR repeats and vector sequence contaminations. GAMOLA2 has already been validated in a wide range of bacterial and archaeal genomes, and its modular concept allows easy addition of further functionality in future releases. A modified and adapted version of the Artemis Genome Viewer (Sanger Institute) has been developed to leverage the additional features and underlying information provided by the GAMOLA2 analysis, and is part of the software distribution. In addition to genome annotations, GAMOLA2 features, among others, supplemental modules that assist in the creation of custom Blast databases, annotation transfers between genome versions, and the preparation of Genbank files for submission via the NCBI Sequin tool. GAMOLA2 is intended to be run under a Linux environment, whereas the subsequent visualization and manual curation in Artemis is mobile and platform independent. The development of GAMOLA2 is ongoing and community driven. New functionality can easily be added upon user requests, ensuring that GAMOLA2 provides information relevant to microbiologists. The software is available free of charge for academic use.

Half a Century of Oman Ophiolite Studies: SSZ or MOR, the Arc Disposal Problem

NASA Astrophysics Data System (ADS)

Gregory, R. T.; Gray, D.

2014-12-01

The Samail Ophiolite, one of the largest and best exposed ophiolite complexes, is a Tethyan ophiolite obducted in the Late Cretaceous onto the formerly passive Arabian platform as Arabia began its most recent >1000 km northward migration towards a Miocene collision with Eurasia. The Oman Mountains, northeastern Arabian Peninsula have yet to collide with Eurasia; present uplift and form of the mountains also date to the Miocene. In addition to the scientific scrutiny of the ophiolite complex, the geologic constraints on the timing and emplacement of the ophiolite are abundant with no consensus on the obduction mechanism or its original tectonic setting. The crustal thickness of the ophiolite is comparable to thicknesses observed for "normal" mid-ocean ridges. Largely on the basis of structural and paleomagnetic arguments, some workers have attributed its origin to Pacific-type fast spreading ridges and complex micro plate geometries. Indeed the lower pillow lava sequences and much of the gabbroic crust have isotope and geochemical signatures consistent with a MORB source. However, because of the geochemistry of the upper pillow lavas, the ophiolite is most often characterized as a supra-subduction zone (SSZ) ophiolite, i.e. it sits in the hanging wall of some large tectonic structure for part of its history. In the absence of a preserved arc, the SSZ designation has little explanatory power only being a declaration of allochthony or about chemical properties of the mantle source. That associated continental shelf and oceanic crustal sections have suffered either clockwise or counterclockwise PT time trajectories requires some type of nascent subduction and hanging wall thrust transport of the young ridge crest. The widespread Late Cretaceous obduction of Tethyan oceanic crust and mantle over thousands of kilometers strike length is a problem for SSZ models (arc, forearc, back arc etc.) because arc initiation results in thick crust on short time scales, none of which is preserved. Similarly, fast spreading models require the subduction of >106 km2 without the initiation and preservation of a magmatic arc. Some Late Cretaceous major plate boundary reorganization that resulted in the current plate motion regime with NNE convergence between Afro-Arabia and Eurasia will be part of any final solution to the Oman problem.

cyvcf2: fast, flexible variant analysis with Python.

PubMed

Pedersen, Brent S; Quinlan, Aaron R

2017-06-15

Variant call format (VCF) files document the genetic variation observed after DNA sequencing, alignment and variant calling of a sample cohort. Given the complexity of the VCF format as well as the diverse variant annotations and genotype metadata, there is a need for fast, flexible methods enabling intuitive analysis of the variant data within VCF and BCF files. We introduce cyvcf2 , a Python library and software package for fast parsing and querying of VCF and BCF files and illustrate its speed, simplicity and utility. bpederse@gmail.com or aaronquinlan@gmail.com. cyvcf2 is available from https://github.com/brentp/cyvcf2 under the MIT license and from common python package managers. Detailed documentation is available at http://brentp.github.io/cyvcf2/. © The Author 2017. Published by Oxford University Press.

ArcGIS Framework for Scientific Data Analysis and Serving

NASA Astrophysics Data System (ADS)

Xu, H.; Ju, W.; Zhang, J.

2015-12-01

ArcGIS is a platform for managing, visualizing, analyzing, and serving geospatial data. Scientific data as part of the geospatial data features multiple dimensions (X, Y, time, and depth) and large volume. Multidimensional mosaic dataset (MDMD), a newly enhanced data model in ArcGIS, models the multidimensional gridded data (e.g. raster or image) as a hypercube and enables ArcGIS's capabilities to handle the large volume and near-real time scientific data. Built on top of geodatabase, the MDMD stores the dimension values and the variables (2D arrays) in a geodatabase table which allows accessing a slice or slices of the hypercube through a simple query and supports animating changes along time or vertical dimension using ArcGIS desktop or web clients. Through raster types, MDMD can manage not only netCDF, GRIB, and HDF formats but also many other formats or satellite data. It is scalable and can handle large data volume. The parallel geo-processing engine makes the data ingestion fast and easily. Raster function, definition of a raster processing algorithm, is a very important component in ArcGIS platform for on-demand raster processing and analysis. The scientific data analytics is achieved through the MDMD and raster function templates which perform on-demand scientific computation with variables ingested in the MDMD. For example, aggregating monthly average from daily data; computing total rainfall of a year; calculating heat index for forecasting data, and identifying fishing habitat zones etc. Addtionally, MDMD with the associated raster function templates can be served through ArcGIS server as image services which provide a framework for on-demand server side computation and analysis, and the published services can be accessed by multiple clients such as ArcMap, ArcGIS Online, JavaScript, REST, WCS, and WMS. This presentation will focus on the MDMD model and raster processing templates. In addtion, MODIS land cover, NDFD weather service, and HYCOM ocean model will be used to illustrate how ArcGIS platform and MDMD model can facilitate scientific data visualization and analytics and how the analysis results can be shared to more audience through ArcGIS Online and Portal.

Spatial Memory Impairment is Associated with Intraneural Amyloid-β Immunoreactivity and Dysfunctional Arc Expression in the Hippocampal-CA3 Region of a Transgenic Mouse Model of Alzheimer's Disease.

PubMed

Morin, Jean-Pascal; Cerón-Solano, Giovanni; Velázquez-Campos, Giovanna; Pacheco-López, Gustavo; Bermúdez-Rattoni, Federico; Díaz-Cintra, Sofía

2016-01-01

Dysfunction of synaptic communication in cortical and hippocampal networks has been suggested as one of the neuropathological hallmarks of the early stages of Alzheimer's disease (AD). Also, several lines of evidence have linked disrupted levels of activity-regulated cytoskeletal associated protein (Arc), an immediate early gene product that plays a central role in synaptic plasticity, with AD "synaptopathy". The mapping of Arc expression patterns in brain networks has been extensively used as a marker of memory-relevant neuronal activity history. Here we evaluated basal and behavior-induced Arc expression in hippocampal networks of the 3xTg-AD mouse model of AD. The basal percentage of Arc-expressing cells in 10-month-old 3xTg-AD mice was higher than wild type in CA3 (4.88% versus 1.77% , respectively) but similar in CA1 (1.75% versus 2.75% ). Noteworthy, this difference was not observed at 3 months of age. Furthermore, although a Morris water maze test probe induced a steep (∼4-fold) increment in the percentage of Arc+ cells in the CA3 region of the 10-month-old wild-type group, no such increment was observed in age-matched 3xTg-AD, whereas the amount of Arc+ cells in CA1 increased in both groups. Further, we detected that CA3 neurons with amyloid-β were much more likely to express Arc protein under basal conditions. We propose that in 3xTg-AD mice, intraneuronal amyloid-β expression in CA3 could increase unspecific neuronal activation and subsequent Arc protein expression, which might impair further memory-stabilizing processes.

Proteomic Analyses of Cysteine Redox in High-Fat-Fed and Fasted Mouse Livers: Implications for Liver Metabolic Homeostasis.

PubMed

Li, Yixing; Luo, Zupeng; Wu, Xilong; Zhu, Jun; Yu, Kai; Jin, Yi; Zhang, Zhiwang; Zhao, Shuhong; Zhou, Lei

2018-01-05

Intensive oxidative stress occurs during high-fat-diet-induced hepatic fat deposition, suggesting a critical role for redox signaling in liver metabolism. Intriguingly, evidence shows that fasting could also result in redox-profile changes largely through reduced oxidant or increased antioxidant levels. However, a comprehensive landscape of redox-modified hepatic substrates is lacking, thereby hindering our understanding of liver metabolic homeostasis. We employed a proteomic approach combining iodoacetyl tandem mass tag and nanoliquid chromatography tandem mass spectrometry to quantitatively probe the effects of high-fat feeding and fasting on in vivo redox-based cysteine modifications. Compared with control groups, ∼60% of cysteine residues exhibited downregulated oxidation ratios by fasting, whereas ∼94% of these ratios were upregulated by high-fat feeding. Importantly, in fasted livers, proteins exhibiting diminished cysteine oxidation were annotated in pathways associated with fatty acid metabolism, carbohydrate metabolism, insulin, peroxisome proliferator-activated receptors, and oxidative respiratory chain signaling, suggesting that fasting-induced redox changes targeted major metabolic pathways and consequently resulted in hepatic lipid accumulation.

Optogenetic Stimulation of Arcuate Nucleus Kiss1 Neurons Reveals a Steroid-Dependent Glutamatergic Input to POMC and AgRP Neurons in Male Mice

PubMed Central

Nestor, Casey C; Qiu, Jian; Padilla, Stephanie L.; Zhang, Chunguang; Bosch, Martha A.; Fan, Wei; Aicher, Sue A.; Palmiter, Richard D.

2016-01-01

Kisspeptin (Kiss1) neurons are essential for reproduction, but their role in the control of energy balance and other homeostatic functions remains unclear. Proopiomelanocortin (POMC) and agouti-related peptide (AgRP) neurons, located in the arcuate nucleus (ARC) of the hypothalamus, integrate numerous excitatory and inhibitory inputs to ultimately regulate energy homeostasis. Given that POMC and AgRP neurons are contacted by Kiss1 neurons in the ARC (Kiss1ARC) and they express androgen receptors, Kiss1ARC neurons may mediate the orexigenic action of testosterone via POMC and/or AgRP neurons. Quantitative PCR analysis of pooled Kiss1ARC neurons revealed that mRNA levels for Kiss1 and vesicular glutamate transporter 2 were higher in castrated male mice compared with gonad-intact males. Single-cell RT-PCR analysis of yellow fluorescent protein (YFP) ARC neurons harvested from males injected with AAV1-EF1α-DIO-ChR2:YFP revealed that 100% and 88% expressed mRNAs for Kiss1 and vesicular glutamate transporter 2, respectively. Whole-cell, voltage-clamp recordings from nonfluorescent postsynaptic ARC neurons showed that low frequency photo-stimulation (0.5 Hz) of Kiss1-ChR2:YFP neurons elicited a fast glutamatergic inward current in POMC and AgRP neurons. Paired-pulse, photo-stimulation revealed paired-pulse depression, which is indicative of greater glutamate release, in the castrated male mice compared with gonad-intact male mice. Group I and group II metabotropic glutamate receptor agonists depolarized and hyperpolarized POMC and AgRP neurons, respectively, which was mimicked by high frequency photo-stimulation (20 Hz) of Kiss1ARC neurons. Therefore, POMC and AgRP neurons receive direct steroid- and frequency-dependent glutamatergic synaptic input from Kiss1ARC neurons in male mice, which may be a critical pathway for Kiss1 neurons to help coordinate energy homeostasis and reproduction. PMID:27093227

An Ontology-Based GIS for Genomic Data Management of Rumen Microbes

PubMed Central

Jelokhani-Niaraki, Saber; Minuchehr, Zarrin; Nassiri, Mohammad Reza

2015-01-01

During recent years, there has been exponential growth in biological information. With the emergence of large datasets in biology, life scientists are encountering bottlenecks in handling the biological data. This study presents an integrated geographic information system (GIS)-ontology application for handling microbial genome data. The application uses a linear referencing technique as one of the GIS functionalities to represent genes as linear events on the genome layer, where users can define/change the attributes of genes in an event table and interactively see the gene events on a genome layer. Our application adopted ontology to portray and store genomic data in a semantic framework, which facilitates data-sharing among biology domains, applications, and experts. The application was developed in two steps. In the first step, the genome annotated data were prepared and stored in a MySQL database. The second step involved the connection of the database to both ArcGIS and Protégé as the GIS engine and ontology platform, respectively. We have designed this application specifically to manage the genome-annotated data of rumen microbial populations. Such a GIS-ontology application offers powerful capabilities for visualizing, managing, reusing, sharing, and querying genome-related data. PMID:25873847

An Ontology-Based GIS for Genomic Data Management of Rumen Microbes.

PubMed

Jelokhani-Niaraki, Saber; Tahmoorespur, Mojtaba; Minuchehr, Zarrin; Nassiri, Mohammad Reza

2015-03-01

During recent years, there has been exponential growth in biological information. With the emergence of large datasets in biology, life scientists are encountering bottlenecks in handling the biological data. This study presents an integrated geographic information system (GIS)-ontology application for handling microbial genome data. The application uses a linear referencing technique as one of the GIS functionalities to represent genes as linear events on the genome layer, where users can define/change the attributes of genes in an event table and interactively see the gene events on a genome layer. Our application adopted ontology to portray and store genomic data in a semantic framework, which facilitates data-sharing among biology domains, applications, and experts. The application was developed in two steps. In the first step, the genome annotated data were prepared and stored in a MySQL database. The second step involved the connection of the database to both ArcGIS and Protégé as the GIS engine and ontology platform, respectively. We have designed this application specifically to manage the genome-annotated data of rumen microbial populations. Such a GIS-ontology application offers powerful capabilities for visualizing, managing, reusing, sharing, and querying genome-related data.

Simultaneous total electron content and all-sky camera measurements of an auroral arc

NASA Astrophysics Data System (ADS)

Kintner, P. M.; Kil, H.; Deehr, C.; Schuck, P.

2002-07-01

We present an example of Global Positioning System (GPS) derived total electron content (TEC) and all-sky camera (ASC) images that show increases of TEC by ~10 × 1016 electrons m-2 (10 TEC units) occurring simultaneously with auroral light in ASC images. The TEC example appears to be an E region density enhancement produced by two discrete auroral arcs occurring in the late morning auroral oval at 1000 LT. This suggests that GPS signal TEC measurements can be used to detect individual auroral arcs and that individual discrete auroral arcs are responsible for some high-latitude phase scintillations. The specific auroral feature detected was a poleward moving auroral form believed to occur in the polar cap where the ionosphere is convecting antisunward. The magnitude of the rate of change of TEC (dTEC/dt) is comparable to that previously reported. However, the timescales associated with the event, the order of 1 min, suggest that the data sampling technique commonly used by chain GPS TEC receivers (averaging and time decimation) will undersample E region TEC perturbations produced by active auroral displays. The localized nature of this example implies that L1 ranging errors of at least 1.6 m will be introduced by auroral arcs into systems relying on differential GPS for navigation or augmentation. Although the TEC and auroral arcs presented herein occurred in the late morning auroral oval, we expect that the effects of discrete auroral arcs on GPS TEC and subsequent ranging errors should occur at all local times. Furthermore, GPS receivers can be used to detect individual discrete arcs.

MICRA: an automatic pipeline for fast characterization of microbial genomes from high-throughput sequencing data.

PubMed

Caboche, Ségolène; Even, Gaël; Loywick, Alexandre; Audebert, Christophe; Hot, David

2017-12-19

The increase in available sequence data has advanced the field of microbiology; however, making sense of these data without bioinformatics skills is still problematic. We describe MICRA, an automatic pipeline, available as a web interface, for microbial identification and characterization through reads analysis. MICRA uses iterative mapping against reference genomes to identify genes and variations. Additional modules allow prediction of antibiotic susceptibility and resistance and comparing the results of several samples. MICRA is fast, producing few false-positive annotations and variant calls compared to current methods, making it a tool of great interest for fully exploiting sequencing data.

Intelligent video storage of visual evidences on site in fast deployment

NASA Astrophysics Data System (ADS)

Desurmont, Xavier; Bastide, Arnaud; Delaigle, Jean-Francois

2004-07-01

In this article we present a generic, flexible, scalable and robust approach for an intelligent real-time forensic visual system. The proposed implementation could be rapidly deployable and integrates minimum logistic support as it embeds low complexity devices (PCs and cameras) that communicate through wireless network. The goal of these advanced tools is to provide intelligent video storage of potential video evidences for fast intervention during deployment around a hazardous sector after a terrorism attack, a disaster, an air crash or before attempt of it. Advanced video analysis tools, such as segmentation and tracking are provided to support intelligent storage and annotation.

New SW Pacific tectonic model: Cyclical intraoceanic magmatic arc construction and near-coeval emplacement along the Australia-Pacific margin in the Cenozoic

NASA Astrophysics Data System (ADS)

Whattam, Scott A.; Malpas, John; Ali, Jason R.; Smith, Ian E. M.

2008-03-01

Various reconstructions of the SW Pacific for the Late Cretaceous and Cenozoic suggest that northeast dipping subduction began in the South Loyalty Basin (SLB) at 55-50 Ma and that subsequent closure of the SLB resulted in the diachronous emplacement of Cretaceous-Paleocene ophiolitic nappes onto the Norfolk Ridge in New Caledonia at 40-34 Ma and in Northland, New Zealand, around 24-21 Ma. A fundamental problem with these models is that they do not account for the fact that NE dipping subduction had already been established offshore Papua New Guinea by at least 65-60 Ma which resulted in the emplacement of the Papuan Ultramafic Belt (PUB) ophiolite at 59-58 Ma. A second issue is that the reconstructions are based largely upon unfounded assumptions as to the age and nature of the basement beneath the Loyalty arc and Three Kings Ridge. Finally, reconstructions of the Northland region are based upon the erroneous assumption that the age of the majority of the igneous component comprising the Northland allochthon is Late Cretaceous-Paleocene, when in fact it is Oligocene. A new model is presented whereby the PUB, New Caledonia, and Northland ophiolites formed and were emplaced in a cyclical fashion above an extensive NE dipping Cenozoic intraoceanic arc system which diachronously propagated (N-S) along the entire eastern margin of the Australian Plate. These "infant arc" ophiolites represent fragments of suprasubduction zone lithosphere (SSZL) generated in the earliest stages of magmatic arc formation that were emplaced shortly after (<20 m.y.) as a result of forearc-Australian Plate collision. Subduction inception was the result of subsidence of older MORB-like lithosphere generated within an extensive "back arc basin" to the east of the Norfolk Ridge during the earliest stages of SLB formation above a southwest dipping Pacific Plate. During emplacement of each ophiolite, a crustal fragment of the older lithosphere was scraped off the NE dipping slab and subsequently back-thrust beneath each ophiolite during its emplacement.

The European ALMA Regional Centre: a model of user support

NASA Astrophysics Data System (ADS)

Andreani, P.; Stoehr, F.; Zwaan, M.; Hatziminaoglou, E.; Biggs, A.; Diaz-Trigo, M.; Humphreys, E.; Petry, D.; Randall, S.; Stanke, T.; van Kampen, E.; Bárta, M.; Brand, J.; Gueth, F.; Hogerheijde, M.; Bertoldi, F.; Muxlow, T.; Richards, A.; Vlemmings, W.

2014-08-01

The ALMA Regional Centres (ARCs) form the interface between the ALMA observatory and the user community from the proposal preparation stage to the delivery of data and their subsequent analysis. The ARCs provide critical services to both the ALMA operations in Chile and to the user community. These services were split by the ALMA project into core and additional services. The core services are financed by the ALMA operations budget and are critical to the successful operation of ALMA. They are contractual obligations and must be delivered to the ALMA project. The additional services are not funded by the ALMA project and are not contractual obligations, but are critical to achieve ALMA full scientific potential. A distributed network of ARC nodes (with ESO being the central ARC) has been set up throughout Europe at the following seven locations: Bologna, Bonn-Cologne, Grenoble, Leiden, Manchester, Ondrejov, Onsala. These ARC nodes are working together with the central node at ESO and provide both core and additional services to the ALMA user community. This paper presents the European ARC, and how it operates in Europe to support the ALMA community. This model, although complex in nature, is turning into a very successful one, providing a service to the scientific community that has been so far highly appreciated. The ARC could become a reference support model in an age where very large collaborations are required to build large facilities, and support is needed for geographically and culturally diverse communities.

Accelerating yield ramp through design and manufacturing collaboration

NASA Astrophysics Data System (ADS)

Sarma, Robin C.; Dai, Huixiong; Smayling, Michael C.; Duane, Michael P.

2004-12-01

Ramping an integrated circuit from first silicon bring-up to production yield levels is a challenge for all semiconductor products on the path to profitable market entry. Two approaches to accelerating yield ramp are presented. The first is the use of laser mask writers for fast throughput, high yield, and cost effective pattern transfer. The second is the use of electrical test to find a defect and identify the physical region to probe in failure analysis that is most likely to uncover the root cause. This provides feedback to the design team on modifications to make to the design to avoid the yield issue in a future tape-out revision. Additionally, the process parameter responsible for the root cause of the defect is forward annotated through the design, mask and wafer coordinate systems so it can be monitored in-line on subsequent lots of the manufacturing run. This results in an improved recipe for the manufacturing equipment to potentially prevent the recurrence of the defect and raise yield levels on the following material. The test diagnostics approach is enabled by the seamless traceability of a feature across the design, photomask and wafer, made possible by a common data model for design, mask pattern generation and wafer fabrication.

The impact of instructional design in a case-based, computer-assisted instruction module on learning liver pathology in a medical school pathology course

NASA Astrophysics Data System (ADS)

Latham, Patricia S.

The purpose of this quantitative experimental study was to test the impact of three learning interventions on student learning and satisfaction when the interventions were embedded in the instructional design of case-based, Computer-Assisted Instruction (CAI) modules for learning liver pathology in an in-class, self-study, laboratory exercise during a Year-2 medical school Pathology course. The hypothesis was that inclusion of the learning interventions would enhance student satisfaction in using the CAI and improve subsequent CAI-directed exam performance. Three learning interventions were studied, including the use of microscopic virtual slides instead of only static images, the use of interactive image annotations instead of only still annotations, and the use of guiding questions before presenting new information. Students were randomly assigned to with one of eight CAI learning modules configured to control for each of the three learning interventions. Effectiveness of the CAI for student learning was assessed by student performance on questions included in subsequent CAI-directed exams in a pretest and on posttests immediately after the lab exercise, at two weeks and two months. Student satisfaction and perceived learning was assessed by a student survey. Results showed that the learning interventions did not improve subsequent student exam performance, although satisfaction and perceived learning with use of the CAI learning modules was enhanced. Student class rank was evaluated to determine if the learning interventions might have a differential effect based on class rank, but there were no significant differences. Class rank at the time of the lab exercise was itself the strongest predictor of exam performance. The findings suggest that the addition of virtual slides, interactive annotations and guiding questions as learning interventions in self-study, case-based CAI for learning liver pathology in a medical class room setting are not likely to increase performance on subsequent MCQ-based exams, but student satisfaction with use of the CAI can be enhanced, which could provide to be an incentive for students to use similar CAI learning modules for future self-directed learning.

Identification of functional candidates amongst hypothetical proteins of Treponema pallidum ssp. pallidum.

PubMed

Naqvi, Ahmad Abu Turab; Shahbaaz, Mohd; Ahmad, Faizan; Hassan, Md Imtaiyaz

2015-01-01

Syphilis is a globally occurring venereal disease, and its infection is propagated through sexual contact. The causative agent of syphilis, Treponema pallidum ssp. pallidum, a Gram-negative sphirochaete, is an obligate human parasite. Genome of T. pallidum ssp. pallidum SS14 strain (RefSeq NC_010741.1) encodes 1,027 proteins, of which 444 proteins are known as hypothetical proteins (HPs), i.e., proteins of unknown functions. Here, we performed functional annotation of HPs of T. pallidum ssp. pallidum using various database, domain architecture predictors, protein function annotators and clustering tools. We have analyzed the sequences of 444 HPs of T. pallidum ssp. pallidum and subsequently predicted the function of 207 HPs with a high level of confidence. However, functions of 237 HPs are predicted with less accuracy. We found various enzymes, transporters, binding proteins in the annotated group of HPs that may be possible molecular targets, facilitating for the survival of pathogen. Our comprehensive analysis helps to understand the mechanism of pathogenesis to provide many novel potential therapeutic interventions.

Phage phenomics: Physiological approaches to characterize novel viral proteins

ScienceCinema

Sanchez, Savannah E. [San Diego State Univ., San Diego, CA (United States); Cuevas, Daniel A. [San Diego State Univ., San Diego, CA (United States); Rostron, Jason E. [San Diego State Univ., San Diego, CA (United States); Liang, Tiffany Y. [San Diego State Univ., San Diego, CA (United States); Pivaroff, Cullen G. [San Diego State Univ., San Diego, CA (United States); Haynes, Matthew R. [San Diego State Univ., San Diego, CA (United States); Nulton, Jim [San Diego State Univ., San Diego, CA (United States); Felts, Ben [San Diego State Univ., San Diego, CA (United States); Bailey, Barbara A. [San Diego State Univ., San Diego, CA (United States); Salamon, Peter [San Diego State Univ., San Diego, CA (United States); Edwards, Robert A. [San Diego State Univ., San Diego, CA (United States); Argonne National Lab. (ANL), Argonne, IL (United States); Burgin, Alex B. [Broad Institute, Cambridge, MA (United States); Segall, Anca M. [San Diego State Univ., San Diego, CA (United States); Rohwer, Forest [San Diego State Univ., San Diego, CA (United States)

2018-06-21

Current investigations into phage-host interactions are dependent on extrapolating knowledge from (meta)genomes. Interestingly, 60 - 95% of all phage sequences share no homology to current annotated proteins. As a result, a large proportion of phage genes are annotated as hypothetical. This reality heavily affects the annotation of both structural and auxiliary metabolic genes. Here we present phenomic methods designed to capture the physiological response(s) of a selected host during expression of one of these unknown phage genes. Multi-phenotype Assay Plates (MAPs) are used to monitor the diversity of host substrate utilization and subsequent biomass formation, while metabolomics provides bi-product analysis by monitoring metabolite abundance and diversity. Both tools are used simultaneously to provide a phenotypic profile associated with expression of a single putative phage open reading frame (ORF). Thus, representative results for both methods are compared, highlighting the phenotypic profile differences of a host carrying either putative structural or metabolic phage genes. In addition, the visualization techniques and high throughput computational pipelines that facilitated experimental analysis are presented.

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

Sanchez, Savannah E.; Cuevas, Daniel A.; Rostron, Jason E.

Current investigations into phage-host interactions are dependent on extrapolating knowledge from (meta)genomes. Interestingly, 60 - 95% of all phage sequences share no homology to current annotated proteins. As a result, a large proportion of phage genes are annotated as hypothetical. This reality heavily affects the annotation of both structural and auxiliary metabolic genes. Here we present phenomic methods designed to capture the physiological response(s) of a selected host during expression of one of these unknown phage genes. Multi-phenotype Assay Plates (MAPs) are used to monitor the diversity of host substrate utilization and subsequent biomass formation, while metabolomics provides bi-product analysismore » by monitoring metabolite abundance and diversity. Both tools are used simultaneously to provide a phenotypic profile associated with expression of a single putative phage open reading frame (ORF). Thus, representative results for both methods are compared, highlighting the phenotypic profile differences of a host carrying either putative structural or metabolic phage genes. In addition, the visualization techniques and high throughput computational pipelines that facilitated experimental analysis are presented.« less

Map showing inventory and regional susceptibility for Holocene debris flows, and related fast-moving landslides in the conterminous United States

USGS Publications Warehouse

Brabb, Earl E.; Colgan, Joseph P.; Best, Timothy C.

2000-01-01

Introduction Debris flows, debris avalanches, mud flows and lahars are fast-moving landslides that occur in a wide variety of environments throughout the world. They are particularly dangerous to life and property because they move quickly, destroy objects in their paths, and often strike without warning. This map represents a significant effort to compile the locations of known debris flows in United Stated and predict where future flows might occur. The files 'dfipoint.e00' and 'dfipoly.e00' contain the locations of over 6600 debris flows from published and unpublished sources. The locations are referenced by numbers that correspond to entries in a bibliography, which is part of the pamphlet 'mf2329pamphlet.pdf'. The areas of possible future debris flows are shown in the file 'susceptibility.tif', which is a georeferenced TIFF file that can be opened in an image editing program or imported into a GIS system like ARC/INFO. All other databases are in ARC/INFO export (.e00) format.

Geologic Surface Effects of Underground Nuclear Testing, Buckboard Mesa, Climax Stock, Dome Mountain, Frenchman Flat, Rainier/Aqueduct Mesa, and Shoshone Mountain, Nevada Test Site, Nevada

USGS Publications Warehouse

Grasso, Dennis N.

2003-01-01

Surface effects maps were produced for 72 of 89 underground detonations conducted at the Frenchman Flat, Rainier Mesa and Aqueduct Mesa, Climax Stock, Shoshone Mountain, Buckboard Mesa, and Dome Mountain testing areas of the Nevada Test Site between August 10, 1957 (Saturn detonation, Area 12) and September 18, 1992 (Hunters Trophy detonation, Area 12). The ?Other Areas? Surface Effects Map Database, which was used to construct the maps shown in this report, contains digital reproductions of these original maps. The database is provided in both ArcGIS (v. 8.2) geodatabase format and ArcView (v. 3.2) shapefile format. This database contains sinks, cracks, faults, and other surface effects having a combined (cumulative) length of 136.38 km (84.74 mi). In GIS digital format, the user can view all surface effects maps simultaneously, select and view the surface effects of one or more sites of interest, or view specific surface effects by area or site. Three map layers comprise the database. They are: (1) the surface effects maps layer (oase_n27f), (2) the bar symbols layer (oase_bar_n27f), and (3) the ball symbols layer (oase_ball_n27f). Additionally, an annotation layer, named 'Ball_and_Bar_Labels,' and a polygon features layer, named 'Area12_features_poly_n27f,' are contained in the geodatabase version of the database. The annotation layer automatically labels all 295 ball-and-bar symbols shown on these maps. The polygon features layer displays areas of ground disturbances, such as rock spall and disturbed ground caused by the detonations. Shapefile versions of the polygon features layer in Nevada State Plane and Universal Transverse Mercator projections, named 'area12_features_poly_n27f.shp' and 'area12_features_poly_u83m.shp,' are also provided in the archive.

GoGene: gene annotation in the fast lane.

PubMed

Plake, Conrad; Royer, Loic; Winnenburg, Rainer; Hakenberg, Jörg; Schroeder, Michael

2009-07-01

High-throughput screens such as microarrays and RNAi screens produce huge amounts of data. They typically result in hundreds of genes, which are often further explored and clustered via enriched GeneOntology terms. The strength of such analyses is that they build on high-quality manual annotations provided with the GeneOntology. However, the weakness is that annotations are restricted to process, function and location and that they do not cover all known genes in model organisms. GoGene addresses this weakness by complementing high-quality manual annotation with high-throughput text mining extracting co-occurrences of genes and ontology terms from literature. GoGene contains over 4,000,000 associations between genes and gene-related terms for 10 model organisms extracted from more than 18,000,000 PubMed entries. It does not cover only process, function and location of genes, but also biomedical categories such as diseases, compounds, techniques and mutations. By bringing it all together, GoGene provides the most recent and most complete facts about genes and can rank them according to novelty and importance. GoGene accepts keywords, gene lists, gene sequences and protein sequences as input and supports search for genes in PubMed, EntrezGene and via BLAST. Since all associations of genes to terms are supported by evidence in the literature, the results are transparent and can be verified by the user. GoGene is available at http://gopubmed.org/gogene.

DeepFruits: A Fruit Detection System Using Deep Neural Networks

PubMed Central

Sa, Inkyu; Ge, Zongyuan; Dayoub, Feras; Upcroft, Ben; Perez, Tristan; McCool, Chris

2016-01-01

This paper presents a novel approach to fruit detection using deep convolutional neural networks. The aim is to build an accurate, fast and reliable fruit detection system, which is a vital element of an autonomous agricultural robotic platform; it is a key element for fruit yield estimation and automated harvesting. Recent work in deep neural networks has led to the development of a state-of-the-art object detector termed Faster Region-based CNN (Faster R-CNN). We adapt this model, through transfer learning, for the task of fruit detection using imagery obtained from two modalities: colour (RGB) and Near-Infrared (NIR). Early and late fusion methods are explored for combining the multi-modal (RGB and NIR) information. This leads to a novel multi-modal Faster R-CNN model, which achieves state-of-the-art results compared to prior work with the F1 score, which takes into account both precision and recall performances improving from 0.807 to 0.838 for the detection of sweet pepper. In addition to improved accuracy, this approach is also much quicker to deploy for new fruits, as it requires bounding box annotation rather than pixel-level annotation (annotating bounding boxes is approximately an order of magnitude quicker to perform). The model is retrained to perform the detection of seven fruits, with the entire process taking four hours to annotate and train the new model per fruit. PMID:27527168

DeepFruits: A Fruit Detection System Using Deep Neural Networks.

PubMed

Sa, Inkyu; Ge, Zongyuan; Dayoub, Feras; Upcroft, Ben; Perez, Tristan; McCool, Chris

2016-08-03

This paper presents a novel approach to fruit detection using deep convolutional neural networks. The aim is to build an accurate, fast and reliable fruit detection system, which is a vital element of an autonomous agricultural robotic platform; it is a key element for fruit yield estimation and automated harvesting. Recent work in deep neural networks has led to the development of a state-of-the-art object detector termed Faster Region-based CNN (Faster R-CNN). We adapt this model, through transfer learning, for the task of fruit detection using imagery obtained from two modalities: colour (RGB) and Near-Infrared (NIR). Early and late fusion methods are explored for combining the multi-modal (RGB and NIR) information. This leads to a novel multi-modal Faster R-CNN model, which achieves state-of-the-art results compared to prior work with the F1 score, which takes into account both precision and recall performances improving from 0 . 807 to 0 . 838 for the detection of sweet pepper. In addition to improved accuracy, this approach is also much quicker to deploy for new fruits, as it requires bounding box annotation rather than pixel-level annotation (annotating bounding boxes is approximately an order of magnitude quicker to perform). The model is retrained to perform the detection of seven fruits, with the entire process taking four hours to annotate and train the new model per fruit.

Transformation of juvenile Izu-Bonin-Mariana oceanic arc into mature continental crust: An example from the Neogene Izu collision zone granitoid plutons, Central Japan

NASA Astrophysics Data System (ADS)

Saito, Satoshi; Tani, Kenichiro

2017-04-01

Granitic rocks (sensulato) are major constituents of upper continental crust. Recent reviews reveal that the average composition of Phanerozoic upper continental crust is granodioritic. Although oceanic arcs are regarded as a site producing continental crust material in an oceanic setting, intermediate to felsic igneous rocks occurring in modern oceanic arcs are dominantly tonalitic to trondhjemitic in composition and have lower incompatible element contents than the average upper continental crust. Therefore, juvenile oceanic arcs require additional processes in order to get transformed into mature continental crust enriched in incompatible elements. Neogene granitoid plutons are widely exposed in the Izu Collision Zone in central Japan, where the northern end of the Izu-Bonin-Mariana (IBM) arc (juvenile oceanic arc) has been colliding with the Honshu arc (mature island arc) since Middle Miocene. The plutons in this area are composed of various types of granitoids ranging from tonalite to trondhjemite, granodiorite, monzogranite and granite. Three main granitoid plutons are distributed in this area: Tanzawa plutonic complex, Kofu granitic complex, and Kaikomagatake granitoid pluton. Tanzawa plutonic complex is dominantly composed of tonalite and trondhjemite and characterized by low concentration of incompatible elements and shows geochemical similarity with modern juvenile oceanic arcs. In contrast, Kofu granitic complex and Kaikomagatake granitoid pluton consists mainly of granodiorite, monzogranite and granite and their incompatible element abundances are comparable to the average upper continental crust. Previous petrogenetic studies on these plutons suggested that (1) the Tanzawa plutonic complex formed by lower crustal anatexis of juvenile basaltic rocks occurring in the IBM arc, (2) the Kofu granitic complex formed by anatexis of 'hybrid lower crust' comprising of both basaltic rocks of the IBM arc and metasedimentary rocks of the Honshu arc, and (3) the Kaikomagatake granitoid pluton formed by anatexis of 'hybrid lower crust' consisting of K-rich rear-arc crust of the IBM arc and metasedimentary rocks of the Honshu arc. These studies collectively suggest that the chemical diversity within the Izu Collision Zone granitoid plutons reflects the chemical variation of basaltic sources (i.e., across-arc chemical variation in the IBM arc) as well as variable contribution of the metasedimentary component in the source region. The petrogenetic models of the Izu Collision Zone granitoid plutons suggest that collision with another mature arc/continent, hybrid lower crust formation and subsequent hybrid source anatexis are required for juvenile oceanic arcs to produce granitoid magmas with enriched compositions. The Izu Collision Zone granitoid plutons provide an exceptional example of the collision-induced transformation from a juvenile oceanic arc to the mature continental crust.

Oxidation State of Iron in the Izu-Bonin Arc Initial Magma and Its Influence Factors

NASA Astrophysics Data System (ADS)

Li, H.; Arculus, R. J.; Brandl, P. A.; Hamada, M.; Savov, I. P.; Zhu, S.; Hickey-Vargas, R.; Tepley, F. J., III; Meffre, S.; Yogodzinski, G. M.; McCarthy, A.; Barth, A. P.; Kanayama, K.; Kusano, Y.; Sun, W.

2014-12-01

The redox state of mantle-derived magmas is a controversial issue, especially whether island arc basalts are more oxidized than those from mid-ocean ridges. Usually, arc magmas have higher Fe3+/Fe2+ and calculated oxygen fugacity (fO2) than mid-ocean ridge basalts (MORB). It is the high fO2 of arc magma that apparently delays onset of sulfide fractionation and sequestration of precious/base metals thereby facilitating the formation of many giant gold-copper deposits typically associated with subduction zones. But due to a paucity of Fe3+/Fe2+ data for primary mantle-derived arc magmas, the cause for high fO2 of these magma types is still controversial; causes may include inter alia subduction-released oxidized material addition to the mantle wedge source of arc magma, partial melting of subducted slab, and redox changes occurring during ascent of the magma. Fortunately, IODP expedition 351 drilling at IODP Site U1438 in the Amami-Sankaku Basin of the northwestern Philipine Sea, adjacent to the proto-Izu-Bonin Arc at the Kyushu-Palau Ridge (KPR), recovered not only volcaniclastics derived from the inception of Izu-Bonin Mariana (IBM) arc in the Eocene, but also similar materials for the Arc's subsequent evolution through to the Late Oligocene and abandonment of the KPR as a remnant arc. Samples of the pre-Arc oceanic crustal basement were also recovered enabling us to determine the fO2of the mantle preceding arc inception. As the oxidation state of iron in basaltic glass directly relates to the fO2 , the Fe3+/∑Fe ratio [Fe3+/(Fe3++ Fe2+)] of basaltic glass are quantified by synchrotron-facilitated micro X-ray Absorption Near Edge Structure (XANES) spectroscopy to reflect its fO2. Fe K-edge µ-XANES spectra were recorded in fluorescence mode at Beamline 15U1, Shanghai Synchrotron Radiation Facility (SSRF). Synthetic silicate glass with known Fe3+/∑Fe ratio was used in data handling. The experimental results as well as preliminary data from IODP Expedition 351 will be presented

Investigation of DC hybrid circuit breaker based on high-speed switch and arc generator

NASA Astrophysics Data System (ADS)

Wu, Yifei; Rong, Mingzhe; Wu, Yi; Yang, Fei; Li, Mei; Zhong, Jianying; Han, Guohui; Niu, Chunping; Hu, Yang

2015-02-01

A new design of DC hybrid circuit breaker based on high-speed switch (HSS) and arc generator (AG), which can drastically profit from low heat loss in normal state and fast current breaking under fault state, is presented and analyzed in this paper. AG is designed according to the magnetic pinch effect of liquid metal. By utilizing the arc voltage generated across AG, the fault current is rapidly commutated from HSS into parallel connected branch. As a consequence, the arcless open of HSS is achieved. The post-arc conducting resume time (Δ tc) of AG and the commutation original voltage (Uc), two key factors in the commutation process, are investigated experimentally. Particularly, influences of the liquid metal channel diameter (Φ) of AG, fault current rate of rise (di/dt) and Uc on Δ tc are focused on. Furthermore, a suitable Uc is determined during the current commutation process, aiming at the reliable arcless open of HSS and short breaking time. Finally, the fault current breaking test is carried out for the current peak value of 11.8 kA, and the validity of the design is confirmed by the experimental results.

Investigation of DC hybrid circuit breaker based on high-speed switch and arc generator.

PubMed

Wu, Yifei; Rong, Mingzhe; Wu, Yi; Yang, Fei; Li, Mei; Zhong, Jianying; Han, Guohui; Niu, Chunping; Hu, Yang

2015-02-01

A new design of DC hybrid circuit breaker based on high-speed switch (HSS) and arc generator (AG), which can drastically profit from low heat loss in normal state and fast current breaking under fault state, is presented and analyzed in this paper. AG is designed according to the magnetic pinch effect of liquid metal. By utilizing the arc voltage generated across AG, the fault current is rapidly commutated from HSS into parallel connected branch. As a consequence, the arcless open of HSS is achieved. The post-arc conducting resume time (Δ tc) of AG and the commutation original voltage (Uc), two key factors in the commutation process, are investigated experimentally. Particularly, influences of the liquid metal channel diameter (Φ) of AG, fault current rate of rise (di/dt) and Uc on Δ tc are focused on. Furthermore, a suitable Uc is determined during the current commutation process, aiming at the reliable arcless open of HSS and short breaking time. Finally, the fault current breaking test is carried out for the current peak value of 11.8 kA, and the validity of the design is confirmed by the experimental results.

Arcmon for Process Control in Silicomanganese Production: A Case Study

NASA Astrophysics Data System (ADS)

Steenkamp, Joalet Dalene; Hockaday, Christopher James; Gous, Johan Petrus; Clark, Wilma; Corfield, Archie

2017-12-01

Arcmon is a device that is used to quantify the amount of arcing (expressed as arc power fraction) that takes place in submerged-arc furnaces (SAFs). During a trial installation on a 48-MVA SAF used for the production of SiMn, differences in arcing behavior between the three different electrodes were observed, with the amount of arcing on one electrode being significantly higher than on the other two. During the subsequent excavation of the SAF, the increased amount of arcing had been attributed to the presence of a hard build-up below the electrode. Phase chemical analysis of the hard build-up indicated that it consisted primarily of portlandite (a reaction product of calcium carbide that probably reacted with the water used to cool down the burden during excavation) and silicon carbide. In comparison, the coke-bed below one of the other electrodes consisted mainly of graphite, silicon carbide, and phases which will typically precipitate from slag upon cooling, i.e. phases expected to be present in a coke-bed. The presence of such a large build-up of carbide material is undesirable as it effectively reduces the volume of coke-bed available for the reduction reactions to occur. The study indicated that Arcmon could potentially be applied as an early warning system to identify the presence of such a build-up.

Record of Current Educational Publications. Bulletin, 1921, No. 52

ERIC Educational Resources Information Center

Bureau of Education, Department of the Interior, 1922

1922-01-01

The titles included in this classified and annotated list are books and articles selected by the compilers from the current educational literature of the final months of 1921, subsequent to the preparation of Bulletin, 1921, no. 49. Monthly Record of Current Educational Publications, October, 1921. The publications are organized into the following…

Motivating Students for Excellence. The Best of ERIC on Educational Management, Number 73.

ERIC Educational Resources Information Center

ERIC Clearinghouse on Educational Management, Eugene, OR.

The first 2 of the 12 publications reviewed in this annotated bibliography use Abraham Maslow's hierarchy of needs to address problems, respectively, of teaching composition and of motivating students by teaching them how to set goals, formulate goal-achievement strategies, and successfully implement their plans. Subsequent reports suggest ways of…

Web 2.0-Based Crowdsourcing for High-Quality Gold Standard Development in Clinical Natural Language Processing

PubMed Central

Deleger, Louise; Li, Qi; Kaiser, Megan; Stoutenborough, Laura

2013-01-01

Background A high-quality gold standard is vital for supervised, machine learning-based, clinical natural language processing (NLP) systems. In clinical NLP projects, expert annotators traditionally create the gold standard. However, traditional annotation is expensive and time-consuming. To reduce the cost of annotation, general NLP projects have turned to crowdsourcing based on Web 2.0 technology, which involves submitting smaller subtasks to a coordinated marketplace of workers on the Internet. Many studies have been conducted in the area of crowdsourcing, but only a few have focused on tasks in the general NLP field and only a handful in the biomedical domain, usually based upon very small pilot sample sizes. In addition, the quality of the crowdsourced biomedical NLP corpora were never exceptional when compared to traditionally-developed gold standards. The previously reported results on medical named entity annotation task showed a 0.68 F-measure based agreement between crowdsourced and traditionally-developed corpora. Objective Building upon previous work from the general crowdsourcing research, this study investigated the usability of crowdsourcing in the clinical NLP domain with special emphasis on achieving high agreement between crowdsourced and traditionally-developed corpora. Methods To build the gold standard for evaluating the crowdsourcing workers’ performance, 1042 clinical trial announcements (CTAs) from the ClinicalTrials.gov website were randomly selected and double annotated for medication names, medication types, and linked attributes. For the experiments, we used CrowdFlower, an Amazon Mechanical Turk-based crowdsourcing platform. We calculated sensitivity, precision, and F-measure to evaluate the quality of the crowd’s work and tested the statistical significance (P<.001, chi-square test) to detect differences between the crowdsourced and traditionally-developed annotations. Results The agreement between the crowd’s annotations and the traditionally-generated corpora was high for: (1) annotations (0.87, F-measure for medication names; 0.73, medication types), (2) correction of previous annotations (0.90, medication names; 0.76, medication types), and excellent for (3) linking medications with their attributes (0.96). Simple voting provided the best judgment aggregation approach. There was no statistically significant difference between the crowd and traditionally-generated corpora. Our results showed a 27.9% improvement over previously reported results on medication named entity annotation task. Conclusions This study offers three contributions. First, we proved that crowdsourcing is a feasible, inexpensive, fast, and practical approach to collect high-quality annotations for clinical text (when protected health information was excluded). We believe that well-designed user interfaces and rigorous quality control strategy for entity annotation and linking were critical to the success of this work. Second, as a further contribution to the Internet-based crowdsourcing field, we will publicly release the JavaScript and CrowdFlower Markup Language infrastructure code that is necessary to utilize CrowdFlower’s quality control and crowdsourcing interfaces for named entity annotations. Finally, to spur future research, we will release the CTA annotations that were generated by traditional and crowdsourced approaches. PMID:23548263

Variation analysis and gene annotation of eight MHC haplotypes: The MHC Haplotype Project

PubMed Central

Horton, Roger; Gibson, Richard; Coggill, Penny; Miretti, Marcos; Allcock, Richard J.; Almeida, Jeff; Forbes, Simon; Gilbert, James G. R.; Halls, Karen; Harrow, Jennifer L.; Hart, Elizabeth; Howe, Kevin; Jackson, David K.; Palmer, Sophie; Roberts, Anne N.; Sims, Sarah; Stewart, C. Andrew; Traherne, James A.; Trevanion, Steve; Wilming, Laurens; Rogers, Jane; de Jong, Pieter J.; Elliott, John F.; Sawcer, Stephen; Todd, John A.; Trowsdale, John

2008-01-01

The human major histocompatibility complex (MHC) is contained within about 4 Mb on the short arm of chromosome 6 and is recognised as the most variable region in the human genome. The primary aim of the MHC Haplotype Project was to provide a comprehensively annotated reference sequence of a single, human leukocyte antigen-homozygous MHC haplotype and to use it as a basis against which variations could be assessed from seven other similarly homozygous cell lines, representative of the most common MHC haplotypes in the European population. Comparison of the haplotype sequences, including four haplotypes not previously analysed, resulted in the identification of >44,000 variations, both substitutions and indels (insertions and deletions), which have been submitted to the dbSNP database. The gene annotation uncovered haplotype-specific differences and confirmed the presence of more than 300 loci, including over 160 protein-coding genes. Combined analysis of the variation and annotation datasets revealed 122 gene loci with coding substitutions of which 97 were non-synonymous. The haplotype (A3-B7-DR15; PGF cell line) designated as the new MHC reference sequence, has been incorporated into the human genome assembly (NCBI35 and subsequent builds), and constitutes the largest single-haplotype sequence of the human genome to date. The extensive variation and annotation data derived from the analysis of seven further haplotypes have been made publicly available and provide a framework and resource for future association studies of all MHC-associated diseases and transplant medicine. PMID:18193213

Singing activity-driven Arc expression associated with vocal acoustic plasticity in juvenile songbird.

PubMed

Hayase, Shin; Wada, Kazuhiro

2018-06-23

Learned vocalization, including birdsong and human speech, is acquired through self-motivated vocal practice during the sensitive period of vocal learning. The zebra finch (Taeniopygia guttata) develops a song characterized by vocal variability and crystalizes a defined song pattern as adulthood. However, it remains unknown how vocal variability is regulated with diurnal singing during the sensorimotor learning period. Here, we investigated the expression of activity-dependent neuroplasticity-related gene Arc during the early plastic song phase to examine its potential association with vocal plasticity. We first confirmed that multiple acoustic features of syllables in the plastic song were dramatically and simultaneously modulated during the first 3 hours of singing in a day and the altered features were maintained until sleep. Concurrently, Arc was intensely induced during morning singing and a subsequent attenuation during afternoon singing in the robust nucleus of the arcopallium (RA) and the interfacial nucleus of the nidopallium (NIf). The singing-driven Arc expression was not altered by circadian rhythm, but rather reduced during the day as juveniles produced more songs. Song stabilization accelerated by testosterone administration in juveniles was accompanied with attenuation of Arc induction in RA and NIf. In contrast, although early-deafened birds produced highly unstable song even at adulthood, singing-driven Arc expression was not different between intact and early-deafened adults. These results suggest a potential functional link between Arc expression in RA and NIf and vocal plasticity during the sensorimotor phase of song learning. Nonetheless, Arc expression did not reflect the quality of bird's own song or auditory feedback. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Expression of c-Fos in Arcuate Nucleus Induced by Electroacupuncture: relations to neurons containing opioids and glutamate

PubMed Central

Guo, Zhi-Ling; Longhurst, John C.

2007-01-01

Electroacupuncture (EA) at the Neiguan-Jianshi acupoints (P5-P6, overlying the median nerve) attenuates sympathoexcitatory reflexes probably through affecting the opioid system. The arcuate nucleus (ARC) within hypothalamus is an important brain area that produces opioid peptides. Current physiological studies have demonstrated that the predominant response to EA is excitation in the ARC and that excitatory projections from the ARC to the ventrolateral periaqueductal gray during EA at P5-P6 contribute to inhibition of sympathoexcitatory cardiovascular reflexes. These data imply that ARC neurons activated by EA also may contain excitatory neurotransmitters. Thus, the present study evaluated activation of the ARC induced by EA at P5-P6, in relation to the opioid system and glutamate, by detecting c-Fos, an immediate early gene, opioid peptides and vesicular glutamate transporter 3 (VGLUT3). To enhance detection of perikarya containing the opioid peptides, colchicine (90–100 µg/kg) was administered in cats 28–30 hours before EA or the sham-operated control. EA was performed at P5-P6 for 30 min. Compared to controls (n=5), c-Fos positive cells and neurons double-labeled with c-Fos and β-endorphin, enkephalin or VGLUT3 in the ARC were significantly increased in EA-treated cats (n=6; all P<0.05). Moreover, neurons triple-labeled with c-Fos, β-endorphin and VGLUT3 were noted in this region following EA stimulation, but not in controls. Thus, EA at P5-P6 activates neurons in the ARC, some of which contain opioids as well as glutamate or both. The results imply that EA at P5-P6 has the potential to influence ARC neurons containing multiple neuronal substances that subsequently modulate cardiovascular function. PMID:17662967

Sensors control gas metal arc welding

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

Siewert, T.A.; Madigan, R.B.; Quinn, T.P.

1997-04-01

The response time of a trained welder from the time a weld problem is identified to the time action is taken is about one second--especially after a long, uneventful period of welding. This is acceptable for manual welding because it is close to the time it takes for the weld pool to solidify. If human response time were any slower, manual welding would not be possible. However, human response time is too slow to respond to some weld events, such as melting of the contact tube in gas metal arc welding (GMAW), and only automated intelligent control systems can reactmore » fast enough to correct or avoid these problems. Control systems incorporate welding knowledge that enables intelligent decisions to be made about weld quality and, ultimately, to keep welding parameters in the range where only high-quality welds are produced. This article discusses the correlation of electrical signals with contact-tube wear, changes in shielding gas, changes in arc length, and other weld process data.« less

DDBJ read annotation pipeline: a cloud computing-based pipeline for high-throughput analysis of next-generation sequencing data.

PubMed

Nagasaki, Hideki; Mochizuki, Takako; Kodama, Yuichi; Saruhashi, Satoshi; Morizaki, Shota; Sugawara, Hideaki; Ohyanagi, Hajime; Kurata, Nori; Okubo, Kousaku; Takagi, Toshihisa; Kaminuma, Eli; Nakamura, Yasukazu

2013-08-01

High-performance next-generation sequencing (NGS) technologies are advancing genomics and molecular biological research. However, the immense amount of sequence data requires computational skills and suitable hardware resources that are a challenge to molecular biologists. The DNA Data Bank of Japan (DDBJ) of the National Institute of Genetics (NIG) has initiated a cloud computing-based analytical pipeline, the DDBJ Read Annotation Pipeline (DDBJ Pipeline), for a high-throughput annotation of NGS reads. The DDBJ Pipeline offers a user-friendly graphical web interface and processes massive NGS datasets using decentralized processing by NIG supercomputers currently free of charge. The proposed pipeline consists of two analysis components: basic analysis for reference genome mapping and de novo assembly and subsequent high-level analysis of structural and functional annotations. Users may smoothly switch between the two components in the pipeline, facilitating web-based operations on a supercomputer for high-throughput data analysis. Moreover, public NGS reads of the DDBJ Sequence Read Archive located on the same supercomputer can be imported into the pipeline through the input of only an accession number. This proposed pipeline will facilitate research by utilizing unified analytical workflows applied to the NGS data. The DDBJ Pipeline is accessible at http://p.ddbj.nig.ac.jp/.

Assessment of protein set coherence using functional annotations

PubMed Central

Chagoyen, Monica; Carazo, Jose M; Pascual-Montano, Alberto

2008-01-01

Background Analysis of large-scale experimental datasets frequently produces one or more sets of proteins that are subsequently mined for functional interpretation and validation. To this end, a number of computational methods have been devised that rely on the analysis of functional annotations. Although current methods provide valuable information (e.g. significantly enriched annotations, pairwise functional similarities), they do not specifically measure the degree of homogeneity of a protein set. Results In this work we present a method that scores the degree of functional homogeneity, or coherence, of a set of proteins on the basis of the global similarity of their functional annotations. The method uses statistical hypothesis testing to assess the significance of the set in the context of the functional space of a reference set. As such, it can be used as a first step in the validation of sets expected to be homogeneous prior to further functional interpretation. Conclusion We evaluate our method by analysing known biologically relevant sets as well as random ones. The known relevant sets comprise macromolecular complexes, cellular components and pathways described for Saccharomyces cerevisiae, which are mostly significantly coherent. Finally, we illustrate the usefulness of our approach for validating 'functional modules' obtained from computational analysis of protein-protein interaction networks. Matlab code and supplementary data are available at PMID:18937846

DDBJ Read Annotation Pipeline: A Cloud Computing-Based Pipeline for High-Throughput Analysis of Next-Generation Sequencing Data

PubMed Central

Nagasaki, Hideki; Mochizuki, Takako; Kodama, Yuichi; Saruhashi, Satoshi; Morizaki, Shota; Sugawara, Hideaki; Ohyanagi, Hajime; Kurata, Nori; Okubo, Kousaku; Takagi, Toshihisa; Kaminuma, Eli; Nakamura, Yasukazu

2013-01-01

High-performance next-generation sequencing (NGS) technologies are advancing genomics and molecular biological research. However, the immense amount of sequence data requires computational skills and suitable hardware resources that are a challenge to molecular biologists. The DNA Data Bank of Japan (DDBJ) of the National Institute of Genetics (NIG) has initiated a cloud computing-based analytical pipeline, the DDBJ Read Annotation Pipeline (DDBJ Pipeline), for a high-throughput annotation of NGS reads. The DDBJ Pipeline offers a user-friendly graphical web interface and processes massive NGS datasets using decentralized processing by NIG supercomputers currently free of charge. The proposed pipeline consists of two analysis components: basic analysis for reference genome mapping and de novo assembly and subsequent high-level analysis of structural and functional annotations. Users may smoothly switch between the two components in the pipeline, facilitating web-based operations on a supercomputer for high-throughput data analysis. Moreover, public NGS reads of the DDBJ Sequence Read Archive located on the same supercomputer can be imported into the pipeline through the input of only an accession number. This proposed pipeline will facilitate research by utilizing unified analytical workflows applied to the NGS data. The DDBJ Pipeline is accessible at http://p.ddbj.nig.ac.jp/. PMID:23657089

A computational model for predicting integrase catalytic domain of retrovirus.

PubMed

Wu, Sijia; Han, Jiuqiang; Zhang, Xinman; Zhong, Dexing; Liu, Ruiling

2017-06-21

Integrase catalytic domain (ICD) is an essential part in the retrovirus for integration reaction, which enables its newly synthesized DNA to be incorporated into the DNA of infected cells. Owing to the crucial role of ICD for the retroviral replication and the absence of an equivalent of integrase in host cells, it is comprehensible that ICD is a promising drug target for therapeutic intervention. However, annotated ICDs in UniProtKB database have still been insufficient for a good understanding of their statistical characteristics so far. Accordingly, it is of great importance to put forward a computational ICD model in this work to annotate these domains in the retroviruses. The proposed model then discovered 11,660 new putative ICDs after scanning sequences without ICD annotations. Subsequently in order to provide much confidence in ICD prediction, it was tested under different cross-validation methods, compared with other database search tools, and verified on independent datasets. Furthermore, an evolutionary analysis performed on the annotated ICDs of retroviruses revealed a tight connection between ICD and retroviral classification. All the datasets involved in this paper and the application software tool of this model can be available for free download at https://sourceforge.net/projects/icdtool/files/?source=navbar. Copyright © 2017 Elsevier Ltd. All rights reserved.

A Computational Model for Predicting RNase H Domain of Retrovirus.

PubMed

Wu, Sijia; Zhang, Xinman; Han, Jiuqiang

2016-01-01

RNase H (RNH) is a pivotal domain in retrovirus to cleave the DNA-RNA hybrid for continuing retroviral replication. The crucial role indicates that RNH is a promising drug target for therapeutic intervention. However, annotated RNHs in UniProtKB database have still been insufficient for a good understanding of their statistical characteristics so far. In this work, a computational RNH model was proposed to annotate new putative RNHs (np-RNHs) in the retroviruses. It basically predicts RNH domains through recognizing their start and end sites separately with SVM method. The classification accuracy rates are 100%, 99.01% and 97.52% respectively corresponding to jack-knife, 10-fold cross-validation and 5-fold cross-validation test. Subsequently, this model discovered 14,033 np-RNHs after scanning sequences without RNH annotations. All these predicted np-RNHs and annotated RNHs were employed to analyze the length, hydrophobicity and evolutionary relationship of RNH domains. They are all related to retroviral genera, which validates the classification of retroviruses to a certain degree. In the end, a software tool was designed for the application of our prediction model. The software together with datasets involved in this paper can be available for free download at https://sourceforge.net/projects/rhtool/files/?source=navbar.

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

PubMed Central

2010-01-01

Background Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) or ChIP followed by genome tiling array analysis (ChIP-chip) have become standard technologies for genome-wide identification of DNA-binding protein target sites. A number of algorithms have been developed in parallel that allow identification of binding sites from ChIP-seq or ChIP-chip datasets and subsequent visualization in the University of California Santa Cruz (UCSC) Genome Browser as custom annotation tracks. However, summarizing these tracks can be a daunting task, particularly if there are a large number of binding sites or the binding sites are distributed widely across the genome. Results We have developed ChIPpeakAnno as a Bioconductor package within the statistical programming environment R to facilitate batch annotation of enriched peaks identified from ChIP-seq, ChIP-chip, cap analysis of gene expression (CAGE) or any experiments resulting in a large number of enriched genomic regions. The binding sites annotated with ChIPpeakAnno can be viewed easily as a table, a pie chart or plotted in histogram form, i.e., the distribution of distances to the nearest genes for each set of peaks. In addition, we have implemented functionalities for determining the significance of overlap between replicates or binding sites among transcription factors within a complex, and for drawing Venn diagrams to visualize the extent of the overlap between replicates. Furthermore, the package includes functionalities to retrieve sequences flanking putative binding sites for PCR amplification, cloning, or motif discovery, and to identify Gene Ontology (GO) terms associated with adjacent genes. Conclusions ChIPpeakAnno enables batch annotation of the binding sites identified from ChIP-seq, ChIP-chip, CAGE or any technology that results in a large number of enriched genomic regions within the statistical programming environment R. Allowing users to pass their own annotation data such as a different Chromatin immunoprecipitation (ChIP) preparation and a dataset from literature, or existing annotation packages, such as GenomicFeatures and BSgenome, provides flexibility. Tight integration to the biomaRt package enables up-to-date annotation retrieval from the BioMart database. PMID:20459804

THERMAL RELAY DEVICE

DOEpatents

Murdoch, R.O.; Record, F.A.

1963-01-29

This invention relates to a fast-acting spring-loaded electrical switch which can break a 1500-volt circuit in one millisecond without arcing. In particular, a springloaded shorting bar is held in tension by a fusible wire. Passage of an electrical current pulse through the fusible wire breaks the fuse thereby releasing the shorting bar to open one and close another electrical circuit. (AEC)

Deformable image registration using convolutional neural networks

NASA Astrophysics Data System (ADS)

Eppenhof, Koen A. J.; Lafarge, Maxime W.; Moeskops, Pim; Veta, Mitko; Pluim, Josien P. W.

2018-03-01

Deformable image registration can be time-consuming and often needs extensive parameterization to perform well on a specific application. We present a step towards a registration framework based on a three-dimensional convolutional neural network. The network directly learns transformations between pairs of three-dimensional images. The outputs of the network are three maps for the x, y, and z components of a thin plate spline transformation grid. The network is trained on synthetic random transformations, which are applied to a small set of representative images for the desired application. Training therefore does not require manually annotated ground truth deformation information. The methodology is demonstrated on public data sets of inspiration-expiration lung CT image pairs, which come with annotated corresponding landmarks for evaluation of the registration accuracy. Advantages of this methodology are its fast registration times and its minimal parameterization.

Developing a diagnostic tool for measuring maximum effective temperature within high pressure electrodeless discharges

NASA Astrophysics Data System (ADS)

Whiting, Michael; Preston, Barry; Mucklejohn, Stuart; Santos, Monica; Lister, Graeme

2016-09-01

Here we present an investigation into the feasibility of creating a diagnostic tool for obtaining maximum arc temperature measurements within a high pressure electrodeless discharge; utilizing integrating sphere measurements of optically thin lines emitted from mercury atoms within commercially available high pressure mercury lamp arc tubes. The optically thin lines chosen were 577 nm and 1014 nm from a 250 W high pressure mercury lamp operated at various powers. The effective temperature could be calculated by considering the relative intensities of the two optically thin lines and comparison with the theoretical ratio of the temperature dependent power emitted from the lines derived from the atomic spectral data provided by NIST. The calculations gave effective arc temperatures of 5755, 5804 and 5820 K at 200, 225, 250 W respectively. This method was subsequently used as a basis for determining maximum effective arc temperature within microwave-driven electrodeless discharge capsules, with varying mercury content of 6.07, 9.4 and 12.95 mg within 1 × 10-6 m3 giving maximum effective temperatures of 5163, 4768 and 4715 K respectively at 240 W.

SU-F-T-625: Optimal Treatment Planning Strategy Among Arc Arrangements for Prostate SBRT with VMAT Technique

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

Chung, J; Kim, J; Eom, K

Purpose: The purpose of this study is to determine the optimal treatment planning strategy among the different arc arrangements for prostate stereotactic body radiotherapy (SBRT) plans with volumetric modulated arc therapy (VMAT). Methods: Ten patients with prostate cancer were selected. The SBRT-VMAT plans for each patient were generated with single-full (181° to 179°; 1FA), single-partial (240° to 120°; 1PA), double-full (181° to 179° and 179° to 181°; 2FA), and double-partial (240° to 120° and 120° to 240°; 2PA) arc arrangements. The prescription dose was 42.7 Gy in 7 fractions. Dose distribution was calculated using a 10-MV flattening-filter-free beam and themore » Acuros XB algorithm. Dosimetric parameters of target volume and organs at risk (OARs) were evaluated from cumulative dose-volume histograms on prostate SBRT-VMAT plans between single-arc (1FA and 1PA) and double-arc (2FA and 2PA) arrangements. Results: All plans using four arc arrangements were highly conformal with conformity index (CI)<1.05 and conformation number (CN)=0.91, and the doses to target volume were homogeneous (homogeneity index (HI)= 0.09 0.12). Pertaining to the dose to the OARs, there were significant differences in the rectum, left and right femoral head doses while having no difference in the bladder dose. The partial-arc (1PA and 2PA) had relatively high reductions for the mean rectum dose compared to full-arc (1FA and 2FA). The near-to-maximum dose (D2%) and mean dose of the left and right femoral head were always lower on prostate SBRT-VMAT plan using the full-arc, when compared to the partial-arc arrangement. Conclusion: This study confirmed that prostate SBRT-VMAT using 1PA was feasible fast delivery time and produced equivalent target coverage and better rectum sparing, although the D2% and mean dose of the left and right femoral head increased slightly. Therefore, the results of this study suggest that the use of 1PA is an attractive choice for delivering prostate SBRT-VMAT.« less

SANSparallel: interactive homology search against Uniprot

PubMed Central

Somervuo, Panu; Holm, Liisa

2015-01-01

Proteins evolve by mutations and natural selection. The network of sequence similarities is a rich source for mining homologous relationships that inform on protein structure and function. There are many servers available to browse the network of homology relationships but one has to wait up to a minute for results. The SANSparallel webserver provides protein sequence database searches with immediate response and professional alignment visualization by third-party software. The output is a list, pairwise alignment or stacked alignment of sequence-similar proteins from Uniprot, UniRef90/50, Swissprot or Protein Data Bank. The stacked alignments are viewed in Jalview or as sequence logos. The database search uses the suffix array neighborhood search (SANS) method, which has been re-implemented as a client-server, improved and parallelized. The method is extremely fast and as sensitive as BLAST above 50% sequence identity. Benchmarks show that the method is highly competitive compared to previously published fast database search programs: UBLAST, DIAMOND, LAST, LAMBDA, RAPSEARCH2 and BLAT. The web server can be accessed interactively or programmatically at http://ekhidna2.biocenter.helsinki.fi/cgi-bin/sans/sans.cgi. It can be used to make protein functional annotation pipelines more efficient, and it is useful in interactive exploration of the detailed evidence supporting the annotation of particular proteins of interest. PMID:25855811

Integrative Functional Genomics for Systems Genetics in GeneWeaver.org.

PubMed

Bubier, Jason A; Langston, Michael A; Baker, Erich J; Chesler, Elissa J

2017-01-01

The abundance of existing functional genomics studies permits an integrative approach to interpreting and resolving the results of diverse systems genetics studies. However, a major challenge lies in assembling and harmonizing heterogeneous data sets across species for facile comparison to the positional candidate genes and coexpression networks that come from systems genetic studies. GeneWeaver is an online database and suite of tools at www.geneweaver.org that allows for fast aggregation and analysis of gene set-centric data. GeneWeaver contains curated experimental data together with resource-level data such as GO annotations, MP annotations, and KEGG pathways, along with persistent stores of user entered data sets. These can be entered directly into GeneWeaver or transferred from widely used resources such as GeneNetwork.org. Data are analyzed using statistical tools and advanced graph algorithms to discover new relations, prioritize candidate genes, and generate function hypotheses. Here we use GeneWeaver to find genes common to multiple gene sets, prioritize candidate genes from a quantitative trait locus, and characterize a set of differentially expressed genes. Coupling a large multispecies repository curated and empirical functional genomics data to fast computational tools allows for the rapid integrative analysis of heterogeneous data for interpreting and extrapolating systems genetics results.

EnsMart: A Generic System for Fast and Flexible Access to Biological Data

PubMed Central

Kasprzyk, Arek; Keefe, Damian; Smedley, Damian; London, Darin; Spooner, William; Melsopp, Craig; Hammond, Martin; Rocca-Serra, Philippe; Cox, Tony; Birney, Ewan

2004-01-01

The EnsMart system (www.ensembl.org/EnsMart) provides a generic data warehousing solution for fast and flexible querying of large biological data sets and integration with third-party data and tools. The system consists of a query-optimized database and interactive, user-friendly interfaces. EnsMart has been applied to Ensembl, where it extends its genomic browser capabilities, facilitating rapid retrieval of customized data sets. A wide variety of complex queries, on various types of annotations, for numerous species are supported. These can be applied to many research problems, ranging from SNP selection for candidate gene screening, through cross-species evolutionary comparisons, to microarray annotation. Users can group and refine biological data according to many criteria, including cross-species analyses, disease links, sequence variations, and expression patterns. Both tabulated list data and biological sequence output can be generated dynamically, in HTML, text, Microsoft Excel, and compressed formats. A wide range of sequence types, such as cDNA, peptides, coding regions, UTRs, and exons, with additional upstream and downstream regions, can be retrieved. The EnsMart database can be accessed via a public Web site, or through a Java application suite. Both implementations and the database are freely available for local installation, and can be extended or adapted to `non-Ensembl' data sets. PMID:14707178

Thermochronology and tectonics of the Leeward Antilles: Evolution of the southern Caribbean Plate boundary zone

USGS Publications Warehouse

van der Lelij, Roelant; Spikings, Richard A.; Kerr, Andrew C.; Kounov, Alexandre; Cosca, Michael; Chew, David; Villagomez, Diego

2010-01-01

Tectonic reconstructions of the Caribbean Plate are severely hampered by a paucity of geochronologic and exhumation constraints from anastomosed basement blocks along its southern margin. New U/Pb, 40Ar/39Ar, apatite fission track, and apatite (U-Th)/He data constrain quantitative thermal and exhumation histories, which have been used to propose a model for the tectonic evolution of the emergent parts of the Bonaire Block and the southern Caribbean Plate boundary zone. An east facing arc system intruded through an oceanic plateau during ~90 to ~87 Ma and crops out on Aruba. Subsequent structural displacements resulted in >80°C of cooling on Aruba during 70–60 Ma. In contrast, exhumation of the island arc sequence exposed on Bonaire occurred at 85–80 Ma and 55–45 Ma. Santonian exhumation on Bonaire occurred immediately subsequent to burial metamorphism and may have been driven by the collision of a west facing island arc with the Caribbean Plate. Island arc rocks intruded oceanic plateau rocks on Gran Roque at ~65 Ma and exhumed rapidly at 55–45 Ma. We attribute Maastrichtian-Danian exhumation on Aruba and early Eocene exhumation on Bonaire and Gran Roque to sequential diachronous accretion of their basement units to the South American Plate. Widespread unconformities indicate late Eocene subaerial exposure. Late Oligocene–early Miocene dextral transtension within the Bonaire Block drove subsidence and burial of crystalline basement rocks of the Leeward Antilles to ≤1 km. Late Miocene–recent transpression caused inversion and ≤1 km of exhumation, possibly as a result of the northward escape of the Maracaibo Block.

Rethinking Recycling in Arcs

NASA Astrophysics Data System (ADS)

Kelemen, P.; Behn, M. D.; Jagoutz, O.

2012-12-01

Hacker et al EPSL 2011 and Behn et al Nature Geosci 2011 investigated pathways for return of buoyant, subducted material to arc crust. These include (1) diapirs rising into the hot mantle wedge, with extensive melts adding a component to arc magmas, (2) flow of material back up a relatively cold "subduction channel", adding solids to the lower crust and small-degree partial melts to the upper crust, (3) flow from the forearc along the base of arc crust, and (4) imbrication of forearc material into arc crust. These processes add felsic, incompatible-element-rich components to arc crust. The flux of incompatible elements such as Th in arc lavas, thought to be mainly recycled from subducted sediments, is > sediment subduction flux. There are large uncertainties: arc crustal growth rates are imprecise; young, primitive arc lavas may not be representative of magmatic flux into arc crust; sediment subduction flux may have varied. Nevertheless, this result is found for all arcs examined, using recently published growth rates. Perhaps arc growth rates that include subduction erosion are systematically overestimated. Instead or in addition, maybe significant Th comes from material other than sediments. Here, we consider the implications of pathways 1-4 for arc growth rates and incompatible element enrichment, in the context of subduction erosion and arc-arc collision. Subducting arc lithologies can become separated, with only felsic components returned to arc crust. Buoyant lithologies are mobile in viscous instabilities at > 700-800°C. Whereas thin layers such as sediments may become mobile all at once, instabilities may periodically strip the hottest parts from the top of thick buoyant layers, replacing them with hot mantle. In arc-arc collision, the top of a subducting plate starts at about 0°C on the seafloor, so heating is slow. In subduction erosion, forearc material in the subducting package can be > 200°C before erosion so buoyant lithologies reach 700-800°C faster, and in larger volumes at a given time. Subduction erosion rarely, if ever, transports significant amounts of buoyant material deep into the convecting mantle. Because buoyant material can remain part of the crust, it may often be a mistake to add all of the eroded material to the observed arc volume to derive crustal growth rates. Buoyancy instabilities during subduction erosion or arc-arc collision will accumulate felsic arc crust. For example, > 50% of Aleutian arc lavas and exposed plutons are more buoyant than mantle peridotite at 700-800°C, 3-4 GPa. The buoyant material has an average of 60-62 wt% SiO2, molar Mg/(Mg+Fe) 0.4-0.5, and trace elements identical to bulk continental crust, though western Aleutian lavas have the most depleted Sr, Nd and Pb isotope ratios of all arc lavas worldwide. In general, density sorting of arc lithologies, and subsequent partial melting as buoyant rocks rise through the mantle wedge or along a subduction channel, could lead to a kind of double and triple distillation. Incompatible elements such as Th would be enriched in arc crust, retaining correlations with isotopic indicators of a recycled sediment component, while Th-poor, dense, mafic lavas and lower crustal cumulates return to the convecting mantle.

The role of apoptosis repressor with a CARD domain (ARC) in the therapeutic resistance of renal cell carcinoma (RCC): the crucial role of ARC in the inhibition of extrinsic and intrinsic apoptotic signalling.

PubMed

Toth, Csaba; Funke, Sarah; Nitsche, Vanessa; Liverts, Anna; Zlachevska, Viktoriya; Gasis, Marcia; Wiek, Constanze; Hanenberg, Helmut; Mahotka, Csaba; Schirmacher, Peter; Heikaus, Sebastian

2017-05-02

Renal cell carcinomas (RCCs) display broad resistance against conventional radio- and chemotherapies, which is due at least in part to impairments in both extrinsic and intrinsic apoptotic pathways. One important anti-apoptotic factor that is strongly overexpressed in RCCs and known to inhibit both apoptotic pathways is ARC (apoptosis repressor with a CARD domain). Expression and subcellular distribution of ARC in RCC tissue samples and RCC cell lines were determined by immunohistochemistry and fluorescent immunohistochemistry, respectively. Extrinsic and intrinsic apoptosis signalling were induced by TRAIL (TNF-related apoptosis-inducing ligand), ABT-263 or topotecan. ARC knock-down was performed in clearCa-12 cells using lentiviral transduction of pGIPZ. shRNAmir constructs. Extrinsic respectively intrinsic apoptosis were induced by TRAIL (TNF-related apoptosis-inducing ligand), ABT263 or topotecan. Potential synergistic effects were tested by pre-treatment with topotecan and subsequent treatment with ABT263. Activation of different caspases and mitochondrial depolarisation (JC-1 staining) were analysed by flow cytometry. Protein expression of Bcl-2 family members and ARC in RCC cell lines was measured by Western blotting. Statistical analysis was performed by Student's t-test. Regarding the extrinsic pathway, ARC knockdown strongly enhanced TRAIL-induced apoptosis by increasing the activation level of caspase-8. Regarding the intrinsic pathway, ARC, which was only weakly expressed in the nuclei of RCCs in vivo, exerted its anti-apoptotic effect by impairing mitochondrial activation rather than inhibiting p53. Topotecan- and ABT-263-induced apoptosis was strongly enhanced following ARC knockdown in RCC cell lines. In addition, topotecan pre-treatment enhanced ABT-263-induced apoptosis and this effect was amplified in ARC-knockdown cells. Taken together, our results are the first to demonstrate the importance of ARC protein in the inhibition of both the extrinsic and intrinsic pathways of apoptosis in RCCs. In this context, ARC cooperates with anti-apoptotic Bcl-2 family members to exert its strong anti-apoptotic effects and is therefore an important factor not only in the therapeutic resistance but also in future therapy strategies (i.e., Bcl-2 inhibitors) in RCC. In sum, targeting of ARC may enhance the therapeutic response in combination therapy protocols.

Skid resistance performance of asphalt wearing courses with electric arc furnace slag aggregates.

PubMed

Kehagia, Fotini

2009-05-01

Metallurgical slags are by-products of the iron and steel industry and are subdivided into blast furnace slag and steel slag according to the different steel-producing processes. In Greece, slags are mostly produced from steelmaking using the electric arc furnace process, and subsequently are either disposed in a random way or utilized by the cement industry. Steel slag has been recently used, worldwide, as hard aggregates in wearing courses in order to improve the skidding resistance of asphalt pavements. At the Highway Laboratory, Department of Civil Engineering of Aristotle University of Thessaloniki research has been carried out in the field of steel slags, and especially in electric arc furnace (EAF) slag, to evaluate their possible use in highway engineering. In this paper, the recent results of anti-skidding performance of steel slag aggregates in highway pavements are presented.

Structure and Evolution of the Forearc-Arc Crust Along the Tonga-Kermadec Subduction System from Integrated Geophysical Data

NASA Astrophysics Data System (ADS)

Funnell, M.; Peirce, C.; Robinson, A. H.; Watts, A. B.; Grevemeyer, I.

2016-12-01

Variations in tectonic forces and inputs to subduction systems generate, alter, and deform overriding crustal material. Although these processes are recorded in the crustal structure of volcanic arcs and their backarcs, the continuous nature of plate convergence superimposes subsequent episodes of crustal evolution on older features. Seismic imaging at modern subduction zones enhances our understanding of forearc development and variations in present-day deformation caused by inherited structures. In 2011 a set of multichannel and wide-angle seismic profiles imaged the forearc-arc crust and upper mantle structure along the 2700 km-long NNE-SSW trending Tonga-Kermadec subduction zone. The Tonga forearc region exhibits an 100 km-wide, 2 km high bathymetric elevation, with a 3 km-thick upper and mid-crust (Vp <6 km s-1), and a lower-crustal ridge 30 km wide comprising velocities up to 7.4 km s-1 that characterize an extinct Eocene ( 50 Ma) arc. By contrast, the active arc is <10 km wide and exhibits lower-crustal velocities below 7.0 km s-1, most likely representing intermediate compositions. This structural change suggests significant evolution, alteration, and modification of the overriding crust since the onset of subduction at this margin. Gravity anomaly modelling suggests that the extinct arc within the Tonga forearc region comprises relatively dense mafic-ultrabasic material that extends south beneath the Kermadec forearc and terminates at 32°S. The apparent southern termination of the extinct arc coincides with the partitioning of morphological features at 32°S, including a 10-km westward-step of the active arc and a 1.5 km deeper backarc to the south. We propose that tectonic partitioning about the 32°S boundary is the result of variations in the inherited crustal structure, which is divided by the presence and absence, to the north and south respectively, of the extinct volcanic arc.

A Guide to Reviews of Books, Plays, Films: A Selected Bibliography.

ERIC Educational Resources Information Center

Miller, Elaine N.

Forty reference sources for book, play, and film reviews are listed in this annotated bibliography: most of the titles cited are periodical indexes. A general section lists sources not restricted by subject or which contain references to all three kinds of reviews. Subsequent sections are the broad subject categories of humanities, science, social…

MobiDB-lite: fast and highly specific consensus prediction of intrinsic disorder in proteins.

PubMed

Necci, Marco; Piovesan, Damiano; Dosztányi, Zsuzsanna; Tosatto, Silvio C E

2017-05-01

Intrinsic disorder (ID) is established as an important feature of protein sequences. Its use in proteome annotation is however hampered by the availability of many methods with similar performance at the single residue level, which have mostly not been optimized to predict long ID regions of size comparable to domains. Here, we have focused on providing a single consensus-based prediction, MobiDB-lite, optimized for highly specific (i.e. few false positive) predictions of long disorder. The method uses eight different predictors to derive a consensus which is then filtered for spurious short predictions. Consensus prediction is shown to outperform the single methods when annotating long ID regions. MobiDB-lite can be useful in large-scale annotation scenarios and has indeed already been integrated in the MobiDB, DisProt and InterPro databases. MobiDB-lite is available as part of the MobiDB database from URL: http://mobidb.bio.unipd.it/. An executable can be downloaded from URL: http://protein.bio.unipd.it/mobidblite/. silvio.tosatto@unipd.it. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

MIPS: analysis and annotation of proteins from whole genomes

PubMed Central

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

2004-01-01

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

MIPS: analysis and annotation of proteins from whole genomes.

PubMed

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

2004-01-01

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

Driven motion and instability of an atmospheric pressure arc

NASA Astrophysics Data System (ADS)

Karasik, Max

Atmospheric pressure arcs are used extensively in applications such as welding and metallurgy. However, comparatively little is known of the physics of such arcs in external magnetic fields and the mechanisms of the instabilities present. In order to address questions of equilibrium and stability of such arcs, an experimental are furnace is constructed and operated in air with graphite cathode and steel anode at currents 100--250 A. The arc is diagnosed with a gated intensified camera and a collimated photodiode array, as well as fast voltage and current probes. Experiments are carried out on the response of the are to applied transverse DC and AC (up to ≈1 kHz) magnetic fields. The arc is found to deflect parabolically for DC field and assumes a growing sinusoidal structure for AC field. A simple analytic two-parameter fluid model of the are dynamics is derived, in which the inertia of the magnetically pumped cathode jet balances the applied J⃗xB⃗ force. Time variation of the applied field allows evaluation of the parameters individually. A fit of the model to the experimental data gives a value for the average jet speed an order of magnitude below Maecker's estimate of the maximum jet speed. A spontaneous instability of the same arc is investigated experimentally and modeled analytically. The presence of the instability is found to depend critically on cathode dimensions. For cylindrical cathodes, instability occurs only for a narrow range of cathode diameters. Cathode spot motion is proposed as the mechanism of the instability. A simple fluid model combining the effect of the cathode spot motion and the inertia of the cathode jet successfully describes the arc shape during low amplitude instability. The amplitude of cathode spot motion required by the model is in agreement with measurements. The average jet velocity required is approximately equal to that inferred from the transverse magnetic field experiments. Reasons for spot motion and for cathode geometry dependence are discussed. An exploratory study of the instability of the arc in applied axial magnetic field is also described. Applicability of the results of the thesis to an industrial steelmaking furnace is considered.

CardioClassifier: disease- and gene-specific computational decision support for clinical genome interpretation.

PubMed

Whiffin, Nicola; Walsh, Roddy; Govind, Risha; Edwards, Matthew; Ahmad, Mian; Zhang, Xiaolei; Tayal, Upasana; Buchan, Rachel; Midwinter, William; Wilk, Alicja E; Najgebauer, Hanna; Francis, Catherine; Wilkinson, Sam; Monk, Thomas; Brett, Laura; O'Regan, Declan P; Prasad, Sanjay K; Morris-Rosendahl, Deborah J; Barton, Paul J R; Edwards, Elizabeth; Ware, James S; Cook, Stuart A

2018-01-25

PurposeInternationally adopted variant interpretation guidelines from the American College of Medical Genetics and Genomics (ACMG) are generic and require disease-specific refinement. Here we developed CardioClassifier (http://www.cardioclassifier.org), a semiautomated decision-support tool for inherited cardiac conditions (ICCs).MethodsCardioClassifier integrates data retrieved from multiple sources with user-input case-specific information, through an interactive interface, to support variant interpretation. Combining disease- and gene-specific knowledge with variant observations in large cohorts of cases and controls, we refined 14 computational ACMG criteria and created three ICC-specific rules.ResultsWe benchmarked CardioClassifier on 57 expertly curated variants and show full retrieval of all computational data, concordantly activating 87.3% of rules. A generic annotation tool identified fewer than half as many clinically actionable variants (64/219 vs. 156/219, Fisher's P = 1.1  ×  10 -18 ), with important false positives, illustrating the critical importance of disease and gene-specific annotations. CardioClassifier identified putatively disease-causing variants in 33.7% of 327 cardiomyopathy cases, comparable with leading ICC laboratories. Through addition of manually curated data, variants found in over 40% of cardiomyopathy cases are fully annotated, without requiring additional user-input data.ConclusionCardioClassifier is an ICC-specific decision-support tool that integrates expertly curated computational annotations with case-specific data to generate fast, reproducible, and interactive variant pathogenicity reports, according to best practice guidelines.GENETICS in MEDICINE advance online publication, 25 January 2018; doi:10.1038/gim.2017.258.

Modeling of breakdown during the post-arc phase of a vacuum circuit breaker

NASA Astrophysics Data System (ADS)

Sarrailh, P.; Garrigues, L.; Boeuf, J. P.; Hagelaar, G. J. M.

2010-12-01

After a high-current interruption in a vacuum circuit breaker (VCB), the electrode gap is filled with a high density copper vapor plasma in a large copper vapor density (~1022 m-3). The copper vapor density is sustained by electrode evaporation. During the post-arc phase, a rapidly increasing voltage is applied to the gap, and a sheath forms and expands, expelling the plasma from the gap when circuit breaking is successful. There is, however, a risk of breakdown during that phase, leading to the failure of the VCB. Preventing breakdown during the post-arc phase is an important issue for the improvement of VCB reliability. In this paper, we analyze the risk of Townsend breakdown in the high copper vapor density during the post-arc phase using a numerical model that takes into account secondary electron emission, volume ionization, and plasma and neutral transport, for given electrode temperatures. The simulations show that fast neutrals created in the cathode sheath by charge exchange collisions with ions generate a very large secondary electron emission current that can lead to Townsend breakdown. The results also show that the risk of failure of the VCB due to Townsend breakdown strongly depends on the electrode temperatures (which govern the copper vapor density) and becomes important for temperatures greater than 2100 K, which can be reached in vacuum arcs. The simulations also predict that a hotter anode tends to increase the risk of Townsend breakdown.

Operating safety of a hot-shot wind tunnel with combined test gas heating in stabilization mode

NASA Astrophysics Data System (ADS)

Shumskii, V. V.; Yaroslavtsev, M. I.

2017-07-01

In the present paper, we analyze emergency situations typical of short-duration wind tunnels with electric-arc or combined test-gas heating in the presence of stabilization and diaphragm-rupturing systems, which occur in the case of no discharge initiation in the settling chamber, with the capacitor battery having remained charged during the start of wind-tunnel systems. For avoiding such emergency situations, some additional changes based on using feedback elements are introduced into the wind-tunnel design: the piston of the fast-response valve is made hollow for increasing the volume of the shutoff cavity and for making the release of pressure from this cavity unnecessary; the high-pressure channel, which connects the piston and the piston rod with the settling-chamber cavity, is filled with a liquid and is closed from the side of the settling chamber with a piston; the device for controlled diaphragm breakdown is provided with an external electric circuit intended to control the diaphragm-rupturing process. Those modifications allow subsequent functioning of the wind-tunnel systems only in the presence of heat-supply-induced pressure growth in the settling chamber of the wind tunnel.

Phage phenomics: Physiological approaches to characterize novel viral proteins

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

Sanchez, Savannah E.; Cuevas, Daniel A.; Rostron, Jason E.

Current investigations into phage-host interactions are dependent on extrapolating knowledge from (meta)genomes. Interestingly, 60 - 95% of all phage sequences share no homology to current annotated proteins. As a result, a large proportion of phage genes are annotated as hypothetical. This reality heavily affects the annotation of both structural and auxiliary metabolic genes. Here we present phenomic methods designed to capture the physiological response(s) of a selected host during expression of one of these unknown phage genes. Multi-phenotype Assay Plates (MAPs) are used to monitor the diversity of host substrate utilization and subsequent biomass formation, while metabolomics provides bi-product analysismore » by monitoring metabolite abundance and diversity. Both tools are used simultaneously to provide a phenotypic profile associated with expression of a single putative phage open reading frame (ORF). Thus, representative results for both methods are compared, highlighting the phenotypic profile differences of a host carrying either putative structural or metabolic phage genes. In addition, the visualization techniques and high throughput computational pipelines that facilitated experimental analysis are presented.« less

Identification of Functional Candidates amongst Hypothetical Proteins of Treponema pallidum ssp. pallidum

PubMed Central

Naqvi, Ahmad Abu Turab; Shahbaaz, Mohd; Ahmad, Faizan; Hassan, Md. Imtaiyaz

2015-01-01

Syphilis is a globally occurring venereal disease, and its infection is propagated through sexual contact. The causative agent of syphilis, Treponema pallidum ssp. pallidum, a Gram-negative sphirochaete, is an obligate human parasite. Genome of T. pallidum ssp. pallidum SS14 strain (RefSeq NC_010741.1) encodes 1,027 proteins, of which 444 proteins are known as hypothetical proteins (HPs), i.e., proteins of unknown functions. Here, we performed functional annotation of HPs of T. pallidum ssp. pallidum using various database, domain architecture predictors, protein function annotators and clustering tools. We have analyzed the sequences of 444 HPs of T. pallidum ssp. pallidum and subsequently predicted the function of 207 HPs with a high level of confidence. However, functions of 237 HPs are predicted with less accuracy. We found various enzymes, transporters, binding proteins in the annotated group of HPs that may be possible molecular targets, facilitating for the survival of pathogen. Our comprehensive analysis helps to understand the mechanism of pathogenesis to provide many novel potential therapeutic interventions. PMID:25894582

Semantics-Based Intelligent Indexing and Retrieval of Digital Images - A Case Study

NASA Astrophysics Data System (ADS)

Osman, Taha; Thakker, Dhavalkumar; Schaefer, Gerald

The proliferation of digital media has led to a huge interest in classifying and indexing media objects for generic search and usage. In particular, we are witnessing colossal growth in digital image repositories that are difficult to navigate using free-text search mechanisms, which often return inaccurate matches as they typically rely on statistical analysis of query keyword recurrence in the image annotation or surrounding text. In this chapter we present a semantically enabled image annotation and retrieval engine that is designed to satisfy the requirements of commercial image collections market in terms of both accuracy and efficiency of the retrieval process. Our search engine relies on methodically structured ontologies for image annotation, thus allowing for more intelligent reasoning about the image content and subsequently obtaining a more accurate set of results and a richer set of alternatives matchmaking the original query. We also show how our well-analysed and designed domain ontology contributes to the implicit expansion of user queries as well as presenting our initial thoughts on exploiting lexical databases for explicit semantic-based query expansion.

Phage phenomics: Physiological approaches to characterize novel viral proteins

DOE PAGES

Sanchez, Savannah E.; Cuevas, Daniel A.; Rostron, Jason E.; ...

2015-06-11

Current investigations into phage-host interactions are dependent on extrapolating knowledge from (meta)genomes. Interestingly, 60 - 95% of all phage sequences share no homology to current annotated proteins. As a result, a large proportion of phage genes are annotated as hypothetical. This reality heavily affects the annotation of both structural and auxiliary metabolic genes. Here we present phenomic methods designed to capture the physiological response(s) of a selected host during expression of one of these unknown phage genes. Multi-phenotype Assay Plates (MAPs) are used to monitor the diversity of host substrate utilization and subsequent biomass formation, while metabolomics provides bi-product analysismore » by monitoring metabolite abundance and diversity. Both tools are used simultaneously to provide a phenotypic profile associated with expression of a single putative phage open reading frame (ORF). Thus, representative results for both methods are compared, highlighting the phenotypic profile differences of a host carrying either putative structural or metabolic phage genes. In addition, the visualization techniques and high throughput computational pipelines that facilitated experimental analysis are presented.« less

Combinatory annotation of cell membrane receptors and signalling pathways of Bombyx mori prothoracic glands

PubMed Central

Moulos, Panagiotis; Samiotaki, Martina; Panayotou, George; Dedos, Skarlatos G.

2016-01-01

The cells of prothoracic glands (PG) are the main site of synthesis and secretion of ecdysteroids, the biochemical products of cholesterol conversion to steroids that shape the morphogenic development of insects. Despite the availability of genome sequences from several insect species and the extensive knowledge of certain signalling pathways that underpin ecdysteroidogenesis, the spectrum of signalling molecules and ecdysteroidogenic cascades is still not fully comprehensive. To fill this gap and obtain the complete list of cell membrane receptors expressed in PG cells, we used combinatory bioinformatic, proteomic and transcriptomic analysis and quantitative PCR to annotate and determine the expression profiles of genes identified as putative cell membrane receptors of the model insect species, Bombyx mori, and subsequently enrich the repertoire of signalling pathways that are present in its PG cells. The genome annotation dataset we report here highlights modules and pathways that may be directly involved in ecdysteroidogenesis and aims to disseminate data and assist other researchers in the discovery of the role of such receptors and their ligands. PMID:27576083

Arcjet power supply and start circuit

NASA Technical Reports Server (NTRS)

Gruber, Robert P. (Inventor)

1988-01-01

A dc power supply for spacecraft arcjet thrusters has an integral automatic starting circuit and an output averaging inductor. The output averaging inductor, in series with the load, provides instantaneous current control, and ignition pulse and an isolated signal proportional to the arc voltage. A pulse width modulated converter, close loop configured, is also incorporated to give fast response output current control.

A unique power supply for the PEP II klystron at SLAC

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

Cassel, R.; Nguyen, M.N.

1997-07-01

Each of the eight 1.2 MW RF klystrons for the PEP-II storage rings require a 2.5 MVA DC power supply of 83 Kv at 23 amps. The design for the supply was base on three factors, low cost, small size to fit existing substation pads, and good protection against damage to the klystron including klystron gun arcs. The supply uses a 12 pulse 12.5 KV primary thyristor star point controller with primary filter inductor to provide rapid voltage control, good voltage regulation, and fast turn off during klystron tube faults. The supply also uses a unique secondary rectifier, filter capacitormore » configuration to minimize the energy available under a klystron fault. The voltage control is from 0--90 KV with a regulation of < 0.1% and voltage ripple of < 1% P-P, (< 0.2% RMS) above 60 KV. The supply utilizes a thyristor crowbar, which under a klystron tube arc limits the energy in the klystron arc to < 5 joules. If the thyristor crowbar is disabled the energy supplied is < 40 joules into the arc. The size of the supply was reduced small enough to fit the existing PEP transformer yard pads. The cost of the power supply was < $140 per KVA.« less

Balancing Value and Risk in Information Sharing Through Obfuscation

DTIC Science & Technology

2012-09-20

California, Los Angeles Chatschik Bisdikian IBM T.J. Watson Research Center Lance M. Kaplan US Army Research Laboratory Abstract—Fast-paced data-to...AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) IBM T.J. Watson Research...giving us annotations for both the white listed activity detection as well as the black listed activity recognition . We implemented five features

PDV2 has a dosage effect on chloroplast division in Arabidopsis.

PubMed

Chang, Ning; Sun, Qingqing; Li, Yiqiong; Mu, Yajuan; Hu, Jinglei; Feng, Yue; Liu, Xiaomin; Gao, Hongbo

2017-03-01

PDV2 has a dosage effect on chloroplast division in Arabidopsis thaliana , but this effect may vary in different plants. Chloroplasts have to be divided as plants grow to maintain an optimized number in the cell. Chloroplasts are divided by protein complexes across the double membranes from the stroma side to the cytosolic side. PDV2 is a chloroplast division protein on the chloroplast outer membrane. It recruits the dynamin-related GTPase ARC5 to the division site. The C-terminus of PDV2 and the C-terminus of ARC6 interact in the intermembrane space, which is important for the localization of PDV2. Previously, it was shown that overexpression of PDV2 can increase the division of chloroplasts in Arabidopsis and moss, so the authors concluded that PDV2 determines the rate of chloroplast division in land plants. PDV2 was also shown to inhibit the GTPase activity of ARC5 by in vitro experiment. These results look to be contradictory. Here, we identified a null allele of PDV2 in Arabidopsis and studied plants with different levels of PDV2. Our results suggested that the chloroplast division phenotype in Arabidopsis is sensitive to the level of PDV2, while this is not the case for ARC6. The level of PDV2 protein is reduced sharply in fast-growing leaves, while the level of ARC6 is not. The levels of PDV2 and ARC6 in several other plant species at different developmental stages were also investigated. The results indicated that their expression pattern varies in different species. Thus, PDV2 is an important positive factor of chloroplast division with an apparent dosage effect in Arabidopsis, but this effect for different chloroplast division proteins in different plants may vary.

Poster — Thur Eve — 31: Dosimetric Effect of Respiratory Motion on RapidArc Lung SBRT Treatment Delivered by TrueBeam Linear Accelerator

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

Jiang, Runqing; Zhan, Lixin; Osei, Ernest

2014-08-15

Volumetric modulated arc therapy (VMAT) allows fast delivery of stereotactic radiotherapy. However, the discrepancies between the calculated and delivered dose distributions due to respiratory motion and dynamic multileaf collimators (MLCs) interplay are not avoidable. The purpose of this study is to investigate RapidArc lung SBRT treatment delivered by the flattening filter-free (FFF) beam and flattened beam with Varian TrueBeam machine. CIRS Dynamic Thorax Phantom with in-house made lung tumor insertion was CT scanned both in free breathing and 4DCT. 4DCT was used to determine the internal target volume. The free breathing CT scan was used for treatment planning. A 5more » mm margin was given to ITV to generate a planning target volume. Varian Eclipse treatment planning was used to generate RapidArc plans based on the 6 MV flattened beam and 6MV FFF beam. The prescription dose was 48 Gy in 4 fractions. At least 95% of PTV was covered by the prescribed dose. The RapidArc plans with 6 MV flattened beam and 6MV FFF beam were delivered with Varian TrueBeam machine. The dosimetric measurements were performed with Gafchromic XR-RV3 film, which was placed in the lung tumor insertion. The interplay between the dynamic MLC-based delivery of VMAT and the respiratory motion of the tumor degraded target coverage and created undesired hot or cold dose spots inside the lung tumor. Lung SBRT RapidArc treatments delivered by the FFF beam of TrueBeam linear accelerator is superior to the flattened beam. Further investigation will be performed by Monte Carlo simulation.« less

Sulphide-sulphate stability and melting in subducted sediment and its role in arc mantle redox and chalcophile cycling in space and time

NASA Astrophysics Data System (ADS)

Canil, Dante; Fellows, Steven A.

2017-07-01

The redox budget during subduction is tied to the evolution of oxygen and biogeochemical cycles on Earth's surface over time. The sulphide-sulphate couple in subducted crust has significant potential for redox and control on extraction of chalcophile metals from the arc mantle. We derive oxygen buffers for sulphide-sulphate stability ('SSO buffers') using mineral assemblages in subducted crust within the eclogite facies, and examine their disposition relative to the fO2 in the arc mantle along various P-T trajectories for subduction. The fO2 required for sulphide stability in subducted crust passing beneath an arc is shifted by variations in the bulk Ca/(Ca + Mg + Fe) of the subducting crust alone. Hotter slabs and more Fe-rich sediments stabilize sulphide and favour chalcophile sequestration deep into the mantle, whereas colder slabs and calcic sediment will stabilize anhydrite, in some cases at depths of melt generation in the arc mantle (<130 km). The released sulphate on melting potentially increases the fO2 of the arc mantle. We performed melting experiments on three subducted sediment compositions varying in bulk Ca/(Ca + Mg + Fe) from 0.3 to 0.6 at 2.5 GPa and 900-1100 °C to confirm how anhydrite stability can change by orders of magnitude the S, Cu, As, Zn, Mo, Pb, and Sb contents of sediment melts, and their subsequent liberation to the arc mantle. Using Cu/Sc as a proxy for the behaviour of S, the effect of variable subducted sediment composition on sulphide-sulphate stability and release of chalcophiles to the arc mantle is recognizable in volcanic suites from several subduction zones in space and time. The fO2 of the SSO buffers in subducted sediment relative to the arc mantle may have changed with time by shifts in the nature of pelagic sedimentation in the oceans over earth history. Oxidation of arc mantle and the proliferation of porphyry Cu deposits may be latter-day advents in earth history partly due to the rise of planktic calcifiers in the oceans in only the past 250 million years.

Upper Cretaceous to Holocene magmatism and evidence for transient Miocene shallowing of the Andean subduction zone under the northern Neuquén Basin

USGS Publications Warehouse

Kay, Suzanne M.; Burns, W. Matthew; Copeland, Peter; Mancilla, Oscar

2006-01-01

Evidence for a Miocene period of transient shallow subduction under the Neuquén Basin in the Andean backarc, and an intermittent Upper Cretaceous to Holocene frontal arc with a relatively stable magma source and arc-to-trench geometry comes from new 40Ar/39Ar, major- and trace-element, and Sr, Pb, and Nd isotopic data on magmatic rocks from a transect at ∼36°–38°S. Older frontal arc magmas include early Paleogene volcanic rocks erupted after a strong Upper Cretaceous contractional deformation and mid-Eocene lavas erupted from arc centers displaced slightly to the east. Following a gap of some 15 m.y., ca. 26–20 Ma mafic to acidic arc-like magmas erupted in the extensional Cura Mallín intra-arc basin, and alkali olivine basalts with intraplate signatures erupted across the backarc. A major change followed as ca. 20–15 Ma basaltic andesite–dacitic magmas with weak arc signatures and 11.7 Ma Cerro Negro andesites with stronger arc signatures erupted in the near to middle backarc. They were followed by ca. 7.2–4.8 Ma high-K basaltic to dacitic hornblende-bearing magmas with arc-like high field strength element depletion that erupted in the Sierra de Chachahuén, some 500 km east of the trench. The chemistry of these Miocene rocks along with the regional deformational pattern support a transient period of shallow subduction that began at ca. 20 Ma and climaxed near 5 Ma. The subsequent widespread eruption of Pliocene to Pleistocene alkaline magmas with an intraplate chemistry in the Payenia large igneous province signaled a thickening mantle wedge above a steepening subduction zone. A pattern of decreasingly arc-like Pliocene to Holocene backarc lavas in the Tromen region culminated with the eruption of a 0.175 ± 0.025 Ma mafic andesite. The northwest-trending Cortaderas lineament, which generally marks the southern limit of Neogene backarc magmatism, is considered to mark the southern boundary of the transient shallow subduction zone.

openBEB: open biological experiment browser for correlative measurements

PubMed Central

2014-01-01

Background New experimental methods must be developed to study interaction networks in systems biology. To reduce biological noise, individual subjects, such as single cells, should be analyzed using high throughput approaches. The measurement of several correlative physical properties would further improve data consistency. Accordingly, a considerable quantity of data must be acquired, correlated, catalogued and stored in a database for subsequent analysis. Results We have developed openBEB (open Biological Experiment Browser), a software framework for data acquisition, coordination, annotation and synchronization with database solutions such as openBIS. OpenBEB consists of two main parts: A core program and a plug-in manager. Whereas the data-type independent core of openBEB maintains a local container of raw-data and metadata and provides annotation and data management tools, all data-specific tasks are performed by plug-ins. The open architecture of openBEB enables the fast integration of plug-ins, e.g., for data acquisition or visualization. A macro-interpreter allows the automation and coordination of the different modules. An update and deployment mechanism keeps the core program, the plug-ins and the metadata definition files in sync with a central repository. Conclusions The versatility, the simple deployment and update mechanism, and the scalability in terms of module integration offered by openBEB make this software interesting for a large scientific community. OpenBEB targets three types of researcher, ideally working closely together: (i) Engineers and scientists developing new methods and instruments, e.g., for systems-biology, (ii) scientists performing biological experiments, (iii) theoreticians and mathematicians analyzing data. The design of openBEB enables the rapid development of plug-ins, which will inherently benefit from the “house keeping” abilities of the core program. We report the use of openBEB to combine live cell microscopy, microfluidic control and visual proteomics. In this example, measurements from diverse complementary techniques are combined and correlated. PMID:24666611

A Fast Alignment-Free Approach for De Novo Detection of Protein Conserved Regions

PubMed Central

Abnousi, Armen; Broschat, Shira L.; Kalyanaraman, Ananth

2016-01-01

Background Identifying conserved regions in protein sequences is a fundamental operation, occurring in numerous sequence-driven analysis pipelines. It is used as a way to decode domain-rich regions within proteins, to compute protein clusters, to annotate sequence function, and to compute evolutionary relationships among protein sequences. A number of approaches exist for identifying and characterizing protein families based on their domains, and because domains represent conserved portions of a protein sequence, the primary computation involved in protein family characterization is identification of such conserved regions. However, identifying conserved regions from large collections (millions) of protein sequences presents significant challenges. Methods In this paper we present a new, alignment-free method for detecting conserved regions in protein sequences called NADDA (No-Alignment Domain Detection Algorithm). Our method exploits the abundance of exact matching short subsequences (k-mers) to quickly detect conserved regions, and the power of machine learning is used to improve the prediction accuracy of detection. We present a parallel implementation of NADDA using the MapReduce framework and show that our method is highly scalable. Results We have compared NADDA with Pfam and InterPro databases. For known domains annotated by Pfam, accuracy is 83%, sensitivity 96%, and specificity 44%. For sequences with new domains not present in the training set an average accuracy of 63% is achieved when compared to Pfam. A boost in results in comparison with InterPro demonstrates the ability of NADDA to capture conserved regions beyond those present in Pfam. We have also compared NADDA with ADDA and MKDOM2, assuming Pfam as ground-truth. On average NADDA shows comparable accuracy, more balanced sensitivity and specificity, and being alignment-free, is significantly faster. Excluding the one-time cost of training, runtimes on a single processor were 49s, 10,566s, and 456s for NADDA, ADDA, and MKDOM2, respectively, for a data set comprised of approximately 2500 sequences. PMID:27552220

Petrologic, tectonic, and metallogenic evolution of the Ancestral Cascades magmatic arc, Washington, Oregon, and northern California

USGS Publications Warehouse

du Bray, Edward A.; John, David A.

2011-01-01

Present-day High Cascades arc magmatism was preceded by ~40 m.y. of nearly cospatial magmatism represented by the ancestral Cascades arc in Washington, Oregon, and northernmost California (United States). Time-space-composition relations for the ancestral Cascades arc have been synthesized from a recent compilation of more than 4000 geochemical analyses and associated age data. Neither the composition nor distribution of ancestral Cascades magmatism was uniform along the length of the ancestral arc through time. Initial (>40 to 36 Ma) ancestral Cascades magmatism (mostly basalt and basaltic andesite) was focused at the north end of the arc between the present-day locations of Mount Rainier and the Columbia River. From 35 to 18 Ma, initial basaltic andesite and andesite magmatism evolved to include dacite and rhyolite; magmatic activity became more voluminous and extended along most of the arc. Between 17 and 8 Ma, magmatism was focused along the part of the arc coincident with the northern two-thirds of Oregon and returned to more mafic compositions. Subsequent ancestral Cascades magmatism was dominated by basaltic andesite to basalt prior to the post–4 Ma onset of High Cascades magmatism. Transitional tholeiitic to calc-alkaline compositions dominated early (before 40 to ca. 25 Ma) ancestral Cascades eruptive products, whereas the majority of the younger arc rocks have a calc-alkaline affinity. Tholeiitic compositions characteristic of the oldest ancestral arc magmas suggest development associated with thin, immature crust and slab window processes, whereas the younger, calc-alkaline magmas suggest interaction with thicker, more evolved crust and more conventional subduction-related magmatic processes. Presumed changes in subducted slab dip through time also correlate with fundamental magma composition variation. The predominance of mafic compositions during latest ancestral arc magmatism and throughout the history of modern High Cascades magmatism probably reflects extensional tectonics that dominated during these periods of arc magmatism. Mineral deposits associated with ancestral Cascades arc rocks are uncommon; most are small and low grade relative to those found in other continental magmatic arcs. The small size, low grade, and dearth of deposits, especially in the southern two-thirds of the ancestral arc, probably reflect many factors, the most important of which may be the prevalence of extensional tectonics within this arc domain during this magmatic episode. Progressive clockwise rotation of the forearc block west of the evolving Oregon part of the ancestral Cascades magmatism produced an extensional regime that did not foster significant mineral deposit formation. In contrast, the Washington arc domain developed in a transpressional to mildly compressive regime that was more conducive to magmatic processes and hydrothermal fluid channeling critical to deposit formation. Small, low-grade porphyry copper deposits in the northern third of the ancestral Cascades arc segment also may be a consequence of more mature continental crust, including a Mesozoic component, beneath Washington north of Mount St. Helens.

PDBe: towards reusable data delivery infrastructure at protein data bank in Europe

PubMed Central

Alhroub, Younes; Anyango, Stephen; Armstrong, David R; Berrisford, John M; Clark, Alice R; Conroy, Matthew J; Dana, Jose M; Gupta, Deepti; Gutmanas, Aleksandras; Haslam, Pauline; Mak, Lora; Mukhopadhyay, Abhik; Nadzirin, Nurul; Paysan-Lafosse, Typhaine; Sehnal, David; Sen, Sanchayita; Smart, Oliver S; Varadi, Mihaly; Kleywegt, Gerard J

2018-01-01

Abstract The Protein Data Bank in Europe (PDBe, pdbe.org) is actively engaged in the deposition, annotation, remediation, enrichment and dissemination of macromolecular structure data. This paper describes new developments and improvements at PDBe addressing three challenging areas: data enrichment, data dissemination and functional reusability. New features of the PDBe Web site are discussed, including a context dependent menu providing links to raw experimental data and improved presentation of structures solved by hybrid methods. The paper also summarizes the features of the LiteMol suite, which is a set of services enabling fast and interactive 3D visualization of structures, with associated experimental maps, annotations and quality assessment information. We introduce a library of Web components which can be easily reused to port data and functionality available at PDBe to other services. We also introduce updates to the SIFTS resource which maps PDB data to other bioinformatics resources, and the PDBe REST API. PMID:29126160

HHsvm: fast and accurate classification of profile–profile matches identified by HHsearch

PubMed Central

Dlakić, Mensur

2009-01-01

Motivation: Recently developed profile–profile methods rival structural comparisons in their ability to detect homology between distantly related proteins. Despite this tremendous progress, many genuine relationships between protein families cannot be recognized as comparisons of their profiles result in scores that are statistically insignificant. Results: Using known evolutionary relationships among protein superfamilies in SCOP database, support vector machines were trained on four sets of discriminatory features derived from the output of HHsearch. Upon validation, it was shown that the automatic classification of all profile–profile matches was superior to fixed threshold-based annotation in terms of sensitivity and specificity. The effectiveness of this approach was demonstrated by annotating several domains of unknown function from the Pfam database. Availability: Programs and scripts implementing the methods described in this manuscript are freely available from http://hhsvm.dlakiclab.org/. Contact: mdlakic@montana.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19773335

Fast-acting self-healing metallic fuse.

NASA Technical Reports Server (NTRS)

Schwartz, F. C.; Renton, C. A.; Rabinovici, B.

1971-01-01

Description of a fast-acting nonmechanical self-healing mercury fuse capable of protecting a high current circuit or device from overcurrent fault damages. Basically the self-healing fuse consists of two enclosed mercury reservoirs connected by a fine capillary tube filled with mercury that serves as the fusing element. It is pointed out that a better understanding of the energy conversion process involved in the operation of the device could help explore other device configurations (such as a tapering geometry and use of magnetic field to drive the arc into the fuse wall on inductive loads, etc.) and thus extend the range of capabilities for this type of protective device.

23RD International Conference on Phenomena in Ionized Gases, Volume 2

DTIC Science & Technology

1998-12-01

able voltage arcs and thermoionic converters [10]. The news for subsequent evolution into a prebiotic structure, XXIII ICPIG (Toulouse, France ) 17...possibilities of a prebiotic [9]. M.Sanduloviciu, Proc XXII ICPIG New Jersey structure in the early Earth atmosphere (a plasma like 1995, Contr. Paper 1, p

Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements

PubMed Central

Jühling, Frank; Pütz, Joern; Bernt, Matthias; Donath, Alexander; Middendorf, Martin; Florentz, Catherine; Stadler, Peter F.

2012-01-01

Transfer RNAs (tRNAs) are present in all types of cells as well as in organelles. tRNAs of animal mitochondria show a low level of primary sequence conservation and exhibit ‘bizarre’ secondary structures, lacking complete domains of the common cloverleaf. Such sequences are hard to detect and hence frequently missed in computational analyses and mitochondrial genome annotation. Here, we introduce an automatic annotation procedure for mitochondrial tRNA genes in Metazoa based on sequence and structural information in manually curated covariance models. The method, applied to re-annotate 1876 available metazoan mitochondrial RefSeq genomes, allows to distinguish between remaining functional genes and degrading ‘pseudogenes’, even at early stages of divergence. The subsequent analysis of a comprehensive set of mitochondrial tRNA genes gives new insights into the evolution of structures of mitochondrial tRNA sequences as well as into the mechanisms of genome rearrangements. We find frequent losses of tRNA genes concentrated in basal Metazoa, frequent independent losses of individual parts of tRNA genes, particularly in Arthropoda, and wide-spread conserved overlaps of tRNAs in opposite reading direction. Direct evidence for several recent Tandem Duplication-Random Loss events is gained, demonstrating that this mechanism has an impact on the appearance of new mitochondrial gene orders. PMID:22139921

Method-centered digital communities on protocols.io for fast-paced scientific innovation.

PubMed

Kindler, Lori; Stoliartchouk, Alexei; Teytelman, Leonid; Hurwitz, Bonnie L

2016-01-01

The Internet has enabled online social interaction for scientists beyond physical meetings and conferences. Yet despite these innovations in communication, dissemination of methods is often relegated to just academic publishing. Further, these methods remain static, with subsequent advances published elsewhere and unlinked. For communities undergoing fast-paced innovation, researchers need new capabilities to share, obtain feedback, and publish methods at the forefront of scientific development. For example, a renaissance in virology is now underway given the new metagenomic methods to sequence viral DNA directly from an environment. Metagenomics makes it possible to "see" natural viral communities that could not be previously studied through culturing methods. Yet, the knowledge of specialized techniques for the production and analysis of viral metagenomes remains in a subset of labs.  This problem is common to any community using and developing emerging technologies and techniques. We developed new capabilities to create virtual communities in protocols.io, an open access platform, for disseminating protocols and knowledge at the forefront of scientific development. To demonstrate these capabilities, we present a virology community forum called VERVENet. These new features allow virology researchers to share protocols and their annotations and optimizations, connect with the broader virtual community to share knowledge, job postings, conference announcements through a common online forum, and discover the current literature through personalized recommendations to promote discussion of cutting edge research. Virtual communities in protocols.io enhance a researcher's ability to: discuss and share protocols, connect with fellow community members, and learn about new and innovative research in the field.  The web-based software for developing virtual communities is free to use on protocols.io. Data are available through public APIs at protocols.io.

Hybrid/Tandem Laser-Arc Welding of Thick Low Carbon Martensitic Stainless Steel Plates =

NASA Astrophysics Data System (ADS)

Mirakhorli, Fatemeh

High efficiency and long-term life of hydraulic turbines and their assemblies are of utmost importance for the hydropower industry. Usually, hydroelectric turbine components are made of thick-walled low carbon martensitic stainless steels. The assembly of large hydroelectric turbine components has been a great challenge. The use of conventional welding processes involves typical large groove design and multi-pass welding to fill the groove which exposes the weld to a high heat input creating relatively large fusion zone and heat affected zone. The newly-developed hybrid/tandem laser-arc welding technique is believed to offer a highly competitive solution to improve the overall hydro-turbine performance by combining the high energy density and fast welding speed of the laser welding technology with the good gap bridging and feeding ability of the gas metal arc welding process to increase the productivity and reduce the consumable material. The main objective of this research work is to understand different challenges appearing during hybrid laser-arc welding (HLAW) of thick gauge assemblies of low carbon 13%Cr- 4%Ni martensitic stainless steel and find a practical solution by adapting and optimizing this relatively new welding process in order to reduce the number of welding passes necessary to fill the groove gap. The joint integrity was evaluated in terms of microstructure, defects and mechanical properties in both as-welded and post-welded conditions. A special focus was given to the hybrid and tandem laser-arc welding technique for the root pass. Based on the thickness of the low carbon martensitic stainless steel plates, this work is mainly focused on the following two tasks: • Single pass hybrid laser-arc welding of 10-mm thick low carbon martensitic stainless steel. • Multi-pass hybrid/tandem laser-arc welding of 25-mm thick martensitic stainless steel.

Improved methods for multi-trait fine mapping of pleiotropic risk loci.

PubMed

Kichaev, Gleb; Roytman, Megan; Johnson, Ruth; Eskin, Eleazar; Lindström, Sara; Kraft, Peter; Pasaniuc, Bogdan

2017-01-15

Genome-wide association studies (GWAS) have identified thousands of regions in the genome that contain genetic variants that increase risk for complex traits and diseases. However, the variants uncovered in GWAS are typically not biologically causal, but rather, correlated to the true causal variant through linkage disequilibrium (LD). To discern the true causal variant(s), a variety of statistical fine-mapping methods have been proposed to prioritize variants for functional validation. In this work we introduce a new approach, fastPAINTOR, that leverages evidence across correlated traits, as well as functional annotation data, to improve fine-mapping accuracy at pleiotropic risk loci. To improve computational efficiency, we describe an new importance sampling scheme to perform model inference. First, we demonstrate in simulations that by leveraging functional annotation data, fastPAINTOR increases fine-mapping resolution relative to existing methods. Next, we show that jointly modeling pleiotropic risk regions improves fine-mapping resolution compared to standard single trait and pleiotropic fine mapping strategies. We report a reduction in the number of SNPs required for follow-up in order to capture 90% of the causal variants from 23 SNPs per locus using a single trait to 12 SNPs when fine-mapping two traits simultaneously. Finally, we analyze summary association data from a large-scale GWAS of lipids and show that these improvements are largely sustained in real data. The fastPAINTOR framework is implemented in the PAINTOR v3.0 package which is publicly available to the research community http://bogdan.bioinformatics.ucla.edu/software/paintor CONTACT: gkichaev@ucla.eduSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Differential root transcriptomics in a polyploid non-model crop: the importance of respiration during osmotic stress

PubMed Central

Zorrilla-Fontanesi, Yasmín; Rouard, Mathieu; Cenci, Alberto; Kissel, Ewaut; Do, Hien; Dubois, Emeric; Nidelet, Sabine; Roux, Nicolas; Swennen, Rony; Carpentier, Sebastien Christian

2016-01-01

To explore the transcriptomic global response to osmotic stress in roots, 18 mRNA-seq libraries were generated from three triploid banana genotypes grown under mild osmotic stress (5% PEG) and control conditions. Illumina sequencing produced 568 million high quality reads, of which 70–84% were mapped to the banana diploid reference genome. Using different uni- and multivariate statistics, 92 genes were commonly identified as differentially expressed in the three genotypes. Using our in house workflow to analyze GO enriched and underlying biochemical pathways, we present the general processes affected by mild osmotic stress in the root and focus subsequently on the most significantly overrepresented classes associated with: respiration, glycolysis and fermentation. We hypothesize that in fast growing and oxygen demanding tissues, mild osmotic stress leads to a lower energy level, which induces a metabolic shift towards (i) a higher oxidative respiration, (ii) alternative respiration and (iii) fermentation. To confirm the mRNA-seq results, a subset of twenty up-regulated transcripts were further analysed by RT-qPCR in an independent experiment at three different time points. The identification and annotation of this set of genes provides a valuable resource to understand the importance of energy sensing during mild osmotic stress. PMID:26935041

An Advanced Deep Learning Approach for Ki-67 Stained Hotspot Detection and Proliferation Rate Scoring for Prognostic Evaluation of Breast Cancer.

PubMed

Saha, Monjoy; Chakraborty, Chandan; Arun, Indu; Ahmed, Rosina; Chatterjee, Sanjoy

2017-06-12

Being a non-histone protein, Ki-67 is one of the essential biomarkers for the immunohistochemical assessment of proliferation rate in breast cancer screening and grading. The Ki-67 signature is always sensitive to radiotherapy and chemotherapy. Due to random morphological, color and intensity variations of cell nuclei (immunopositive and immunonegative), manual/subjective assessment of Ki-67 scoring is error-prone and time-consuming. Hence, several machine learning approaches have been reported; nevertheless, none of them had worked on deep learning based hotspots detection and proliferation scoring. In this article, we suggest an advanced deep learning model for computerized recognition of candidate hotspots and subsequent proliferation rate scoring by quantifying Ki-67 appearance in breast cancer immunohistochemical images. Unlike existing Ki-67 scoring techniques, our methodology uses Gamma mixture model (GMM) with Expectation-Maximization for seed point detection and patch selection and deep learning, comprises with decision layer, for hotspots detection and proliferation scoring. Experimental results provide 93% precision, 0.88% recall and 0.91% F-score value. The model performance has also been compared with the pathologists' manual annotations and recently published articles. In future, the proposed deep learning framework will be highly reliable and beneficial to the junior and senior pathologists for fast and efficient Ki-67 scoring.

Cold starting of fluorescent lamps - part II: experiments on glow times and electrode damaging

NASA Astrophysics Data System (ADS)

Langer, Reinhard; Paul, Irina; Hilscher, Achim; Horn, Siegfried; Tidecks, Reinhard

2017-01-01

In the present work we present experiments on cold start and the resulting electrode damaging (reducing lamp life) of AC driven fluorescent lamps. The crucial parameter is the glow time, determined from time resolved measurements of lamp voltage and current. The relation between the energy consumed during glow phase and the glow time is studied. It turns out that there is no common threshold of energy until the glow-to-arc transition takes place, but strong energy input into the lamp yields short glow times. The transient behaviour from the glow to the arc regime is investigated and the stable operation points of the arc discharge are determined, yielding an arc discharge voltage-current characteristics of the lamp type investigated. The electrode damage is investigated as a function of the open source voltage and the ballast resistance. Subsequent cold starts lead to an increase of the glow time due to electrode damaging, i.e., the electrode damage accumulates. Different regeneration procedures and their effectiveness are compared. Regeneration burning turns out to be more effective than heating up the electrode. A criterion for avoiding high electrode damage is obtained, indicating that the average power during glow time should exceed 20 W.

Beam loss detection system in the arcs of the LHC

NASA Astrophysics Data System (ADS)

Arauzo, A.; Bovet, C.

2000-11-01

Over the whole circumference of the LHC, Beam Loss Monitors (BLM) will be needed for a continuous surveillance of fast and slow beam losses. In this paper, the location of the BLMs set outside the magnet cryostats in the arcs is proposed. In order to know the number of protons lost on the beam screen, the sensitivity of each BLM has been computed using the program GEANT 3.21, which generates the shower inside the cryostat. The material and the magnetic fields have been described thoroughly in 3-D and the simulation results show the best locations for 6 BLMs needed around each quadrupole. The number of minimum ionizing particles received for each lost proton serves to define local thresholds to dump the beam when the losses are menacing to quench a magnet.

RF Conditioning of the Photo-Cathode RF Gun at the Advanced Photon Source - NWA RF Measurements

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

Smith, T. L.; DiMonte, N.; Nassiri, A.

A new S-band Photo-cathode (PC) gun was recently installed and RF conditioned at the Advanced Photon Source (APS) Injector Test-stand (ITS) at Argonne National Lab (ANL). The APS PC gun is a LCLS type gun fabricated at SLAC [1]. The PC gun was delivered to the APS in October 2013 and installed in the APS ITS in December 2013. At ANL, we developed a new method of fast detection and mitigation of the guns internal arcs during the RF conditioning process to protect the gun from arc damage and to RF condition more efficiently. Here, we report the results ofmore » RF measurements for the PC gun and an Auto-Restart method for high power RF conditioning.« less

Increasing clinicians' EBT exploration and preparation behavior in youth mental health services by changing organizational culture with ARC.

PubMed

Glisson, Charles; Williams, Nathaniel J; Hemmelgarn, Anthony; Proctor, Enola; Green, Philip

2016-01-01

Clinician EBT exploration and preparation behavior is essential to the ongoing implementation of new EBTs. This study examined the effect of the ARC organizational intervention on clinician EBT exploration and preparation behavior and assessed the mediating role of organizational culture as a linking mechanism. Fourteen community mental health agencies that serve youth in a major Midwestern metropolis along with 475 clinicians who worked in those agencies, were randomly assigned to either the three-year ARC intervention or control condition. Organizational culture was assessed with the Organizational Social Context (OSC) measure at baseline and follow-up. EBT exploration and preparation behavior was measured as clinician participation in nine separate community EBT workshops held over a three-year period. There was 69 percent greater odds (OR = 1.69, p < .003) of clinicians in the ARC condition (versus control) attending each subsequent workshop. Workshop attendance in the control group remained under two percent and declined over three years while attendance in the ARC condition grew from 3.6 percent in the first workshop to 12 percent in the ninth and final workshop. Improvement in proficient organizational culture mediated the positive effect of the ARC intervention on clinicians' workshop attendance (a × b = .21; 95% CI:LL = .05, UL = .40). Organizational interventions that create proficient mental health agency cultures can increase clinician EBT exploration and preparation behavior that is essential to the ongoing implementation of new EBTs in community youth mental health settings. Copyright © 2015 Elsevier Ltd. All rights reserved.

Permian arc evolution associated with Panthalassa subduction along the eastern margin of the South China block, based on sandstone provenance and U-Pb detrital zircon ages of the Kurosegawa belt, Southwest Japan

NASA Astrophysics Data System (ADS)

Hara, Hidetoshi; Hirano, Miho; Kurihara, Toshiyuki; Takahashi, Toshiro; Ueda, Hayato

2018-01-01

We have studied the petrography, geochemistry, and detrital zircon U-Pb ages of sandstones from shallow-marine forearc sediments, accretionary complexes (ACs), and metamorphosed accretionary complexes (Meta-ACs) within the Kurosegawa belt of Southwest Japan. Those rocks formed in a forearc region of a Permian island arc associated with subduction of the Panthalassa oceanic crust along the eastern margin of the South China block (Yangtze block). The provenance of the shallow-marine sediments was dominated by basaltic to andesitic volcanic rocks and minor granitic rocks during the late Middle to Late Permian. The ACs were derived from felsic to andesitic volcanic rocks during the Late Permian. The provenance of Meta-ACs was dominated by andesitic volcanic rocks in the Middle Permian. The provenance, source rock compositions, and zircon age distribution for the forearc sediments, ACs and Meta-ACs have allowed us to reconstruct the geological history of the Permian arc system of the Kurosegawa belt. During the Middle Permian, the ACs were accreted along the eastern margin of the South China block. The Middle Permian arc was an immature oceanic island arc consisting of andesitic volcanic rocks. During the Late Permian, the ACs formed in a mature arc, producing voluminous felsic to andesitic volcanic rocks. A forearc basin developed during the late Middle to Late Permian. Subsequently, the Middle Permian ACs and part of the Late Permian AC underwent low-grade metamorphism in the Late to Early Jurassic, presenting the Meta-ACs.

FAST TRACK COMMUNICATION: First prediction of the direct effect of a confined atom on photoionization of the confining fullerene

NASA Astrophysics Data System (ADS)

McCune, Matthew A.; De, Ruma; Madjet, Mohamed E.; Chakraborty, Himadri S.

2010-09-01

We predict that the confined atom can qualitatively modify the energetic photoionization of some cage levels, even though these levels are of very dominant fullerene character. The effect imposes strong new oscillations in the cross sections which are forbidden to the ionization of empty fullerenes. Results are presented for the Ar@C60 endofullerene compound.

The ARC (Astrophysical Research Consortium) telescope project.

NASA Astrophysics Data System (ADS)

Anderson, K. S.

A consortium of universities intends to construct a 3.5 meter optical-infrared telescope at a site in south-central New Mexico. The use of innovative mirror technology, a fast primary, and an alt-azimuth mounting results in a compact and lightweight instrument. This telescope will be uniquely well-suited for addressing certain observational programs by virtue of its capability for fully remote operation and rapid instrument changes.

SANSparallel: interactive homology search against Uniprot.

PubMed

Somervuo, Panu; Holm, Liisa

2015-07-01

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

Model for turbidite-to-contourite continuum and multiple process transport in deep marine settings: examples in the rock record

NASA Astrophysics Data System (ADS)

Stanley, Daniel Jean

1993-01-01

Petrological analysis of geological sections in St. Croix in the Caribbean, the Niesenflysch in Switzerland and the Annot Sandstone in the French Maritime Alps sheds light on multiple process transport in deep marine settings. A model depicting a turbidite-to-contourite continuum of stratal types is applied to these three rock units. Recognition of a diverse suite of bedforms, coupled with analysis of paleocurrents, helps to better interpret depositional origin and basin paleogeography. The St. Croix strata record emplacement by gravity flows and, subsequently, by bottom currents flowing parallel to the base of slope; these sediments accumulated on a lower slope apron. A Niesenflysch section in the Swiss Alps west of Adelboden includes turbidites which were deposited at fairly regular intervals beyond the base of slope, in a setting more distal than that of the St. Croix sequences. Most of these turbidites appear to have been partially reworked by bottom currents related to basin circulation or to density flows from the basin margins. In the Annot Sandstone, reworked turbidites (termed transitional variants) and packets of entirely rippled strata are observed in submarine fan and slope sequences in the Peira-Cava area. In contrast to those in St. Croix and the Niesenflysch, the current-emplaced deposits of the Annot Sandstone are directly associated with fan-valley deposits. Such rippled strata in channels are deposits of gravity flow origin which were subsequently reworked downslope by currents generated by successive gravity flows; they also occur on levees by overbank flow. Consideration of multiple process transport is of special help to interpret sections which are poorly exposed, or which can be examined in cores, or which are located in sequences that have been highly deformed structurally.

Developing a knowledge base to support the annotation of ultrasound images of ectopic pregnancy.

PubMed

Dhombres, Ferdinand; Maurice, Paul; Friszer, Stéphanie; Guilbaud, Lucie; Lelong, Nathalie; Khoshnood, Babak; Charlet, Jean; Perrot, Nicolas; Jauniaux, Eric; Jurkovic, Davor; Jouannic, Jean-Marie

2017-01-31

Ectopic pregnancy is a frequent early complication of pregnancy associated with significant rates of morbidly and mortality. The positive diagnosis of this condition is established through transvaginal ultrasound scanning. The timing of diagnosis depends on the operator expertise in identifying the signs of ectopic pregnancy, which varies dramatically among medical staff with heterogeneous training. Developing decision support systems in this context is expected to improve the identification of these signs and subsequently improve the quality of care. In this article, we present a new knowledge base for ectopic pregnancy, and we demonstrate its use on the annotation of clinical images. The knowledge base is supported by an application ontology, which provides the taxonomy, the vocabulary and definitions for 24 types and 81 signs of ectopic pregnancy, 484 anatomical structures and 32 technical elements for image acquisition. The knowledge base provides a sign-centric model of the domain, with the relations of signs to ectopic pregnancy types, anatomical structures and the technical elements. The evaluation of the ontology and knowledge base demonstrated a positive feedback from a panel of 17 medical users. Leveraging these semantic resources, we developed an application for the annotation of ultrasound images. Using this application, 6 operators achieved a precision of 0.83 for the identification of signs in 208 ultrasound images corresponding to 35 clinical cases of ectopic pregnancy. We developed a new ectopic pregnancy knowledge base for the annotation of ultrasound images. The use of this knowledge base for the annotation of ultrasound images of ectopic pregnancy showed promising results from the perspective of clinical decision support system development. Other gynecological disorders and fetal anomalies may benefit from our approach.

The first step in the development of text mining technology for cancer risk assessment: identifying and organizing scientific evidence in risk assessment literature

PubMed Central

Korhonen, Anna; Silins, Ilona; Sun, Lin; Stenius, Ulla

2009-01-01

Background One of the most neglected areas of biomedical Text Mining (TM) is the development of systems based on carefully assessed user needs. We have recently investigated the user needs of an important task yet to be tackled by TM -- Cancer Risk Assessment (CRA). Here we take the first step towards the development of TM technology for the task: identifying and organizing the scientific evidence required for CRA in a taxonomy which is capable of supporting extensive data gathering from biomedical literature. Results The taxonomy is based on expert annotation of 1297 abstracts downloaded from relevant PubMed journals. It classifies 1742 unique keywords found in the corpus to 48 classes which specify core evidence required for CRA. We report promising results with inter-annotator agreement tests and automatic classification of PubMed abstracts to taxonomy classes. A simple user test is also reported in a near real-world CRA scenario which demonstrates along with other evaluation that the resources we have built are well-defined, accurate, and applicable in practice. Conclusion We present our annotation guidelines and a tool which we have designed for expert annotation of PubMed abstracts. A corpus annotated for keywords and document relevance is also presented, along with the taxonomy which organizes the keywords into classes defining core evidence for CRA. As demonstrated by the evaluation, the materials we have constructed provide a good basis for classification of CRA literature along multiple dimensions. They can support current manual CRA as well as facilitate the development of an approach based on TM. We discuss extending the taxonomy further via manual and machine learning approaches and the subsequent steps required to develop TM technology for the needs of CRA. PMID:19772619

Hypothalamic CaMKKβ mediates glucagon anorectic effect and its diet-induced resistance.

PubMed

Quiñones, Mar; Al-Massadi, Omar; Gallego, Rosalía; Fernø, Johan; Diéguez, Carlos; López, Miguel; Nogueiras, Ruben

2015-12-01

Glucagon receptor antagonists and humanized glucagon antibodies are currently studied as promising therapies for obesity and type II diabetes. Among its variety of actions, glucagon reduces food intake, but the molecular mechanisms mediating this effect as well as glucagon resistance are totally unknown. Glucagon and adenoviral vectors were administered in specific hypothalamic nuclei of lean and diet-induced obese rats. The expression of neuropeptides controlling food intake was performed by in situ hybridization. The regulation of factors of the glucagon signaling pathway was assessed by western blot. The central injection of glucagon decreased feeding through a hypothalamic pathway involving protein kinase A (PKA)/Ca(2+)-calmodulin-dependent protein kinase kinase β (CaMKKβ)/AMP-activated protein kinase (AMPK)-dependent mechanism. More specifically, the central injection of glucagon increases PKA activity and reduces protein levels of CaMKKβ and its downstream target phosphorylated AMPK in the hypothalamic arcuate nucleus (ARC). Consistently, central glucagon significantly decreased AgRP expression. Inhibition of PKA and genetic activation of AMPK in the ARC blocked glucagon-induced anorexia in lean rats. Genetic down-regulation of glucagon receptors in the ARC stimulates fasting-induced hyperphagia. Although glucagon was unable to decrease food intake in DIO rats, glucagon sensitivity was restored after inactivation of CaMKKβ, specifically in the ARC. Thus, glucagon decreases food intake acutely via PKA/CaMKKβ/AMPK dependent pathways in the ARC, and CaMKKβ mediates its obesity-induced hypothalamic resistance. This work reveals the molecular underpinnings by which glucagon controls feeding that may lead to a better understanding of disease states linked to anorexia and cachexia.

Resequencing and annotation of the Nostoc punctiforme ATTC 29133 genome: facilitating biofuel and high-value chemical production

DOE PAGES

Moraes, Luis E.; Blow, Matthew J.; Hawley, Erik R.; ...

2017-02-16

Cyanobacteria have the potential to produce bulk and fine chemicals and members belonging to Nostoc sp. have received particular attention due to their relatively fast growth rate and the relative ease with which they can be harvested. Nostoc punctiforme is an aerobic, motile, Gram-negative, filamentous cyanobacterium that has been studied intensively to enhance our understanding of microbial carbon and nitrogen fixation. The genome of the type strain N. punctiforme ATCC 29133 was sequenced in 2001 and the scientific community has used these genome data extensively since then. Advances in bioinformatics tools for sequence annotation and the importance of this organismmore » prompted us to resequence and reanalyze its genome and to make both, the initial and improved annotation, available to the scientific community. The new draft genome has a total size of 9.1 Mbp and consists of 65 contiguous pieces of DNA with a GC content of 41.38% and 7664 protein-coding genes. Furthermore, the resequenced genome is slightly (5152 bp) larger and contains 987 more genes with functional prediction when compared to the previously published version. We deposited the annotation of both genomes in the Department of Energy’s IMG database to facilitate easy genome exploration by the scientific community without the need of in-depth bioinformatics skills. We expect that an facilitated access and ability to search the N. punctiforme ATCC 29133 for genes of interest will significantly facilitate metabolic engineering and genome prospecting efforts and ultimately the synthesis of biofuels and natural products from this keystone organism and closely related cyanobacteria.« less

Resequencing and annotation of the Nostoc punctiforme ATTC 29133 genome: facilitating biofuel and high-value chemical production

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

Moraes, Luis E.; Blow, Matthew J.; Hawley, Erik R.

Cyanobacteria have the potential to produce bulk and fine chemicals and members belonging to Nostoc sp. have received particular attention due to their relatively fast growth rate and the relative ease with which they can be harvested. Nostoc punctiforme is an aerobic, motile, Gram-negative, filamentous cyanobacterium that has been studied intensively to enhance our understanding of microbial carbon and nitrogen fixation. The genome of the type strain N. punctiforme ATCC 29133 was sequenced in 2001 and the scientific community has used these genome data extensively since then. Advances in bioinformatics tools for sequence annotation and the importance of this organismmore » prompted us to resequence and reanalyze its genome and to make both, the initial and improved annotation, available to the scientific community. The new draft genome has a total size of 9.1 Mbp and consists of 65 contiguous pieces of DNA with a GC content of 41.38% and 7664 protein-coding genes. Furthermore, the resequenced genome is slightly (5152 bp) larger and contains 987 more genes with functional prediction when compared to the previously published version. We deposited the annotation of both genomes in the Department of Energy’s IMG database to facilitate easy genome exploration by the scientific community without the need of in-depth bioinformatics skills. We expect that an facilitated access and ability to search the N. punctiforme ATCC 29133 for genes of interest will significantly facilitate metabolic engineering and genome prospecting efforts and ultimately the synthesis of biofuels and natural products from this keystone organism and closely related cyanobacteria.« less

Statistical assessment of crosstalk enrichment between gene groups in biological networks.

PubMed

McCormack, Theodore; Frings, Oliver; Alexeyenko, Andrey; Sonnhammer, Erik L L

2013-01-01

Analyzing groups of functionally coupled genes or proteins in the context of global interaction networks has become an important aspect of bioinformatic investigations. Assessing the statistical significance of crosstalk enrichment between or within groups of genes can be a valuable tool for functional annotation of experimental gene sets. Here we present CrossTalkZ, a statistical method and software to assess the significance of crosstalk enrichment between pairs of gene or protein groups in large biological networks. We demonstrate that the standard z-score is generally an appropriate and unbiased statistic. We further evaluate the ability of four different methods to reliably recover crosstalk within known biological pathways. We conclude that the methods preserving the second-order topological network properties perform best. Finally, we show how CrossTalkZ can be used to annotate experimental gene sets using known pathway annotations and that its performance at this task is superior to gene enrichment analysis (GEA). CrossTalkZ (available at http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/) is implemented in C++, easy to use, fast, accepts various input file formats, and produces a number of statistics. These include z-score, p-value, false discovery rate, and a test of normality for the null distributions.

Fasting insulin, insulin resistance and risk of hypertension in the general population: A meta-analysis.

PubMed

Wang, Feng; Han, Lili; Hu, Dayi

2017-01-01

Studies on the association of fasting insulin concentrations or insulin resistance with subsequent risk of hypertension have yielded conflicting results. To quantitatively assess the association of fasting insulin concentrations or homeostasis model assessment insulin resistance (HOMA-IR) with incident hypertension in a general population by performing a meta-analysis. We searched the PubMed and Embase databases until August 31, 2016 for prospective observational studies investigating the elevated fasting insulin concentrations or HOMA-IR with subsequent risk of hypertension in the general population. Pooled risk ratio (RR) and 95% confidence interval (CI) of hypertension was calculated for the highest versus the lowest category of fasting insulin or HOMA-IR. Eleven studies involving 10,230 hypertension cases were identified from 55,059 participants. Meta-analysis showed that the pooled adjusted RR of hypertension was 1.54 (95% CI 1.34-1.76) for fasting insulin concentrations and 1.43 (95% CI 1.27-1.62) for HOMA-IR comparing the highest to the lowest category. Subgroup analysis results showed that the association of fasting insulin concentrations with subsequent risk of hypertension seemed more pronounced in women (RR 2.07; 95% CI 1.19-3.60) than in men (RR 1.48; 95% CI 1.17-1.88). This meta-analysis suggests that elevated fasting insulin concentrations or insulin resistance as estimated by homeostasis model assessment is independently associated with an exacerbated risk of hypertension in the general population. Early intervention of hyperinsulinemia or insulin resistance may help clinicians to identify the high risk of hypertensive population. Copyright © 2016 Elsevier B.V. All rights reserved.

Microstructural changes of a thermally aged stainless steel submerged arc weld overlay cladding of nuclear reactor pressure vessels

NASA Astrophysics Data System (ADS)

Takeuchi, T.; Kameda, J.; Nagai, Y.; Toyama, T.; Matsukawa, Y.; Nishiyama, Y.; Onizawa, K.

2012-06-01

The effect of thermal aging on microstructural changes in stainless steel submerged arc weld-overlay cladding of reactor pressure vessels was investigated using atom probe tomography (APT). In as-received materials subjected to post-welding heat treatments (PWHTs), with a subsequent furnace cooling, a slight fluctuation of the Cr concentration was observed due to spinodal decomposition in the δ-ferrite phase but not in the austenitic phase. Thermal aging at 400 °C for 10,000 h caused not only an increase in the amplitude of spinodal decomposition but also the precipitation of G phases with composition ratios of Ni:Si:Mn = 16:7:6 in the δ-ferrite phase. The degree of the spinodal decomposition in the submerged arc weld sample was similar to that in the electroslag weld one reported previously. We also observed a carbide on the γ-austenite and δ-ferrite interface. There were no Cr depleted zones around the carbide.

Age constraints on the evolution of the Quetico belt, Superior Province, Ontario

NASA Technical Reports Server (NTRS)

Percival, J. A.; Sullivan, R. W.

1986-01-01

Much attention has been focused on the nature of Archean tectonic processes and the extent to which they were different from modern rigid-plate tectonics. The Archean Superior Province has linear metavolcanic and metasediment-dominated subprovinces of similar scale to cenozoic island arc-trench systems of the western Pacific, suggesting an origin by accreting arcs. Models of the evolution of metavolcanic belts in parts of the Superior Province suggest an arc setting but the tectonic environment and evolution of the intervening metasedimentary belts are poorly understood. In addition to explaining the setting giving rise to a linear sedimentary basin, models must account for subsequent shortening and high-temperature, low-pressure metamorphism. Correlation of rock units and events in adjacent metavolcanic and metasedimentary belts is a first step toward understanding large-scale crustal interactions. To this end, zircon geochronology has been applied to metavolcanic belts of the western Superior Province; new age data for the Quetico metasedimentary belt is reported, permitting correlation with the adjacent Wabigoon and Wawa metavolcanic subprovinces.

Tracing halogen and B cycling in subduction zones based on obducted, subducted and forearc serpentinites of the Dominican Republic.

PubMed

Pagé, Lilianne; Hattori, Keiko

2017-12-19

Serpentinites are important reservoirs of fluid-mobile elements in subduction zones, contributing to volatiles in arc magmas and their transport into the Earth's mantle. This paper reports halogen (F, Cl, Br, I) and B abundances of serpentinites from the Dominican Republic, including obducted and subducted abyssal serpentinites and forearc mantle serpentinites. Abyssal serpentinite compositions indicate the incorporation of these elements from seawater and sediments during serpentinization on the seafloor and at slab bending. During their subduction and subsequent lizardite-antigorite transition, F and B are retained in serpentinites, whilst Cl, Br and I are expelled. Forearc mantle serpentinite compositions suggest their hydration by fluids released from subducting altered oceanic crust and abyssal serpentinites, with only minor sediment contribution. This finding is consistent with the minimal subduction of sediments in the Dominican Republic. Forearc mantle serpentinites have F/Cl and B/Cl ratios similar to arc magmas, suggesting the importance of serpentinite dehydration in the generation of arc magmatism in the mantle wedge.

Optical Tracking Data Validation and Orbit Estimation for Sparse Observations of Satellites by the OWL-Net.

PubMed

Choi, Jin; Jo, Jung Hyun; Yim, Hong-Suh; Choi, Eun-Jung; Cho, Sungki; Park, Jang-Hyun

2018-06-07

An Optical Wide-field patroL-Network (OWL-Net) has been developed for maintaining Korean low Earth orbit (LEO) satellites' orbital ephemeris. The OWL-Net consists of five optical tracking stations. Brightness signals of reflected sunlight of the targets were detected by a charged coupled device (CCD). A chopper system was adopted for fast astrometric data sampling, maximum 50 Hz, within a short observation time. The astrometric accuracy of the optical observation data was validated with precise orbital ephemeris such as Consolidated Prediction File (CPF) data and precise orbit determination result with onboard Global Positioning System (GPS) data from the target satellite. In the optical observation simulation of the OWL-Net for 2017, an average observation span for a single arc of 11 LEO observation targets was about 5 min, while an average optical observation separation time was 5 h. We estimated the position and velocity with an atmospheric drag coefficient of LEO observation targets using a sequential-batch orbit estimation technique after multi-arc batch orbit estimation. Post-fit residuals for the multi-arc batch orbit estimation and sequential-batch orbit estimation were analyzed for the optical measurements and reference orbit (CPF and GPS data). The post-fit residuals with reference show few tens-of-meters errors for in-track direction for multi-arc batch and sequential-batch orbit estimation results.

Reliability of serum creatinine-based formulae estimating renal function in non-critically ill surgery patients: Focus on augmented renal clearance.

PubMed

Declercq, Peter; Gijsen, Matthias; Meijers, Björn; Schetz, Marie; Nijs, Stefaan; D'Hoore, André; Wauters, Joost; Spriet, Isabel

2018-05-07

Formulae estimating glomerular filtration rate (GFR) are frequently used to guide drug dosing. The objectives of this prospective single-center study were to evaluate agreement between these equations and measured creatinine clearance (CrCl) in non-critically ill surgery patients with normal kidney function and augmented renal clearance (ARC, CrCl ≥ 130 mL/min/1.73 m²), to determine predictors for disagreement, define a GFR estimator cut-off value identifying ARC and determine the ARC prevalence and duration in non-critically ill surgical patients. Hospitalized adult non-critically ill abdominal and trauma surgery patients were eligible for inclusion. Measured CrCl based on an 8-hour urinary collection (CrCl 8h ) was used as the primary method for determining kidney function. Agreement between equations and measured CrCl 8h was assessed in terms of precision, defined as a bias within ±10 mL/min/1.73 m². Predictors for disagreement were identified for the most precise estimator using an ordinal logistic regression model with negative bias, agreement and positive bias as outcome variables. A receiver operating characteristic (ROC) analysis was performed to identify an estimator cut-off predicting ARC, which was subsequently applied for the daily proportion of patients displaying ARC and ARC duration. During the study period (14/11/2013 - 13/05/2014), in 232 adult non-critically ill abdominal and trauma surgery patients, all estimators tend to underestimate CrCl 8h (mean bias ranging from 17 to 22 mL/min/1.73 m²), especially in patients displaying ARC (mean bias ranging from 44 to 56 mL/min/1.73 m²). eGFR CKD-EPI performed the best. Younger age and low ASA score independently predicted underestimation of CrCl 8h . Three different eGFR CKD-EPI cut-offs with decreasing sensitivity and increasing specificity (84, 95 and 112 mL/min/1.73 m²) identified, respectively, 65%, 44% and 14% patients displaying ARC. The median ARC duration was 4, 4 and 3 days, respectively. In surgical patients, eGFR frequently underestimates measured CrCl, especially in young patients with low ASA score. eGFR cut-offs predicting ARC were identified. © 2018 John Wiley & Sons Ltd.

Back-arc with frontal-arc component origin of Triassic Karmutsen basalt, British Columbia, Canada

USGS Publications Warehouse

Barker, F.; Sutherland, Brown A.; Budahn, J.R.; Plafker, G.

1989-01-01

The largely basaltic, ???4.5-6.2-km-thick, Middle to Upper Triassic Karmutsen Formation is a prominent part of the Wrangellian sequence. Twelve analyses of major and minor elements of representative samples of pillowed and massive basalt flows and sills from Queen Charlotte and Vancouver Islands are ferrotholeiites that show a range of 10.2-3.8% MgO (as normalized, H2O- and CO2-free) and related increases in TiO2 (1.0-2.5%), Zr (43-147 ppm) and Nb (5-16 ppm). Other elemental abundances are not related simply to MgO: distinct groupings are evident in Al2O3, Na2O and Cr, but considerable scatter is present in FeO* (FeO + 0.9Fe2O3) and CaO. Some of the variation is attributed to alteration during low-rank metamorphism or by seawater - including variation of Ba, Rb, Sr and Cu, but high-field-strength elements (Sc, Ti, Y, Zr and Nb) as well as Cr, Ni, Cu and rare-earth elements (REE's) were relatively immobile. REE's show chondrite-normalized patterns ranging from light-REE depleted to moderately light-REE enriched. On eleven discriminant plots these analyses fall largely into or across fields of within-plate basalt (WIP), normal or enriched mid-ocean-ridge tholeiite (MORB) and island-arc tholeiite (IAT). Karmutsen basalts are chemically identical to the stratigraphically equivalent Nikolai Greenstone of southern Alaska and Yukon Territory. These data and the fact that the Karmutsen rests on Sicker Group island-arc rocks of Paleozoic age suggest to us that: 1. (1) the basal arc, after minor carbonate-shale deposition, underwent near-axial back-arc rifting (as, e.g., the Mariana arc rifted at different times); 2. (2) the Karmutsen basalts were erupted along this rift or basin as "arc-rift" tholeiitite; and 3. (3) after subsequent deposition of carbonates and other rocks, and Jurassic magmatism, a large fragment of this basalt-sediment-covered island arc was accreted to North America as Wrangellia. The major- and minor-elemental abundances of Karmutsen basalt is modeled by first mixing primitive arc magma with enriched basaltic liquid derived either from garnet peridotite or metasomatized mantle, followed by fractionation of olivine, pyroxenes, plagioclase and spinel. ?? 1989.

Short Pulse Switches for Airborne High Power Supplies

DTIC Science & Technology

1973-10-01

IB 8. Rotary Mechanical Switch 20 9. Mechanical Switch, Essential Elements 24 10. Motor , Torsion Bar Electrodynamic Drive 28 11. Fast Acting...Gas Valve 31 12. Motor Test, Conductance, and Torque 33 13. Measured Motor Characteristics 34 14. Motor Structural Test Sample 36 15. Motor ...Fig. 42. Fig. 43. Fig. 44. Fig. 45. Fig. 46. Fig. 47. Fig. 48. Mechanical Switch 49 Arcing Contacts 51 Nonarcing Contacts 53 Motor

An Agent Based Collaborative Simplification of 3D Mesh Model

NASA Astrophysics Data System (ADS)

Wang, Li-Rong; Yu, Bo; Hagiwara, Ichiro

Large-volume mesh model faces the challenge in fast rendering and transmission by Internet. The current mesh models obtained by using three-dimensional (3D) scanning technology are usually very large in data volume. This paper develops a mobile agent based collaborative environment on the development platform of mobile-C. Communication among distributed agents includes grasping image of visualized mesh model, annotation to grasped image and instant message. Remote and collaborative simplification can be efficiently conducted by Internet.

Review of the Scientific Literature and Preparation of an Annotated Bibliography on Effects of Cigarette Smoking and Nicotine on Human Performance. Volume 1

DTIC Science & Technology

1986-01-01

physiological changes that contribute to the state of arousal upon which a smoking habit may depend. TheI radial muscle of the iris in the eye contracts...studied the vestibular nystagnus pattern of smokers; amplitude, frequency, speed of slow component, speed of fast component, and angular deviation of eyes ...carbon monoxide was measured before and after treatment in order to estimate the degree of inhalation, and cigarette butts were collected for analysis

Integrating shape into an interactive segmentation framework

NASA Astrophysics Data System (ADS)

Kamalakannan, S.; Bryant, B.; Sari-Sarraf, H.; Long, R.; Antani, S.; Thoma, G.

2013-02-01

This paper presents a novel interactive annotation toolbox which extends a well-known user-steered segmentation framework, namely Intelligent Scissors (IS). IS, posed as a shortest path problem, is essentially driven by lower level image based features. All the higher level knowledge about the problem domain is obtained from the user through mouse clicks. The proposed work integrates one higher level feature, namely shape up to a rigid transform, into the IS framework, thus reducing the burden on the user and the subjectivity involved in the annotation procedure, especially during instances of occlusions, broken edges, noise and spurious boundaries. The above mentioned scenarios are commonplace in medical image annotation applications and, hence, such a tool will be of immense help to the medical community. As a first step, an offline training procedure is performed in which a mean shape and the corresponding shape variance is computed by registering training shapes up to a rigid transform in a level-set framework. The user starts the interactive segmentation procedure by providing a training segment, which is a part of the target boundary. A partial shape matching scheme based on a scale-invariant curvature signature is employed in order to extract shape correspondences and subsequently predict the shape of the unsegmented target boundary. A `zone of confidence' is generated for the predicted boundary to accommodate shape variations. The method is evaluated on segmentation of digital chest x-ray images for lung annotation which is a crucial step in developing algorithms for screening Tuberculosis.

Hypothalamic over-expression of VGF in the Siberian hamster increases energy expenditure and reduces body weight gain

PubMed Central

Brameld, John M.; Hill, Phil; Cocco, Cristina; Noli, Barbara; Ferri, Gian-Luca; Barrett, Perry; Ebling, Francis J. P.; Jethwa, Preeti H.

2017-01-01

VGF (non-acronymic) was first highlighted to have a role in energy homeostasis through experiments involving dietary manipulation in mice. Fasting increased VGF mRNA in the Arc and levels were subsequently reduced upon refeeding. This anabolic role for VGF was supported by observations in a VGF null (VGF-/-) mouse and in the diet-induced and gold-thioglucose obese mice. However, this anabolic role for VGF has not been supported by a number of subsequent studies investigating the physiological effects of VGF-derived peptides. Intracerebroventricular (ICV) infusion of TLQP-21 increased resting energy expenditure and rectal temperature in mice and protected against diet-induced obesity. Similarly, ICV infusion of TLQP-21 into Siberian hamsters significantly reduced body weight, but this was due to a decrease in food intake, with no effect on energy expenditure. Subsequently NERP-2 was shown to increase food intake in rats via the orexin system, suggesting opposing roles for these VGF-derived peptides. Thus to further elucidate the role of hypothalamic VGF in the regulation of energy homeostasis we utilised a recombinant adeno-associated viral vector to over-express VGF in adult male Siberian hamsters, thus avoiding any developmental effects or associated functional compensation. Initially, hypothalamic over-expression of VGF in adult Siberian hamsters produced no effect on metabolic parameters, but by 12 weeks post-infusion hamsters had increased oxygen consumption and a tendency to increased carbon dioxide production; this attenuated body weight gain, reduced interscapular white adipose tissue and resulted in a compensatory increase in food intake. These observed changes in energy expenditure and food intake were associated with an increase in the hypothalamic contents of the VGF-derived peptides AQEE, TLQP and NERP-2. The complex phenotype of the VGF-/- mice is a likely consequence of global ablation of the gene and its derived peptides during development, as well as in the adult. PMID:28235047

Hypothalamic over-expression of VGF in the Siberian hamster increases energy expenditure and reduces body weight gain.

PubMed

Lewis, Jo E; Brameld, John M; Hill, Phil; Cocco, Cristina; Noli, Barbara; Ferri, Gian-Luca; Barrett, Perry; Ebling, Francis J P; Jethwa, Preeti H

2017-01-01

VGF (non-acronymic) was first highlighted to have a role in energy homeostasis through experiments involving dietary manipulation in mice. Fasting increased VGF mRNA in the Arc and levels were subsequently reduced upon refeeding. This anabolic role for VGF was supported by observations in a VGF null (VGF-/-) mouse and in the diet-induced and gold-thioglucose obese mice. However, this anabolic role for VGF has not been supported by a number of subsequent studies investigating the physiological effects of VGF-derived peptides. Intracerebroventricular (ICV) infusion of TLQP-21 increased resting energy expenditure and rectal temperature in mice and protected against diet-induced obesity. Similarly, ICV infusion of TLQP-21 into Siberian hamsters significantly reduced body weight, but this was due to a decrease in food intake, with no effect on energy expenditure. Subsequently NERP-2 was shown to increase food intake in rats via the orexin system, suggesting opposing roles for these VGF-derived peptides. Thus to further elucidate the role of hypothalamic VGF in the regulation of energy homeostasis we utilised a recombinant adeno-associated viral vector to over-express VGF in adult male Siberian hamsters, thus avoiding any developmental effects or associated functional compensation. Initially, hypothalamic over-expression of VGF in adult Siberian hamsters produced no effect on metabolic parameters, but by 12 weeks post-infusion hamsters had increased oxygen consumption and a tendency to increased carbon dioxide production; this attenuated body weight gain, reduced interscapular white adipose tissue and resulted in a compensatory increase in food intake. These observed changes in energy expenditure and food intake were associated with an increase in the hypothalamic contents of the VGF-derived peptides AQEE, TLQP and NERP-2. The complex phenotype of the VGF-/- mice is a likely consequence of global ablation of the gene and its derived peptides during development, as well as in the adult.

Dynamic Modeling of Back-arc Extension in the Aegean Sea and Western Anatolia

NASA Astrophysics Data System (ADS)

Mazlum, Ziya; Göğüş, Oğuz H.; Sözbilir, Hasan; Karabulut, Hayrullah; Pysklywec, Russell N.

2015-04-01

Western Anatolian-Aegean regions are characterized by large-scale lithospheric thinning and extensional deformation. While many geological observations suggest the formation of rift basins, normal faulting, exhumation of metamorphic rocks, and back-arc volcanism, the primary cause and the geodynamic driving mechanisms for the lithospheric thinning and extension are not well understood. Previous studies suggest three primary geodynamic hypotheses to address the extension in the Aegean-west Anatolia: 1) Slab retreat/roll-back model, inferred by the southward younging magmatism and metamorphic exhumations; 2) Gravitational collapse of the overthickened (post orogenic) lithosphere, interpreted by the structural studies that suggests tectonic mode switching from contraction to extension; 3) Lateral extrusion (escape tectonics) associated with the continental collision in East Anatolia. We use 2-D thermo-mechanical numerical subduction experiments to investigate how subduction retreat and related back-arc basin opening are controlled by a) changing length and thickness of the subducting plate, b) the dip angle of the subducting slab and c) various thickness and thermal properties of the back-arc lithosphere. Subsequently, we explore the surface response to the subduction retreat model in conjunction with the gravitational (orogenic) collapse in the presumed back-arc region. Quantitative model predictions (e.g., crustal thickness, extension rate) are tested against a wide range of available geological and geophysical observations from the Aegean and west Anatolia regions and these results are reconciled with regional tectonic observations. Our model results are interpreted in the context of different surface response in the extensional regime (back-arc) for the Aegean and western Anatolia, where these two regions have been presumably segmented by the right lateral transfer fault system (Izmir-Balıkesir transfer zone).

Local concentration of fast-food outlets is associated with poor nutrition and obesity.

PubMed

Kruger, Daniel J; Greenberg, Emily; Murphy, Jillian B; DiFazio, Lindsay A; Youra, Kathryn R

2014-01-01

We investigated the relationship of the local availability of fast-food restaurant locations with diet and obesity. We geocoded addresses of survey respondents and fast-food restaurant locations to assess the association between the local concentration of fast-food outlets, BMI, and fruit and vegetable consumption. The survey was conducted in Genesee County, Michigan. There were 1345 individuals included in this analysis, and the response rate was 25%. The Speak to Your Health! Community Survey included fruit and vegetable consumption items from the Behavioral Risk Factor Surveillance System, height, weight, and demographics. We used ArcGIS to map fast-food outlets and survey respondents. Stepwise linear regressions identified unique predictors of body mass index (BMI) and fruit and vegetable consumption. Survey respondents had 8 ± 7 fast-food outlets within 2 miles of their home. Individuals living in close proximity to fast-food restaurants had higher BMIs t(1342) = 3.21, p < .001, and lower fruit and vegetable consumption, t(1342) = 2.67, p = .008. Individuals may be at greater risk for adverse consequences of poor nutrition because of the patterns in local food availability, which may constrain the success of nutrition promotion efforts. Efforts to decrease the local availability of unhealthy foods as well as programs to help consumers identify strategies for obtaining healthy meals at fast-food outlets may improve health outcomes.

Immunodiagnosis of sheep infections with Echinococcus granulosus: in 35 years where have we come?

PubMed

McManus, D P

2014-03-01

W. K. Yong and D. D. Heath published in 1979 a seminal paper in the first issue of Parasite immunology describing their efforts to determine whether the arc 5 precipitin band, formed when test human serum is reacted against electrophoresed hydatid cyst fluid antigen, would be a suitable immunodiagnostic test for the identification of sheep infected with Echinococcus granulosus. Although they found antibodies to arc 5 in the sera of hydatid-infected sheep, the sera of some sheep harbouring Taenia ovis and T. hydatigena also precipitated the hydatid cyst fluid arc 5 antigen, so they concluded arc 5 antibodies were not suitable for the specific immunodiagnosis of E. granulosus infection in sheep in New Zealand. Subsequent work has shown that the existence of multiple infections with different taeniid species, antigenic cross-reactivity between these related parasites and the low level of specific antibody response to infection continue to hinder efforts to improve the diagnosis of hydatid infection in sheep and other natural intermediate hosts, thereby preventing the development of any practical test. In particular, the poor antibody response of ruminants to naturally acquired hydatid infection may prove an insurmountable barrier in future efforts to develop a reliable and accurate immunological test. © 2013 John Wiley & Sons Ltd.

Annotated Bibliography for Gas Mask and Chemical Defense Gear Related Papers

DTIC Science & Technology

1988-01-15

protective clothing and equipment on combat efficiency (Technical Report No. AMSAA--TR-313). Aberdeen Proving Ground, MD: Army Material Systems Analysis ...atmosphere containing a known concentration of a harmless test aerosol or gas and subsequent analysis of the concentration inside the mask. Qualitative...exercise. Ergonomics , 21, 531-538. Eleven healthy males performed steady--s:ate bicycle exercise while breathing at each of 6 added inspiratory resist

Magmatic evolution of Panama Canal volcanic rocks: A record of arc processes and tectonic change.

PubMed

Farris, David W; Cardona, Agustin; Montes, Camilo; Foster, David; Jaramillo, Carlos

2017-01-01

Volcanic rocks along the Panama Canal present a world-class opportunity to examine the relationship between arc magmatism, tectonic forcing, wet and dry magmas, and volcanic structures. Major and trace element geochemistry of Canal volcanic rocks indicate a significant petrologic transition at 21-25 Ma. Oligocene Bas Obispo Fm. rocks have large negative Nb-Ta anomalies, low HREE, fluid mobile element enrichments, a THI of 0.88, and a H2Ocalc of >3 wt. %. In contrast, the Miocene Pedro Miguel and Late Basalt Fm. exhibit reduced Nb-Ta anomalies, flattened REE curves, depleted fluid mobile elements, a THI of 1.45, a H2Ocalc of <1 wt. %, and plot in mid-ocean ridge/back-arc basin fields. Geochemical modeling of Miocene rocks indicates 0.5-0.1 kbar crystallization depths of hot (1100-1190°C) magmas in which most compositional diversity can be explained by fractional crystallization (F = 0.5). However, the most silicic lavas (Las Cascadas Fm.) require an additional mechanism, and assimilation-fractional-crystallization can reproduce observed compositions at reasonable melt fractions. The Canal volcanic rocks, therefore, change from hydrous basaltic pyroclastic deposits typical of mantle-wedge-derived magmas, to hot, dry bi-modal magmatism at the Oligocene-Miocene boundary. We suggest the primary reason for the change is onset of arc perpendicular extension localized to central Panama. High-resolution mapping along the Panama Canal has revealed a sequence of inward dipping maar-diatreme pyroclastic pipes, large basaltic sills, and bedded silicic ignimbrites and tuff deposits. These volcanic bodies intrude into the sedimentary Canal Basin and are cut by normal and subsequently strike-slip faults. Such pyroclastic pipes and basaltic sills are most common in extensional arc and large igneous province environments. Overall, the change in volcanic edifice form and geochemistry are related to onset of arc perpendicular extension, and are consistent with the idea that Panama arc crust fractured during collision with South America forming the observed Canal extensional zone.

Moderate caloric restriction during gestation results in lower arcuate nucleus NPY- and alphaMSH-neurons and impairs hypothalamic response to fed/fasting conditions in weaned rats.

PubMed

García, A P; Palou, M; Priego, T; Sánchez, J; Palou, A; Picó, C

2010-05-01

We aimed to characterize the developmental programming effects of moderate caloric restriction during early pregnancy on factors involved in hypothalamic control of energy balance. Twenty-five-days-old offspring Wistar rats from 20% caloric restricted dams (from 1 to 12 days of pregnancy) (CR) and from control dams were studied under fed and 12 h fasting conditions. Morphometric studies on arcuate nucleus (ARC) and determinations of circulating parameters and hypothalamic levels of neuropeptide Y (NPY), proopiomelanocortin (POMC), long-form leptin receptor (ObRb), insulin receptor (InsR) and suppressor of cytokine signalling-3 (SOCS-3) mRNA were performed. CR animals did not show different body weight with respect to their controls, but presented higher food intake. They exhibited lower neuropeptide Y- and alpha-melanocyte-stimulating hormone-neurons (decreases of 18 and 13% in males, and 10 and 18% in females respectively) and lower total cells (decrease of 3% in males and 18% in females) in ARC. Under fed conditions, CR animals presented lower circulating leptin and ghrelin levels (decreases of 37 and 43% in males, and 15 and 34% in females respectively); furthermore, hypothalamic POMC, NPY (only in females), ObRb and InsR mRNA levels were reduced (39, 16 and 26% in males, and 112, 33, 61 and 56% in females), and those of SOCS-3 were increased (86% in males and 74% in females). Unlike control animals, under fasting conditions, ObRb, InsR and POMC mRNA levels did not decrease in CR females, and NPY mRNA decreased instead of increase in CR males. Moderate caloric restriction during gestation affects offspring hypothalamic structure and function, impairing its response to fed/fasting conditions, which suggests a predisposition to insulin and leptin resistance.

Modeling of plasma and thermo-fluid transport in hybrid welding

NASA Astrophysics Data System (ADS)

Ribic, Brandon D.

Hybrid welding combines a laser beam and electrical arc in order to join metals within a single pass at welding speeds on the order of 1 m min -1. Neither autonomous laser nor arc welding can achieve the weld geometry obtained from hybrid welding for the same process parameters. Depending upon the process parameters, hybrid weld depth and width can each be on the order of 5 mm. The ability to produce a wide weld bead increases gap tolerance for square joints which can reduce machining costs and joint fitting difficulty. The weld geometry and fast welding speed of hybrid welding make it a good choice for application in ship, pipeline, and aerospace welding. Heat transfer and fluid flow influence weld metal mixing, cooling rates, and weld bead geometry. Cooling rate affects weld microstructure and subsequent weld mechanical properties. Fluid flow and heat transfer in the liquid weld pool are affected by laser and arc energy absorption. The laser and arc generate plasmas which can influence arc and laser energy absorption. Metal vapors introduced from the keyhole, a vapor filled cavity formed near the laser focal point, influence arc plasma light emission and energy absorption. However, hybrid welding plasma properties near the opening of the keyhole are not known nor is the influence of arc power and heat source separation understood. A sound understanding of these processes is important to consistently achieving sound weldments. By varying process parameters during welding, it is possible to better understand their influence on temperature profiles, weld metal mixing, cooling rates, and plasma properties. The current literature has shown that important process parameters for hybrid welding include: arc power, laser power, and heat source separation distance. However, their influence on weld temperatures, fluid flow, cooling rates, and plasma properties are not well understood. Modeling has shown to be a successful means of better understanding the influence of processes parameters on heat transfer, fluid flow, and plasma characteristics for arc and laser welding. However, numerical modeling of laser/GTA hybrid welding is just beginning. Arc and laser welding plasmas have been previously analyzed successfully using optical emission spectroscopy in order to better understand arc and laser plasma properties as a function of plasma radius. Variation of hybrid welding plasma properties with radial distance is not known. Since plasma properties can affect arc and laser energy absorption and weld integrity, a better understanding of the change in hybrid welding plasma properties as a function of plasma radius is important and necessary. Material composition influences welding plasma properties, arc and laser energy absorption, heat transfer, and fluid flow. The presence of surface active elements such as oxygen and sulfur can affect weld pool fluid flow and bead geometry depending upon the significance of heat transfer by convection. Easily vaporized and ionized alloying elements can influence arc plasma characteristics and arc energy absorption. The effects of surface active elements on heat transfer and fluid flow are well understood in the case of arc and conduction mode laser welding. However, the influence of surface active elements on heat transfer and fluid flow during keyhole mode laser welding and laser/arc hybrid welding are not well known. Modeling has been used to successfully analyze the influence of surface active elements during arc and conduction mode laser welding in the past and offers promise in the case of laser/arc hybrid welding. A critical review of the literature revealed several important areas for further research and unanswered questions. (1) The understanding of heat transfer and fluid flow during hybrid welding is still beginning and further research is necessary. (2) Why hybrid welding weld bead width is greater than that of laser or arc welding is not well understood. (3) The influence of arc power and heat source separation distance on cooling rates during hybrid welding are not known. (4) Convection during hybrid welding is not well understood despite its importance to weld integrity. (5) The influence of surface active elements on weld geometry, weld pool temperatures, and fluid flow during high power density laser and laser/arc hybrid welding are not known. (6) Although the arc power and heat source separation distance have been experimentally shown to influence arc stability and plasma light emission during hybrid welding, the influence of these parameters on plasma properties is unknown. (7) The electrical conductivity of hybrid welding plasmas is not known, despite its importance to arc stability and weld integrity. In this study, heat transfer and fluid flow are analyzed for laser, gas tungsten arc (GTA), and laser/GTA hybrid welding using an experimentally validated three dimensional phenomenological model. By evaluating arc and laser welding using similar process parameters, a better understanding of the hybrid welding process is expected. The role of arc power and heat source separation distance on weld depth, weld pool centerline cooling rates, and fluid flow profiles during CO2 laser/GTA hybrid welding of 321 stainless steel are analyzed. Laser power is varied for a constant heat source separation distance to evaluate its influence on weld temperatures, weld geometry, and fluid flow during Nd:YAG laser/GTA hybrid welding of A131 structural steel. The influence of oxygen and sulfur on keyhole and weld bead geometry, weld temperatures, and fluid flow are analyzed for high power density Yb doped fiber laser welding of (0.16 %C, 1.46 %Mn) mild steel. Optical emission spectroscopy was performed on GTA, Nd:YAG laser, and Nd:YAG laser/GTA hybrid welding plasmas for welding of 304L stainless steel. Emission spectroscopy provides a means of determining plasma temperatures and species densities using deconvoluted measured spectral intensities, which can then be used to calculate plasma electrical conductivity. In this study, hybrid welding plasma temperatures, species densities, and electrical conductivities were determined using various heat source separation distances and arc currents using an analytical method coupled calculated plasma compositions. As a result of these studies heat transfer by convection was determined to be dominant during hybrid welding of steels. The primary driving forces affecting hybrid welding fluid flow are the surface tension gradient and electromagnetic force. Fiber laser weld depth showed a negligible change when increasing the (0.16 %C, 1.46 %Mn) mild steel sulfur concentration from 0.006 wt% to 0.15 wt%. Increasing the dissolved oxygen content in weld pool from 0.0038 wt% to 0.0257 wt% increased the experimental weld depth from 9.3 mm to 10.8 mm. Calculated partial pressure of carbon monoxide increased from 0.1 atm to 0.75 atm with the 0.0219 wt% increase in dissolved oxygen in the weld metal and may explain the increase in weld depth. Nd:YAG laser/GTA hybrid welding plasma temperatures were calculated to be approximately between 7927 K and 9357 K. Increasing the Nd:YAG laser/GTA hybrid welding heat source separation distance from 4 mm to 6 mm reduced plasma temperatures between 500 K and 900 K. Hybrid welding plasma total electron densities and electrical conductivities were on the order of 1 x 1022 m-3 and 3000 S m-1, respectively.

Morphological and behavioral limit of visual resolution in temperate (Hippocampus abdominalis) and tropical (Hippocampus taeniopterus) seahorses.

PubMed

Lee, Hie Rin; O'Brien, Keely M Bumsted

2011-07-01

Seahorses are visually guided feeders that prey upon small fast-moving crustaceans. Seahorse habitats range from clear tropical to turbid temperate waters. How are seahorse retinae specialized to mediate vision in these diverse environments? Most species of seahorse have a specialization in their retina associated with acute vision, the fovea. The purpose of this study was to characterize the fovea of temperate Hippocampus abdominalis and tropical H. taeniopterus seahorses and to investigate their theoretical and behavioral limits of visual resolution. Their foveae were identified and photoreceptor (PR) and ganglion cell (GC) densities determined throughout the retina and topographically mapped. The theoretical limit of visual resolution was calculated using formulas taking into account lens radius and either cone PR or GC densities. Visual resolution was determined behaviorally using reactive distance. Both species possess a rod-free convexiclivate fovea. PR and GC densities were highest along the foveal slope, with a density decrease within the foveal center. Outside the fovea, there was a gradual density decrease towards the periphery. The theoretically calculated visual resolution on the foveal slope was poorer for H. abdominalis (5.25 min of arc) compared with H. taeniopterus (4.63 min of arc) based on PR density. Using GC density, H. abdominalis (9.81 min of arc) had a lower resolution compared with H. taeniopterus (9.04 min of arc). Behaviorally, H. abdominalis had a resolution limit of 1090.64 min of arc, while H. taeniopterus was much smaller, 692.86 min of arc. Although both species possess a fovea and the distribution of PR and GC is similar, H. taeniopterus has higher PR and GC densities on the foveal slope and better theoretical and behaviorally measured visual resolution compared to H. abdominalis. These data indicate that seahorses have a well-developed acute visual system, and tropical seahorses have higher visual resolution compared to temperate seahorses.

Collaboration Between NASA Centers of Excellence on Autonomous System Software Development

NASA Technical Reports Server (NTRS)

Goodrich, Charles H.; Larson, William E.; Delgado, H. (Technical Monitor)

2001-01-01

Software for space systems flight operations has its roots in the early days of the space program when computer systems were incapable of supporting highly complex and flexible control logic. Control systems relied on fast data acquisition and supervisory control from a roomful of systems engineers on the ground. Even though computer hardware and software has become many orders of magnitude more capable, space systems have largely adhered to this original paradigm In an effort to break this mold, Kennedy Space Center (KSC) has invested in the development of model-based diagnosis and control applications for ten years having broad experience in both ground and spacecraft systems and software. KSC has now partnered with Ames Research Center (ARC), NASA's Center of Excellence in Information Technology, to create a new paradigm for the control of dynamic space systems. ARC has developed model-based diagnosis and intelligent planning software that enables spacecraft to handle most routine problems automatically and allocate resources in a flexible way to realize mission objectives. ARC demonstrated the utility of onboard diagnosis and planning with an experiment aboard Deep Space I in 1999. This paper highlights the software control system collaboration between KSC and ARC. KSC has developed a Mars In-situ Resource Utilization testbed based on the Reverse Water Gas Shift (RWGS) reaction. This plant, built in KSC's Applied Chemistry Laboratory, is capable of producing the large amount of Oxygen that would be needed to support a Human Mars Mission. KSC and ARC are cooperating to develop an autonomous, fault-tolerant control system for RWGS to meet the need for autonomy on deep space missions. The paper will also describe how the new system software paradigm will be applied to Vehicle Health Monitoring, tested on the new X vehicles and integrated into future launch processing systems.

Detecting slab structure beneath the Banda Arc from waveform analysis of deep focus earthquakes

NASA Astrophysics Data System (ADS)

Miller, M. S.; Sun, D.; Holt, A. F.

2017-12-01

We investigate the structure of the subducting Australian slab by utilizing 30 recently installed, temporary broadband seismometers (YS network) in the Banda Arc region of the Indonesia archipelago. This region is of particular tectonic interest as it is the archetypal example of a young arc-continent collision along with known varied lithospheric structure of the incoming Australian plate. Previous (e.g. Widiyantoro et al. 2011) and preliminary body wave tomography (Harris et al., this session) indicate complex subducted slab structures, where gaps in fast velocity anomalies in the upper mantle are interpreted as slab tears and are linked to the variation in the incoming plate structures. The detailed shape and location of these tears are important for kinematic reconstructions and for understanding the evolution of the entire subduction system. However, tomographic images are inherently smooth due to being produced with damped inversions and therefore underestimate the sharpness of these structures. We investigate possible sharp-sided structures within and at the edges of the subducted plate from deep focus earthquakes beneath the Banda Arc that occur beneath the seismic stations. Preliminary results show that the energy associated with the P-wave first arrival exhibits large variability between waveforms recorded at different stations along the arc, both in terms of frequency content and maximum amplitudes. Three main observations are shown with these initial results: (i) Variation in frequency content along strike from the deep events; (ii) There are two "regions" that have low frequency signals which possibly correspond to subducted continental lithosphere; (iii) There are two "regions" that have high frequency signals which possibly correspond to subducted oceanic lithosphere.

Investigating the Subduction History of the Southwest Pacific using Coupled Plate Tectonic-Mantle Convection Models

NASA Astrophysics Data System (ADS)

Matthews, K. J.; Flament, N. E.; Williams, S.; Müller, D.; Gurnis, M.

2014-12-01

The Late Cretaceous to mid Eocene (~85-45 Ma) evolution of the southwest Pacific has been the subject of starkly contrasting plate reconstruction models, reflecting sparse and ambiguous data. Disparate models of (1) west-dipping subduction and back-arc basin opening to the east of the Lord Howe Rise, (2) east-dipping subduction and back-arc basin closure to the east of the Lord Howe Rise, and (3) tectonic quiescence with no subduction have all been proposed for this time frame. To help resolve this long-standing problem we test a new southwest Pacific reconstruction using global mantle flow models with imposed plate motions. The kinematic model incorporates east to northeast directed rollback of a west-dipping subduction zone between 85 and 55 Ma, accommodating opening of the South Loyalty back-arc basin to the east of New Caledonia. At 55 Ma there is a plate boundary reorganization in the region. West-dipping subduction and back-arc basin spreading end, and there is initiation of northeast dipping subduction within the back-arc basin. Consumption of South Loyalty Basin seafloor continues until 45 Ma, when obduction onto New Caledonia begins. West-dipping Tonga-Kermadec subduction initiates at this time at the relict Late Cretaceous-earliest Eocene subduction boundary. We use the 3D spherical mantle convection code CitcomS coupled to the plate reconstruction software GPlates, with plate motions and evolving plate boundaries imposed since 230 Ma. The predicted present-day mantle structure is compared to S- and P-wave seismic tomography models, which can be used to infer the presence of slab material in the mantle at locations where fast velocity anomalies are imaged. This workflow enables us to assess the forward-modeled subduction history of the region.

Hypothalamic CaMKKβ mediates glucagon anorectic effect and its diet-induced resistance

PubMed Central

Quiñones, Mar; Al-Massadi, Omar; Gallego, Rosalía; Fernø, Johan; Diéguez, Carlos; López, Miguel; Nogueiras, Ruben

2015-01-01

Objective Glucagon receptor antagonists and humanized glucagon antibodies are currently studied as promising therapies for obesity and type II diabetes. Among its variety of actions, glucagon reduces food intake, but the molecular mechanisms mediating this effect as well as glucagon resistance are totally unknown. Methods Glucagon and adenoviral vectors were administered in specific hypothalamic nuclei of lean and diet-induced obese rats. The expression of neuropeptides controlling food intake was performed by in situ hybridization. The regulation of factors of the glucagon signaling pathway was assessed by western blot. Results The central injection of glucagon decreased feeding through a hypothalamic pathway involving protein kinase A (PKA)/Ca2+-calmodulin-dependent protein kinase kinase β (CaMKKβ)/AMP-activated protein kinase (AMPK)-dependent mechanism. More specifically, the central injection of glucagon increases PKA activity and reduces protein levels of CaMKKβ and its downstream target phosphorylated AMPK in the hypothalamic arcuate nucleus (ARC). Consistently, central glucagon significantly decreased AgRP expression. Inhibition of PKA and genetic activation of AMPK in the ARC blocked glucagon-induced anorexia in lean rats. Genetic down-regulation of glucagon receptors in the ARC stimulates fasting-induced hyperphagia. Although glucagon was unable to decrease food intake in DIO rats, glucagon sensitivity was restored after inactivation of CaMKKβ, specifically in the ARC. Thus, glucagon decreases food intake acutely via PKA/CaMKKβ/AMPK dependent pathways in the ARC, and CaMKKβ mediates its obesity-induced hypothalamic resistance. Conclusions This work reveals the molecular underpinnings by which glucagon controls feeding that may lead to a better understanding of disease states linked to anorexia and cachexia. PMID:26909312

PDBe: towards reusable data delivery infrastructure at protein data bank in Europe.

PubMed

Mir, Saqib; Alhroub, Younes; Anyango, Stephen; Armstrong, David R; Berrisford, John M; Clark, Alice R; Conroy, Matthew J; Dana, Jose M; Deshpande, Mandar; Gupta, Deepti; Gutmanas, Aleksandras; Haslam, Pauline; Mak, Lora; Mukhopadhyay, Abhik; Nadzirin, Nurul; Paysan-Lafosse, Typhaine; Sehnal, David; Sen, Sanchayita; Smart, Oliver S; Varadi, Mihaly; Kleywegt, Gerard J; Velankar, Sameer

2018-01-04

The Protein Data Bank in Europe (PDBe, pdbe.org) is actively engaged in the deposition, annotation, remediation, enrichment and dissemination of macromolecular structure data. This paper describes new developments and improvements at PDBe addressing three challenging areas: data enrichment, data dissemination and functional reusability. New features of the PDBe Web site are discussed, including a context dependent menu providing links to raw experimental data and improved presentation of structures solved by hybrid methods. The paper also summarizes the features of the LiteMol suite, which is a set of services enabling fast and interactive 3D visualization of structures, with associated experimental maps, annotations and quality assessment information. We introduce a library of Web components which can be easily reused to port data and functionality available at PDBe to other services. We also introduce updates to the SIFTS resource which maps PDB data to other bioinformatics resources, and the PDBe REST API. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

STRAP PTM: Software Tool for Rapid Annotation and Differential Comparison of Protein Post-Translational Modifications.

PubMed

Spencer, Jean L; Bhatia, Vivek N; Whelan, Stephen A; Costello, Catherine E; McComb, Mark E

2013-12-01

The identification of protein post-translational modifications (PTMs) is an increasingly important component of proteomics and biomarker discovery, but very few tools exist for performing fast and easy characterization of global PTM changes and differential comparison of PTMs across groups of data obtained from liquid chromatography-tandem mass spectrometry experiments. STRAP PTM (Software Tool for Rapid Annotation of Proteins: Post-Translational Modification edition) is a program that was developed to facilitate the characterization of PTMs using spectral counting and a novel scoring algorithm to accelerate the identification of differential PTMs from complex data sets. The software facilitates multi-sample comparison by collating, scoring, and ranking PTMs and by summarizing data visually. The freely available software (beta release) installs on a PC and processes data in protXML format obtained from files parsed through the Trans-Proteomic Pipeline. The easy-to-use interface allows examination of results at protein, peptide, and PTM levels, and the overall design offers tremendous flexibility that provides proteomics insight beyond simple assignment and counting.

ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life.

PubMed

Pafilis, Evangelos; Frankild, Sune P; Schnetzer, Julia; Fanini, Lucia; Faulwetter, Sarah; Pavloudi, Christina; Vasileiadou, Katerina; Leary, Patrick; Hammock, Jennifer; Schulz, Katja; Parr, Cynthia Sims; Arvanitidis, Christos; Jensen, Lars Juhl

2015-06-01

The association of organisms to their environments is a key issue in exploring biodiversity patterns. This knowledge has traditionally been scattered, but textual descriptions of taxa and their habitats are now being consolidated in centralized resources. However, structured annotations are needed to facilitate large-scale analyses. Therefore, we developed ENVIRONMENTS, a fast dictionary-based tagger capable of identifying Environment Ontology (ENVO) terms in text. We evaluate the accuracy of the tagger on a new manually curated corpus of 600 Encyclopedia of Life (EOL) species pages. We use the tagger to associate taxa with environments by tagging EOL text content monthly, and integrate the results into the EOL to disseminate them to a broad audience of users. The software and the corpus are available under the open-source BSD and the CC-BY-NC-SA 3.0 licenses, respectively, at http://environments.hcmr.gr. © The Author 2015. Published by Oxford University Press.

From damage response to action potentials: early evolution of neural and contractile modules in stem eukaryotes.

PubMed

Brunet, Thibaut; Arendt, Detlev

2016-01-05

Eukaryotic cells convert external stimuli into membrane depolarization, which in turn triggers effector responses such as secretion and contraction. Here, we put forward an evolutionary hypothesis for the origin of the depolarization-contraction-secretion (DCS) coupling, the functional core of animal neuromuscular circuits. We propose that DCS coupling evolved in unicellular stem eukaryotes as part of an 'emergency response' to calcium influx upon membrane rupture. We detail how this initial response was subsequently modified into an ancient mechanosensory-effector arc, present in the last eukaryotic common ancestor, which enabled contractile amoeboid movement that is widespread in extant eukaryotes. Elaborating on calcium-triggered membrane depolarization, we reason that the first action potentials evolved alongside the membrane of sensory-motile cilia, with the first voltage-sensitive sodium/calcium channels (Nav/Cav) enabling a fast and coordinated response of the entire cilium to mechanosensory stimuli. From the cilium, action potentials then spread across the entire cell, enabling global cellular responses such as concerted contraction in several independent eukaryote lineages. In animals, this process led to the invention of mechanosensory contractile cells. These gave rise to mechanosensory receptor cells, neurons and muscle cells by division of labour and can be regarded as the founder cell type of the nervous system. © 2015 The Authors.

From damage response to action potentials: early evolution of neural and contractile modules in stem eukaryotes

PubMed Central

Brunet, Thibaut; Arendt, Detlev

2016-01-01

Eukaryotic cells convert external stimuli into membrane depolarization, which in turn triggers effector responses such as secretion and contraction. Here, we put forward an evolutionary hypothesis for the origin of the depolarization–contraction–secretion (DCS) coupling, the functional core of animal neuromuscular circuits. We propose that DCS coupling evolved in unicellular stem eukaryotes as part of an ‘emergency response’ to calcium influx upon membrane rupture. We detail how this initial response was subsequently modified into an ancient mechanosensory–effector arc, present in the last eukaryotic common ancestor, which enabled contractile amoeboid movement that is widespread in extant eukaryotes. Elaborating on calcium-triggered membrane depolarization, we reason that the first action potentials evolved alongside the membrane of sensory-motile cilia, with the first voltage-sensitive sodium/calcium channels (Nav/Cav) enabling a fast and coordinated response of the entire cilium to mechanosensory stimuli. From the cilium, action potentials then spread across the entire cell, enabling global cellular responses such as concerted contraction in several independent eukaryote lineages. In animals, this process led to the invention of mechanosensory contractile cells. These gave rise to mechanosensory receptor cells, neurons and muscle cells by division of labour and can be regarded as the founder cell type of the nervous system. PMID:26598726

Recycling and transport of continental material through the mantle wedge above subduction zones: A Caribbean example

NASA Astrophysics Data System (ADS)

Rojas-Agramonte, Yamirka; Garcia-Casco, Antonio; Kemp, Anthony; Kröner, Alfred; Proenza, Joaquín A.; Lázaro, Concepción; Liu, Dunyi

2016-02-01

Estimates of global growth rates of continental crust critically depend upon knowledge of the rate at which crustal material is delivered back into the mantle at subduction zones and is then returned to the crust as a component of mantle-derived magma. Quantification of crustal recycling by subduction-related magmatism relies on indirect chemical and isotopic tracers and is hindered by the large range of potential melt sources (e.g., subducted oceanic crust and overlying chemical and clastic sediment, sub-arc lithospheric mantle, arc crust), whose composition may not be accurately known. There is also uncertainty about how crustal material is transferred from subducted lithosphere and mixed into the mantle source of arc magmas. We use the resilient mineral zircon to track crustal recycling in mantle-derived rocks of the Caribbean (Greater Antilles) intra-oceanic arc of Cuba, whose inception was triggered after the break-up of Pangea. Despite juvenile Sr and Nd isotope compositions, the supra-subduction zone ophiolitic and volcanic arc rocks of this Cretaceous (∼135-70 Ma) arc contain old zircons (∼200-2525 Ma) attesting to diverse crustal inputs. The Hf-O isotope systematics of these zircons suggest derivation from exposed crustal terranes in northern Central America (e.g. Mexico) and South America. Modeling of the sedimentary component in the most mafic lavas suggests a contribution of no more than 2% for the case of source contamination or less than 4% for sediment assimilation by the magma. We discuss several possibilities for the presence of inherited zircons and conclude that they were transported as detrital grains into the mantle beneath the Caribbean Plate via subduction of oceanic crust. The detrital zircons were subsequently entrained by mafic melts that were rapidly emplaced into the Caribbean volcanic arc crust and supra-subduction mantle. These findings suggest transport of continental detritus, through the mantle wedge above subduction zones, in magmas that otherwise do not show strong evidence for crustal input and imply that crustal recycling rates in some arcs may be higher than hitherto realized.

Chemical models for simulating single-walled nanotube production in arc vaporization and laser ablation processes

NASA Technical Reports Server (NTRS)

Scott, Carl D.

2004-01-01

Chemical kinetic models for the nucleation and growth of clusters and single-walled carbon nanotube (SWNT) growth are developed for numerical simulations of the production of SWNTs. Two models that involve evaporation and condensation of carbon and metal catalysts, a full model involving all carbon clusters up to C80, and a reduced model are discussed. The full model is based on a fullerene model, but nickel and carbon/nickel cluster reactions are added to form SWNTs from soot and fullerenes. The full model has a large number of species--so large that to incorporate them into a flow field computation for simulating laser ablation and arc processes requires that they be simplified. The model is reduced by defining large clusters that represent many various sized clusters. Comparisons are given between these models for cases that may be applicable to arc and laser ablation production. Solutions to the system of chemical rate equations of these models for a ramped temperature profile show that production of various species, including SWNTs, agree to within about 50% for a fast ramp, and within 10% for a slower temperature decay time.

Automated synovium segmentation in doppler ultrasound images for rheumatoid arthritis assessment

NASA Astrophysics Data System (ADS)

Yeung, Pak-Hei; Tan, York-Kiat; Xu, Shuoyu

2018-02-01

We need better clinical tools to improve monitoring of synovitis, synovial inflammation in the joints, in rheumatoid arthritis (RA) assessment. Given its economical, safe and fast characteristics, ultrasound (US) especially Doppler ultrasound is frequently used. However, manual scoring of synovitis in US images is subjective and prone to observer variations. In this study, we propose a new and robust method for automated synovium segmentation in the commonly affected joints, i.e. metacarpophalangeal (MCP) and metatarsophalangeal (MTP) joints, which would facilitate automation in quantitative RA assessment. The bone contour in the US image is firstly detected based on a modified dynamic programming method, incorporating angular information for detecting curved bone surface and using image fuzzification to identify missing bone structure. K-means clustering is then performed to initialize potential synovium areas by utilizing the identified bone contour as boundary reference. After excluding invalid candidate regions, the final segmented synovium is identified by reconnecting remaining candidate regions using level set evolution. 15 MCP and 15 MTP US images were analyzed in this study. For each image, segmentations by our proposed method as well as two sets of annotations performed by an experienced clinician at different time-points were acquired. Dice's coefficient is 0.77+/-0.12 between the two sets of annotations. Similar Dice's coefficients are achieved between automated segmentation and either the first set of annotations (0.76+/-0.12) or the second set of annotations (0.75+/-0.11), with no significant difference (P = 0.77). These results verify that the accuracy of segmentation by our proposed method and by clinician is comparable. Therefore, reliable synovium identification can be made by our proposed method.

A portable platform to collect and review behavioral data simultaneously with neurophysiological signals.

PubMed

Tianxiao Jiang; Siddiqui, Hasan; Ray, Shruti; Asman, Priscella; Ozturk, Musa; Ince, Nuri F

2017-07-01

This paper presents a portable platform to collect and review behavioral data simultaneously with neurophysiological signals. The whole system is comprised of four parts: a sensor data acquisition interface, a socket server for real-time data streaming, a Simulink system for real-time processing and an offline data review and analysis toolbox. A low-cost microcontroller is used to acquire data from external sensors such as accelerometer and hand dynamometer. The micro-controller transfers the data either directly through USB or wirelessly through a bluetooth module to a data server written in C++ for MS Windows OS. The data server also interfaces with the digital glove and captures HD video from webcam. The acquired sensor data are streamed under User Datagram Protocol (UDP) to other applications such as Simulink/Matlab for real-time analysis and recording. Neurophysiological signals such as electroencephalography (EEG), electrocorticography (ECoG) and local field potential (LFP) recordings can be collected simultaneously in Simulink and fused with behavioral data. In addition, we developed a customized Matlab Graphical User Interface (GUI) software to review, annotate and analyze the data offline. The software provides a fast, user-friendly data visualization environment with synchronized video playback feature. The software is also capable of reviewing long-term neural recordings. Other featured functions such as fast preprocessing with multithreaded filters, annotation, montage selection, power-spectral density (PSD) estimate, time-frequency map and spatial spectral map are also implemented.

Complete genome sequence, metabolic model construction and phenotypic characterization of Geobacillus LC300, an extremely thermophilic, fast growing, xylose-utilizing bacterium.

PubMed

Cordova, Lauren T; Long, Christopher P; Venkataramanan, Keerthi P; Antoniewicz, Maciek R

2015-11-01

We have isolated a new extremely thermophilic fast-growing Geobacillus strain that can efficiently utilize xylose, glucose, mannose and galactose for cell growth. When grown aerobically at 72 °C, Geobacillus LC300 has a growth rate of 2.15 h(-1) on glucose and 1.52 h(-1) on xylose (doubling time less than 30 min). The corresponding specific glucose and xylose utilization rates are 5.55 g/g/h and 5.24 g/g/h, respectively. As such, Geobacillus LC300 grows 3-times faster than E. coli on glucose and xylose, and has a specific xylose utilization rate that is 3-times higher than the best metabolically engineered organism to date. To gain more insight into the metabolism of Geobacillus LC300 its genome was sequenced using PacBio's RS II single-molecule real-time (SMRT) sequencing platform and annotated using the RAST server. Based on the genome annotation and the measured biomass composition a core metabolic network model was constructed. To further demonstrate the biotechnological potential of this organism, Geobacillus LC300 was grown to high cell-densities in a fed-batch culture, where cells maintained a high xylose utilization rate under low dissolved oxygen concentrations. All of these characteristics make Geobacillus LC300 an attractive host for future metabolic engineering and biotechnology applications. Copyright © 2015 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Investigation of the effects of shear on arc-electrode erosion using a modified arc-electrode mass loss model

NASA Astrophysics Data System (ADS)

Webb, Bryan T.

The electrodes are the attachment points for an electric arc where electrons and positive ions enter and leave the gas, creating a flow of current. Electrons enter the gas at the cathode and are removed at the anode. Electrons then flow out through the leads on the anode and are replenished from the power supply through the leads on the cathode. Electric arc attachment to the electrode surface causes intensive heating and subsequent melting and vaporization. At that point a multitude of factors can contribute to mass loss, to include vaporization (boiling), material removal via shear forces, chemical reactions, evaporation, and ejection of material in jets due to pressure effects. If these factors were more thoroughly understood and could be modeled, this knowledge would guide the development of an electrode design with minimal erosion. An analytic model was developed by a previous researcher that models mass loss by melting, evaporation and boiling with a moving arc attachment point. This pseudo one-dimensional model includes surface heat flux in periodic cycles of heating and cooling to model motion of a spinning arc in an annular electrode where the arc periodically returns to the same spot. This model, however, does not account for removal of material due to shear or pressure induced effects, or the effects of chemical reactions. As a result of this, the model under-predicts material removal by about 50%. High velocity air flowing over an electrode will result in a shear force which has the potential to remove molten material as the arc melts the surface on its path around the electrode. In order to study the effects of shear on mass loss rate, the model from this previous investigator has been altered to include this mass loss mechanism. The results of this study have shown that shear is a viable mechanism for mass loss in electrodes and can account for the mismatch between theoretical and experimental rates determined by previous investigators. The results of a parametric study of arc attachment factors - including spot size, fall voltage, arc spot rotation rate, ambient bore heat rate, and air mass flow rate - are presented. The parametric study resulted in improving estimates of both the arc spot size and electrode fall voltage, two critical factors affecting electrode heating. Little sensitivity of electrode erosion rate to ambient bore heat rate and rotation rate was found. The erosion rate is found to be sensitive to the mass flow rate of air injected in the arc heater and validation of the model by comparison with more run condition data should be carried out as the data become available.

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

Larsen, M.J.; Klingensmith, W.C. III; Kuni, C.C.

Radionuclide hepatobiliary imaging demonstrated nonvisualization of the gallbladder in four patients who were studied after fasting from 14 hr to 12 days. Two patients subsequently had normal gallbladders at autopsy, and two gave normal gallbladder visualization on repeat imaging studies after fasts of 2 to 3 hr. These findings suggest that prolonged fasting may be a cause for nonvisualization of a normal gallbladder.

High-resolution seismic data regularization and wavefield separation

NASA Astrophysics Data System (ADS)

Cao, Aimin; Stump, Brian; DeShon, Heather

2018-04-01

We present a new algorithm, non-equispaced fast antileakage Fourier transform (NFALFT), for irregularly sampled seismic data regularization. Synthetic tests from 1-D to 5-D show that the algorithm may efficiently remove leaked energy in the frequency wavenumber domain, and its corresponding regularization process is accurate and fast. Taking advantage of the NFALFT algorithm, we suggest a new method (wavefield separation) for the detection of the Earth's inner core shear wave with irregularly distributed seismic arrays or networks. All interfering seismic phases that propagate along the minor arc are removed from the time window around the PKJKP arrival. The NFALFT algorithm is developed for seismic data, but may also be used for other irregularly sampled temporal or spatial data processing.

Solar radiometry at millimeter wavelengths. [Fast Fourier Transformation solutions

NASA Technical Reports Server (NTRS)

Henze, W.

1974-01-01

In the area of resolution enhancement, the use of Fast Fourier Transform programs was investigated for possible application to millimeter wavelength maps of the sun. A difficulty arises with the La Posta maps in that they are limited to 35 arc-minutes square while the smeared out solar image is larger than that. A list of possible cometary emission lines near 13 millimeters is presented. Although preparation of the list was inspired by the appearance of Comet Kohoutek, the results are applicable to any future comet. The brightness temperature of the sun at 8.6 millimeters was measured using the moon as a calibration source. The result does not confirm a deep absorption feature as apparently observed by earlier workers.

Amphibious Magnetotelluric Investigation of the Aleutian Arc: Mantle Melt Generation and Migration beneath Okmok Caldera

NASA Astrophysics Data System (ADS)

Zelenak, G.; Key, K.; Bennington, N. L.; Bedrosian, P.

2015-12-01

Understanding the factors controlling the release of volatiles from the downgoing slab, the subsequent generation of melt in the overlying mantle wedge, the migration of melt to the crust, and its evolution and emplacement within the crust are important for advancing our understanding of arc magmatism and crustal genesis. Because melt and aqueous fluids are a few orders of magnitude more electrically conductive than unmelted peridotite, the conductivity-mapping magnetotelluric (MT) method is well-suited to imaging fluids and melt beneath arc volcanoes. Here we present conductivity results from an amphibious MT profile crossing Okmok volcano in the central Aleutian arc. The Aleutian arc is one of the most volcanically active regions in North America, making it an ideal location for studying arc magnetism. Okmok volcano, located on the northeastern portion of Umnak Island, is among the most active volcanoes in the Aleutian chain. In addition to two caldera-forming events in the Holocene, numerous eruptions in the past century indicate a robust magmatic supply. Previous coarse resolution seismic studies have inferred a crustal magma reservoir. In order to investigate the role fluids play in melting the mantle wedge, how melts ascend through the corner flow regime of the mantle wedge, how melt migrates and is stored within the upper mantle and crust, and how this impacts explosive caldera forming eruptions, we carried out an amphibious geophysical survey across the arc in June-July 2015. Twenty-nine onshore MT stations and 10 offshore stations were collected in a 3D array covering Okmok, and 43 additional offshore MT stations completed a 300 km amphibious profile starting at the trench, crossing the forearc, arc and backarc. Thirteen onshore passive seismic stations were also installed and will remain in place for one year to supplement the twelve permanent stations on the island. Data collected by this project will be used to map seismic velocity and electrical conductivity variations within the arc, providing unique constraints
on temperature, mineralogy and fluid content. This abstract covers preliminary MT constraints on the mantle and deep crust as inferred from the 300 km long amphibious profile. A companion abstract (Bennington et al.) considers the crustal magma chamber imaged by the 3D array.

Sequencing, Analysis, and Annotation of Expressed Sequence Tags for Camelus dromedarius

PubMed Central

Al-Swailem, Abdulaziz M.; Shehata, Maher M.; Abu-Duhier, Faisel M.; Al-Yamani, Essam J.; Al-Busadah, Khalid A.; Al-Arawi, Mohammed S.; Al-Khider, Ali Y.; Al-Muhaimeed, Abdullah N.; Al-Qahtani, Fahad H.; Manee, Manee M.; Al-Shomrani, Badr M.; Al-Qhtani, Saad M.; Al-Harthi, Amer S.; Akdemir, Kadir C.; Otu, Hasan H.

2010-01-01

Despite its economical, cultural, and biological importance, there has not been a large scale sequencing project to date for Camelus dromedarius. With the goal of sequencing complete DNA of the organism, we first established and sequenced camel EST libraries, generating 70,272 reads. Following trimming, chimera check, repeat masking, cluster and assembly, we obtained 23,602 putative gene sequences, out of which over 4,500 potentially novel or fast evolving gene sequences do not carry any homology to other available genomes. Functional annotation of sequences with similarities in nucleotide and protein databases has been obtained using Gene Ontology classification. Comparison to available full length cDNA sequences and Open Reading Frame (ORF) analysis of camel sequences that exhibit homology to known genes show more than 80% of the contigs with an ORF>300 bp and ∼40% hits extending to the start codons of full length cDNAs suggesting successful characterization of camel genes. Similarity analyses are done separately for different organisms including human, mouse, bovine, and rat. Accompanying web portal, CAGBASE (http://camel.kacst.edu.sa/), hosts a relational database containing annotated EST sequences and analysis tools with possibility to add sequences from public domain. We anticipate our results to provide a home base for genomic studies of camel and other comparative studies enabling a starting point for whole genome sequencing of the organism. PMID:20502665

Generation of Ground Truth Datasets for the Analysis of 3d Point Clouds in Urban Scenes Acquired via Different Sensors

NASA Astrophysics Data System (ADS)

Xu, Y.; Sun, Z.; Boerner, R.; Koch, T.; Hoegner, L.; Stilla, U.

2018-04-01

In this work, we report a novel way of generating ground truth dataset for analyzing point cloud from different sensors and the validation of algorithms. Instead of directly labeling large amount of 3D points requiring time consuming manual work, a multi-resolution 3D voxel grid for the testing site is generated. Then, with the help of a set of basic labeled points from the reference dataset, we can generate a 3D labeled space of the entire testing site with different resolutions. Specifically, an octree-based voxel structure is applied to voxelize the annotated reference point cloud, by which all the points are organized by 3D grids of multi-resolutions. When automatically annotating the new testing point clouds, a voting based approach is adopted to the labeled points within multiple resolution voxels, in order to assign a semantic label to the 3D space represented by the voxel. Lastly, robust line- and plane-based fast registration methods are developed for aligning point clouds obtained via various sensors. Benefiting from the labeled 3D spatial information, we can easily create new annotated 3D point clouds of different sensors of the same scene directly by considering the corresponding labels of 3D space the points located, which would be convenient for the validation and evaluation of algorithms related to point cloud interpretation and semantic segmentation.

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi.

PubMed

Schoch, Conrad L; Robbertse, Barbara; Robert, Vincent; Vu, Duong; Cardinali, Gianluigi; Irinyi, Laszlo; Meyer, Wieland; Nilsson, R Henrik; Hughes, Karen; Miller, Andrew N; Kirk, Paul M; Abarenkov, Kessy; Aime, M Catherine; Ariyawansa, Hiran A; Bidartondo, Martin; Boekhout, Teun; Buyck, Bart; Cai, Qing; Chen, Jie; Crespo, Ana; Crous, Pedro W; Damm, Ulrike; De Beer, Z Wilhelm; Dentinger, Bryn T M; Divakar, Pradeep K; Dueñas, Margarita; Feau, Nicolas; Fliegerova, Katerina; García, Miguel A; Ge, Zai-Wei; Griffith, Gareth W; Groenewald, Johannes Z; Groenewald, Marizeth; Grube, Martin; Gryzenhout, Marieka; Gueidan, Cécile; Guo, Liangdong; Hambleton, Sarah; Hamelin, Richard; Hansen, Karen; Hofstetter, Valérie; Hong, Seung-Beom; Houbraken, Jos; Hyde, Kevin D; Inderbitzin, Patrik; Johnston, Peter R; Karunarathna, Samantha C; Kõljalg, Urmas; Kovács, Gábor M; Kraichak, Ekaphan; Krizsan, Krisztina; Kurtzman, Cletus P; Larsson, Karl-Henrik; Leavitt, Steven; Letcher, Peter M; Liimatainen, Kare; Liu, Jian-Kui; Lodge, D Jean; Luangsa-ard, Janet Jennifer; Lumbsch, H Thorsten; Maharachchikumbura, Sajeewa S N; Manamgoda, Dimuthu; Martín, María P; Minnis, Andrew M; Moncalvo, Jean-Marc; Mulè, Giuseppina; Nakasone, Karen K; Niskanen, Tuula; Olariaga, Ibai; Papp, Tamás; Petkovits, Tamás; Pino-Bodas, Raquel; Powell, Martha J; Raja, Huzefa A; Redecker, Dirk; Sarmiento-Ramirez, J M; Seifert, Keith A; Shrestha, Bhushan; Stenroos, Soili; Stielow, Benjamin; Suh, Sung-Oui; Tanaka, Kazuaki; Tedersoo, Leho; Telleria, M Teresa; Udayanga, Dhanushka; Untereiner, Wendy A; Diéguez Uribeondo, Javier; Subbarao, Krishna V; Vágvölgyi, Csaba; Visagie, Cobus; Voigt, Kerstin; Walker, Donald M; Weir, Bevan S; Weiß, Michael; Wijayawardene, Nalin N; Wingfield, Michael J; Xu, J P; Yang, Zhu L; Zhang, Ning; Zhuang, Wen-Ying; Federhen, Scott

2014-01-01

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi. Database URL: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353. Published by Oxford University Press 2013. This work is written by US Government employees and is in the public domain in the US.

High Voltage Test-Stand Research Done on ICRF Antenna Elements of the High-Harmonic Fast-Wave System of NSTX

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

Perkins, R. J.; Ahn, J.W.; Bortolon, A.

The twelve-strap high-harmonic fast-wave (HHFW) antenna on NSTX has exhibited a high-voltage standoff around 25 kV during previous experimental campaigns; this standoff needs to be improved for increased power coupling. During the recent NSTX-U upgrade period, a test-stand was set up with two antenna straps along with Faraday screens for testing purposes. Using a diagnostic suite consisting of a fast camera, a residual gas analyzer, a pressure gage, high-voltage probes, and an infrared camera, several interesting discoveries were made, leading to possible improvements of the antenna RF voltage operation level. First, arcing was observed outside the Faraday shields towards themore » low-voltage ("grounded") end of the straps (faraday shield box ends); this arcing was successfully eliminated by installing an additional grounding point between the Faraday shield box and the vessel wall. Second, considerable outgassing was observed during the RF pulse and the amount of outgassing was found to decrease with increasing RF power, possibly indicative of multipacting. Finally, infrared camera measurements of heating on the Faraday shield assembly suggest that the return currents on the Faraday shield box are highly localized at the box sides and possibly account for the pressure increase observed. Computations of these RF currents using Microwave Studio show qualitative agreement with the heated regions. New grounding points between the antenna box and the vessel have been implemented in NSTX-U, where future tests will be done to determine if the high-voltage standoff has improved. Further antenna improvements will be sought through future experiments on the test stand.« less

Geodynamic Modeling of the Subduction Zone around the Japanese Islands

NASA Astrophysics Data System (ADS)

Honda, S.

2017-06-01

In this review, which focuses on our research, we describe the development of the thermomechanical modeling of subduction zones, paying special attention to those around the Japanese Islands. Without a sufficient amount of data and observations, models tended to be conceptual and general. However, the increasing power of computational tools has resulted in simple analytical and numerical models becoming more realistic, by incorporating the mantle flow around the subducting slab. The accumulation of observations and data has made it possible to construct regional models to understand the detail of the subduction processes. Recent advancements in the study of the seismic tomography and geology around the Japanese Islands has enabled new aspects of modeling the mantle processes. A good correlation between the seismic velocity anomalies and the finger-like distribution of volcanoes in northeast Japan has been recognized and small-scale convection (SSC) in the mantle wedge has been proposed to explain such a feature. The spatial and temporal evolution of the distribution of past volcanoes may reflect the characteristics of the flow in the mantle wedge, and points to the possibility of the flip-flopping of the finger-like pattern of the volcano distribution and the migration of volcanic activity from the back-arc side to the trench side. These observations are found to be qualitatively consistent with the results of the SSC model. We have also investigated the expected seismic anisotropy in the presence of SSC. The fast direction of the P-wave anisotropy generally shows the trench-normal direction with a reduced magnitude compared to the case without SSC. An analysis of full 3D seismic anisotropy is necessary to confirm the existence and nature of SSC. The 3D mantle flow around the subduction zone of plate-size scale has been modeled. It was found that the trench-parallel flow in the sub-slab mantle around the northern edge of the Pacific plate at the junction between the Aleutian arc and the Kurile arc is generally weak and we have suggested the possible contribution of a hot anomaly in the sub-slab mantle as the origin of possible trench-parallel flow there. A 3D mantle flow model of the back-arc around the junction between the northeast Japan arc and the Kurile arc shows a trench-normal flow at a shallow depth. As a result, the expected seismic anisotropy shows the fast direction normal to the arc, even in the region of oblique subduction. This result is generally consistent with observations there. The existence of a hot anomaly in the sub-slab mantle under the Pacific plate was proposed from an analysis of the seismic tomography, and we have studied its possible origins. The origin of a hot anomaly adjacent to the cold downgoing flow, typically observed in internally heated convection, is preferable to that of a hot anomaly, such as a plume head, carried far from the subduction zone. The nature of the western edge of the stagnant slab under northeast China has been investigated with modeling studies, which take into account the subduction history and the phase changes in the mantle. It is likely to be a ridge-type plate boundary between the extinct Izanagi plate and the Pacific plate. Thus, we have concluded that the slab gap under northeast China is not a breakage of the stagnant slab. Further studies have suggested that the existence of the rheological weakening of the slab in the transition zone, and the additional effects of a hot anomaly in the sub-slab mantle under the Pacific plate, may explain the differences in slab morphology under the northern Okhotsk arc and the northeast Japan arc.

Lateral heterogeneity and azimuthal anistropy of the upper mantle: Love and Rayleigh waves 100-250 sec

NASA Technical Reports Server (NTRS)

Tanimoto, T.; Anderson, D. L.

1983-01-01

The lateral heterogeneity and apparent anisotropy of the upper mantle are studied by measuring Rayleigh and Love wave phase velocities in the period range 100-250 sec. Spherical harmonic descriptions of the lateral heterogeneity are obtained for order and degree up to 1=m=10. Slow regions are evident at the East Pacific rise, northeast Africa, Tibet, Tasman sea, southwestern North America and triple junctions in the Northern Atlantic and Indian oceans. Fast regions occur in Australia, western Pacific and the eastern Atlantic. Details which are not evident in previous studies include two fast regions in the central Pacific and the subduction zone in the Scotia Arc region. Inversion for azimuthal dependence showed (1) little correlation between the fast phase velocity directions and the plate motion vector in plate interiors, but (2) correlation of the fast direction with the perpendicular direction to trenches and ridges. Phase velocity is high when waves propagate perpendicular to these structures. Severe tradeoffs exist between heterogeneity and azimuthal dependence because of the yet unsatisfactory path coverage.

Lateral heterogeneity and azimuthal anisotropy of the upper mantle - Love and Rayleigh waves 100-250 sec

NASA Technical Reports Server (NTRS)

Tanimoto, T.; Anderson, D. L.

1985-01-01

The lateral heterogeneity and apparent anisotropy of the upper mantle are studied by measuring Rayleigh and Love wave phase velocities in the period range 100-250 sec. Spherical harmonic descriptions of the lateral heterogeneity are obtained for order and degree up to 1=m=10. Slow regions are evident at the East Pacific rise, northeast Africa, Tibet, Tasman sea, southwestern North America and triple junctions in the Northern Atlantic and Indian oceans. Fast regions occur in Australia, western Pacific and the eastern Atlantic. Details which are not evident in previous studies include two fast regions in the central Pacific and the subduction zone in the Scotia Arc region. Inversion for azimuthal dependence showed (1) little correlation between the fast phase velocity directions and the plate motion vector in plate interiors, but (2) correlation of the fast direction with the perpendicular direction to trenches and ridges. Phase velocity is high when waves propagate perpendicular to these structures. Severe tradeoffs exist between heterogeneity and azimuthal dependence because of the yet unsatisfactory path coverage.

Comparison of fast electric field changes from subsequent return strokes of natural and triggered lightning

NASA Technical Reports Server (NTRS)

Le Vine, D. M.; Willett, J.

1988-01-01

Fast electric field changes from subsequent return strokes of natural and triggered lightning with propagation paths almost entirely over water are compared. Data were collected at the Kennedy Space Center, Florida. Comparisons have been made of the average shape, the rise time and the spectrum of the electric field changes. The electric field changes from the triggered flashes tend to rise to peak faster and decay faster than do their counterparts in natural cloud-to-ground flashes.

Alternative Fuels Data Center: Maps and Data

Science.gov Websites

1992 (EPAct) and subsequent legislation require federal government agencies to incorporate alternative : Federal Fleet FAST Data The Energy Policy Act of 1992 (EPAct) and subsequent legislation require federal

Synthesis and electrochemical properties of silicon nanosheets by DC arc discharge for lithium-ion batteries.

PubMed

Yu, Xiuhong; Xue, Fanghong; Huang, Hao; Liu, Chunjing; Yu, Jieyi; Sun, Yuejun; Dong, Xinglong; Cao, Guozhong; Jung, Youngguan

2014-06-21

Two-dimensional (2D) ultrathin silicon nanosheets (Si NSs) were synthesized by DC arc discharge method and investigated as anode material for Li-ion batteries. The 2D ultrathin characteristics of Si NSs is confirmed by means of transmission electron microscopy (TEM) and atomic force microscopy (AFM). The average size of Si NSs is about 20 nm, with thickness less than 2.5 nm. The characteristic Raman peak of Si NSs is found to have an appreciable (20 nm) shift to low frequency, presumably due to the size effect. The synergistic effects of Ar(+) and H(+) lead to 2D growth of Si NSs under high temperature and energy. Electrochemical analyses reveal that Si NSs anode possesses stable cycling performance and fast diffusion of Li-ions with insertion/extraction processes. Such Si NSs might be a promising candidate for anode of Li-ion batteries.

In Vitro Analysis of Electrophoretic Deposited Fluoridated Hydroxyapatite Coating on Micro-arc Oxidized AZ91 Magnesium Alloy for Biomaterials Applications

NASA Astrophysics Data System (ADS)

Razavi, Mehdi; Fathi, Mohammadhossein; Savabi, Omid; Vashaee, Daryoosh; Tayebi, Lobat

2015-03-01

Magnesium (Mg) alloys have been recently introduced as a biodegradable implant for orthopedic applications. However, their fast corrosion, low bioactivity, and mechanical integrity have limited their clinical applications. The main aim of this research was to improve such properties of the AZ91 Mg alloy through surface modifications. For this purpose, nanostructured fluoridated hydroxyapatite (FHA) was coated on AZ91 Mg alloy by micro-arc oxidation and electrophoretic deposition method. The coated alloy was characterized through scanning electron microscopy, transmission electron microscopy, X-ray diffraction, in vitro corrosion tests, mechanical tests, and cytocompatibility evaluation. The results confirmed the improvement of the corrosion resistance, in vitro bioactivity, mechanical integrity, and the cytocompatibility of the coated Mg alloy. Therefore, the nanostructured FHA coating can offer a promising way to improve the properties of the Mg alloy for orthopedic applications.

Hypothalamic KLF4 mediates leptin's effects on food intake via AgRP

PubMed Central

Imbernon, Monica; Sanchez-Rebordelo, Estrella; Gallego, Rosalia; Gandara, Marina; Lear, Pamela; Lopez, Miguel; Dieguez, Carlos; Nogueiras, Ruben

2014-01-01

Krüppel-like factor 4 (KLF4) is a zinc-finger-type transcription factor expressed in a range of tissues that plays multiple functions. We report that hypothalamic KLF4 represents a new transcription factor specifically modulating agouti-related protein (AgRP) expression in vivo. Hypothalamic KLF4 colocalizes with AgRP neurons and is modulated by nutritional status and leptin. Over-expression of KLF4 in the hypothalamic arcuate nucleus (ARC) induces food intake and increases body weight through the specific stimulation of AgRP, as well as blunting leptin sensitivity in lean rats independent of forkhead box protein 01 (FoxO1). Down-regulation of KLF4 in the ARC inhibits fasting-induced food intake in both lean and diet-induced obese (DIO) rats. Silencing KLF4, however, does not, on its own, enhance peripheral leptin sensitivity in DIO rats. PMID:24944903

Hypothalamic KLF4 mediates leptin's effects on food intake via AgRP.

PubMed

Imbernon, Monica; Sanchez-Rebordelo, Estrella; Gallego, Rosalia; Gandara, Marina; Lear, Pamela; Lopez, Miguel; Dieguez, Carlos; Nogueiras, Ruben

2014-07-01

Krüppel-like factor 4 (KLF4) is a zinc-finger-type transcription factor expressed in a range of tissues that plays multiple functions. We report that hypothalamic KLF4 represents a new transcription factor specifically modulating agouti-related protein (AgRP) expression in vivo. Hypothalamic KLF4 colocalizes with AgRP neurons and is modulated by nutritional status and leptin. Over-expression of KLF4 in the hypothalamic arcuate nucleus (ARC) induces food intake and increases body weight through the specific stimulation of AgRP, as well as blunting leptin sensitivity in lean rats independent of forkhead box protein 01 (FoxO1). Down-regulation of KLF4 in the ARC inhibits fasting-induced food intake in both lean and diet-induced obese (DIO) rats. Silencing KLF4, however, does not, on its own, enhance peripheral leptin sensitivity in DIO rats.

Interactive approach to segment organs at risk in radiotherapy treatment planning

NASA Astrophysics Data System (ADS)

Dolz, Jose; Kirisli, Hortense A.; Viard, Romain; Massoptier, Laurent

2014-03-01

Accurate delineation of organs at risk (OAR) is required for radiation treatment planning (RTP). However, it is a very time consuming and tedious task. The use in clinic of image guided radiation therapy (IGRT) becomes more and more popular, thus increasing the need of (semi-)automatic methods for delineation of the OAR. In this work, an interactive segmentation approach to delineate OAR is proposed and validated. The method is based on the combination of watershed transformation, which groups small areas of similar intensities in homogeneous labels, and graph cuts approach, which uses these labels to create the graph. Segmentation information can be added in any view - axial, sagittal or coronal -, making the interaction with the algorithm easy and fast. Subsequently, this information is propagated within the whole volume, providing a spatially coherent result. Manual delineations made by experts of 6 OAR - lungs, kidneys, liver, spleen, heart and aorta - over a set of 9 computed tomography (CT) scans were used as reference standard to validate the proposed approach. With a maximum of 4 interactions, a Dice similarity coefficient (DSC) higher than 0.87 was obtained, which demonstrates that, with the proposed segmentation approach, only few interactions are required to achieve similar results as the ones obtained manually. The integration of this method in the RTP process may save a considerable amount of time, and reduce the annotation complexity.

EHR-based phenotyping: Bulk learning and evaluation.

PubMed

Chiu, Po-Hsiang; Hripcsak, George

2017-06-01

In data-driven phenotyping, a core computational task is to identify medical concepts and their variations from sources of electronic health records (EHR) to stratify phenotypic cohorts. A conventional analytic framework for phenotyping largely uses a manual knowledge engineering approach or a supervised learning approach where clinical cases are represented by variables encompassing diagnoses, medicinal treatments and laboratory tests, among others. In such a framework, tasks associated with feature engineering and data annotation remain a tedious and expensive exercise, resulting in poor scalability. In addition, certain clinical conditions, such as those that are rare and acute in nature, may never accumulate sufficient data over time, which poses a challenge to establishing accurate and informative statistical models. In this paper, we use infectious diseases as the domain of study to demonstrate a hierarchical learning method based on ensemble learning that attempts to address these issues through feature abstraction. We use a sparse annotation set to train and evaluate many phenotypes at once, which we call bulk learning. In this batch-phenotyping framework, disease cohort definitions can be learned from within the abstract feature space established by using multiple diseases as a substrate and diagnostic codes as surrogates. In particular, using surrogate labels for model training renders possible its subsequent evaluation using only a sparse annotated sample. Moreover, statistical models can be trained and evaluated, using the same sparse annotation, from within the abstract feature space of low dimensionality that encapsulates the shared clinical traits of these target diseases, collectively referred to as the bulk learning set. Copyright © 2017 Elsevier Inc. All rights reserved.

Some difficulties in the assessment of electric arc welding fume.

PubMed

Hewitt, P J; Gray, C N

1983-10-01

During electric arc welding of metals, particulate fume in a variety of chemical compositions and physical forms is produced with consequent complex solution chemistry. Mechanisms of fume formation include condensation of vaporized metals to produce submicron diameter chains, and spatter of larger particles with subsequent oxidation to yield mixed metal oxide fumes in the respirable range. Complete dissolution of certain constituent metals such as chromium, can be achieved by fusion with potassium hydrogen sulphate. Extraction of hexavalent chromium by sodium carbonate/hydroxide solution is efficient and rapid, while some other extractants give erroneous results. Investigations show that constituent metals are released from the fume at different rates both in vitro and in vivo. The implications arising from the complex nature of welding fume for industrial hygiene assessment are discussed.

JNSViewer—A JavaScript-based Nucleotide Sequence Viewer for DNA/RNA secondary structures

PubMed Central

Dong, Min; Graham, Mitchell; Yadav, Nehul

2017-01-01

Many tools are available for visualizing RNA or DNA secondary structures, but there is scarce implementation in JavaScript that provides seamless integration with the increasingly popular web computational platforms. We have developed JNSViewer, a highly interactive web service, which is bundled with several popular tools for DNA/RNA secondary structure prediction and can provide precise and interactive correspondence among nucleotides, dot-bracket data, secondary structure graphs, and genic annotations. In JNSViewer, users can perform RNA secondary structure predictions with different programs and settings, add customized genic annotations in GFF format to structure graphs, search for specific linear motifs, and extract relevant structure graphs of sub-sequences. JNSViewer also allows users to choose a transcript or specific segment of Arabidopsis thaliana genome sequences and predict the corresponding secondary structure. Popular genome browsers (i.e., JBrowse and BrowserGenome) were integrated into JNSViewer to provide powerful visualizations of chromosomal locations, genic annotations, and secondary structures. In addition, we used StructureFold with default settings to predict some RNA structures for Arabidopsis by incorporating in vivo high-throughput RNA structure profiling data and stored the results in our web server, which might be a useful resource for RNA secondary structure studies in plants. JNSViewer is available at http://bioinfolab.miamioh.edu/jnsviewer/index.html. PMID:28582416

Breaking the 1000-gene barrier for Mimivirus using ultra-deep genome and transcriptome sequencing.

PubMed

Legendre, Matthieu; Santini, Sébastien; Rico, Alain; Abergel, Chantal; Claverie, Jean-Michel

2011-03-04

Mimivirus, a giant dsDNA virus infecting Acanthamoeba, is the prototype of the mimiviridae family, the latest addition to the family of the nucleocytoplasmic large DNA viruses (NCLDVs). Its 1.2 Mb-genome was initially predicted to encode 917 genes. A subsequent RNA-Seq analysis precisely mapped many transcript boundaries and identified 75 new genes. We now report a much deeper analysis using the SOLiD™ technology combining RNA-Seq of the Mimivirus transcriptome during the infectious cycle (202.4 Million reads), and a complete genome re-sequencing (45.3 Million reads). This study corrected the genome sequence and identified several single nucleotide polymorphisms. Our results also provided clear evidence of previously overlooked transcription units, including an important RNA polymerase subunit distantly related to Euryarchea homologues. The total Mimivirus gene count is now 1018, 11% greater than the original annotation. This study highlights the huge progress brought about by ultra-deep sequencing for the comprehensive annotation of virus genomes, opening the door to a complete one-nucleotide resolution level description of their transcriptional activity, and to the realistic modeling of the viral genome expression at the ultimate molecular level. This work also illustrates the need to go beyond bioinformatics-only approaches for the annotation of short protein and non-coding genes in viral genomes.

Comprehensive cellular‐resolution atlas of the adult human brain

PubMed Central

Royall, Joshua J.; Sunkin, Susan M.; Ng, Lydia; Facer, Benjamin A.C.; Lesnar, Phil; Guillozet‐Bongaarts, Angie; McMurray, Bergen; Szafer, Aaron; Dolbeare, Tim A.; Stevens, Allison; Tirrell, Lee; Benner, Thomas; Caldejon, Shiella; Dalley, Rachel A.; Dee, Nick; Lau, Christopher; Nyhus, Julie; Reding, Melissa; Riley, Zackery L.; Sandman, David; Shen, Elaine; van der Kouwe, Andre; Varjabedian, Ani; Write, Michelle; Zollei, Lilla; Dang, Chinh; Knowles, James A.; Koch, Christof; Phillips, John W.; Sestan, Nenad; Wohnoutka, Paul; Zielke, H. Ronald; Hohmann, John G.; Jones, Allan R.; Bernard, Amy; Hawrylycz, Michael J.; Hof, Patrick R.; Fischl, Bruce

2016-01-01

ABSTRACT Detailed anatomical understanding of the human brain is essential for unraveling its functional architecture, yet current reference atlases have major limitations such as lack of whole‐brain coverage, relatively low image resolution, and sparse structural annotation. We present the first digital human brain atlas to incorporate neuroimaging, high‐resolution histology, and chemoarchitecture across a complete adult female brain, consisting of magnetic resonance imaging (MRI), diffusion‐weighted imaging (DWI), and 1,356 large‐format cellular resolution (1 µm/pixel) Nissl and immunohistochemistry anatomical plates. The atlas is comprehensively annotated for 862 structures, including 117 white matter tracts and several novel cyto‐ and chemoarchitecturally defined structures, and these annotations were transferred onto the matching MRI dataset. Neocortical delineations were done for sulci, gyri, and modified Brodmann areas to link macroscopic anatomical and microscopic cytoarchitectural parcellations. Correlated neuroimaging and histological structural delineation allowed fine feature identification in MRI data and subsequent structural identification in MRI data from other brains. This interactive online digital atlas is integrated with existing Allen Institute for Brain Science gene expression atlases and is publicly accessible as a resource for the neuroscience community. J. Comp. Neurol. 524:3127–3481, 2016. © 2016 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc. PMID:27418273

Functional Immunomics of the Squash Bug, Anasa tristis (De Geer) (Heteroptera: Coreidae)

PubMed Central

Shelby, Kent S.

2013-01-01

The Squash bug, Anasa tristis (De Geer), is a major piercing/sucking pest of cucurbits, causing extensive damage to plants and fruits, and transmitting phytopathogens. No genomic resources to facilitate field and laboratory studies of this pest were available; therefore the first de novo exome for this destructive pest was assembled. RNA was extracted from insects challenged with bacterial and fungal immunoelicitors, insects fed on different cucurbit species, and insects from all life stages from egg to adult. All treatments and replicates were separately barcoded for subsequent analyses, then pooled for sequencing in a single lane using the Illumina HiSeq2000 platform. Over 211 million 100-base tags generated in this manner were trimmed, filtered, and cleaned, then assembled into a de novo reference transcriptome using the Broad Institute Trinity assembly algorithm. The assembly was annotated using NCBIx NR, BLAST2GO, KEGG and other databases. Of the >130,000 total assemblies 37,327 were annotated identifying the sequences of candidate gene silencing targets from immune, endocrine, reproductive, cuticle, and other physiological systems. Expression profiling of the adult immune response was accomplished by aligning the 100-base tags from each biological replicate from each treatment and controls to the annotated reference assembly of the A. tristis transcriptome. PMID:26462532

A three-dimensional single-cell-resolution whole-brain atlas using CUBIC-X expansion microscopy and tissue clearing.

PubMed

Murakami, Tatsuya C; Mano, Tomoyuki; Saikawa, Shu; Horiguchi, Shuhei A; Shigeta, Daichi; Baba, Kousuke; Sekiya, Hiroshi; Shimizu, Yoshihiro; Tanaka, Kenji F; Kiyonari, Hiroshi; Iino, Masamitsu; Mochizuki, Hideki; Tainaka, Kazuki; Ueda, Hiroki R

2018-04-01

A three-dimensional single-cell-resolution mammalian brain atlas will accelerate systems-level identification and analysis of cellular circuits underlying various brain functions. However, its construction requires efficient subcellular-resolution imaging throughout the entire brain. To address this challenge, we developed a fluorescent-protein-compatible, whole-organ clearing and homogeneous expansion protocol based on an aqueous chemical solution (CUBIC-X). The expanded, well-cleared brain enabled us to construct a point-based mouse brain atlas with single-cell annotation (CUBIC-Atlas). CUBIC-Atlas reflects inhomogeneous whole-brain development, revealing a significant decrease in the cerebral visual and somatosensory cortical areas during postnatal development. Probabilistic activity mapping of pharmacologically stimulated Arc-dVenus reporter mouse brains onto CUBIC-Atlas revealed the existence of distinct functional structures in the hippocampal dentate gyrus. CUBIC-Atlas is shareable by an open-source web-based viewer, providing a new platform for whole-brain cell profiling.

53rd Course Molecular Physics and Plasmas in Hypersonics 2

DTIC Science & Technology

2013-09-09

between CO2 symmetric and bending modes ( 11 ) proceeds fast due to the Fermi resonance between the frequencies of these modes and can be considered as...of local maximization of the collision frequency given by Eq. ( 11 ) allows a strong reduction of the computational cost and it is verified a...called arc-jets or DC-Plasmatron [25, 26]. PWTs using Inductively Coupled Plasma (ICP) torch, based on Radio - Frequency (RF) discharge, are so- called

Seismic imaging of deep crustal melt sills beneath Costa Rica suggests a method for the formation of the Archean continental crust

NASA Astrophysics Data System (ADS)

Harmon, Nicholas; Rychert, Catherine A.

2015-11-01

Continental crust formed billions of years ago but cannot be explained by a simple evolution of primary mantle magmas. A multi-step process is required that likely includes re-melting of wet metamorphosed basalt at high pressures. Such a process could occur at depth in oceanic crust that has been thickened by a large magmatic event. In Central America, variations in geologically inferred, pre-existing oceanic crustal thickness beneath the arc provides an excellent opportunity to study its effect on magma storage, re-melting of meta-basalts, and the potential for creating continental crust. We use surface waves derived from ambient noise tomography to image 6% radially anisotropic structures in the thickened oceanic plateau crust of Costa Rica that likely represent deep crustal melt sills. In Nicaragua, where the arc is forming on thinner oceanic crust, we do not image these deep crustal melt sills. The presence of these deep sills correlates with more felsic arc outputs from the Costa Rican Arc suggesting pre-existing thickened crust accelerates processing of primary basalts to continental compositions. In the Archean, reprocessing thickened oceanic crust by subsequent hydrated hotspot volcanism or subduction zone volcanism may have similarly enhanced formation of early continental crust. This mechanism may have been particularly important if subduction did not initiate until 3 Ga.

A new method of automatic landmark tagging for shape model construction via local curvature scale

NASA Astrophysics Data System (ADS)

Rueda, Sylvia; Udupa, Jayaram K.; Bai, Li

2008-03-01

Segmentation of organs in medical images is a difficult task requiring very often the use of model-based approaches. To build the model, we need an annotated training set of shape examples with correspondences indicated among shapes. Manual positioning of landmarks is a tedious, time-consuming, and error prone task, and almost impossible in the 3D space. To overcome some of these drawbacks, we devised an automatic method based on the notion of c-scale, a new local scale concept. For each boundary element b, the arc length of the largest homogeneous curvature region connected to b is estimated as well as the orientation of the tangent at b. With this shape description method, we can automatically locate mathematical landmarks selected at different levels of detail. The method avoids the use of landmarks for the generation of the mean shape. The selection of landmarks on the mean shape is done automatically using the c-scale method. Then, these landmarks are propagated to each shape in the training set, defining this way the correspondences among the shapes. Altogether 12 strategies are described along these lines. The methods are evaluated on 40 MRI foot data sets, the object of interest being the talus bone. The results show that, for the same number of landmarks, the proposed methods are more compact than manual and equally spaced annotations. The approach is applicable to spaces of any dimensionality, although we have focused in this paper on 2D shapes.

Transcriptomic resources for the medicinal legume Mucuna pruriens: de novo transcriptome assembly, annotation, identification and validation of EST-SSR markers.

PubMed

Sathyanarayana, N; Pittala, Ranjith Kumar; Tripathi, Pankaj Kumar; Chopra, Ratan; Singh, Heikham Russiachand; Belamkar, Vikas; Bhardwaj, Pardeep Kumar; Doyle, Jeff J; Egan, Ashley N

2017-05-25

The medicinal legume Mucuna pruriens (L.) DC. has attracted attention worldwide as a source of the anti-Parkinson's drug L-Dopa. It is also a popular green manure cover crop that offers many agronomic benefits including high protein content, nitrogen fixation and soil nutrients. The plant currently lacks genomic resources and there is limited knowledge on gene expression, metabolic pathways, and genetics of secondary metabolite production. Here, we present transcriptomic resources for M. pruriens, including a de novo transcriptome assembly and annotation, as well as differential transcript expression analyses between root, leaf, and pod tissues. We also develop microsatellite markers and analyze genetic diversity and population structure within a set of Indian germplasm accessions. One-hundred ninety-one million two hundred thirty-three thousand two hundred forty-two bp cleaned reads were assembled into 67,561 transcripts with mean length of 626 bp and N50 of 987 bp. Assembled sequences were annotated using BLASTX against public databases with over 80% of transcripts annotated. We identified 7,493 simple sequence repeat (SSR) motifs, including 787 polymorphic repeats between the parents of a mapping population. 134 SSRs from expressed sequenced tags (ESTs) were screened against 23 M. pruriens accessions from India, with 52 EST-SSRs retained after quality control. Population structure analysis using a Bayesian framework implemented in fastSTRUCTURE showed nearly similar groupings as with distance-based (neighbor-joining) and principal component analyses, with most of the accessions clustering per geographical origins. Pair-wise comparison of transcript expression in leaves, roots and pods identified 4,387 differentially expressed transcripts with the highest number occurring between roots and leaves. Differentially expressed transcripts were enriched with transcription factors and transcripts annotated as belonging to secondary metabolite pathways. The M. pruriens transcriptomic resources generated in this study provide foundational resources for gene discovery and development of molecular markers. Polymorphic SSRs identified can be used for genetic diversity, marker-trait analyses, and development of functional markers for crop improvement. The results of differential expression studies can be used to investigate genes involved in L-Dopa synthesis and other key metabolic pathways in M. pruriens.

Liver Transcriptome Analysis of the Large Yellow Croaker (Larimichthys crocea) during Fasting by Using RNA-Seq

PubMed Central

Qian, Baoying; Xue, Liangyi; Huang, Hongli

2016-01-01

The large yellow croaker (Larimichthys crocea) is an economically important fish species in Chinese mariculture industry. To understand the molecular basis underlying the response to fasting, Illumina HiSeqTM 2000 was used to analyze the liver transcriptome of fasting large yellow croakers. A total of 54,933,550 clean reads were obtained and assembled into 110,364 contigs. Annotation to the NCBI database identified a total of 38,728 unigenes, of which 19,654 were classified into Gene Ontology and 22,683 were found in Kyoto Encyclopedia of Genes and Genomes (KEGG). Comparative analysis of the expression profiles between fasting fish and normal-feeding fish identified a total of 7,623 differentially expressed genes (P < 0.05), including 2,500 upregulated genes and 5,123 downregulated genes. Dramatic differences were observed in the genes involved in metabolic pathways such as fat digestion and absorption, citrate cycle, and glycolysis/gluconeogenesis, and the similar results were also found in the transcriptome of skeletal muscle. Further qPCR analysis confirmed that the genes encoding the factors involved in those pathways significantly changed in terms of expression levels. The results of the present study provide insights into the molecular mechanisms underlying the metabolic response of the large yellow croaker to fasting as well as identified areas that require further investigation. PMID:26967898

Magmatic evolution of Panama Canal volcanic rocks: A record of arc processes and tectonic change

PubMed Central

Cardona, Agustin; Montes, Camilo; Foster, David; Jaramillo, Carlos

2017-01-01

Volcanic rocks along the Panama Canal present a world-class opportunity to examine the relationship between arc magmatism, tectonic forcing, wet and dry magmas, and volcanic structures. Major and trace element geochemistry of Canal volcanic rocks indicate a significant petrologic transition at 21–25 Ma. Oligocene Bas Obispo Fm. rocks have large negative Nb-Ta anomalies, low HREE, fluid mobile element enrichments, a THI of 0.88, and a H2Ocalc of >3 wt. %. In contrast, the Miocene Pedro Miguel and Late Basalt Fm. exhibit reduced Nb-Ta anomalies, flattened REE curves, depleted fluid mobile elements, a THI of 1.45, a H2Ocalc of <1 wt. %, and plot in mid-ocean ridge/back-arc basin fields. Geochemical modeling of Miocene rocks indicates 0.5–0.1 kbar crystallization depths of hot (1100–1190°C) magmas in which most compositional diversity can be explained by fractional crystallization (F = 0.5). However, the most silicic lavas (Las Cascadas Fm.) require an additional mechanism, and assimilation-fractional-crystallization can reproduce observed compositions at reasonable melt fractions. The Canal volcanic rocks, therefore, change from hydrous basaltic pyroclastic deposits typical of mantle-wedge-derived magmas, to hot, dry bi-modal magmatism at the Oligocene-Miocene boundary. We suggest the primary reason for the change is onset of arc perpendicular extension localized to central Panama. High-resolution mapping along the Panama Canal has revealed a sequence of inward dipping maar-diatreme pyroclastic pipes, large basaltic sills, and bedded silicic ignimbrites and tuff deposits. These volcanic bodies intrude into the sedimentary Canal Basin and are cut by normal and subsequently strike-slip faults. Such pyroclastic pipes and basaltic sills are most common in extensional arc and large igneous province environments. Overall, the change in volcanic edifice form and geochemistry are related to onset of arc perpendicular extension, and are consistent with the idea that Panama arc crust fractured during collision with South America forming the observed Canal extensional zone. PMID:28489866

Line plus arc source trajectories and their R-line coverage for long-object cone-beam imaging with a C-arm system

NASA Astrophysics Data System (ADS)

Yu, Zhicong; Wunderlich, Adam; Dennerlein, Frank; Lauritsch, Günter; Noo, Frédéric

2011-06-01

Cone-beam imaging with C-arm systems has become a valuable tool in interventional radiology. Currently, a simple circular trajectory is used, but future applications should use more sophisticated source trajectories, not only to avoid cone-beam artifacts but also to allow extended volume imaging. One attractive strategy to achieve these two goals is to use a source trajectory that consists of two parallel circular arcs connected by a line segment, possibly with repetition. In this work, we address the question of R-line coverage for such a trajectory. More specifically, we examine to what extent R-lines for such a trajectory cover a central cylindrical region of interest (ROI). An R-line is a line segment connecting any two points on the source trajectory. Knowledge of R-line coverage is crucial because a general theory for theoretically exact and stable image reconstruction from axially truncated data is only known for the points in the scanned object that lie on R-lines. Our analysis starts by examining the R-line coverage for the elemental trajectories consisting of (i) two parallel circular arcs and (ii) a circular arc connected orthogonally to a line segment. Next, we utilize our understanding of the R-lines for the aforementioned elemental trajectories to determine the R-line coverage for the trajectory consisting of two parallel circular arcs connected by a tightly fit line segment. For this trajectory, we find that the R-line coverage is insufficient to completely cover any central ROI. Because extension of the line segment beyond the circular arcs helps to increase the R-line coverage, we subsequently propose a trajectory composed of two parallel circular arcs connected by an extended line. We show that the R-lines for this trajectory can fully cover a central ROI if the line extension is long enough. Our presentation includes a formula for the minimum line extension needed to achieve full R-line coverage of an ROI with a specified size, and also includes a preliminary study on the required detector size, showing that the R-lines added by the line extension are not constraining.

Retrieval-induced NMDA receptor-dependent Arc expression in two models of cocaine-cue memory.

PubMed

Alaghband, Yasaman; O'Dell, Steven J; Azarnia, Siavash; Khalaj, Anna J; Guzowski, John F; Marshall, John F

2014-12-01

The association of environmental cues with drugs of abuse results in persistent drug-cue memories. These memories contribute significantly to relapse among addicts. While conditioned place preference (CPP) is a well-established paradigm frequently used to examine the modulation of drug-cue memories, very few studies have used the non-preference-based model conditioned activity (CA) for this purpose. Here, we used both experimental approaches to investigate the neural substrates of cocaine-cue memories. First, we directly compared, in a consistent setting, the involvement of cortical and subcortical brain regions in cocaine-cue memory retrieval by quantifying activity-regulated cytoskeletal-associated (Arc) protein expression in both the CPP and CA models. Second, because NMDA receptor activation is required for Arc expression, we investigated the NMDA receptor dependency of memory persistence using the CA model. In both the CPP and CA models, drug-paired animals showed significant increases in Arc immunoreactivity in regions of the frontal cortex and amygdala compared to unpaired controls. Additionally, administration of a NMDA receptor antagonist (MK-801 or memantine) immediately after cocaine-CA memory reactivation impaired the subsequent conditioned locomotion associated with the cocaine-paired environment. The enhanced Arc expression evident in a subset of corticolimbic regions after retrieval of a cocaine-context memory, observed in both the CPP and CA paradigms, likely signifies that these regions: (i) are activated during retrieval of these memories irrespective of preference-based decisions, and (ii) undergo neuroplasticity in order to update information about cues previously associated with cocaine. This study also establishes the involvement of NMDA receptors in maintaining memories established using the CA model, a characteristic previously demonstrated using CPP. Overall, these results demonstrate the utility of the CA model for studies of cocaine-context memory and suggest the involvement of an NMDA receptor-dependent Arc induction pathway in drug-cue memory interference. Copyright © 2014 Elsevier Inc. All rights reserved.

Retrieval-induced NMDA receptor-dependent Arc expression in two models of cocaine-cue memory

PubMed Central

Alaghband, Yasaman; O'Dell, Steven J.; Azarnia, Siavash; Khalaj, Anna J.; Guzowski, John F.; Marshall, John F.

2014-01-01

The association of environmental cues with drugs of abuse results in persistent drug-cue memories. These memories contribute significantly to relapse among addicts. While conditioned place preference (CPP) is a well-established paradigm frequently used to examine the modulation of drug-cue memories, very few studies have used the non-preference-based model conditioned activity (CA) for this purpose. Here, we used both experimental approaches to investigate the neural substrates of cocaine-cue memories. First, we directly compared, in a consistent setting, the involvement of cortical and subcortical brain regions in cocaine-cue memory retrieval by quantifying activity-regulated cytoskeletal associated gene (Arc) protein expression in both the CPP and CA models. Second, because NMDA receptor activation is required for Arc expression, we investigated the NMDA receptor dependency of memory persistence using the CA model. In both the CPP and CA models, drug-paired animals showed significant increases in Arc immunoreactivity in regions of the frontal cortex and amygdala compared to unpaired controls. Additionally, administration of a NMDA receptor antagonist (MK-801 or memantine) immediately after cocaine-CA memory reactivation impaired the subsequent conditioned locomotion associated with the cocaine-paired environment. The enhanced Arc expression evident in a subset of corticolimbic regions after retrieval of a cocaine-context memory, observed in both the CPP and CA paradigms, likely signifies that these regions: (i) are activated during retrieval of these memories irrespective of preference-based decisions, and (ii) undergo neuroplasticity in order to update information about cues previously associated with cocaine. This study also establishes the involvement of NMDA receptors in maintaining memories established using the CA model, a characteristic previously demonstrated using CPP. Overall, these results demonstrate the utility of the CA model for studies of cocaine-context memory and suggest the involvement of an NMDA receptor-dependent Arc induction pathway in drug-cue memory interference. PMID:25225165

Aqueous stream characterization from biomass fast pyrolysis and catalytic fast pyrolysis

DOE PAGES

Black, Brenna A.; Michener, William E.; Ramirez, Kelsey J.; ...

2016-09-05

Here, biomass pyrolysis offers a promising means to rapidly depolymerize lignocellulosic biomass for subsequent catalytic upgrading to renewable fuels. Substantial efforts are currently ongoing to optimize pyrolysis processes including various fast pyrolysis and catalytic fast pyrolysis schemes. In all cases, complex aqueous streams are generated containing solubilized organic compounds that are not converted to target fuels or chemicals and are often slated for wastewater treatment, in turn creating an economic burden on the biorefinery. Valorization of the species in these aqueous streams, however, offers significant potential for substantially improving the economics and sustainability of thermochemical biorefineries. To that end, heremore » we provide a thorough characterization of the aqueous streams from four pilot-scale pyrolysis processes: namely, from fast pyrolysis, fast pyrolysis with downstream fractionation, in situ catalytic fast pyrolysis, and ex situ catalytic fast pyrolysis. These configurations and processes represent characteristic pyrolysis processes undergoing intense development currently. Using a comprehensive suite of aqueous-compatible analytical techniques, we quantitatively characterize between 12 g kg -1 of organic carbon of a highly aqueous catalytic fast pyrolysis stream and up to 315 g kg -1 of organic carbon present in the fast pyrolysis aqueous streams. In all cases, the analysis ranges between 75 and 100% of mass closure. The composition and stream properties closely match the nature of pyrolysis processes, with high contents of carbohydrate-derived compounds in the fast pyrolysis aqueous phase, high acid content in nearly all streams, and mostly recalcitrant phenolics in the heavily deoxygenated ex situ catalytic fast pyrolysis stream. Overall, this work provides a detailed compositional analysis of aqueous streams from leading thermochemical processes -- analyses that are critical for subsequent development of selective valorization strategies for these waste streams.« less

Aqueous stream characterization from biomass fast pyrolysis and catalytic fast pyrolysis

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

Black, Brenna A.; Michener, William E.; Ramirez, Kelsey J.

Here, biomass pyrolysis offers a promising means to rapidly depolymerize lignocellulosic biomass for subsequent catalytic upgrading to renewable fuels. Substantial efforts are currently ongoing to optimize pyrolysis processes including various fast pyrolysis and catalytic fast pyrolysis schemes. In all cases, complex aqueous streams are generated containing solubilized organic compounds that are not converted to target fuels or chemicals and are often slated for wastewater treatment, in turn creating an economic burden on the biorefinery. Valorization of the species in these aqueous streams, however, offers significant potential for substantially improving the economics and sustainability of thermochemical biorefineries. To that end, heremore » we provide a thorough characterization of the aqueous streams from four pilot-scale pyrolysis processes: namely, from fast pyrolysis, fast pyrolysis with downstream fractionation, in situ catalytic fast pyrolysis, and ex situ catalytic fast pyrolysis. These configurations and processes represent characteristic pyrolysis processes undergoing intense development currently. Using a comprehensive suite of aqueous-compatible analytical techniques, we quantitatively characterize between 12 g kg -1 of organic carbon of a highly aqueous catalytic fast pyrolysis stream and up to 315 g kg -1 of organic carbon present in the fast pyrolysis aqueous streams. In all cases, the analysis ranges between 75 and 100% of mass closure. The composition and stream properties closely match the nature of pyrolysis processes, with high contents of carbohydrate-derived compounds in the fast pyrolysis aqueous phase, high acid content in nearly all streams, and mostly recalcitrant phenolics in the heavily deoxygenated ex situ catalytic fast pyrolysis stream. Overall, this work provides a detailed compositional analysis of aqueous streams from leading thermochemical processes -- analyses that are critical for subsequent development of selective valorization strategies for these waste streams.« less

Neutral beam dump with cathodic arc titanium gettering

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

Smirnov, A.; Korepanov, S. A.; Putvinski, S.

An incomplete neutral beam capture can degrade the plasma performance in neutral beam driven plasma machines. The beam dumps mitigating the shine-through beam recycling must entrap and retain large particle loads while maintaining the beam-exposed surfaces clean of the residual impurities. The cathodic arc gettering, which provides high evaporation rate coupled with a fast time response, is a powerful and versatile technique for depositing clean getter films in vacuum. A compact neutral beam dump utilizing the titanium arc gettering was developed for a field-reversed configuration plasma sustained by 1 MW, 20-40 keV neutral hydrogen beams. The titanium evaporator features amore » new improved design. The beam dump is capable of handling large pulsed gas loads, has a high sorption capacity, and is robust and reliable. With the beam particle flux density of 5 x 10{sup 17} H/(cm{sup 2}s) sustained for 3-10 ms, the beam recycling coefficient, defined as twice the ratio of the hydrogen molecular flux leaving the beam dump to the incident flux of high-energy neutral atoms, is {approx}0.7. The use of the beam dump allows us to significantly reduce the recycling of the shine-through neutral beam as well as to improve the vacuum conditions in the machine.« less

A community detection algorithm using network topologies and rule-based hierarchical arc-merging strategies

PubMed Central

2017-01-01

The authors use four criteria to examine a novel community detection algorithm: (a) effectiveness in terms of producing high values of normalized mutual information (NMI) and modularity, using well-known social networks for testing; (b) examination, meaning the ability to examine mitigating resolution limit problems using NMI values and synthetic networks; (c) correctness, meaning the ability to identify useful community structure results in terms of NMI values and Lancichinetti-Fortunato-Radicchi (LFR) benchmark networks; and (d) scalability, or the ability to produce comparable modularity values with fast execution times when working with large-scale real-world networks. In addition to describing a simple hierarchical arc-merging (HAM) algorithm that uses network topology information, we introduce rule-based arc-merging strategies for identifying community structures. Five well-studied social network datasets and eight sets of LFR benchmark networks were employed to validate the correctness of a ground-truth community, eight large-scale real-world complex networks were used to measure its efficiency, and two synthetic networks were used to determine its susceptibility to two resolution limit problems. Our experimental results indicate that the proposed HAM algorithm exhibited satisfactory performance efficiency, and that HAM-identified and ground-truth communities were comparable in terms of social and LFR benchmark networks, while mitigating resolution limit problems. PMID:29121100

Microstructure and Tensile Behavior of Laser Arc Hybrid Welded Dissimilar Al and Ti Alloys

PubMed Central

Gao, Ming; Chen, Cong; Gu, Yunze; Zeng, Xiaoyan

2014-01-01

Fiber laser-cold metal transfer arc hybrid welding was developed to welding-braze dissimilar Al and Ti alloys in butt configuration. Microstructure, interface properties, tensile behavior, and their relationships were investigated in detail. The results show the cross-weld tensile strength of the joints is up to 213 MPa, 95.5% of same Al weld. The optimal range of heat input for accepted joints was obtained as 83–98 J·mm−1. Within this range, the joint is stronger than 200 MPa and fractures in weld metal, or else, it becomes weaker and fractures at the intermetallic compounds (IMCs) layer. The IMCs layer of an accepted joint is usually thin and continuous, which is about 1μm-thick and only consists of TiAl2 due to fast solidification rate. However, the IMCs layer at the top corner of fusion zone/Ti substrate is easily thickened with increasing heat input. This thickened IMCs layer consists of a wide TiAl3 layer close to FZ and a thin TiAl2 layer close to Ti substrate. Furthermore, both bead shape formation and interface growth were discussed by laser-arc interaction and melt flow. Tensile behavior was summarized by interface properties. PMID:28788533

The influence of a subduction component on magmatism in the Okinawa Trough: Evidence from thorium and related trace element ratios

NASA Astrophysics Data System (ADS)

Guo, Kun; Zeng, Zhi-Gang; Chen, Shuai; Zhang, Yu-Xiang; Qi, Hai-Yan; Ma, Yao

2017-09-01

The Okinawa Trough (OT) is a back-arc, initial continental marginal sea basin located behind the Ryukyu Arc-Trench System. Formation and evolution of the OT have been intimately related to subduction of the Philippine Sea Plate (PSP) since the late Miocene; thus, the magma source of the trough has been affected by subduction components, as in the case of other active back-arc basins, including the Lau Basin (LB) and Mariana Trough (MT). We review all the available geochemical data relating to basaltic lavas from the OT and the middle Ryukyu Arc (RA) in this paper in order to determine the influence of the subduction components on the formation of arc and back-arc magmas within this subduction system. The results of this study reveal that the abundances of Th in OT basalts (OTBs) are higher than that in LB (LBBs) and MT basalts (MTBs) due to the mixing of subducted sediments and EMI-like enriched materials. The geochemical characteristics of Th and other trace element ratios indicate that the OTB originated from a more enriched mantle source (compared to N-mid-ocean ridge basalt, N-MORB) and was augmented by subducted sediments. Data show that the magma sources of the south OT (SOT) and middle Ryukyu Arc (MRA) basalts were principally influenced by subducted aqueous fluids and bulk sediments, which were potentially added into magma sources by accretion and underplating. At the same time, the magma sources of the middle OT (MOT) and Kobi-syo and Sekibi-Syo (KBS+SBS) basalts were impacted by subducted aqueous fluids from both altered oceanic crust (AOC) and sediment. The variable geochemical characteristics of these basalts are due to different Wadati-Benioff depths and tectonic environments of formation, while the addition of subducted bulk sediment to SOT and MRA basalts may be due to accretion and underplating, and subsequent to form mélange formation, which would occur partial melting after aqueous fluids are added. The addition of AOC and sediment aqueous fluid to MOT and KBS+SBS basalts is therefore the result of cold subducted slab dehydration combined with a rapid subduction rate (82 mm/a), leading to the migration of fluids into the mantle wedge. The presence of these attributes is likely because the OT was a back-arc, initial continental marginal sea basin.

Fast and automated functional classification with MED-SuMo: an application on purine-binding proteins.

PubMed

Doppelt-Azeroual, Olivia; Delfaud, François; Moriaud, Fabrice; de Brevern, Alexandre G

2010-04-01

Ligand-protein interactions are essential for biological processes, and precise characterization of protein binding sites is crucial to understand protein functions. MED-SuMo is a powerful technology to localize similar local regions on protein surfaces. Its heuristic is based on a 3D representation of macromolecules using specific surface chemical features associating chemical characteristics with geometrical properties. MED-SMA is an automated and fast method to classify binding sites. It is based on MED-SuMo technology, which builds a similarity graph, and it uses the Markov Clustering algorithm. Purine binding sites are well studied as drug targets. Here, purine binding sites of the Protein DataBank (PDB) are classified. Proteins potentially inhibited or activated through the same mechanism are gathered. Results are analyzed according to PROSITE annotations and to carefully refined functional annotations extracted from the PDB. As expected, binding sites associated with related mechanisms are gathered, for example, the Small GTPases. Nevertheless, protein kinases from different Kinome families are also found together, for example, Aurora-A and CDK2 proteins which are inhibited by the same drugs. Representative examples of different clusters are presented. The effectiveness of the MED-SMA approach is demonstrated as it gathers binding sites of proteins with similar structure-activity relationships. Moreover, an efficient new protocol associates structures absent of cocrystallized ligands to the purine clusters enabling those structures to be associated with a specific binding mechanism. Applications of this classification by binding mode similarity include target-based drug design and prediction of cross-reactivity and therefore potential toxic side effects.

Fast and automated functional classification with MED-SuMo: An application on purine-binding proteins

PubMed Central

Doppelt-Azeroual, Olivia; Delfaud, François; Moriaud, Fabrice; de Brevern, Alexandre G

2010-01-01

Ligand–protein interactions are essential for biological processes, and precise characterization of protein binding sites is crucial to understand protein functions. MED-SuMo is a powerful technology to localize similar local regions on protein surfaces. Its heuristic is based on a 3D representation of macromolecules using specific surface chemical features associating chemical characteristics with geometrical properties. MED-SMA is an automated and fast method to classify binding sites. It is based on MED-SuMo technology, which builds a similarity graph, and it uses the Markov Clustering algorithm. Purine binding sites are well studied as drug targets. Here, purine binding sites of the Protein DataBank (PDB) are classified. Proteins potentially inhibited or activated through the same mechanism are gathered. Results are analyzed according to PROSITE annotations and to carefully refined functional annotations extracted from the PDB. As expected, binding sites associated with related mechanisms are gathered, for example, the Small GTPases. Nevertheless, protein kinases from different Kinome families are also found together, for example, Aurora-A and CDK2 proteins which are inhibited by the same drugs. Representative examples of different clusters are presented. The effectiveness of the MED-SMA approach is demonstrated as it gathers binding sites of proteins with similar structure-activity relationships. Moreover, an efficient new protocol associates structures absent of cocrystallized ligands to the purine clusters enabling those structures to be associated with a specific binding mechanism. Applications of this classification by binding mode similarity include target-based drug design and prediction of cross-reactivity and therefore potential toxic side effects. PMID:20162627

Maui-VIA: A User-Friendly Software for Visual Identification, Alignment, Correction, and Quantification of Gas Chromatography–Mass Spectrometry Data

PubMed Central

Kuich, P. Henning J. L.; Hoffmann, Nils; Kempa, Stefan

2015-01-01

A current bottleneck in GC–MS metabolomics is the processing of raw machine data into a final datamatrix that contains the quantities of identified metabolites in each sample. While there are many bioinformatics tools available to aid the initial steps of the process, their use requires both significant technical expertise and a subsequent manual validation of identifications and alignments if high data quality is desired. The manual validation is tedious and time consuming, becoming prohibitively so as sample numbers increase. We have, therefore, developed Maui-VIA, a solution based on a visual interface that allows experts and non-experts to simultaneously and quickly process, inspect, and correct large numbers of GC–MS samples. It allows for the visual inspection of identifications and alignments, facilitating a unique and, due to its visualization and keyboard shortcuts, very fast interaction with the data. Therefore, Maui-Via fills an important niche by (1) providing functionality that optimizes the component of data processing that is currently most labor intensive to save time and (2) lowering the threshold of expertise required to process GC–MS data. Maui-VIA projects are initiated with baseline-corrected raw data, peaklists, and a database of metabolite spectra and retention indices used for identification. It provides functionality for retention index calculation, a targeted library search, the visual annotation, alignment, correction interface, and metabolite quantification, as well as the export of the final datamatrix. The high quality of data produced by Maui-VIA is illustrated by its comparison to data attained manually by an expert using vendor software on a previously published dataset concerning the response of Chlamydomonas reinhardtii to salt stress. In conclusion, Maui-VIA provides the opportunity for fast, confident, and high-quality data processing validation of large numbers of GC–MS samples by non-experts. PMID:25654076

Real-Time Detection and Measurement of Eye Features from Color Images

PubMed Central

Borza, Diana; Darabant, Adrian Sergiu; Danescu, Radu

2016-01-01

The accurate extraction and measurement of eye features is crucial to a variety of domains, including human-computer interaction, biometry, and medical research. This paper presents a fast and accurate method for extracting multiple features around the eyes: the center of the pupil, the iris radius, and the external shape of the eye. These features are extracted using a multistage algorithm. On the first stage the pupil center is localized using a fast circular symmetry detector and the iris radius is computed using radial gradient projections, and on the second stage the external shape of the eye (of the eyelids) is determined through a Monte Carlo sampling framework based on both color and shape information. Extensive experiments performed on a different dataset demonstrate the effectiveness of our approach. In addition, this work provides eye annotation data for a publicly-available database. PMID:27438838

Fast Detection of Airports on Remote Sensing Images with Single Shot MultiBox Detector

NASA Astrophysics Data System (ADS)

Xia, Fei; Li, HuiZhou

2018-01-01

This paper introduces a method for fast airport detection on remote sensing images (RSIs) using Single Shot MultiBox Detector (SSD). To our knowledge, this could be the first study which introduces an end-to-end detection model into airport detection on RSIs. Based on the common low-level features between natural images and RSIs, a convolution neural network trained on large amounts of natural images was transferred to tackle the airport detection problem with limited annotated data. To deal with the specific characteristics of RSIs, some related parameters in the SSD, such as the scales and layers, were modified for more accurate and rapider detection. The experiments show that the proposed method could achieve 83.5% Average Recall at 8 FPS on RSIs with the size of 1024*1024. In contrast to Faster R-CNN, an improvement on AP and speed could be obtained.

Oligocene to Recent tectonic history of the Central Solomon intra-arc basin as determined from marine seismic reflection data and compilation of onland geology

NASA Astrophysics Data System (ADS)

Cowley, Shane; Mann, Paul; Coffin, M. F.; Shipley, Thomas H.

2004-10-01

Systematic analysis of a grid of 3450 km of multichannel seismic reflection lines from the Solomon Islands constrains the late Tertiary sedimentary and tectonic history of the Solomon Island arc and its convergent interaction with the Cretaceous Ontong Java oceanic plateau (OJP). The OJP, the largest oceanic plateau on Earth, subducted beneath the northern edge of the Solomon arc in the late Neogene, but the timing and consequences of this obliquely convergent event and its role in the subduction polarity reversal process remain poorly constrained. The Central Solomon intra-arc basin (CSB), which developed in Oligocene to Recent time above the Solomon arc, provides a valuable record of the tectonic environment prior to and accompanying the OJP convergent event and the subsequent arc polarity reversal. Recognition of regionally extensive stratigraphic sequences—whose ages can be inferred from marine sedimentary sections exposed onland in the Solomon Islands—indicate four distinct tectonic phases affecting the Solomon Island arc. Phase 1: Late Oligocene-Late Miocene rifting of the northeast-facing Solomon Island arc produced basal, normal-fault-controlled, asymmetrical sequences of the CSB; the proto-North Solomon trench was probably much closer to the CSB and is inferred to coincide with the trace of the present-day Kia-Kaipito-Korigole (KKK) fault zone; this protracted period of intra-arc extension shows no evidence for interruption by an early Miocene period of convergent "soft docking" of the Ontong Java Plateau as proposed by previous workers. Phase 2: Late Miocene-Pliocene oblique convergence of the Ontong Java Plateau at the proto-North Solomon trench (KKK fault zone) and folding of the CSB and formation of the Malaita accretionary prism (MAP); the highly oblique and diachronous convergence between the Ontong Java plateau and the Solomon arc terminates intra-arc extension first in the southeast (Russell subbasin of the CSB) during the Late Miocene and later during the Pliocene in the northwest (Shortland subbasin of the CSB); folds in the CSB form by inversion of normal faults formed during Phase 1; Phinney et al. [Sequence stratigraphy, structural style, and age of deformation of the Malaita accretionary prism (Solomon arc-Ontong Java Plateau convergent zone)] show a coeval pattern of southeast to northwest younging in folding and faulting of the MAP. Phase 3: Late Pliocene-early Pleistocene arc polarity reversal and subduction initiation at the San Cristobal trench. Effects of this event in the CSB include the formation of a chain of volcanoes above the subducting Australia plate at the San Cristobal trench, the formation of the broad synclinal structure of the CSB with evidence for truncation at the uplifted flanks, and widespread occurrence of slides and "seismites" (deposits formed by seismic shaking). Phase 4: Pleistocene to Recent continued shortening and synclinal subsidence of the CSB. Continued Australia-Pacific oblique plate convergence has led to deepening of the submarine, elongate basin axis of the synclinal CSB and uplift of the dual chain of the islands on its flanks.

Molecular and behavioral profiling of Dbx1-derived neurons in the arcuate, lateral and ventromedial hypothalamic nuclei.

PubMed

Sokolowski, Katie; Tran, Tuyen; Esumi, Shigeyuki; Kamal, Yasmin; Oboti, Livio; Lischinsky, Julieta; Goodrich, Meredith; Lam, Andrew; Carter, Margaret; Nakagawa, Yasushi; Corbin, Joshua G

2016-05-21

Neurons in the hypothalamus function to regulate the state of the animal during both learned and innate behaviors, and alterations in hypothalamic development may contribute to pathological conditions such as anxiety, depression or obesity. Despite many studies of hypothalamic development and function, the link between embryonic development and innate behaviors remains unexplored. Here, focusing on the embryonically expressed homeodomain-containing gene Developing Brain Homeobox 1 (Dbx1), we explored the relationship between embryonic lineage, post-natal neuronal identity and lineage-specific responses to innate cues. We found that Dbx1 is widely expressed across multiple developing hypothalamic subdomains. Using standard and inducible fate-mapping to trace the Dbx1-derived neurons, we identified their contribution to specific neuronal subtypes across hypothalamic nuclei and further mapped their activation patterns in response to a series of well-defined innate behaviors. Dbx1-derived neurons occupy multiple postnatal hypothalamic nuclei including the lateral hypothalamus (LH), arcuate nucleus (Arc) and the ventral medial hypothalamus (VMH). Within these nuclei, Dbx1 (+) progenitors generate a large proportion of the Pmch-, Nesfatin-, Cart-, Hcrt-, Agrp- and ERα-expressing neuronal populations, and to a lesser extent the Pomc-, TH- and Aromatase-expressing populations. Inducible fate-mapping reveals distinct temporal windows for development of the Dbx1-derived LH and Arc populations, with Agrp(+) and Cart(+) populations in the Arc arising early (E7.5-E9.5), while Pmch(+) and Hcrt(+) populations in the LH derived from progenitors expressing Dbx1 later (E9.5-E11.5). Moreover, as revealed by c-Fos labeling, Dbx1-derived cells in male and female LH, Arc and VMH are responsive during mating and aggression. In contrast, Dbx1-lineage cells in the Arc and LH have a broader behavioral tuning, which includes responding to fasting and predator odor cues. We define a novel fate map of the hypothalamus with respect to Dbx1 expression in hypothalamic progenitor zones. We demonstrate that in a temporally regulated manner, Dbx1-derived neurons contribute to molecularly distinct neuronal populations in the LH, Arc and VMH that have been implicated in a variety of hypothalamic-driven behaviors. Consistent with this, Dbx1-derived neurons in the LH, Arc and VMH are activated during stress and other innate behavioral responses, implicating their involvement in these diverse behaviors.

Real-time 3D internal marker tracking during arc radiotherapy by the use of combined MV kV imaging

NASA Astrophysics Data System (ADS)

Liu, W.; Wiersma, R. D.; Mao, W.; Luxton, G.; Xing, L.

2008-12-01

To minimize the adverse dosimetric effect caused by tumor motion, it is desirable to have real-time knowledge of the tumor position throughout the beam delivery process. A promising technique to realize the real-time image guided scheme in external beam radiation therapy is through the combined use of MV and onboard kV beam imaging. The success of this MV-kV triangulation approach for fixed-gantry radiation therapy has been demonstrated. With the increasing acceptance of modern arc radiotherapy in the clinics, a timely and clinically important question is whether the image guidance strategy can be extended to arc therapy to provide the urgently needed real-time tumor motion information. While conceptually feasible, there are a number of theoretical and practical issues specific to the arc delivery that need to be resolved before clinical implementation. The purpose of this work is to establish a robust procedure of system calibration for combined MV and kV imaging for internal marker tracking during arc delivery and to demonstrate the feasibility and accuracy of the technique. A commercially available LINAC equipped with an onboard kV imager and electronic portal imaging device (EPID) was used for the study. A custom built phantom with multiple ball bearings was used to calibrate the stereoscopic MV-kV imaging system to provide the transformation parameters from imaging pixels to 3D world coordinates. The accuracy of the fiducial tracking system was examined using a 4D motion phantom capable of moving in accordance with a pre-programmed trajectory. Overall, spatial accuracy of MV-kV fiducial tracking during the arc delivery process for normal adult breathing amplitude and period was found to be better than 1 mm. For fast motion, the results depended on the imaging frame rates. The RMS error ranged from ~0.5 mm for the normal adult breathing pattern to ~1.5 mm for more extreme cases with a low imaging frame rate of 3.4 Hz. In general, highly accurate real-time tracking of implanted markers using hybrid MV-kV imaging is achievable and the technique should be useful to improve the beam targeting accuracy of arc therapy.

Lesser Antillean Arc Initiation and Migration as a Proxy of Slab Dynamics: Geothermochronology, Thermobarometry and Structure of Saint Martin Granodiorites

NASA Astrophysics Data System (ADS)

Noury, M.; Münch, P.; Philippon, M. M.; Bernet, M.; Bruguier, O.; Balvay, M.

2017-12-01

In subduction zones, volcanic arc initiation, cessation, migration and associated upper plate deformation -i.e faulting and vertical motions- reflect large-scale slab dynamics. At the northeastern edge of the Caribbean plate, the Greater Caribbean subduction zone waned out during the Mid Eocene, following the subduction of the Bahamas bank. This arc cessation was contemporaneous with (i) a plate boundary re-organization (evolving from subduction to transform), (ii) upper plate deformation and (iii) arc initiation in the Lesser Antilles. As part of the GAARANTI project that aims at unraveling the relationships between the evolution of terrestrial Caribbean biodiversity and vertical motions resulting from the Lesser Antilles subduction zone dynamic, we study the Saint Martin granodiorites, one of the two Oligocene plutons outcropping in the Lesser Antillean forearc. We investigate the birth and evolution of the Lesser Antillean arc and its thermo-mechanical impact on the Caribbean upper plate. In order to characterize the P,T,t path of the pluton we performed several thermochronological analyses covering a wide range of temperature (U-Pb on zircon -Tc 850°C, Ar/Ar on amphibole -Tc 550°C- and biotite -Tc 325°C-, zircon and apatite fission-tracks -Tc 250 and 110°C, respectively as well as U-Th/He on apatite -Tc 60°C) coupled with in-situ thermobarometry analyses (Al in hornblendes) and structural data. Geochronology and thermobarometry reveal that the granodiorites emplaced at ca. 28 Ma, at a depth of 5 km. Based on the age difference between amphibole and biotite Ar/Ar ages, we show that the northern pluton cooled faster than the southern one. Preliminary thermochronological results show a fast cooling between 29 and 25 Ma and then a continuous and slow cooling since 25 Ma and inverse modeling points to a 10 Ma cooling event. Our investigations give insights on the thermo-mechanical evolution of the arc-forearc region of the Lesser Antilles subduction zone. Considering a mean high of 1200m for the volcanic edifice, the pluton emplaced at shallow depth (ca. 4 km) within the Caribbean plate. The pluton is bounded by N-S faults that could possibly be responsible for the 10 Ma exhumation event. This thermal event may be contemporaneous with the westward arc migration during Miocene times and may reflect slab flattening.

Real-time 3D internal marker tracking during arc radiotherapy by the use of combined MV-kV imaging.

PubMed

Liu, W; Wiersma, R D; Mao, W; Luxton, G; Xing, L

2008-12-21

To minimize the adverse dosimetric effect caused by tumor motion, it is desirable to have real-time knowledge of the tumor position throughout the beam delivery process. A promising technique to realize the real-time image guided scheme in external beam radiation therapy is through the combined use of MV and onboard kV beam imaging. The success of this MV-kV triangulation approach for fixed-gantry radiation therapy has been demonstrated. With the increasing acceptance of modern arc radiotherapy in the clinics, a timely and clinically important question is whether the image guidance strategy can be extended to arc therapy to provide the urgently needed real-time tumor motion information. While conceptually feasible, there are a number of theoretical and practical issues specific to the arc delivery that need to be resolved before clinical implementation. The purpose of this work is to establish a robust procedure of system calibration for combined MV and kV imaging for internal marker tracking during arc delivery and to demonstrate the feasibility and accuracy of the technique. A commercially available LINAC equipped with an onboard kV imager and electronic portal imaging device (EPID) was used for the study. A custom built phantom with multiple ball bearings was used to calibrate the stereoscopic MV-kV imaging system to provide the transformation parameters from imaging pixels to 3D world coordinates. The accuracy of the fiducial tracking system was examined using a 4D motion phantom capable of moving in accordance with a pre-programmed trajectory. Overall, spatial accuracy of MV-kV fiducial tracking during the arc delivery process for normal adult breathing amplitude and period was found to be better than 1 mm. For fast motion, the results depended on the imaging frame rates. The RMS error ranged from approximately 0.5 mm for the normal adult breathing pattern to approximately 1.5 mm for more extreme cases with a low imaging frame rate of 3.4 Hz. In general, highly accurate real-time tracking of implanted markers using hybrid MV-kV imaging is achievable and the technique should be useful to improve the beam targeting accuracy of arc therapy.

On the development of the calc-alkaline and tholeiitic magma series: A deep crustal cumulate perspective

NASA Astrophysics Data System (ADS)

Chin, Emily J.; Shimizu, Kei; Bybee, Grant M.; Erdman, Monica E.

2018-01-01

Two distinct igneous differentiation trends - the tholeiitic and calc-alkaline - give rise to Earth's oceanic and continental crust, respectively. Mantle melting at mid-ocean ridges produces dry magmas that differentiate at low-pressure conditions, resulting in early plagioclase saturation, late oxide precipitation, and Fe-enrichment in mid-ocean ridge basalts (MORBs). In contrast, magmas formed above subduction zones are Fe-depleted, have elevated water contents and are more oxidized relative to MORBs. It is widely thought that subduction of hydrothermally altered, oxidized oceanic crust at convergent margins oxidizes the mantle source of arc magmas, resulting in erupted lavas that inherit this oxidized signature. Yet, because our understanding of the calc-alkaline and tholeiitic trends largely comes from studies of erupted melts, the signals from shallow crustal contamination by potentially oxidized, Si-rich, Fe-poor materials, which may also generate calc-alkaline rocks, are obscured. Here, we use deep crustal cumulates to "see through" the effects of shallow crustal processes. We find that the tholeiitic and calc-alkaline trends are indeed reflected in Fe-poor mid-ocean ridge cumulates and Fe-rich arc cumulates, respectively. A key finding is that with increasing crustal thickness, arc cumulates become more Fe-enriched. We propose that the thickness of the overlying crustal column modulates the melting degree of the mantle wedge (lower F beneath thick arcs and vice versa) and thus water and Fe3+ contents in primary melts, which subsequently controls the onset and extent of oxide fractionation. Deep crustal cumulates beneath thick, mature continental arcs are the most Fe-enriched, and therefore may be the "missing" Fe-rich reservoir required to balance the Fe-depleted upper continental crust.

Geochemistry, petrography, and zircon U-Pb geochronology of Paleozoic metaigneous rocks in the Mount Veta area of east-central Alaska: implications for the evolution of the westernmost part of the Yukon-Tanana terrane

USGS Publications Warehouse

Dusel-Bacon, Cynthia; Day, Warren C.; Aleinikoff, John N.

2013-01-01

We report the results of new mapping, whole-rock major, minor, and trace-element geochemistry, and petrography for metaigneous rocks from the Mount Veta area in the westernmost part of the allochthonous Yukon–Tanana terrane (YTT) in east-central Alaska. These rocks include tonalitic mylonite gneiss and mafic metaigneous rocks from the Chicken metamorphic complex and the Nasina and Fortymile River assemblages. Whole-rock trace-element data from the tonalitic gneiss, whose igneous protolith was dated by SHRIMP U–Pb zircon geochronology at 332.6 ± 5.6 Ma, indicate derivation from tholeiitic arc basalt. Whole-rock analyses of the mafic rocks suggest that greenschist-facies rocks from the Chicken metamorphic complex, a mafic metavolcanic rock from the Nasina assemblage, and an amphibolite from the Fortymile River assemblage formed as island-arc tholeiite in a back-arc setting; another Nasina assemblage greenschist has MORB geochemical characteristics, and another mafic metaigneous rock from the Fortymile River assemblage has geochemical characteristics of calc-alkaline basalt. Our geochemical results imply derivation in an arc and back-arc spreading region within the allochthonous YTT crustal fragment, as previously proposed for correlative units in other parts of the terrane. We also describe the petrography and geochemistry of a newly discovered tectonic lens of Alpine-type metaharzburgite. The metaharzburgite is interpreted to be a sliver of lithospheric mantle from beneath the Seventymile ocean basin or from sub-continental mantle lithosphere of the allochthonous YTT or the western margin of Laurentia that was tectonically emplaced within crustal rocks during closure of the Seventymile ocean basin and subsequently displaced and fragmented by faults.

Arc-heated gas flow experiments for hypersonic propulsion applications

NASA Astrophysics Data System (ADS)

Roseberry, Christopher Matthew

Although hydrogen is an attractive fuel for a hypersonic air-breathing vehicle in terms of reaction rate, flame temperature, and energy content per unit mass, the substantial tank volume required to store hydrogen imposes a drag penalty to performance that tends to offset these advantages. An alternative approach is to carry a hydrocarbon fuel and convert it on-board into a hydrogen-rich gas mixture to be injected into the engine combustors. To investigate this approach, the UTA Arc-Heated Wind Tunnel facility was modified to run on methane rather than the normally used nitrogen. Previously, this facility was extensively developed for the purpose of eventually performing experiments simulating scramjet engine flow along a single expansion ramp nozzle (SERN) in addition to more generalized applications. This formidable development process, which involved modifications to every existing subsystem along with the incorporation of new subsystems, is described in detail. Fortunately, only a minor plumbing reconfiguration was required to prepare the facility for the fuel reformation research. After a failure of the arc heater power supply, a 5.6 kW plasma-cutting torch was modified in order to continue the arc pyrolysis experiments. The outlet gas flow from the plasma torch was sampled and subsequently analyzed using gas chromatography. The experimental apparatus converted the methane feedstock almost completely into carbon, hydrogen and acetylene. A high yield of hydrogen, consisting of a product mole fraction of roughly 0.7, was consistently obtained. Unfortunately, the energy consumption of the apparatus was too excessive to be feasible for a flight vehicle. However, other researchers have pyrolyzed hydrocarbons using electric arcs with much less power input per unit mass.

Kisspeptin Expression in Guinea Pig Hypothalamus: Effects of 17β-Estradiol

PubMed Central

Bosch, Martha A.; Xue, Changhui; Rønnekleiv, Oline K.

2013-01-01

Kisspeptin is essential for reproductive functions in humans. As a model for the human we have used the female guinea pig, which has a long ovulatory cycle similar to that of primates. Initially, we cloned a guinea pig kisspeptin cDNA sequence and subsequently explored the distribution and 17β-estradiol (E2) regulation of kisspeptin mRNA (Kiss1) and protein (kisspeptin) by using in situ hybridization, real-time PCR and immunocytochemistry. In ovariectomized females, Kiss1 neurons were scattered throughout the preoptic periventricular areas (PV), but the vast majority of Kiss1 neurons were localized in the arcuate nucleus (Arc). An E2 treatment that first inhibits (negative feedback) and then augments (positive feedback) serum luteinizing hormone (LH) increased Kiss1 mRNA density and number of cells expressing Kiss1 in the PV at both time points. Within the Arc, Kiss1 mRNA density was reduced at both time points. Quantitative real-time PCR confirmed the in situ hybridization results during positive feedback. E2 reduced the number of immunoreactive kisspeptin cells in the PV at both time points, perhaps an indication of increased release. Within the Arc, the kisspeptin immunoreactivity was decreased during negative feedback but increased during positive feedback. Therefore, it appears that in guinea pig both the PV and the Arc kisspeptin neurons act cooperatively to excite gonadotropin-releasing hormone (GnRH) neurons during positive feedback. We conclude that E2 regulation of negative and positive feedback may reflect a complex interaction of the kisspeptin circuitry, and both the PV and the Arc respond to hormone signals to encode excitation of GnRH neurons during the ovulatory cycle. PMID:22173890

Ambient noise tomography of Ecuador: Fore- and back-arc velocity structure and radial anisotropy

NASA Astrophysics Data System (ADS)

Lynner, C.; Beck, S. L.; Porritt, R.; Meltzer, A.; Alvarado, A. P.; Gabriela, P.; Ruiz, M. C.; Hoskins, M.; Stachnik, J.; Rietbrock, A.; Leon-Rios, S.; Regnier, M. M.; Agurto-Detzel, H.; Font, Y.; Charvis, P.

2017-12-01

In northern South America, the oceanic Nazca plate subducts beneath the South American continent, giving rise to the high mountains of the northern Andes. The Ecuador subduction zone has a history of large megathrust earthquakes, most recently the Mw=7.8 April 16, 2016, Pedernales earthquake. The volcanic arc in Ecuador is broad with active volcanoes along both the western and eastern cordilleras. Many of these volcanoes surround the city of Quito putting millions of people at risk. A recent international broadband aftershock deployment was conducted for approximately one year after the Pedernales mainshock and this data combined with a sub-set of data from from the permanent IGEPN national network provide an ideal data set to use for ambient noise tomography (ANT) to constrain absolute Vsh and Vsv across Ecuador. ANT studies use noise-generated surface wave dispersion measurements to invert for 3D shear velocity in the crust. Having a precise understanding of crustal velocity structure is necessary to advance a number of projects, including better earthquake locations of the April 16, 2016 Pedernales-earthquake aftershock sequence and identifying large-scale partial melt zones associated with the active volcanic arc. The majority of ANT studies use only Rayleigh waves to constrain Vsv structure. Initial Rayleigh wave ANT results, using periods between 8 and 40 seconds, show a fast phase velocities for the forearc and much slower phase velocities for the high elevation volcanic arc. Including Love wave dispersion measurements can improve overall crustal velocity models, as well as provide constraints on radial anisotropy. Radial anisotropy can develop in a variety of ways but most typically arises from the deformation-induced alignment of anisotropic minerals. Radial anisotropy, therefore, can inform on patterns of ductile crustal flow. Strong radial anisotropy at mid-crustal depths from ANT has already been observed south of Ecuador, in the Central Andean Plateau, raising the question, does the radial anisotropy signal persist as far north as the Ecuadorian Andes? Here we present Vsh, Vsv, and radial anisotropy results from Love and Rayleigh wave ambient noise tomography in Ecuador from the fore-arc to the back-arc region.

Unravelling the pre-Variscan evolution of the Habach terrane (Tauern Window, Austria) by U-Pb SHRIMP zircon data

NASA Astrophysics Data System (ADS)

Eichhorn, Roland; Loth, Georg; Kennedy, Allen

2001-08-01

The U-Pb SHRIMP age determinations of zircons from the Habach terrane (Tauern Window, Austria) reveal a complex evolution of this basement unit, which is exposed in the Penninic domain of the Alpine orogen. The oldest components are found in zircons of a metamorphosed granitoid clast, of a migmatitic leucosome, and of a meta-rhyolitic (Variscan) tuff which bear cores of Archean age. The U-Pb ages of discordant zircon cores of the same rocks range between 540 and 520 Ma. It is assumed that the latter zircons were originally also of Archean origin and suffered severe lead loss, whilst being incorporated into Early-Cambrian volcanic arc magmas. The provenance region of the Archean (2.64-2.06 Ga) zircons is assumed to be a terrane of Gondwana affinity: i.e., the West African craton (Hoggar Shield, Reguibat Shield). The Caledonian metamorphism left a pervasive structural imprint in amphibolite facies on rocks of the Habach terrane; it is postdated by discordant zircons of a migmatitic leucosome at <440 Ma (presumably ca. 420 Ma). Alpine and Variscan upper greenschist- to amphibolite-facies conditions caused partial lead loss in zircons of a muscovite gneiss ('white schist') only, where extensive fluid flow and brittle deformation due to its position near a nappe-sole thrust enhanced the grains' susceptibility to isotopic disturbance. The Habach terrane - an active continental margin with ensialic back-arc development - showed subduction-induced magmatic activity approx. between 550 and 507 Ma. Back-arc diorites and arc basalts were intruded by ultramafic sills and subsequently by small patches of mantle-dominated unaltered and (in the vicinity of a major tungsten deposit) altered granitoids. Fore-arc (shales) and back-arc (greywackes, cherts) basin sediments as well as arc and back-arc magmatites were not only nappe-stacked by the Caledonian compressional regime closing the presumably narrow oceanic back-arc basin and squeezing mafic to ultramafic cumulates out of high-level magma chambers (496-482 Ma). It also induced uplift and erosion of deeply rooted crystalline complexes and triggered the development of a successor basin filled with predominantly clastic greywacke-arkosic sediments. The study demonstrates that the basement rocks exposed in the Habach terrane might be the 'missing link' between similar units of the more westerly positioned External domain (i.e., Aar, Aiguilles Rouges, Mont Blanc) and the Austroalpine domain to the east (Oetztal, Silvretta).

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

PubMed

Büssow, Konrad; Hoffmann, Steve; Sievert, Volker

2002-12-19

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

SurfaceSlide: a multitouch digital pathology platform.

PubMed

Wang, Yinhai; Williamson, Kate E; Kelly, Paul J; James, Jacqueline A; Hamilton, Peter W

2012-01-01

Digital pathology provides a digital environment for the management and interpretation of pathological images and associated data. It is becoming increasing popular to use modern computer based tools and applications in pathological education, tissue based research and clinical diagnosis. Uptake of this new technology is stymied by its single user orientation and its prerequisite and cumbersome combination of mouse and keyboard for navigation and annotation. In this study we developed SurfaceSlide, a dedicated viewing platform which enables the navigation and annotation of gigapixel digitised pathological images using fingertip touch. SurfaceSlide was developed using the Microsoft Surface, a 30 inch multitouch tabletop computing platform. SurfaceSlide users can perform direct panning and zooming operations on digitised slide images. These images are downloaded onto the Microsoft Surface platform from a remote server on-demand. Users can also draw annotations and key in texts using an on-screen virtual keyboard. We also developed a smart caching protocol which caches the surrounding regions of a field of view in multi-resolutions thus providing a smooth and vivid user experience and reducing the delay for image downloading from the internet. We compared the usability of SurfaceSlide against Aperio ImageScope and PathXL online viewer. SurfaceSlide is intuitive, fast and easy to use. SurfaceSlide represents the most direct, effective and intimate human-digital slide interaction experience. It is expected that SurfaceSlide will significantly enhance digital pathology tools and applications in education and clinical practice.

SurfaceSlide: A Multitouch Digital Pathology Platform

PubMed Central

Wang, Yinhai; Williamson, Kate E.; Kelly, Paul J.; James, Jacqueline A.; Hamilton, Peter W.

2012-01-01

Background Digital pathology provides a digital environment for the management and interpretation of pathological images and associated data. It is becoming increasing popular to use modern computer based tools and applications in pathological education, tissue based research and clinical diagnosis. Uptake of this new technology is stymied by its single user orientation and its prerequisite and cumbersome combination of mouse and keyboard for navigation and annotation. Methodology In this study we developed SurfaceSlide, a dedicated viewing platform which enables the navigation and annotation of gigapixel digitised pathological images using fingertip touch. SurfaceSlide was developed using the Microsoft Surface, a 30 inch multitouch tabletop computing platform. SurfaceSlide users can perform direct panning and zooming operations on digitised slide images. These images are downloaded onto the Microsoft Surface platform from a remote server on-demand. Users can also draw annotations and key in texts using an on-screen virtual keyboard. We also developed a smart caching protocol which caches the surrounding regions of a field of view in multi-resolutions thus providing a smooth and vivid user experience and reducing the delay for image downloading from the internet. We compared the usability of SurfaceSlide against Aperio ImageScope and PathXL online viewer. Conclusion SurfaceSlide is intuitive, fast and easy to use. SurfaceSlide represents the most direct, effective and intimate human–digital slide interaction experience. It is expected that SurfaceSlide will significantly enhance digital pathology tools and applications in education and clinical practice. PMID:22292040

microRNAs Databases: Developmental Methodologies, Structural and Functional Annotations.

PubMed

Singh, Nagendra Kumar

2017-09-01

microRNA (miRNA) is an endogenous and evolutionary conserved non-coding RNA, involved in post-transcriptional process as gene repressor and mRNA cleavage through RNA-induced silencing complex (RISC) formation. In RISC, miRNA binds in complementary base pair with targeted mRNA along with Argonaut proteins complex, causes gene repression or endonucleolytic cleavage of mRNAs and results in many diseases and syndromes. After the discovery of miRNA lin-4 and let-7, subsequently large numbers of miRNAs were discovered by low-throughput and high-throughput experimental techniques along with computational process in various biological and metabolic processes. The miRNAs are important non-coding RNA for understanding the complex biological phenomena of organism because it controls the gene regulation. This paper reviews miRNA databases with structural and functional annotations developed by various researchers. These databases contain structural and functional information of animal, plant and virus miRNAs including miRNAs-associated diseases, stress resistance in plant, miRNAs take part in various biological processes, effect of miRNAs interaction on drugs and environment, effect of variance on miRNAs, miRNAs gene expression analysis, sequence of miRNAs, structure of miRNAs. This review focuses on the developmental methodology of miRNA databases such as computational tools and methods used for extraction of miRNAs annotation from different resources or through experiment. This study also discusses the efficiency of user interface design of every database along with current entry and annotations of miRNA (pathways, gene ontology, disease ontology, etc.). Here, an integrated schematic diagram of construction process for databases is also drawn along with tabular and graphical comparison of various types of entries in different databases. Aim of this paper is to present the importance of miRNAs-related resources at a single place.

Study of electrochemical properties of thin film materials obtained using plasma technologies for production of electrodes for pacemakers

NASA Astrophysics Data System (ADS)

Obrezkov, O. I.; Vinogradov, V. P.; Krauz, V. I.; Mozgrin, D. V.; Guseva, I. A.; Andreev, E. S.; Zverev, A. A.; Starostin, A. L.

2016-09-01

Studies of thin film materials (TFM) as coatings of tips of pacemaker electrodes implanted into the human heart have been performed. TFM coatings were deposited in vacuum by arc magnetron discharge plasma, by pulsed discharge of “Plasma Focus”, and by electron beam evaporation. Simulation of electric charge transfer to the heart in physiological blood- imitator solution and determination of electrochemical properties of the coatings were carried out. TFM of highly developed surface of contact with tissue was produced by argon plasma spraying of titanium powder with subsequent coating by titanium nitride in vacuum arc assisted by Ti ion implantation. The TFM coatings of pacemaker electrode have passed necessary clinical tests and were used in medical practice. They provide low voltage myocardium stimulation thresholds within the required operating time.

Effect of laser power on clad metal in laser-TIG combined metal cladding

NASA Astrophysics Data System (ADS)

Utsumi, Akihiro; Hino, Takanori; Matsuda, Jun; Tasoda, Takashi; Yoneda, Masafumi; Katsumura, Munehide; Yano, Tetsuo; Araki, Takao

2003-03-01

TIG arc welding has been used to date as a method for clad welding of white metal as bearing material. We propose a new clad welding process that combines a CO2 laser and a TIG arc, as a method for cladding at high speed. We hypothesized that this method would permit appropriate control of the melted quantity of base metal by varying the laser power. We carried out cladding while varying the laser power, and investigated the structure near the boundary between the clad layer and the base metal. Using the laser-TIG combined cladding, we found we were able to control appropriately the degree of dilution with the base metal. By applying this result to subsequent cladding, we were able to obtain a clad layer of high quality, which was slightly diluted with the base metal.

What collided with India at ~50 Ma? Constraints from the sedimentary record in the NW Himalaya, Ladakh.

NASA Astrophysics Data System (ADS)

Najman, Y.; Jenks, D.; Godin, L.; BouDagher-Fadel, M. K.; Bown, P. R.; Horstwood, M. S.; Garzanti, E.; Bracciali, L.; Millar, I.

2014-12-01

The timing of India-Asia collision is critical to the understanding of crustal deformation processes. In the NW Himalaya, a number of workers have proposed a ~55-50 Ma age for collision along the Indus suture zone which separates India from the Kohistan-Ladakh Intraoceanic Island arc (KLA) to the north. This is based on a number of factors including the age of youngest marine sediments in the suture (e.g. Green et al. 2008), age of eclogites indicative of onset of Indian continental subduction (e.g. de Sigoyer et al. 2000), and first evidence of detritus from north of the suture zone deposited on the Indian plate (e.g. Clift et al. 2002). Such evidence can be interpreted as documenting the age of India-Asia collision if one takes the KLA to have collided with the Asian plate prior to its collision with India (e.g. Petterson 2010 and refs therein). However, an increasing number of workers propose that the KLA collided with Asia subsequent to its earlier collision with India, dated variously at 85 Ma (Chatterjee et al. 2013), 61 Ma (Khan et al. 2009) and 50 Ma (Bouilhol et al. 2013). If correct, then the previous constraints to dating the collision as outlined above have in fact been dating the timing of India-arc collision, rather than the final ocean closure and terminal collision of India+arc with Asia as previously believed. This, plus the questioning of earlier provenance work of Clift et al. (2002) regarding the validity of their data for constraining the time when detritus from north of the suture first arrived on the Indian plate (Henderson et al. 2011) suggests that the time is right for a reappraisal of this topic. But which method to use? A provenance study now brings with it a requirement to distinguish between detritus from the KLA and Southern margin of Asia. Recently, Bouilhol et al (2013) undertook a detailed study of the KLA, using temporal and spatial variation of zircon U-Pb and Hf as well as Sr-Nd bulk analyses, to document the arc's collision with India at 50 Ma and its subsequent collision with Asia at 40 Ma. Such variation should be reflected in the detrital record of material eroded from the arc. We use zircon U-Pb and Hf analyses from Palaeogene sediments deposited in and adjacent to the Indus suture in Ladakh, to further explore the interpretations presented in that research.

A Western Pacific Hotspot?

NASA Astrophysics Data System (ADS)

MacPherson, C. G.; Hall, R.

2002-12-01

The petrology of volcanic rocks from the St. Andrew Strait and helium isotope ratios of backarc lavas from the Manus Basin have been used to propose the existence of an active hotspot beneath the eastern Bismarck Sea [1,2]. The possible influence of this hotspot can be assessed by mapping its present location onto a plate tectonic reconstruction of the western Pacific [3,4]. During the Middle Eocene the nascent Izu-Bonin-Mariana (IBM) arc lay above the hotspot. The volume of magma emplaced at the IBM arc at that time substantially exceeds the average magma production rate for mature island arcs. Furthermore, the ultramafic (boninitic) character of much of this magmatism requires elevated temperatures in the mantle. The geochemistry of contemporaneous magmatism in the backarc resembles melts usually found at ocean islands and much of the backarc region experienced significant uplift at that time. All of these features can be explained by the influx of hot, buoyant, chemically distinct mantle beneath the IBM and its hinterland. The plates lying above the hotspot during the later Eocene were subsequently subducted, but plate reconstruction suggests that during the Oligo-Miocene it was crossed by parts of the Caroline Plate where the Euripik Rise is found. This is an aseismic rise that possesses the geophysical characteristics of thickened oceanic crust formed by excess, basaltic magmatism and is the type of structure that would result from the passage of relatively young oceanic lithosphere over a mantle hotspot. Plate reconstruction for the western Pacific predicts a hotspot trail that is consistent with the Middle Eocene and Oligo-Miocene geology of the IBM and Caroline Plates, respectively. Parts of the trail have been disrupted by subsequent sea-floor spreading or lost through subduction but the remaining vestiges are consistent with the action of a thermal anomaly throughout much of the Cenozoic. More speculatively, the difference in buoyancy between the IBM, supported by hot mantle, and older, colder lithosphere of the adjacent Pacific Plate may have provided a mechanism to propagate widespread subduction at the nascent IBM arc, which has recently been shown to predate the postulated change in direction of the Pacific Plate during the Eocene [5]. [1] Johnson et al. 1978, BMR J. Aus. Geol. and Geophys. 3, 55. [2] Macpherson et al. 1998, Geology 26, 1007. [3] Hall 2002, J. Asian. Earth Sci. 20, 353. [4] Macpherson et al. 2001 EPSL 186, 215. [5] Cosca et al. 1998 Island Arc 7, 579.

deFUME: Dynamic exploration of functional metagenomic sequencing data.

PubMed

van der Helm, Eric; Geertz-Hansen, Henrik Marcus; Genee, Hans Jasper; Malla, Sailesh; Sommer, Morten Otto Alexander

2015-07-31

Functional metagenomic selections represent a powerful technique that is widely applied for identification of novel genes from complex metagenomic sources. However, whereas hundreds to thousands of clones can be easily generated and sequenced over a few days of experiments, analyzing the data is time consuming and constitutes a major bottleneck for experimental researchers in the field. Here we present the deFUME web server, an easy-to-use web-based interface for processing, annotation and visualization of functional metagenomics sequencing data, tailored to meet the requirements of non-bioinformaticians. The web-server integrates multiple analysis steps into one single workflow: read assembly, open reading frame prediction, and annotation with BLAST, InterPro and GO classifiers. Analysis results are visualized in an online dynamic web-interface. The deFUME webserver provides a fast track from raw sequence to a comprehensive visual data overview that facilitates effortless inspection of gene function, clustering and distribution. The webserver is available at cbs.dtu.dk/services/deFUME/and the source code is distributed at github.com/EvdH0/deFUME.

ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life

PubMed Central

Pafilis, Evangelos; Frankild, Sune P.; Schnetzer, Julia; Fanini, Lucia; Faulwetter, Sarah; Pavloudi, Christina; Vasileiadou, Katerina; Leary, Patrick; Hammock, Jennifer; Schulz, Katja; Parr, Cynthia Sims; Arvanitidis, Christos; Jensen, Lars Juhl

2015-01-01

Summary: The association of organisms to their environments is a key issue in exploring biodiversity patterns. This knowledge has traditionally been scattered, but textual descriptions of taxa and their habitats are now being consolidated in centralized resources. However, structured annotations are needed to facilitate large-scale analyses. Therefore, we developed ENVIRONMENTS, a fast dictionary-based tagger capable of identifying Environment Ontology (ENVO) terms in text. We evaluate the accuracy of the tagger on a new manually curated corpus of 600 Encyclopedia of Life (EOL) species pages. We use the tagger to associate taxa with environments by tagging EOL text content monthly, and integrate the results into the EOL to disseminate them to a broad audience of users. Availability and implementation: The software and the corpus are available under the open-source BSD and the CC-BY-NC-SA 3.0 licenses, respectively, at http://environments.hcmr.gr Contact: pafilis@hcmr.gr or lars.juhl.jensen@cpr.ku.dk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25619994

Integration of human pancreatic islet genomic data refines regulatory mechanisms at Type 2 Diabetes susceptibility loci

PubMed Central

Thurner, Matthias; van de Bunt, Martijn; Torres, Jason M; Mahajan, Anubha; Nylander, Vibe; Bennett, Amanda J; Gaulton, Kyle J; Barrett, Amy; Burrows, Carla; Bell, Christopher G; Lowe, Robert; Beck, Stephan; Rakyan, Vardhman K; Gloyn, Anna L

2018-01-01

Human genetic studies have emphasised the dominant contribution of pancreatic islet dysfunction to development of Type 2 Diabetes (T2D). However, limited annotation of the islet epigenome has constrained efforts to define the molecular mechanisms mediating the, largely regulatory, signals revealed by Genome-Wide Association Studies (GWAS). We characterised patterns of chromatin accessibility (ATAC-seq, n = 17) and DNA methylation (whole-genome bisulphite sequencing, n = 10) in human islets, generating high-resolution chromatin state maps through integration with established ChIP-seq marks. We found enrichment of GWAS signals for T2D and fasting glucose was concentrated in subsets of islet enhancers characterised by open chromatin and hypomethylation, with the former annotation predominant. At several loci (including CDC123, ADCY5, KLHDC5) the combination of fine-mapping genetic data and chromatin state enrichment maps, supplemented by allelic imbalance in chromatin accessibility pinpointed likely causal variants. The combination of increasingly-precise genetic and islet epigenomic information accelerates definition of causal mechanisms implicated in T2D pathogenesis. PMID:29412141

Automatic cerebrospinal fluid segmentation in non-contrast CT images using a 3D convolutional network

NASA Astrophysics Data System (ADS)

Patel, Ajay; van de Leemput, Sil C.; Prokop, Mathias; van Ginneken, Bram; Manniesing, Rashindra

2017-03-01

Segmentation of anatomical structures is fundamental in the development of computer aided diagnosis systems for cerebral pathologies. Manual annotations are laborious, time consuming and subject to human error and observer variability. Accurate quantification of cerebrospinal fluid (CSF) can be employed as a morphometric measure for diagnosis and patient outcome prediction. However, segmenting CSF in non-contrast CT images is complicated by low soft tissue contrast and image noise. In this paper we propose a state-of-the-art method using a multi-scale three-dimensional (3D) fully convolutional neural network (CNN) to automatically segment all CSF within the cranial cavity. The method is trained on a small dataset comprised of four manually annotated cerebral CT images. Quantitative evaluation of a separate test dataset of four images shows a mean Dice similarity coefficient of 0.87 +/- 0.01 and mean absolute volume difference of 4.77 +/- 2.70 %. The average prediction time was 68 seconds. Our method allows for fast and fully automated 3D segmentation of cerebral CSF in non-contrast CT, and shows promising results despite a limited amount of training data.

Comparative Proteomic and Transcriptomic Analysis of Follistatin-Induced Skeletal Muscle Hypertrophy.

PubMed

Barbé, Caroline; Bray, Fabrice; Gueugneau, Marine; Devassine, Stéphanie; Lause, Pascale; Tokarski, Caroline; Rolando, Christian; Thissen, Jean-Paul

2017-10-06

Skeletal muscle, the most abundant body tissue, plays vital roles in locomotion and metabolism. Myostatin is a negative regulator of skeletal muscle mass. In addition to increasing muscle mass, Myostatin inhibition impacts muscle contractility and energy metabolism. To decipher the mechanisms of action of the Myostatin inhibitors, we used proteomic and transcriptomic approaches to investigate the changes induced in skeletal muscles of transgenic mice overexpressing Follistatin, a physiological Myostatin inhibitor. Our proteomic workflow included a fractionation step to identify weakly expressed proteins and a comparison of fast versus slow muscles. Functional annotation of altered proteins supports the phenotypic changes induced by Myostatin inhibition, including modifications in energy metabolism, fiber type, insulin and calcium signaling, as well as membrane repair and regeneration. Less than 10% of the differentially expressed proteins were found to be also regulated at the mRNA level but the Biological Process annotation, and the KEGG pathways analysis of transcriptomic results shows a great concordance with the proteomic data. Thus this study describes the most extensive omics analysis of muscle overexpressing Follistatin, providing molecular-level insights to explain the observed muscle phenotypic changes.

Ensembl BioMarts: a hub for data retrieval across taxonomic space.

PubMed

Kinsella, Rhoda J; Kähäri, Andreas; Haider, Syed; Zamora, Jorge; Proctor, Glenn; Spudich, Giulietta; Almeida-King, Jeff; Staines, Daniel; Derwent, Paul; Kerhornou, Arnaud; Kersey, Paul; Flicek, Paul

2011-01-01

For a number of years the BioMart data warehousing system has proven to be a valuable resource for scientists seeking a fast and versatile means of accessing the growing volume of genomic data provided by the Ensembl project. The launch of the Ensembl Genomes project in 2009 complemented the Ensembl project by utilizing the same visualization, interactive and programming tools to provide users with a means for accessing genome data from a further five domains: protists, bacteria, metazoa, plants and fungi. The Ensembl and Ensembl Genomes BioMarts provide a point of access to the high-quality gene annotation, variation data, functional and regulatory annotation and evolutionary relationships from genomes spanning the taxonomic space. This article aims to give a comprehensive overview of the Ensembl and Ensembl Genomes BioMarts as well as some useful examples and a description of current data content and future objectives. Database URLs: http://www.ensembl.org/biomart/martview/; http://metazoa.ensembl.org/biomart/martview/; http://plants.ensembl.org/biomart/martview/; http://protists.ensembl.org/biomart/martview/; http://fungi.ensembl.org/biomart/martview/; http://bacteria.ensembl.org/biomart/martview/.

Architecture and mineral deposit settings of the Altaid orogenic collage: a revised model

NASA Astrophysics Data System (ADS)

Yakubchuk, Alexander

2004-09-01

The Altaids are an orogenic collage of Neoproterozoic-Paleozoic rocks located in the center of Eurasia. This collage consists of only three oroclinally bent Neoproterozoic-Early Paleozoic magmatic arcs (Kipchak, Tuva-Mongol, and Mugodzhar-Rudny Altai), separated by sutures of their former backarc basins, which were stitched by new generations of overlapping magmatic arcs. In addition, the Altaids host accreted fragments of the Neoproterozoic to Early Paleozoic oceanic island chains and Neoproterozoic to Cenozoic plume-related magmatic rocks superimposed on the accreted fragments. All these assemblages host important, many world-class, Late Proterozoic to Early Mesozoic gold, copper-molybdenum, lead-zinc, nickel and other deposits of various types. In the Late Proterozoic, during breakup of the supercontinent Rodinia, the Kipchak and Tuva-Mongol magmatic arcs were rifted off Eastern Europe-Siberia and Laurentia to produce oceanic backarc basins. In the Late Ordovician, the Siberian craton began its clockwise rotation with respect to Eastern Europe and this coincides with the beginning of formation of the Mugodzhar-Rudny Altai arc behind the Kipchak arc. These earlier arcs produced mostly Cu-Pb-Zn VMS deposits, although some important intrusion-related orogenic Au deposits formed during arc-arc collision events in the Middle Cambrian and Late Ordovician. The clockwise rotation of Siberia continued through the Paleozoic until the Early Permian producing several episodes of oroclinal bending, strike-slip duplication and reorganization of the magmatic arcs to produce the overlapping Kazakh-Mongol and Zharma-Saur-Valerianov-Beltau-Kurama arcs that welded the extinct Kipchak and Tuva-Mongol arcs. This resulted in amalgamation of the western portion of the Altaid orogenic collage in the Late Paleozoic. Its eastern portion amalgamated only in the early Mesozoic and was overlapped by the Transbaikal magmatic arc, which developed in response to subduction of the oceanic crust of the Paleo-Pacific Ocean. Several world-class Cu-(Mo)-porphyry, Cu-Pb-Zn VMS and intrusion-related Au mineral camps, which formed in the Altaids at this stage, coincided with the episodes of plate reorganization and oroclinal bending of magmatic arcs. Major Pb-Zn and Cu sedimentary rock-hosted deposits of Kazakhstan and Central Asia formed in backarc rifts, which developed on the earlier amalgamated fragments. Major orogenic gold deposits are intrusion-related deposits, often occurring within black shale-bearing sutured backarc basins with oceanic crust. After amalgamation of the western Altaids, this part of the collage and adjacent cratons were affected by the Siberian superplume, which ascended at the Permian-Triassic transition. This plume-related magmatism produced various deposits, such as famous Ni-Cu-PGE deposits of Norilsk in the northwest of the Siberian craton. In the early Mesozoic, the eastern Altaids were oroclinally bent together with the overlapping Transbaikal magmatic arc in response to the northward migration and anti-clockwise rotation of the North China craton. The following collision of the eastern portion of the Altaid collage with the Siberian craton formed the Mongol-Okhotsk suture zone, which still links the accretionary wedges of central Mongolia and Circum-Pacific belts. In the late Mesozoic, a system of continent-scale conjugate northwest-trending and northeast-trending strike-slip faults developed in response to the southward propagation of the Siberian craton with subsequent post-mineral offset of some metallogenic belts for as much as 70-400 km, possibly in response to spreading in the Canadian basin. India-Asia collision rejuvenated some of these faults and generated a system of impact rifts.

Bibliography of Publications and Presentations from July 1971 Through December 1981

DTIC Science & Technology

1982-01-01

Bureau of Business Education, Los Angeles, California, Los Angeles, CA., January 1972; issued as Professional Paper 6-73, June 1973. PB-221 830. ED-130...Cert:. .n Types of Uniforms and Accessories (Department of the Army) Changes in Morale Subsequent to Issue Infantry Blue Clothin2 Items, by Robert L...34Bibliography of Publications as of 30 June 1971," listing and annotating the research reports issued during HumRRO’s first 20 years, 1951-71. This

Microstructure and Mechanical Properties of Hybrid Welded Joints with Laser and CO2-Shielded Arc

NASA Astrophysics Data System (ADS)

Wahba, M.; Mizutani, M.; Katayama, S.

2016-07-01

With the objective of reducing the operating costs, argon-rich shielding gas was replaced by 100% CO2 gas in hybrid laser-arc welding of shipbuilding steel. The welding parameters were optimized to obtain buried-arc transfer in order to mitigate spatter formation. Sound butt joints could be successfully produced for plates of 14 and 17 mm thickness in one welding pass. Subsequently, the welded joints were subjected to different tests to evaluate the influence of CO2 shielding gas on the mechanical properties of the welded joints. All tensile-tested specimens failed in the base material, indicating the higher strength of the welded joints. The impact toughness of the welded joints, measured at -20 °C, reached approximately 76% of that of the base material, which was well above the limit set by the relevant standard. The microstructure of the fusion zone consisted of grain boundary ferrite and acicular ferrite uniformly over the plate thickness except for the joint root where the microstructure was chiefly ferrite with an aligned second phase. This resulted in higher hardness in the root region compared with the top and middle parts of the fusion zone.

Convection in Neptune's magnetosphere

NASA Technical Reports Server (NTRS)

Hill, T. W.; Dessler, A. J.

1990-01-01

It is assumed that nonthermal escape from Triton's atmosphere produces a co-orbiting torus of unionized gas (presumably nitrogen and hydrogen) that subsequently becomes ionized by electron impact to populate a partial Triton plasma torus analogous to the Io plasma torus in Jupiter's magnetosphere. Centrifugal and magnetic-mirror forces confine the ions to a plasma sheet located between the magnetic and centrifugal equators. The ionization rate, and hence the torus ion concentration, is strongly peaked at the two points (approximately 180 deg apart in longitude) at which Triton's orbit intersects the plasma equator. During the course of Neptune's rotation these intersection points trace out two arcs roughly 75 deg in longitudinal extent, which we take to be the configuration of the resulting (partial) plasma torus. The implied partial ring currents produce a quadrupolar (four-cell) convection system that provides rapid outward transport of plasma from the arcs. Ring-current shielding, however, prevents this convection system from penetrating very far inside the plasma-arc distance. It is suggested that this convection/shielding process accounts for the radial confinement of trapped particles (150 keV or greater) within L = 14.3 as observed by the Voyager LECP instrument.

The gene normalization task in BioCreative III

PubMed Central

2011-01-01

Background We report the Gene Normalization (GN) challenge in BioCreative III where participating teams were asked to return a ranked list of identifiers of the genes detected in full-text articles. For training, 32 fully and 500 partially annotated articles were prepared. A total of 507 articles were selected as the test set. Due to the high annotation cost, it was not feasible to obtain gold-standard human annotations for all test articles. Instead, we developed an Expectation Maximization (EM) algorithm approach for choosing a small number of test articles for manual annotation that were most capable of differentiating team performance. Moreover, the same algorithm was subsequently used for inferring ground truth based solely on team submissions. We report team performance on both gold standard and inferred ground truth using a newly proposed metric called Threshold Average Precision (TAP-k). Results We received a total of 37 runs from 14 different teams for the task. When evaluated using the gold-standard annotations of the 50 articles, the highest TAP-k scores were 0.3297 (k=5), 0.3538 (k=10), and 0.3535 (k=20), respectively. Higher TAP-k scores of 0.4916 (k=5, 10, 20) were observed when evaluated using the inferred ground truth over the full test set. When combining team results using machine learning, the best composite system achieved TAP-k scores of 0.3707 (k=5), 0.4311 (k=10), and 0.4477 (k=20) on the gold standard, representing improvements of 12.4%, 21.8%, and 26.6% over the best team results, respectively. Conclusions By using full text and being species non-specific, the GN task in BioCreative III has moved closer to a real literature curation task than similar tasks in the past and presents additional challenges for the text mining community, as revealed in the overall team results. By evaluating teams using the gold standard, we show that the EM algorithm allows team submissions to be differentiated while keeping the manual annotation effort feasible. Using the inferred ground truth we show measures of comparative performance between teams. Finally, by comparing team rankings on gold standard vs. inferred ground truth, we further demonstrate that the inferred ground truth is as effective as the gold standard for detecting good team performance. PMID:22151901

The gene normalization task in BioCreative III.

PubMed

Lu, Zhiyong; Kao, Hung-Yu; Wei, Chih-Hsuan; Huang, Minlie; Liu, Jingchen; Kuo, Cheng-Ju; Hsu, Chun-Nan; Tsai, Richard Tzong-Han; Dai, Hong-Jie; Okazaki, Naoaki; Cho, Han-Cheol; Gerner, Martin; Solt, Illes; Agarwal, Shashank; Liu, Feifan; Vishnyakova, Dina; Ruch, Patrick; Romacker, Martin; Rinaldi, Fabio; Bhattacharya, Sanmitra; Srinivasan, Padmini; Liu, Hongfang; Torii, Manabu; Matos, Sergio; Campos, David; Verspoor, Karin; Livingston, Kevin M; Wilbur, W John

2011-10-03

We report the Gene Normalization (GN) challenge in BioCreative III where participating teams were asked to return a ranked list of identifiers of the genes detected in full-text articles. For training, 32 fully and 500 partially annotated articles were prepared. A total of 507 articles were selected as the test set. Due to the high annotation cost, it was not feasible to obtain gold-standard human annotations for all test articles. Instead, we developed an Expectation Maximization (EM) algorithm approach for choosing a small number of test articles for manual annotation that were most capable of differentiating team performance. Moreover, the same algorithm was subsequently used for inferring ground truth based solely on team submissions. We report team performance on both gold standard and inferred ground truth using a newly proposed metric called Threshold Average Precision (TAP-k). We received a total of 37 runs from 14 different teams for the task. When evaluated using the gold-standard annotations of the 50 articles, the highest TAP-k scores were 0.3297 (k=5), 0.3538 (k=10), and 0.3535 (k=20), respectively. Higher TAP-k scores of 0.4916 (k=5, 10, 20) were observed when evaluated using the inferred ground truth over the full test set. When combining team results using machine learning, the best composite system achieved TAP-k scores of 0.3707 (k=5), 0.4311 (k=10), and 0.4477 (k=20) on the gold standard, representing improvements of 12.4%, 21.8%, and 26.6% over the best team results, respectively. By using full text and being species non-specific, the GN task in BioCreative III has moved closer to a real literature curation task than similar tasks in the past and presents additional challenges for the text mining community, as revealed in the overall team results. By evaluating teams using the gold standard, we show that the EM algorithm allows team submissions to be differentiated while keeping the manual annotation effort feasible. Using the inferred ground truth we show measures of comparative performance between teams. Finally, by comparing team rankings on gold standard vs. inferred ground truth, we further demonstrate that the inferred ground truth is as effective as the gold standard for detecting good team performance.

Depth variations of P-wave azimuthal anisotropy beneath East Asia

NASA Astrophysics Data System (ADS)

Wei, W.; Zhao, D.; Xu, J.

2017-12-01

We present a new P-wave anisotropic tomographic model beneath East Asia by inverting a total of 1,488,531 P wave arrival-time data recorded by the regional seismic networks in East Asia and temporary seismic arrays deployed on the Tibetan Plateau. Our results provide important new insights into the subducting Indian, Pacific and Philippine Sea plates and mantle dynamics in East Asia. Our tomographic images show that the northern limit of the subducting Indian plate has reached the Jinsha River suture in eastern Tibet. A striking variation of P-wave azimuthal anisotropy is revealed in the Indian lithosphere: the fast velocity direction (FVD) is NE-SW beneath the Indian continent, whereas the FVD is arc parallel beneath the Himalaya and Tibetan Plateau, which may reflect re-orientation of minerals due to lithospheric extension, in response to the India-Eurasia collision. The FVD in the subducting Philippine Sea plate beneath the Ryukyu arc is NE-SW(trench parallel), which is consistent with the spreading direction of the West Philippine Basin during its initial opening stage, suggesting that it may reflect the fossil anisotropy. A circular pattern of FVDs is revealed around the Philippine Sea slab beneath SE China. We suggest that it reflects asthenospheric strain caused by toroidal mantle flow around the edge of the subducting slab. We find a striking variation of the FVD with depth in the subducting Pacific slab beneath the Northeast Japan arc. It may be caused by slab dehydration that changed elastic properties of the slab with depth. The FVD in the mantle wedge beneath the Northeast Japan and Ryukyu arcs is trench normal, which reflects subduction-induced convection. Beneath the Kuril and Izu-Bonin arcs where oblique subduction occurs, the FVD in the mantle wedge is nearly normal to the moving direction of the downgoing Pacific plate, suggesting that the oblique subduction together with the complex slab morphology have disturbed the mantle flow.

Analysis of the Genome and Chromium Metabolism-Related Genes of Serratia sp. S2.

PubMed

Dong, Lanlan; Zhou, Simin; He, Yuan; Jia, Yan; Bai, Qunhua; Deng, Peng; Gao, Jieying; Li, Yingli; Xiao, Hong

2018-05-01

This study is to investigate the genome sequence of Serratia sp. S2. The genomic DNA of Serratia sp. S2 was extracted and the sequencing library was constructed. The sequencing was carried out by Illumina 2000 and complete genomic sequences were obtained. Gene function annotation and bioinformatics analysis were performed by comparing with the known databases. The genome size of Serratia sp. S2 was 5,604,115 bp and the G+C content was 57.61%. There were 5373 protein coding genes, and 3732, 3614, and 3942 genes were respectively annotated into the GO, KEGG, and COG databases. There were 12 genes related to chromium metabolism in the Serratia sp. S2 genome. The whole genome sequence of Serratia sp. S2 is submitted to the GenBank database with gene accession number of LNRP00000000. Our findings may provide theoretical basis for the subsequent development of new biotechnology to repair environmental chromium pollution.

Leveraging biomedical ontologies and annotation services to organize microbiome data from Mammalian hosts.

PubMed

Sarkar, Indra Neil

2010-11-13

A better understanding of commensal microbiotic communities ("microbiomes") may provide valuable insights to human health. Towards this goal, an essential step may be the development of approaches to organize data that can enable comparative hypotheses across mammalian microbiomes. The present study explores the feasibility of using existing biomedical informatics resources - especially focusing on those available at the National Center for Biomedical Ontology - to organize microbiome data contained within large sequence repositories, such as GenBank. The results indicate that the Foundational Model of Anatomy and SNOMED CT can be used to organize greater than 90% of the bacterial organisms associated with 10 domesticated mammalian species. The promising findings suggest that the current biomedical informatics infrastructure may be used towards the organizing of microbiome data beyond humans. Furthermore, the results identify key concepts that might be organized into a semantic structure for incorporation into subsequent annotations that could facilitate comparative biomedical hypotheses pertaining to human health.

Surfactant-directed synthesis of mesoporous films made single-step by a tandem photosol-gel/photocalcination route

NASA Astrophysics Data System (ADS)

De Paz-Simon, Héloïse; Chemtob, Abraham; Croutxé-Barghorn, Céline; Rigolet, Séverinne; Michelin, Laure; Vidal, Loïc; Lebeau, Bénédicte

2014-11-01

In view of their technological impact in materials chemistry, a simplified and more efficient synthetic route to mesoporous films is highly sought. We report, herein, a smart UV-mediated approach coupling in a one-stage process sol-gel photopolymerization and photoinduced template decomposition/ablation to making mesoporous silica films. Performed at room temperature with a solvent-free solution of silicate precursor and amphiphilic poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) block copolymer, the synthesis relies on photoacid generation to induce the fast formation (≈10 min) of mesostructured silica/surfactant domains. Continuation of UV exposure for three additional hours enables subsequent and complete photodegradation of the polyether copolymer, resulting in ordered or disordered mesoporous silica film. One of the most attractive features is that the one-step procedure relies on a continuous illumination provided by the same conventional medium-pressure Hg-Xe arc lamp equipped with a 254 nm reflector to enhance the emission of energetic photons <300 nm. In addition to X-ray diffraction and transmission electron microscopy, time-resolved Fourier transform infrared spectroscopy has proved to be a powerful in situ technique to probe the different chemical transformations accompanying irradiation. Photocalcination strengthens the inorganic network, while allowing to preserve a higher fraction of residual silanol groups compared with thermal calcination. A polyether chain degradation mechanism based on oxygen reactive species-mediated photo-oxidation is proposed.

Time-resolved ion energy and charge state distributions in pulsed cathodic arc plasmas of Nb‑Al cathodes in high vacuum

NASA Astrophysics Data System (ADS)

Zöhrer, Siegfried; Anders, André; Franz, Robert

2018-05-01

Cathodic arcs have been utilized in various applications including the deposition of thin films and coatings, ion implantation, and high current switching. Despite substantial progress in recent decades, the physical mechanisms responsible for the observed plasma properties are still a matter of dispute, particularly for multi-element cathodes, which can play an essential role in applications. The analysis of plasma properties is complicated by the generally occurring neutral background of metal atoms, which perturbs initial ion properties. By using a time-resolved method in combination with pulsed arcs and a comprehensive Nb‑Al cathode model system, we investigate the influence of cathode composition on the plasma, while making the influence of neutrals visible for the observed time frame. The results visualize ion detections of 600 μs plasma pulses, extracted 0.27 m from the cathode, resolved in mass-per-charge, energy-per-charge and time. Ion properties are found to be strongly dependent on the cathode material in a way that cannot be deduced by simple linear extrapolation. Subsequently, current hypotheses in cathodic arc physics applying to multi-element cathodes, like the so-called ‘velocity rule’ or the ‘cohesive energy rule’, are tested for early and late stages of the pulse. Apart from their fundamental character, the findings could be useful in optimizing or designing plasma properties for applications, by actively utilizing effects on ion distributions caused by composite cathode materials and charge exchange with neutrals.

Volcano flank instability in the Lesser Antilles Arc: Diversity of scale, processes, and temporal recurrence

NASA Astrophysics Data System (ADS)

Boudon, Georges; Le Friant, Anne; Komorowski, Jean-Christophe; Deplus, Christine; Semet, Michel P.

2007-08-01

The 1997 Boxing Day collapse, a remarkable feature of the ongoing eruption of Soufrière Hills on Montserrat, has prompted new interest in the study of volcano stability in the Lesser Antilles. Building on a few cases documented in the literature, we have now identified at least 47 flank collapse events on volcanoes of the Caribbean arc where this type of behavior is characteristic and repetitive. About 15 events occurred on active volcanoes within the last 12,000 years. In the northern part of the arc, flank collapses are repetitive, do not exceed 1 km3 in volume, occur in all directions, and are promoted by intense hydrothermal alteration and well-developed fracturing of the summit part of the edifices. In contrast, infrequent but large sector collapses, with volumes up to tens of km3, are typical of the southern volcanoes. They are always directed to the west as a result of the high overall slopes of the islands toward the deep back-arc Grenada Basin. Because Caribbean islands are small, a large part of the resulting debris avalanches have flowed into the sea thus contributing voluminous and sudden inputs of volcaniclastic sediments to the Grenada Basin. Deposits from such submarine flows have been identified during the recent AGUADOMAR and CARAVAL oceanographic cruises and traced to their source structures on land. Edifice collapses have a major influence on subsequent volcanic activity but also are of high concern because of their tsunamigenic potential.

Lipolysis - a highly regulated multi-enzyme complex mediates the catabolism of cellular fat stores.

PubMed

Lass, Achim; Zimmermann, Robert; Oberer, Monika; Zechner, Rudolf

2011-01-01

Lipolysis is the biochemical pathway responsible for the catabolism of triacylglycerol (TAG) stored in cellular lipid droplets. The hydrolytic cleavage of TAG generates non-esterified fatty acids, which are subsequently used as energy substrates, essential precursors for lipid and membrane synthesis, or mediators in cell signaling processes. Consistent with its central importance in lipid and energy homeostasis, lipolysis occurs in essentially all tissues and cell types, it is most abundant, however, in white and brown adipose tissue. Over the last 5years, important enzymes and regulatory protein factors involved in lipolysis have been identified. These include an essential TAG hydrolase named adipose triglyceride lipase (ATGL) [annotated as patatin-like phospholipase domain-containing protein A2], the ATGL activator comparative gene identification-58 [annotated as α/β hydrolase containing protein 5], and the ATGL inhibitor G0/G1 switch gene 2. Together with the established hormone-sensitive lipase [annotated as lipase E] and monoglyceride lipase, these proteins constitute the basic "lipolytic machinery". Additionally, a large number of hormonal signaling pathways and lipid droplet-associated protein factors regulate substrate access and the activity of the "lipolysome". This review summarizes the current knowledge concerning the enzymes and regulatory processes governing lipolysis of fat stores in adipose and non-adipose tissues. Special emphasis will be given to ATGL, its regulation, and physiological function. Copyright © 2010 Elsevier Ltd. All rights reserved.

pyGeno: A Python package for precision medicine and proteogenomics.

PubMed

Daouda, Tariq; Perreault, Claude; Lemieux, Sébastien

2016-01-01

pyGeno is a Python package mainly intended for precision medicine applications that revolve around genomics and proteomics. It integrates reference sequences and annotations from Ensembl, genomic polymorphisms from the dbSNP database and data from next-gen sequencing into an easy to use, memory-efficient and fast framework, therefore allowing the user to easily explore subject-specific genomes and proteomes. Compared to a standalone program, pyGeno gives the user access to the complete expressivity of Python, a general programming language. Its range of application therefore encompasses both short scripts and large scale genome-wide studies.

pyGeno: A Python package for precision medicine and proteogenomics

PubMed Central

Daouda, Tariq; Perreault, Claude; Lemieux, Sébastien

2016-01-01

pyGeno is a Python package mainly intended for precision medicine applications that revolve around genomics and proteomics. It integrates reference sequences and annotations from Ensembl, genomic polymorphisms from the dbSNP database and data from next-gen sequencing into an easy to use, memory-efficient and fast framework, therefore allowing the user to easily explore subject-specific genomes and proteomes. Compared to a standalone program, pyGeno gives the user access to the complete expressivity of Python, a general programming language. Its range of application therefore encompasses both short scripts and large scale genome-wide studies. PMID:27785359

Comparison of fast electric field changes from subsequent return strokes of natural and triggered lightning

NASA Technical Reports Server (NTRS)

Le Vine, D. M.; Willett, J. C.; Bailey, J. C.

1989-01-01

Fast electric field changes from subsequent return strokes of natural and triggered lightning with propagation paths almost entirely over water are compared. Data were collected at the Kennedy Space Center, Florida, during the summer of 1987. Comparisons have been made of the average shape, the risetime, and the spectrum of the electric field changes. To a first approximation, the waveforms are very similar; however, the electric field changes from the triggered flashes tend to rise to peak faster and decay faster than do their counterparts in natural cloud-to-ground flashes.

Semi-automatic semantic annotation of PubMed Queries: a study on quality, efficiency, satisfaction

PubMed Central

Névéol, Aurélie; Islamaj-Doğan, Rezarta; Lu, Zhiyong

2010-01-01

Information processing algorithms require significant amounts of annotated data for training and testing. The availability of such data is often hindered by the complexity and high cost of production. In this paper, we investigate the benefits of a state-of-the-art tool to help with the semantic annotation of a large set of biomedical information queries. Seven annotators were recruited to annotate a set of 10,000 PubMed® queries with 16 biomedical and bibliographic categories. About half of the queries were annotated from scratch, while the other half were automatically pre-annotated and manually corrected. The impact of the automatic pre-annotations was assessed on several aspects of the task: time, number of actions, annotator satisfaction, inter-annotator agreement, quality and number of the resulting annotations. The analysis of annotation results showed that the number of required hand annotations is 28.9% less when using pre-annotated results from automatic tools. As a result, the overall annotation time was substantially lower when pre-annotations were used, while inter-annotator agreement was significantly higher. In addition, there was no statistically significant difference in the semantic distribution or number of annotations produced when pre-annotations were used. The annotated query corpus is freely available to the research community. This study shows that automatic pre-annotations are found helpful by most annotators. Our experience suggests using an automatic tool to assist large-scale manual annotation projects. This helps speed-up the annotation time and improve annotation consistency while maintaining high quality of the final annotations. PMID:21094696

Origin of the high plateau in the Central Andes, Bolivia, South America

NASA Astrophysics Data System (ADS)

Lamb, Simon; Hoke, Leonore

1997-08-01

The Bolivian Altiplano, in the Central Andes of South America, is part of the second largest high plateau on Earth. It is an elongate region of subdued relief, ˜1.2 × 105 km2 and ˜4 km above sea level, bounded by the Eastern Cordillera and volcanic arc (Western Cordillera). Here the crust is up to ˜75 km thick. We describe the Cenozoic geological evolution of this region, using a revised chronostratigraphy and an analysis of the crustal and lithospheric structure. Crustal shortening and magmatic addition and, locally, sedimentation are the main mechanisms of Cenozoic crustal thickening, leading to nearly 4 km of surface uplift since the Paleocene. Addition of mafic melts appears to be a first-order mechanism of Cenozoic crustal growth, contributing ˜40% of the crustal thickening beneath the volcanic arc. Removal of the basal part of the lithosphere may have caused two episodes of widespread arc and behind-arc mafic volcanism, at ˜23 Ma and 0 - ˜5 Ma, contributing to the surface uplift. The Altiplano originated as a sedimentary basin, several hundred kilometers wide, between the proto-Western Cordillera and a narrow zone of uplift (proto-Eastern Cordillera) farther east. The latter zone formed by inversion of the center of a wide lacustrine or marine Cretaceous - Paleocene basin close to sea-level at ˜45 Ma. A thickness of 2-4 km of Paleogene continental elastics accumulated in the proto-Altiplano basin. Subsequently, in the Oligocene, we estimate that this region and the western margin of the Eastern Cordillera were technically shortened ˜22% (˜65 km), resulting in ˜9 km of average crustal thickening. The Altiplano basin was rejuvenated at ˜25 Ma and subsequently flooded with up to 8 km thickness of detritus eroded from the uplifting Eastern and Western Cordilleras. Between ˜25 and 5 Ma, folding and thrusting in the western margin of the Eastern Cordillera migrated westward into the center of the Altiplano basin, essentially terminating deposition, except in local subbasins, and accommodating ˜13% (˜30 km) of shortening and an estimated ˜7 km of average crustal thickening. Subsequently, there has been strike-slip deformation and limited local thrusting (< 5 km of shortening). Geomorphological and geochronological evidence for 1.5-2 km of surface uplift of this region since the Late Miocene suggests ˜14 km of lower crustal thickening beneath an essentially rigid "lid", and can be explained by ˜100-150 km of underthrusting of the Brazilian shield and adjacent regions beneath the eastern margin of the Central Andes. The present subdued relief in the Altiplano may be a result of ductile flow in the lower crust and sedimentation and erosion in an internal drainage basin.

Automatic acquisition of motion trajectories: tracking hockey players

NASA Astrophysics Data System (ADS)

Okuma, Kenji; Little, James J.; Lowe, David

2003-12-01

Computer systems that have the capability of analyzing complex and dynamic scenes play an essential role in video annotation. Scenes can be complex in such a way that there are many cluttered objects with different colors, shapes and sizes, and can be dynamic with multiple interacting moving objects and a constantly changing background. In reality, there are many scenes that are complex, dynamic, and challenging enough for computers to describe. These scenes include games of sports, air traffic, car traffic, street intersections, and cloud transformations. Our research is about the challenge of inventing a descriptive computer system that analyzes scenes of hockey games where multiple moving players interact with each other on a constantly moving background due to camera motions. Ultimately, such a computer system should be able to acquire reliable data by extracting the players" motion as their trajectories, querying them by analyzing the descriptive information of data, and predict the motions of some hockey players based on the result of the query. Among these three major aspects of the system, we primarily focus on visual information of the scenes, that is, how to automatically acquire motion trajectories of hockey players from video. More accurately, we automatically analyze the hockey scenes by estimating parameters (i.e., pan, tilt, and zoom) of the broadcast cameras, tracking hockey players in those scenes, and constructing a visual description of the data by displaying trajectories of those players. Many technical problems in vision such as fast and unpredictable players' motions and rapid camera motions make our challenge worth tackling. To the best of our knowledge, there have not been any automatic video annotation systems for hockey developed in the past. Although there are many obstacles to overcome, our efforts and accomplishments would hopefully establish the infrastructure of the automatic hockey annotation system and become a milestone for research in automatic video annotation in this domain.

Combinatorial synthesis of phosphors using arc-imaging furnace

PubMed Central

Ishigaki, Tadashi; Toda, Kenji; Yoshimura, Masahiro; Uematsu, Kazuyoshi; Sato, Mineo

2011-01-01

We have applied a novel ‘melt synthesis technique’ rather than a conventional solid-state reaction to rapidly synthesize phosphor materials. During a synthesis, the mixture of oxides or their precursors is melted by light pulses (10–60 s) in an arc-imaging furnace on a water-cooled copper hearth to form a globule of 1–5 mm diameter, which is then rapidly cooled by turning off the light. Using this method, we synthesized several phosphor compounds including Y3Al5O12:Ce(YAG) and SrAl2O4:Eu,Dy. Complex phosphor oxides are difficult to produce by conventional solid-state reaction techniques because of the slow reaction rates among solid oxides; as a result, the oxides form homogeneous compounds or solid solutions. On the other hand, melt reactions are very fast (10–60 s) and result in homogeneous compounds owing to rapid diffusion and mixing in the liquid phase. Therefore, melt synthesis techniques are suitable for preparing multi component homogeneous compounds and solid solutions. PMID:27877432

Combinatorial synthesis of phosphors using arc-imaging furnace

NASA Astrophysics Data System (ADS)

Ishigaki, Tadashi; Toda, Kenji; Yoshimura, Masahiro; Uematsu, Kazuyoshi; Sato, Mineo

2011-10-01

We have applied a novel 'melt synthesis technique' rather than a conventional solid-state reaction to rapidly synthesize phosphor materials. During a synthesis, the mixture of oxides or their precursors is melted by light pulses (10-60 s) in an arc-imaging furnace on a water-cooled copper hearth to form a globule of 1-5 mm diameter, which is then rapidly cooled by turning off the light. Using this method, we synthesized several phosphor compounds including Y3Al5O12:Ce(YAG) and SrAl2O4:Eu,Dy. Complex phosphor oxides are difficult to produce by conventional solid-state reaction techniques because of the slow reaction rates among solid oxides; as a result, the oxides form homogeneous compounds or solid solutions. On the other hand, melt reactions are very fast (10-60 s) and result in homogeneous compounds owing to rapid diffusion and mixing in the liquid phase. Therefore, melt synthesis techniques are suitable for preparing multi component homogeneous compounds and solid solutions.

Advances in solar radio astronomy

NASA Technical Reports Server (NTRS)

Kundu, M. R.

1982-01-01

The status of the observations and interpretations of the sun's radio emission covering the entire radio spectrum from millimeter wavelengths to hectometer and kilometer wavelengths is reviewed. Emphasis is given to the progress made in solar radio physics as a result of recent advances in plasma and radiation theory. It is noted that the capability now exists of observing the sun with a spatial resolution of approximately a second of arc and a temporal resolution of about a millisecond at centimeter wavelengths and of obtaining fast multifrequency two-dimensional pictures of the sun at meter and decameter wavelengths. A summary is given of the properties of nonflaring active regions at millimeter, centimeter, and meter-decameter wavelengths. The properties of centimeter wave bursts are discussed in connection with the high spatial resolution observations. The observations of the preflare build-up of an active region are reviewed. High spatial resolution observations (a few seconds of arc to approximately 1 arcsec) are discussed, with particular attention given to the one- and two-dimensional maps of centimeter-wavelength burst sources.

Microstructures and mechanical properties of bonding layers between low carbon steel and alloy 625 processed by gas tungsten arc welding

NASA Astrophysics Data System (ADS)

Lou, Shuai; Lee, Seul Bi; Nam, Dae-Geun; Choi, Yoon Suk

2017-11-01

A filler metal wire, Alloy 625, was cladded on a plate of a low carbon streel, SS400, by gas tungsten arc welding, and the morphology of the weld bead and resulting dilution ratio were investigated under different welding parameter values (the input current, weld speed and wire feed speed). The wire feed speed was found to be most influential in controlling the dilution ratio of the weld bead, and seemed to limit the influence of other welding parameters. Two extreme welding conditions (with the minimum and maximum dilution ratios) were identified, and the corresponding microstructures, hardness and tensile properties near the bond line were compared between the two cases. The weld bead with the minimum dilution ratio showed superior hardness and tensile properties, while the formation lath martensite (due to relatively fast cooling) affected mechanical properties in the heat affected zone of the base metal with the maximum dilution ratio.

ADVANCEMENT OF THE RHIC BEAM ABORT KICKER SYSTEM.

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

ZHANG,W.AHRENS,L.MI,J.OERTER,B.SANDBERG,J.WARBURTON,D.

2003-05-12

As one of the most critical system for RHIC operation, the beam abort kicker system has to be highly available, reliable, and stable for the entire operating range. Along with the RHIC commission and operation, consistent efforts have been spend to cope with immediate issues as well as inherited design issues. Major design changes have been implemented to achieve the higher operating voltage, longer high voltage hold-off time, fast retriggering and redundant triggering, and improved system protection, etc. Recent system test has demonstrated for the first time that both blue ring and yellow ring beam abort systems have achieved moremore » than 24 hours hold off time at desired operating voltage. In this paper, we report break down, thyratron reverse arcing, and to build a fast re-trigger system to reduce beam spreading in event of premature discharge.« less

Dynamic relations between fast-food restaurant and body weight status: a longitudinal and multilevel analysis of Chinese adults

PubMed Central

Xu, Hongwei; Short, Susan E; Liu, Tao

2013-01-01

Background Mixed findings have been reported on the association between Western fast-food restaurants and body weight status. Results vary across study contexts and are sensitive to the samples, measures and methods used. Most studies have failed to examine the temporally dynamic associations between community exposure to fast-food restaurants and weight changes. Methods Bayesian hierarchical regressions are used to model changes in body mass index, waist-to-height ratio (WHtR) and waist-to-hip ratio (WHpR) as a function of changes in Western fast-food restaurants in 216 communities for more than 9000 Chinese adults followed up multiple times between 2000 and 2009. Results Number of Western fast-food restaurants is positively associated with subsequent increases in WHtR and WHpR among rural population. More fast-food restaurants are positively associated with a future increase in WHpR for urban women. Increased availability of fast food between two waves is related to increased WHtR for urban men over the same period. A past increase in number of fast-food restaurants is associated with subsequent increases in WHtR and WHpR for rural population. Conclusions The associations between community exposure to Western fast food and weight changes are temporally dynamic rather than static. Improved measures of exposure to community environment are needed to achieve more precise estimates and better understanding of these relationships. In light of the findings in this study and China’s rapid economic growth, further investigation and increased public health monitoring is warranted since Western fast food is likely to be more accessible and affordable in the near future. PMID:22923769

Dynamic relations between fast-food restaurant and body weight status: a longitudinal and multilevel analysis of Chinese adults.

PubMed

Xu, Hongwei; Short, Susan E; Liu, Tao

2013-03-01

Mixed findings have been reported on the association between Western fast-food restaurants and body weight status. Results vary across study contexts and are sensitive to the samples, measures and methods used. Most studies have failed to examine the temporally dynamic associations between community exposure to fast-food restaurants and weight changes. Bayesian hierarchical regressions are used to model changes in body mass index, waist-to-height ratio (WHtR) and waist-to-hip ratio (WHpR) as a function of changes in Western fast-food restaurants in 216 communities for more than 9000 Chinese adults followed up multiple times between 2000 and 2009. Number of Western fast-food restaurants is positively associated with subsequent increases in WHtR and WHpR among rural population. More fast-food restaurants are positively associated with a future increase in WHpR for urban women. Increased availability of fast food between two waves is related to increased WHtR for urban men over the same period. A past increase in number of fast-food restaurants is associated with subsequent increases in WHtR and WHpR for rural population. The associations between community exposure to Western fast food and weight changes are temporally dynamic rather than static. Improved measures of exposure to community environment are needed to achieve more precise estimates and better understanding of these relationships. In light of the findings in this study and China's rapid economic growth, further investigation and increased public health monitoring is warranted since Western fast food is likely to be more accessible and affordable in the near future.

Epigenomic Elements Analyses for Promoters Identify ESRRG as a New Susceptibility Gene for Obesity-related Traits

PubMed Central

Dong, Shan-Shan; Guo, Yan; Zhu, Dong-Li; Chen, Xiao-Feng; Wu, Xiao-Ming; Shen, Hui; Chen, Xiang-Ding; Tan, Li-Jun; Tian, Qing; Deng, Hong-Wen; Yang, Tie-Lin

2016-01-01

OBJECTIVES With ENCODE epigenomic data and results from published genome-wide association studies (GWASs), we aimed to find regulatory signatures of obesity genes and discover novel susceptibility genes. METHODS Obesity genes were obtained from public GWASs databases and their promoters were annotated based on the regulatory elements information. Significantly enriched or depleted epigenomic elements in the promoters of obesity genes were evaluated and all human genes were then prioritized according to the existence of the selected elements to predict new candidate genes. Top ranked genes were subsequently applied to validate their associations with obesity-related traits in three independent in-house GWASs samples. RESULTS We identified RAD21 and EZH2 as over-represented, STAT2 and IRF3 as depleted transcription factors. Histone modification of H3K9me3 and chromatin state segmentation of “poised promoter” and “repressed” were overrepresented. All genes were prioritized and we selected the top five genes for validation at population level. Combined results from the three GWASs samples, rs7522101 in ESRRG remained significantly associated with BMI after multiple testing corrections (P = 7.25 × 10−5). It was also associated with β-cell function (P = 1.99 × 10−3) and fasting glucose level (P < 0.05) in the meta-analyses of glucose and insulin-related traits consortium (MAGIC) dataset. CONCLUSIONS In summary, we identified epigenomic characteristics for obesity genes and suggested ESRRG as a novel obesity susceptibility gene. PMID:27113491

Applications of Mobile GIS in Forestry South Australia

NASA Astrophysics Data System (ADS)

Battad, D. T.; Mackenzie, P.

2012-07-01

South Australian Forestry Corporation (ForestrySA) had been actively investigating the applications of mobile GIS in forestry for the past few years. The main objective is to develop an integrated mobile GIS capability that allows staff to collect new spatial information, verify existing data, and remotely access and post data from the field. Two (2) prototype mobile GIS applications have been developed already using the Environmental Systems Research Institute (ESRI) ARCGISR technology as the main spatial component. These prototype systems are the Forest Health Surveillance System and the Mobile GIS for Wetlands System. The Forest Health Surveillance System prototype is used primarily for aerial forest health surveillance. It was developed using a tablet PC with ArcMapR GIS. A customised toolbar was developed using ArcObjectsR in the Visual Basic 6 Integrated Development Environment (IDE). The resulting dynamic linked library provides a suite of custom tools which enables the following: - quickly create spatial features and attribute the data - full utilisation of global positioning system (GPS) technology - excellent screen display navigation tools, i.e. pan, rotate map, capture of flight path - seamless integration of data into GIS as geodatabase (GDB) feature classes - screen entry of text and conversion to annotation feature classes The Mobile GIS for Wetlands System prototype was developed for verifying existing wetland areas within ForestrySA's plantation estate, collect new wetland data, and record wetland conditions. Mapping of actual wetlands within ForestrySA's plantation estate is very critical because of the need to establish protection buffers around these features during the implementation of plantation operations. System development has been focussed on a mobile phone platform (HTC HD2R ) with WindowsR Mobile 6, ESRI's ArcGISR Mobile software development kit (SDK) employing ArcObjectsR written on C#.NET IDE, and ArcGIS ServerR technology. The system is also implemented in the VILIVR X70. The system has undergone testing by ForestrySA staff and the refinements had been incorporated in the latest version of the system. The system has the following functionalities: - display and query strategic data layers - collect and edit spatial and attribute data - full utilisation of global positioning GPS technology - distance and area measurements - display of high resolution imagery - seamless integration of data into GIS as feature classes - screen display and navigation tools, i.e. pan, zoom in/out, rotate map - capture of flight path The next stages in the development of mobile GIS technologies at ForestrySA are to enhance the systems' capabilities as one of the organization main data capture systems. These include incorporating other applications, e.g. roads/tracks mapping, mapping of significant sites, etc., and migration of the system to Windows Phone7.

A New Method to Produce Ni-Cr Ferroalloy Used for Stainless Steel Production

NASA Astrophysics Data System (ADS)

Chen, Pei-Xian; Chu, Shao-Jun; Zhang, Guo-Hua

2016-08-01

A new electrosilicothermic method has been proposed in the present paper to produce Ni-Cr ferroalloy, which can be used for the production of 300 series stainless steel. Based on this new process, the Ni-Si ferroalloy is first produced as the intermediate alloy, and then the desiliconization process of Ni-Si ferroalloy melt with chromium concentrate is carried out to generate Ni-Cr ferroalloy. The silicon content in the Ni-Si ferroalloy produced in the submerged arc furnace should be more than 15 mass% (for the propose of reducing dephosphorization), in order to make sure the phosphorus content in the subsequently produced Ni-Cr ferroalloy is less than 0.03 mass%. A high utilization ratio of Si and a high recovery ratio of Cr can be obtained after the desiliconization reaction between Ni-Si ferroalloy and chromium concentrate in the electric arc furnace (EAF)-shaking ladle (SL) process.

Reliability evaluation of a multistate network subject to time constraint under routing policy

NASA Astrophysics Data System (ADS)

Lin, Yi-Kuei

2013-08-01

A multistate network is a stochastic network composed of multistate arcs in which each arc has several possible capacities and may fail due to failure, maintenance, etc. The quality of a multistate network depends on how to meet the customer's requirements and how to provide the service in time. The system reliability, the probability that a given amount of data can be transmitted through a pair of minimal paths (MPs) simultaneously under the time constraint, is a proper index to evaluate the quality of a multistate network. An efficient solution procedure is first proposed to calculate it. In order to further enhance the system reliability, the network administrator decides the routing policy in advance to indicate the first and the second priority pairs of MPs. The second priority pair of MPs takes charge of the transmission duty if the first fails. The system reliability under the routing policy can be subsequently evaluated.

Study of Radiographic Linear Indications and Subsequent Microstructural Features in Gas Tungsten Arc Welds of Inconel 718

NASA Technical Reports Server (NTRS)

Walley, J. L.; Nunes, A. C.; Clounch, J. L.; Russell, C. K.

2007-01-01

This study presents examples and considerations for differentiating linear radiographic indications produced by gas tungsten arc welds in a 0.05-in-thick sheet of Inconel 718. A series of welds with different structural features, including the enigma indications and other defect indications such as lack of fusion and penetration, were produced, radiographed, and examined metallographically. The enigma indications were produced by a large columnar grain running along the center of the weld nugget occurring when the weld speed was reduced sufficiently below nominal. Examples of respective indications, including the effect of changing the x-ray source location, are presented as an aid to differentiation. Enigma, nominal, and hot-weld specimens were tensile tested to demonstrate the harmlessness of the enigma indication. Statistical analysis showed that there is no difference between the strengths of these three weld conditions.

Nuclear valve manufacturer selects stainless forgings

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

None

1976-02-01

Forged type 316 stainless steel components for nuclear valves are described. Automatic plasma arc welding with powder filler alloys is employed for hardfacing. Seat ring forgings are surfaced four-at-a-time with Stellite No. 156 in a sequential manner to minimize heat input to the individual components. After cladding and machining, seat rings are welded into the valve body using a semiautomatic, hot-wire gas tungsten-arc process. Disc faces and guide slots are surfaced with Stellite No. 6. The valve stem is machined from 17-4PH forged bar stock in the H-1100 condition. The heat treatment is specified to minimize pitting under prolonged exposuremore » to wet packing. A 12 rms (0.3 $mu$m) surface finish minimizes tearing of the packing and subsequent leakage. The link and stem pin are SA 564 Grade 660 (in the H-1100 condition) and ASTM A637 Grade 718 respectively. (JRD)« less

Geochemical and modal data for igneous rocks associated with epithermal mineral deposits

USGS Publications Warehouse

du Bray, Edward A.

2014-01-01

The purposes of this report are to (1) present available geochemical and modal data for igneous rocks associated with epithermal mineral deposits and (2) to make those data widely and readily available for subsequent, more in-depth consideration and interpretation. Epithermal precious and base-metal deposits are commonly associated with subduction-related calc-alkaline to alkaline arc magmatism as well as back-arc continental rift magmatism. These deposits form in association with compositionally diverse extrusive and intrusive igneous rocks. Temperature and depth regimes prevailing during deposit formation are highly variable. The deposits form from hydrothermal fluids that range from acidic to near-neutral pH, and they occur in a variety of structural settings. The disparate temperature, pressure, fluid chemistry, and structural controls have resulted in deposits with wide ranging characteristics. Economic geologists have employed these characteristics to develop classification schemes for epithermal deposits and to constrain the important genetic processes responsible for their formation.

Difluoro-lambda(5)-phosphinonitrile F(2)P[triple bond]N: matrix isolation and photoisomerization into FP=NF.

PubMed

Zeng, Xiaoqing; Beckers, Helmut; Willner, Helge

2009-01-01

Splendid isolation: Monomeric phosphazene F(2)PN ((1)A(1)) was prepared for the first time through irradiation of F(2)PN(3) in an argon matrix with an ArF excimer laser (lambda=193 nm). Upon subsequent irradiation with a high-pressure mercury arc lamp (lambda=255 nm), F(2)PN undergoes a 1,2-fluorine shift to give iminophosphane cis-FP=NF.

Allorecognition triggers autophagy and subsequent necrosis in the cnidarian Hydractinia symbiolongicarpus.

PubMed

Buss, Leo W; Anderson, Christopher; Westerman, Erica; Kritzberger, Chad; Poudyal, Monita; Moreno, Maria A; Lakkis, Fadi G

2012-01-01

Transitory fusion is an allorecognition phenotype displayed by the colonial hydroid Hydractinia symbiolongicarpus when interacting colonies share some, but not all, loci within the allorecognition gene complex (ARC). The phenotype is characterized by an initial fusion followed by subsequent cell death resulting in separation of the two incompatible colonies. We here characterize this cell death process using scanning electron microscopy (SEM), transmission electron microscopy (TEM), and continuous in vivo digital microscopy. These techniques reveal widespread autophagy and subsequent necrosis in both colony and grafted polyp assays. Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assays and ultrastructural observations revealed no evidence of apoptosis. Pharmacological inhibition of autophagy using 3-methyladenine (3-MA) completely suppressed transitory fusion in vivo in colony assays. Rapamycin did not have a significant effect in the same assays. These results establish the hydroid allorecognition system as a novel model for the study of cell death.

Illumination system development using design and analysis of computer experiments

NASA Astrophysics Data System (ADS)

Keresztes, Janos C.; De Ketelaere, Bart; Audenaert, Jan; Koshel, R. J.; Saeys, Wouter

2015-09-01

Computer assisted optimal illumination design is crucial when developing cost-effective machine vision systems. Standard local optimization methods, such as downhill simplex optimization (DHSO), often result in an optimal solution that is influenced by the starting point by converging to a local minimum, especially when dealing with high dimensional illumination designs or nonlinear merit spaces. This work presents a novel nonlinear optimization approach, based on design and analysis of computer experiments (DACE). The methodology is first illustrated with a 2D case study of four light sources symmetrically positioned along a fixed arc in order to obtain optimal irradiance uniformity on a flat Lambertian reflecting target at the arc center. The first step consists of choosing angular positions with no overlap between sources using a fast, flexible space filling design. Ray-tracing simulations are then performed at the design points and a merit function is used for each configuration to quantify the homogeneity of the irradiance at the target. The obtained homogeneities at the design points are further used as input to a Gaussian Process (GP), which develops a preliminary distribution for the expected merit space. Global optimization is then performed on the GP more likely providing optimal parameters. Next, the light positioning case study is further investigated by varying the radius of the arc, and by adding two spots symmetrically positioned along an arc diametrically opposed to the first one. The added value of using DACE with regard to the performance in convergence is 6 times faster than the standard simplex method for equal uniformity of 97%. The obtained results were successfully validated experimentally using a short-wavelength infrared (SWIR) hyperspectral imager monitoring a Spectralon panel illuminated by tungsten halogen sources with 10% of relative error.

SU-E-T-422: Fast Analytical Beamlet Optimization for Volumetric Intensity-Modulated Arc Therapy

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

Chan, Kenny S K; Lee, Louis K Y; Xing, L

2015-06-15

Purpose: To implement a fast optimization algorithm on CPU/GPU heterogeneous computing platform and to obtain an optimal fluence for a given target dose distribution from the pre-calculated beamlets in an analytical approach. Methods: The 2D target dose distribution was modeled as an n-dimensional vector and estimated by a linear combination of independent basis vectors. The basis set was composed of the pre-calculated beamlet dose distributions at every 6 degrees of gantry angle and the cost function was set as the magnitude square of the vector difference between the target and the estimated dose distribution. The optimal weighting of the basis,more » which corresponds to the optimal fluence, was obtained analytically by the least square method. Those basis vectors with a positive weighting were selected for entering into the next level of optimization. Totally, 7 levels of optimization were implemented in the study.Ten head-and-neck and ten prostate carcinoma cases were selected for the study and mapped to a round water phantom with a diameter of 20cm. The Matlab computation was performed in a heterogeneous programming environment with Intel i7 CPU and NVIDIA Geforce 840M GPU. Results: In all selected cases, the estimated dose distribution was in a good agreement with the given target dose distribution and their correlation coefficients were found to be in the range of 0.9992 to 0.9997. Their root-mean-square error was monotonically decreasing and converging after 7 cycles of optimization. The computation took only about 10 seconds and the optimal fluence maps at each gantry angle throughout an arc were quickly obtained. Conclusion: An analytical approach is derived for finding the optimal fluence for a given target dose distribution and a fast optimization algorithm implemented on the CPU/GPU heterogeneous computing environment greatly reduces the optimization time.« less

Pulsed-focusing recirculating linacs for muon acceleration

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

Johnson, Rolland

2014-12-31

Since the muon has a short lifetime, fast acceleration is essential for high-energy applications such as muon colliders, Higgs factories, or neutrino factories. The best one can do is to make a linear accelerator with the highest possible accelerating gradient to make the accelerating time as short as possible. However, the cost of such a single linear accelerator is prohibitively large due to expensive power sources, cavities, tunnels, and related infrastructure. As was demonstrated in the Thomas Jefferson Accelerator Facility (Jefferson Lab) Continuous Electron Beam Accelerator Facility (CEBAF), an elegant solution to reduce cost is to use magnetic return arcsmore » to recirculate the beam through the accelerating RF cavities many times, where they gain energy on each pass. In such a Recirculating Linear Accelerator (RLA), the magnetic focusing strength diminishes as the beam energy increases in a conventional linac that has constant strength quadrupoles. After some number of passes the focusing strength is insufficient to keep the beam from going unstable and being lost. In this project, the use of fast pulsed quadrupoles in the linac sections was considered for stronger focusing as a function of time to allow more successive passes of a muon beam in a recirculating linear accelerator. In one simulation, it was shown that the number of passes could be increased from 8 to 12 using pulsed magnet designs that have been developed and tested. This could reduce the cost of linac sections of a muon RLA by 8/12, where more improvement is still possible. The expense of a greater number of passes and corresponding number of return arcs was also addressed in this project by exploring the use of ramped or FFAG-style magnets in the return arcs. A better solution, invented in this project, is to use combined-function dipole-quadrupole magnets to simultaneously transport two beams of different energies through one magnet string to reduce costs of return arcs by almost a factor of two. A patent application was filed for this invention and a detailed report published in Physical Review Special Topics. A scaled model using an electron beam was developed and proposed to test the concept of a dog bone RLA with combined-function return arcs. The efforts supported by this grant were reported in a series of contributions to particle accelerator conferences that are reproduced in the appendices and summarized in the body of this report.« less

The 'Soil Cover App' - a new tool for fast determination of dead and living biomass on soil

NASA Astrophysics Data System (ADS)

Bauer, Thomas; Strauss, Peter; Riegler-Nurscher, Peter; Prankl, Johann; Prankl, Heinrich

2017-04-01

Worldwide many agricultural practices aim on soil protection strategies using living or dead biomass as soil cover. Especially for the case when management practices are focusing on soil erosion mitigation the effectiveness of these practices is directly driven by the amount of soil coverleft on the soil surface. Hence there is a need for quick and reliable methods of soil cover estimation not only for living biomass but particularly for dead biomass (mulch). Available methods for the soil cover measurement are either subjective, depending on an educated guess or time consuming, e.g., if the image is analysed manually at grid points. We therefore developed a mobile application using an algorithm based on entangled forest classification. The final output of the algorithm gives classified labels for each pixel of the input image as well as the percentage of each class which are living biomass, dead biomass, stones and soil. Our training dataset consisted of more than 250 different images and their annotated class information. Images have been taken in a set of different environmental conditions such as light, soil coverages from between 0% to 100%, different materials such as living plants, residues, straw material and stones. We compared the results provided by our mobile application with a data set of 180 images that had been manually annotated A comparison between both methods revealed a regression slope of 0.964 with a coefficient of determination R2 = 0.92, corresponding to an average error of about 4%. While average error of living plant classification was about 3%, dead residue classification resulted in an 8% error. Thus the new mobile application tool offers a fast and easy way to obtain information on the protective potential of a particular agricultural management site.

Effect of an acute fast on energy compensation and feeding behaviour in lean men and women.

PubMed

Johnstone, A M; Faber, P; Gibney, E R; Elia, M; Horgan, G; Golden, B E; Stubbs, R J

2002-12-01

Humans appear to defend against energy deficit to a greater extent than energy surplus. Severe dietary energy restriction resulting in 5-30% weight loss often leads to hyperphagia and weight regain in lean subjects. However, the period of time over which fasting is often endured in Western society are far shorter, approximately 1-2 days. This study examined how a 36 h fast effected the subsequent day's energy and nutrient intake in a group of 24 healthy, lean men and women. Subjects underwent two 2 day treatments, termed 'fast' and 'maintenance'. During the 'fast' treatment, subjects were fed a maintenance diet on the day prior to the fast (day -1) to prevent overeating. They then consumed non-energy drinks only, from 20:00 h on day -1 to 08:00 h on day 2 (ad libitum feeding day), thus fasting for 36 h. On the 'maintenance' protocol, subjects received a maintenance diet throughout day 1. Throughout day 2 they had ad libitum access to a range of familiar foods, which were the same for both treatments. Body weight, blood glucose and respiratory quotient were used as compliance checks. Hunger was monitored on day's -1, 1 and 2 for the fast treatment only. On day 2, average energy intake was 10.2 vs 12.2 MJ/day (s.e.d. 1.0) on the post-maintenance and post-fast periods, respectively (P=0.049). Subjects altered feeding behaviour, in response to the fast, only at breakfast time, selecting a higher-fat meal (P<0.005). Compared to day -1, motivation to eat was elevated during the fast (P<0.05). This continued until breakfast was consumed during the re-feeding period (day 2), when values then returned to baseline. These data suggest that a 36 h fast, which generated a negative energy balance of approximately 12 MJ, did not induce a powerful, unconditioned stimulus to compensate on the subsequent day.

Slope-apron deposition in an ordovician arc-related setting: The Vuelta de Las Tolas Member (Suri Formation), Famatina Basin, northwest Argentina

USGS Publications Warehouse

Mangano, M.G.; Buatois, L.A.

1997-01-01

The Ordovician Suri Formation is part of the infill of the Famatina Basin of northwest Argentina, which formed in an active setting along the western margin of early Paleozoic Gondwana. The lower part of this formation, the Vuelta de Las Tolas Member, records sedimentation on a slope apron formed in an intra-arc basin situated on a flooded continental arc platform. The coincidence of a thick Arenig-Llanvirn sedimentary succession and volcanic-plutonic arc rocks suggests an extensional or transtensional arc setting, and is consistent with evidence of an extensional regime within the volcanic arc in the northern Puna region. The studied stratigraphic sections consist of volcanic rocks and six sedimentary facies. The facies can be clustered into four facies associations. Association 1, composed of facies A (laminated siltstones and mudstones) and B (massive mudstones and siltstones), is interpreted to have accumulated from silty-muddy high-and low-density turbidity currents and highly fluid, silty debris flows, with subsequent reworking by bottom currents, and to a lesser extent, hemipelagic suspension in an open-slope setting. Facies association 2 is dominated by facies C (current-rippled siltstones) strata. These deposits are interpreted to record overbank sedimentation from fine-grained turbidity currents. Facies E (matrix-supported volcanic breccias) interbedded with andesitic lava units comprises facies association 3. Deposition was contemporaneous with subaqueous volcanic activity, and accumulated from cohesive debris flows in a coarse-grained wedge at the base of slope. Facies association 4 is typified by facies D (vitric fine-grained sandstones and siltstones) and F (channelized and graded volcanic conglomerates and breccias) deposits. These strata commonly display thinning-and fining-upward trends, indicating sedimentation from highly-concentrated volcaniclastic turbidity currents in a channelized system. The general characteristics of these deposits of fresh pyroclastic detritus suggest that their accumulation was contemporaneous with, or post-dated shallow-water or subaereal explosive volcanism. The Vuelta de Las Tolas Member tends to show an overall random facies patterns reflecting the strong influence of non-cyclical episodic processes related to arc volcanism and slope sedimentation. The scarcity of resident ichnofaunas and the presence of thick packages of uniform mudstones suggest deposition under oxygen-depleted conditions in a topographically confined, ponded sub-basin. Interbasinal correlations favor comparison with Middle Arenig slope-apron successions formed in the northern Puna Basin and suggest a southward prolongation of the Arenig volcanic arc.

LH launcher Arcs Formation and Detection on JET

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

Baranov, Yu. F.; Challis, C. D.; Kirov, K.

2011-12-23

Mechanisms of arc formation have been analyzed and the critical electric fields for the multipactor effect calculated, compared to the experimental values and found to be within the normal operational space of the LH system on JET. It has been shown that the characteristic electron energy (20-1000)eV for the highest multipactor resonances (N = 4-9) are within the limits of secondary electron yield above 1 required for multipactoring. Electrons with these energies provide the highest gas desorption efficiency when hitting the waveguide walls. The effect of higher waveguide modes and magnetic field on the multipactor was also considered. The distributionmore » function for electrons accelerated by LH waves in front of the launcher has been calculated. The field emission currents have been estimated and found to be small. It is proposed that emission of Fel5, 16 lines, which can be obtained with improved diagnostics, could be used to detect arcs that are missed by a protection system based on the reflected power. The reliability and time response of these signals are discussed. A similar technique based on the observation of the emission of low ionized atoms can be used for a fast detection of other undesirable events to avoid sputtering or melting of the plasma facing components such as RF antenna. These techniques are especially powerful if they are based on emission uniquely associated with specific locations and components.« less

Peripheral cannabinoid-1 receptor blockade restores hypothalamic leptin signaling.

PubMed

Tam, Joseph; Szanda, Gergő; Drori, Adi; Liu, Ziyi; Cinar, Resat; Kashiwaya, Yoshihiro; Reitman, Marc L; Kunos, George

2017-10-01

In visceral obesity, an overactive endocannabinoid/CB 1 receptor (CB 1 R) system promotes increased caloric intake and decreases energy expenditure, which are mitigated by global or peripheral CB 1 R blockade. In mice with diet-induced obesity (DIO), inhibition of food intake by the peripherally restricted CB 1 R antagonist JD5037 could be attributed to endogenous leptin due to the rapid reversal of hyperleptinemia that maintains leptin resistance, but the signaling pathway engaged by leptin has remained to be determined. We analyzed the hypothalamic circuitry targeted by leptin following chronic treatment of DIO mice with JD5037. Leptin treatment or an increase in endogenous leptin following fasting/refeeding induced STAT3 phosphorylation in neurons in the arcuate nucleus (ARC) in lean and JD5037-treated DIO mice, but not in vehicle-treated DIO animals. Co-localization of pSTAT3 in leptin-treated mice was significantly less common with NPY + than with POMC + ARC neurons. The hypophagic effect of JD5037 was absent in melanocortin-4 receptor (MC4R) deficient obese mice or DIO mice treated with a MC4R antagonist, but was maintained in NPY -/- mice kept on a high-fat diet. Peripheral CB 1 R blockade in DIO restores sensitivity to endogenous leptin, which elicits hypophagia via the re-activation of melanocortin signaling in the ARC. Copyright © 2017 The Authors. Published by Elsevier GmbH.. All rights reserved.

Metamorphic and tectonic evolution of Ceuta peninsula (Internal Rif): new interpretation in the framework of arc and back arc evolution

NASA Astrophysics Data System (ADS)

Homonnay, Emmanuelle; Lardeaux, Jean-Marc; Corsini, Michel; Cenki-Tok, Bénédicte; Bosch, Delphine; Munch, Philippe; Romagny, Adrien; Ouazzani-Touhami, Mohamed

2016-04-01

In the last twenty years, various geophysical investigations have established that the Western Mediterranean opened in a subduction context as a back arc domain. In the Alboran basin the dip of the subduction plane is eastwards or southeastwards depending of considered models. If the geological records of back-arc opening are well-known, the arc-related tectonic and petrologic evolutions are still poorly documented. In order to decipher these markers, we focalised structural, petrological and thermo-chronological studies on the Ceuta peninsula located in the Rif belt, on the western part of the Gibraltar arc to the North of Morocco. The present-day tectonic pile is constituted by: (1) the upper Ceuta unit, composed of High Pressure and High Temperature metapelites retromorphosed under Amphibolite-facies condition, with Ultra-High Pressure relicts, and pyrigarnite and spinel bearing peridotites boudins at its base, (2) the lower Monte Hacho unit, with orthogneisses metamorphosed under Amphibolite-facies conditions. Structural analysis indicates a polyphase tectonic evolution: (1) an earlier deformation phase only observed in the UHP metapelites and characterized by a steep S1 foliation plane, (2) a main deformation phase associated to a pervasive gently dipping S2 foliation plane bearing a L2 stretching lineation and synschistose folds whose axes are parallel to L2 and (3) a late deformation phase which developed S3 foliation plane and L3 stretching lineation coeval with development of narrow normal ductile shear zones. A zone of increasing deformation, several dozen meters wide, is identified as a major ductile shear zone involving the peridotitic lenses at the base of the metapelites of the Ceuta unit and overlaying this upper unit on top of the orthogneisses of the Monte Hacho lower unit. The attitude of mylonitic foliation and stretching and mineral lineations as well as the numerous shear sense indicators observed in the shear zone are consistent with a thrusting toward the NE. Furthermore, biotite-sillimanite bearing S2 foliation affecting the whole of crustal rocks is contemporaneous with the movement on this main ductile thrusting. We combined garnet-biotite and GASP thermo-barometers with thermodynamic modelling (Theriak-Domino) in order to constrain pressure and temperature conditions of D2 and D3 tectono-metamorphic events. P-T conditions of D2 deformation are in the range 7-10kbar and 770-820°C and are compatible with syn-tectonic partial melting. D3 deformation event occurred at 1-7kbar and 400-550°C. These metamorphic conditions reflect abnormally high geothermal gradients during both shortening and thinning and are clearly compatible with the thermal evolution recognized in continental arcs. Preliminary U-Th-Pb (monazite, zircon and xenotime) and previous Ar39/Ar40 (micas) analyses, furnished similar ages around 21 Ma for D2 and D3 events, suggesting a very fast transition from arc to back-arc dynamics.

Genomes as geography: using GIS technology to build interactive genome feature maps

PubMed Central

Dolan, Mary E; Holden, Constance C; Beard, M Kate; Bult, Carol J

2006-01-01

Background Many commonly used genome browsers display sequence annotations and related attributes as horizontal data tracks that can be toggled on and off according to user preferences. Most genome browsers use only simple keyword searches and limit the display of detailed annotations to one chromosomal region of the genome at a time. We have employed concepts, methodologies, and tools that were developed for the display of geographic data to develop a Genome Spatial Information System (GenoSIS) for displaying genomes spatially, and interacting with genome annotations and related attribute data. In contrast to the paradigm of horizontally stacked data tracks used by most genome browsers, GenoSIS uses the concept of registered spatial layers composed of spatial objects for integrated display of diverse data. In addition to basic keyword searches, GenoSIS supports complex queries, including spatial queries, and dynamically generates genome maps. Our adaptation of the geographic information system (GIS) model in a genome context supports spatial representation of genome features at multiple scales with a versatile and expressive query capability beyond that supported by existing genome browsers. Results We implemented an interactive genome sequence feature map for the mouse genome in GenoSIS, an application that uses ArcGIS, a commercially available GIS software system. The genome features and their attributes are represented as spatial objects and data layers that can be toggled on and off according to user preferences or displayed selectively in response to user queries. GenoSIS supports the generation of custom genome maps in response to complex queries about genome features based on both their attributes and locations. Our example application of GenoSIS to the mouse genome demonstrates the powerful visualization and query capability of mature GIS technology applied in a novel domain. Conclusion Mapping tools developed specifically for geographic data can be exploited to display, explore and interact with genome data. The approach we describe here is organism independent and is equally useful for linear and circular chromosomes. One of the unique capabilities of GenoSIS compared to existing genome browsers is the capacity to generate genome feature maps dynamically in response to complex attribute and spatial queries. PMID:16984652

OPERATION SUNBEAM, SHOT SMALL BOY. Project Officer’s Report - Project 2.2, Measurement of Fast-Neutron Dose Rate as a Function of Time

DTIC Science & Technology

1985-09-01

Calibration 44 3.1.3 The SPIDER Calibration 45 3.1.*» Thermistor Temperature Detector Calibration. . 45 3.2 Amplifier Calibration 45 3.2.1...of a material with high conductivity and preferably high permeability. For the bunker construction, welded one-inch soft-steel plates were chosen for...Kovar flanges (metal- to-ceramic seal). The external plates are hel1arc- welded to the flanges. The external plate facing away from the incoming

Extracting spatial information from large aperture exposures of diffuse sources

NASA Technical Reports Server (NTRS)

Clarke, J. T.; Moos, H. W.

1981-01-01

The spatial properties of large aperture exposures of diffuse emission can be used both to investigate spatial variations in the emission and to filter out camera noise in exposures of weak emission sources. Spatial imaging can be accomplished both parallel and perpendicular to dispersion with a resolution of 5-6 arc sec, and a narrow median filter running perpendicular to dispersion across a diffuse image selectively filters out point source features, such as reseaux marks and fast particle hits. Spatial information derived from observations of solar system objects is presented.

Producing carbon stripper foils containing boron

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

Stoner, J. O. Jr.

2012-12-19

Parameters being actively tested by the accelerator community for the purpose of extending carbon stripper foil lifetimes in fast ion beams include methods of deposition, parting agents, mounting techniques, support (fork) materials, and inclusion of alloying elements, particularly boron. Specialized production apparatus is required for either sequential deposition or co-deposition of boron in carbon foils. A dual-use vacuum evaporator for arc evaporation of carbon and electron-beam evaporation of boron and other materials has been built for such development. Production of both carbon and boron foils has begun and improvements are in progress.

The intra-oceanic Cretaceous (~ 108 Ma) Kata-Rash arc fragment in the Kurdistan segment of Iraqi Zagros suture zone: Implications for Neotethys evolution and closure

NASA Astrophysics Data System (ADS)

Ali, Sarmad A.; Ismail, Sabah A.; Nutman, Allen P.; Bennett, Vickie C.; Jones, Brian G.; Buckman, Solomon

2016-09-01

The Kata-Rash arc fragment is an allochthonous thrust-bound body situated near Penjween, 100 km northeast of Sulymannia city, Kurdistan Region, within the Iraqi portion of the Zagros suture zone. It forms part of the suprasubduction zone 'Upper Allochthon' terranes (designated as the Gimo-Qandil Group), which is dominated by calc-alkaline andesite and basaltic-andesite, rhyodacite to rhyolite, crosscut by granitic, granodioritic, and dioritic dykes. Previously, rocks of the Kata-Rash arc fragment were interpreted as a part of the Eocene Walash volcanic group. However, SHRIMP zircon U-Pb dates on them of 108.1 ± 2.9 Ma (Harbar volcanic rocks) and 107.7 ± 1.9 Ma (Aulan intrusion) indicate an Albian-Cenomanian age, which is interpreted as the time of igneous crystallisation. The Aulan intrusion zircons have initial εHf values of + 8.6 ± 0.2. On a Nb/Yb-Th/Yb diagram, all Kata-Rash samples fall within the compositional field of arc-related rocks, i.e. above the mid-ocean-ridge basalt (MORB)-ocean island basalt (OIB) mantle array. Primitive-mantle-normalised trace-element patterns for the Kata-Rash samples show enrichment in the large ion lithophile elements and depletion in the high-field-strength elements supporting their subduction-related character. Low Ba/La coupled with low La/Yb and Hf/Hf* < 1 for the Aulan sample with initial εHf of + 8.6 ± 0.2 is interpreted as the magma dominated by contributions from fluid fluxing of the mantle wedge and lesser contributions of low temperature melt from subducted slab sediment, in an oceanic setting. This mechanism can explain the sub-DM initial εHf value, without the need to invoke melting of significantly older (continental) crust in an Andean setting. We interpret the Kata-Rash igneous rocks as a fragment of the Late Cretaceous suprasubduction zone system (named here the Kata-Rash arc) that most likely developed within the Neotethys Ocean rather than at a continental margin. Subsequently during the latest Cretaceous to Paleocene, the arc was accreted to the northern margin of the Arabian plate. The results indicate a > 3000 km continuity of Cretaceous arc activity (Oman to Cyprus), that consumed Neotethyian oceanic crust between Eurasia and the Gondwanan fragment Arabia.

Computational annotation of genes differentially expressed along olive fruit development

PubMed Central

Galla, Giulio; Barcaccia, Gianni; Ramina, Angelo; Collani, Silvio; Alagna, Fiammetta; Baldoni, Luciana; Cultrera, Nicolò GM; Martinelli, Federico; Sebastiani, Luca; Tonutti, Pietro

2009-01-01

Background Olea europaea L. is a traditional tree crop of the Mediterranean basin with a worldwide economical high impact. Differently from other fruit tree species, little is known about the physiological and molecular basis of the olive fruit development and a few sequences of genes and gene products are available for olive in public databases. This study deals with the identification of large sets of differentially expressed genes in developing olive fruits and the subsequent computational annotation by means of different software. Results mRNA from fruits of the cv. Leccino sampled at three different stages [i.e., initial fruit set (stage 1), completed pit hardening (stage 2) and veraison (stage 3)] was used for the identification of differentially expressed genes putatively involved in main processes along fruit development. Four subtractive hybridization libraries were constructed: forward and reverse between stage 1 and 2 (libraries A and B), and 2 and 3 (libraries C and D). All sequenced clones (1,132 in total) were analyzed through BlastX against non-redundant NCBI databases and about 60% of them showed similarity to known proteins. A total of 89 out of 642 differentially expressed unique sequences was further investigated by Real-Time PCR, showing a validation of the SSH results as high as 69%. Library-specific cDNA repertories were annotated according to the three main vocabularies of the gene ontology (GO): cellular component, biological process and molecular function. BlastX analysis, GO terms mapping and annotation analysis were performed using the Blast2GO software, a research tool designed with the main purpose of enabling GO based data mining on sequence sets for which no GO annotation is yet available. Bioinformatic analysis pointed out a significantly different distribution of the annotated sequences for each GO category, when comparing the three fruit developmental stages. The olive fruit-specific transcriptome dataset was used to query all known KEGG (Kyoto Encyclopaedia of Genes and Genomes) metabolic pathways for characterizing and positioning retrieved EST records. The integration of the olive sequence datasets within the MapMan platform for microarray analysis allowed the identification of specific biosynthetic pathways useful for the definition of key functional categories in time course analyses for gene groups. Conclusion The bioinformatic annotation of all gene sequences was useful to shed light on metabolic pathways and transcriptional aspects related to carbohydrates, fatty acids, secondary metabolites, transcription factors and hormones as well as response to biotic and abiotic stresses throughout olive drupe development. These results represent a first step toward both functional genomics and systems biology research for understanding the gene functions and regulatory networks in olive fruit growth and ripening. PMID:19852839

An approach to multiobjective optimization of rotational therapy. II. Pareto optimal surfaces and linear combinations of modulated blocked arcs for a prostate geometry.

PubMed

Pardo-Montero, Juan; Fenwick, John D

2010-06-01

The purpose of this work is twofold: To further develop an approach to multiobjective optimization of rotational therapy treatments recently introduced by the authors [J. Pardo-Montero and J. D. Fenwick, "An approach to multiobjective optimization of rotational therapy," Med. Phys. 36, 3292-3303 (2009)], especially regarding its application to realistic geometries, and to study the quality (Pareto optimality) of plans obtained using such an approach by comparing them with Pareto optimal plans obtained through inverse planning. In the previous work of the authors, a methodology is proposed for constructing a large number of plans, with different compromises between the objectives involved, from a small number of geometrically based arcs, each arc prioritizing different objectives. Here, this method has been further developed and studied. Two different techniques for constructing these arcs are investigated, one based on image-reconstruction algorithms and the other based on more common gradient-descent algorithms. The difficulty of dealing with organs abutting the target, briefly reported in previous work of the authors, has been investigated using partial OAR unblocking. Optimality of the solutions has been investigated by comparison with a Pareto front obtained from inverse planning. A relative Euclidean distance has been used to measure the distance of these plans to the Pareto front, and dose volume histogram comparisons have been used to gauge the clinical impact of these distances. A prostate geometry has been used for the study. For geometries where a blocked OAR abuts the target, moderate OAR unblocking can substantially improve target dose distribution and minimize hot spots while not overly compromising dose sparing of the organ. Image-reconstruction type and gradient-descent blocked-arc computations generate similar results. The Pareto front for the prostate geometry, reconstructed using a large number of inverse plans, presents a hockey-stick shape comprising two regions: One where the dose to the target is close to prescription and trade-offs can be made between doses to the organs at risk and (small) changes in target dose, and one where very substantial rectal sparing is achieved at the cost of large target underdosage. Plans computed following the approach using a conformal arc and four blocked arcs generally lie close to the Pareto front, although distances of some plans from high gradient regions of the Pareto front can be greater. Only around 12% of plans lie a relative Euclidean distance of 0.15 or greater from the Pareto front. Using the alternative distance measure of Craft ["Calculating and controlling the error of discrete representations of Pareto surfaces in convex multi-criteria optimization," Phys. Medica (to be published)], around 2/5 of plans lie more than 0.05 from the front. Computation of blocked arcs is quite fast, the algorithms requiring 35%-80% of the running time per iteration needed for conventional inverse plan computation. The geometry-based arc approach to multicriteria optimization of rotational therapy allows solutions to be obtained that lie close to the Pareto front. Both the image-reconstruction type and gradient-descent algorithms produce similar modulated arcs, the latter one perhaps being preferred because it is more easily implementable in standard treatment planning systems. Moderate unblocking provides a good way of dealing with OARs which abut the PTV. Optimization of geometry-based arcs is faster than usual inverse optimization of treatment plans, making this approach more rapid than an inverse-based Pareto front reconstruction.

BigQ: a NoSQL based framework to handle genomic variants in i2b2.

PubMed

Gabetta, Matteo; Limongelli, Ivan; Rizzo, Ettore; Riva, Alberto; Segagni, Daniele; Bellazzi, Riccardo

2015-12-29

Precision medicine requires the tight integration of clinical and molecular data. To this end, it is mandatory to define proper technological solutions able to manage the overwhelming amount of high throughput genomic data needed to test associations between genomic signatures and human phenotypes. The i2b2 Center (Informatics for Integrating Biology and the Bedside) has developed a widely internationally adopted framework to use existing clinical data for discovery research that can help the definition of precision medicine interventions when coupled with genetic data. i2b2 can be significantly advanced by designing efficient management solutions of Next Generation Sequencing data. We developed BigQ, an extension of the i2b2 framework, which integrates patient clinical phenotypes with genomic variant profiles generated by Next Generation Sequencing. A visual programming i2b2 plugin allows retrieving variants belonging to the patients in a cohort by applying filters on genomic variant annotations. We report an evaluation of the query performance of our system on more than 11 million variants, showing that the implemented solution scales linearly in terms of query time and disk space with the number of variants. In this paper we describe a new i2b2 web service composed of an efficient and scalable document-based database that manages annotations of genomic variants and of a visual programming plug-in designed to dynamically perform queries on clinical and genetic data. The system therefore allows managing the fast growing volume of genomic variants and can be used to integrate heterogeneous genomic annotations.

A tool for selecting SNPs for association studies based on observed linkage disequilibrium patterns.

PubMed

De La Vega, Francisco M; Isaac, Hadar I; Scafe, Charles R

2006-01-01

The design of genetic association studies using single-nucleotide polymorphisms (SNPs) requires the selection of subsets of the variants providing high statistical power at a reasonable cost. SNPs must be selected to maximize the probability that a causative mutation is in linkage disequilibrium (LD) with at least one marker genotyped in the study. The HapMap project performed a genome-wide survey of genetic variation with about a million SNPs typed in four populations, providing a rich resource to inform the design of association studies. A number of strategies have been proposed for the selection of SNPs based on observed LD, including construction of metric LD maps and the selection of haplotype tagging SNPs. Power calculations are important at the study design stage to ensure successful results. Integrating these methods and annotations can be challenging: the algorithms required to implement these methods are complex to deploy, and all the necessary data and annotations are deposited in disparate databases. Here, we present the SNPbrowser Software, a freely available tool to assist in the LD-based selection of markers for association studies. This stand-alone application provides fast query capabilities and swift visualization of SNPs, gene annotations, power, haplotype blocks, and LD map coordinates. Wizards implement several common SNP selection workflows including the selection of optimal subsets of SNPs (e.g. tagging SNPs). Selected SNPs are screened for their conversion potential to either TaqMan SNP Genotyping Assays or the SNPlex Genotyping System, two commercially available genotyping platforms, expediting the set-up of genetic studies with an increased probability of success.

Fast time-resolved aerosol collector: proof of concept

NASA Astrophysics Data System (ADS)

Yu, X.-Y.; Cowin, J. P.; Iedema, M. J.; Ali, H.

2010-10-01

Atmospheric particles can be collected in the field on substrates for subsequent laboratory analysis via chemically sensitive single particle methods such as scanning electron microscopy with energy dispersive x-ray analysis. With moving substrates time resolution of seconds to minutes can be achieved. In this paper, we demonstrate how to increase the time resolution when collecting particles on a substrate to a few milliseconds to provide real-time information. Our fast time-resolved aerosol collector ("Fast-TRAC") microscopically observes the particle collection on a substrate and records an on-line video. Particle arrivals are resolved to within a single frame (4-17 ms in this setup), and the spatial locations are matched to the subsequent single particle analysis. This approach also provides in-situ information on particle size and number concentration. Applications are expected in airborne studies of cloud microstructure, pollution plumes, and surface long-term monitoring.

Fast time-resolved aerosol collector: proof of concept

NASA Astrophysics Data System (ADS)

Yu, X.-Y.; Cowin, J. P.; Iedema, M. J.; Ali, H.

2010-06-01

Atmospheric particles can be collected in the field on substrates for subsequent laboratory analysis via chemically sensitive single particle methods such as scanning electron microscopy with energy dispersive x-ray analysis. With moving substrates time resolution of seconds to minutes can be achieved. In this paper, we demonstrate how to increase the time resolution when collecting particles on a substrate to a few milliseconds to provide real-time information. Our fast time-resolved aerosol collector ("Fast-TRAC") microscopically observes the particle collection on a substrate and records an on-line video. Particle arrivals are resolved to within a single frame (4-17 ms in this setup), and the spatial locations are matched to the subsequent single particle analysis. This approach also provides in-situ information on particle size and number concentration. Applications are expected in airborne studies of cloud microstructure, pollution plumes, and surface long-term monitoring.

Community annotation experiment for ground truth generation for the i2b2 medication challenge

PubMed Central

Solti, Imre; Xia, Fei; Cadag, Eithon

2010-01-01

Objective Within the context of the Third i2b2 Workshop on Natural Language Processing Challenges for Clinical Records, the authors (also referred to as ‘the i2b2 medication challenge team’ or ‘the i2b2 team’ for short) organized a community annotation experiment. Design For this experiment, the authors released annotation guidelines and a small set of annotated discharge summaries. They asked the participants of the Third i2b2 Workshop to annotate 10 discharge summaries per person; each discharge summary was annotated by two annotators from two different teams, and a third annotator from a third team resolved disagreements. Measurements In order to evaluate the reliability of the annotations thus produced, the authors measured community inter-annotator agreement and compared it with the inter-annotator agreement of expert annotators when both the community and the expert annotators generated ground truth based on pooled system outputs. For this purpose, the pool consisted of the three most densely populated automatic annotations of each record. The authors also compared the community inter-annotator agreement with expert inter-annotator agreement when the experts annotated raw records without using the pool. Finally, they measured the quality of the community ground truth by comparing it with the expert ground truth. Results and conclusions The authors found that the community annotators achieved comparable inter-annotator agreement to expert annotators, regardless of whether the experts annotated from the pool. Furthermore, the ground truth generated by the community obtained F-measures above 0.90 against the ground truth of the experts, indicating the value of the community as a source of high-quality ground truth even on intricate and domain-specific annotation tasks. PMID:20819855

A Western Pacific Hotspot?

NASA Astrophysics Data System (ADS)

MacPherson, C. G.; Hall, R.

2003-04-01

The petrology of volcanic rocks from the St. Andrew Strait and helium isotope ratios of backarc lavas from the Manus Basin have been used to propose the existence of an active hotspot beneath the eastern Bismarck Sea (Johnson et al., 1978; Macpherson et al., 1998). The past influence of this hotspot can be assessed by mapping its present location onto a plate tectonic reconstruction of the western Pacific (Macpherson and Hall, 2001). During the Middle Eocene the nascent Izu-Bonin-Mariana (IBM) arc lay above the hotspot. The volume of magma emplaced at the IBM arc at that time substantially exceeds the average magma production rate for mature island arcs. Furthermore, the ultramafic (boninitic) character of much of this magmatism requires elevated temperatures. The geochemistry of contemporaneous magmatism in the backarc resembles ocean island basalts and much of the backarc region experienced significant uplift at that time. All of these features can be explained by the influx of hot, buoyant, chemically distinct mantle beneath the IBM and its hinterland. The lithosphere lying above the hotspot during the later Eocene was subsequently subducted. During the Oligo-Miocene the hotspot was traversed by parts of the Caroline Plate where the Euripik Rise is found. This is an aseismic rise that possesses the geophysical characteristics of thickened oceanic crust formed by excess, basaltic magmatism and is the type of structure that would result from the passage of relatively young oceanic lithosphere over a mantle hotspot. Plate reconstruction for the western Pacific predicts a hotspot trail that is consistent with the Middle Eocene and Oligo-Miocene geology of the IBM and Caroline Plates, respectively (Macpherson and Hall, 2001). Parts of the trail have been disrupted by subsequent sea-floor spreading or lost through subduction but the remaining vestiges are consistent with the action of a thermal anomaly throughout much of the Cenozoic. More speculatively, buoyancy differences between the IBM, supported by hot mantle, and older, colder lithosphere of the adjacent Pacific Plate may have provided a mechanism to propagate widespread subduction at the nascent IBM arc. Johnson RW, Smith IEM, &Taylor SR, BMR J. Aus. Geol. Geophys. 3, 55-69, (1978). Macpherson CG, Hilton, DR, Sinton, JM, Poreda RJ &Craig H. Geology 26, 1007-1010, (1998). Macpherson CG &Hall R, Earth Planet. Sci. Lett. 186, 215-230, (2001).

Initial magmatism and evolution of the Izu-Bonin-Mariana Arc

NASA Astrophysics Data System (ADS)

Arculus, R. J.

2016-12-01

Expedition 351 of the IODP targeted site U1438 in the Amami Sankaku Basin, northwestern Philippine Sea , 70 km west of the northern Kyushu-Palau Ridge (KPR). The latter formed a chain of stratovolcanoes of the Izu-Bonin-Mariana (IBM) arc, and a remnant arc following migration of the volcanic front eastwards during Shikoku backarc basin formation in the Miocene. Unravelling causes of subduction initiation drove the primary aims of the Expedition involving recovery of igneous basement below the KPR, and a history of the magmatic evolution of the KPR preserved in a clastic record. All these aims were achieved, but with some surprises. Out of 1600m drilled in 4700m water depth, 150m of igneous oceanic crust comprising low-K, tholeiitic basalt lava flows were recovered at U1438. The lavas are variably glassy to microphyric, Cr-spinel-olivine-plagioclase-clinopyroxene-bearing, have high V/Ti, very low absolute rare earth element abundances and low La/Yb, and radiogenic Hf at a given 143/144Nd compared to basalts of mid-ocean ridges. The basement is geochemically and petrologically similar to so-called "forearc basalts" recovered trenchward of the active IBM volcanic front, and of similar or older age (≥52Ma). Highly melt-depleted mantle source(s) were involved and high-temperature, low-pressure dehydration of the subducting Pacific Plate. Compositions of glass (formerly melt) inclusions in clinopyroxene-bearing clasts and sandstones in sediments overlying the basement show a change from medium-Fe (aka "calcalkaline") to low-Fe (tholeiitic) magmas during the Eocene-Oligocene evolution of the KPR. Widespread magmatism along- and across-strike of the nascent IBM system coupled with geologic constraints from the western Philippine Sea, indicate subduction initiation at the IBM arc likely propagated adjacent to Mesozoic-aged arcs/basins to the west of the KPR, following plate reorganization subsequent to the demise of the Izanagi-Pacific Ridge along eastern Asia at 60Ma. Neither the spontaneous nor induced models of subduction initiation adequately capture the inception of the IBM arc. Geographic modifiers of basalt types such as "forearc" are overly restrictive and potentially misleading.

Petrology and Geochemistry of Serpentinized Peridotites from a Bonin Fore-arc Seamount

NASA Astrophysics Data System (ADS)

Tian, L.; Tuoyu, W.; Dong, Y. H.; Gao, J.; Wu, S.

2016-12-01

Serpentinites, which contain up to 13 wt.% of water, are an important reservoir for chemical recycling in subduction zones. During the last two decades, many observations documented the occurrence of fore-arc mantle serpentinites in different locations. Here, we present petrology and whole rock chemistry for serpentinized peridotites dredged from the Hahajima Seamount, which is located 20-60 km west of the junction of the Bonin Trench and the Mariana Trench. Combined with published geochemical data of serpentinites from the Torishima Seamount, Conical Seamount and South Chamorro Seamount in the Izu-Bonin-Mariana fore-arc region, it will allow us to better understand the average composition of serpentinized fore-arc mantle overlying the subducting slab and the role of serpentinized mantle playing in the subduction zone geochemical cycle. The studied ultramafic rocks from the Hahajima Seamount are extensively serpentinized and hydrated (73 to 83%), with loss of ignition values ranging between 13 and 15 wt.%. Our results show that the serpentinized peridotites have Mg number from 88 to 90, and the average MgO/SiO2 is 0.93. The average Al2O3 (0.48 wt.%) and CaO (0.23 wt.%) contents are very low, consistent with low clinopyroxene abundances, and the overall depleted character of the mantle harzburgite protoliths. The serpentinized peridotites from the Hahajima Seamount exhibit similar "U" shape rare earth element (REE) patterns ([La/Sm]N = 3.1-3.6), at higher overall abundances, to the Conical and South Chamorro Seamount suites. One exceptional sample shows the similar REE pattern as serpentinized peridotites from the Torishima Seamount, with depleted light REE concentration ([La/Sm]N =0.7). All the serpentinized peridotites from these four fore-arc seamounts show strong enrichment in fluid-mobile and lithophile elements (U, Pb, Sr and Li). The geochemical signature of the serpentinized peridotites from the seamounts in the Izu-Bonin-Mariana fore-arc region could be interpreted as the result of the combination of extensive partial melting and subsequent percolation of sediment-derived fluids through the mantle wedge [1]. References: [1] Deschamps et al. (2013), Lithos, 178, 96-127.

Geochemical and isotopic constraints on island arc, synorogenic, post-orogenic and anorogenic granitoids in the Arabian Shield, Saudi Arabia

NASA Astrophysics Data System (ADS)

Robinson, F. A.; Foden, J. D.; Collins, A. S.

2015-04-01

The Arabian Shield preserves a protracted magmatic record of repeated amalgamation of juvenile subduction terranes that host granite intrusions ranging in age from the early Neoproterozoic to the Cambrian, which were emplaced into convergent and within-plate settings. Geochronology and whole-rock geochemistry of sampled Saudi Arabian granitoids define and distinguish four discrete age groups: 1) ~ 845-700 Ma island arc and synorogenic granitoids (IA + Syn), 2) ~ 640-610 Ma granitoids from the Nabitah and Halaban Suture (NHSG), 3) ~ 610-600 Ma post-orogenic perthitic (hypersolvus) granitoids (POPG), and 4) < 600 Ma anorogenic aegirine-bearing perthitic (hypersolvus) granitoids (AAPG). Groups 1, 2 and 3 include suites ranging from I-S- to A-type granites that have REE signatures typical of volcanic arc settings and show intra-suite variation that could be controlled by a combination of crustal assimilation and fractional crystallisation. Their mafic parental magmas have N-MORB-, or arc-tholeiite-like geochemistry. By contrast, group 4 A-type granites are more enriched in HREE and in incompatible elements such as Nb, Rb, Ga, Nd, Zr and Y and have lower Ce/Yb and higher Y/Nb ratios. These granitoids are interpreted to have been emplaced into within-plate and back-arc settings. Granitoid data also provide evidence that there may be two distinct mantle sources to the mafic parents of the granite suites. These are distinguished as contaminated and enriched mantle using Nb and Y and Nd isotopes. All granitoid suites are isotopically juvenile (ɛNd + 3 to + 6) and fall between the upper field crustal values of the Paleoproterozoic Khida terrane (ɛNd + 1) and contemporary depleted mantle. However, Nd isotopes distinguish contamination in group 1-3 mafic end-members beneath sutures which are interpreted to be derived from the contemporary MORB-type mantle wedge with subsequent crustal assimilation and fractionation to I- and A-type granitoids. The youngest (after 600 Ma) A-types (group 4) emplaced into extensional within-plate and back-arc settings require a new enriched mantle source that this study interprets to be associated with delamination.

Link between SSZ ophiolite formation, emplacement and arc inception, Northland, New Zealand: U Pb SHRIMP constraints; Cenozoic SW Pacific tectonic implications

NASA Astrophysics Data System (ADS)

Whattam, Scott A.; Malpas, John; Smith, Ian E. M.; Ali, Jason R.

2006-10-01

New U-Pb age-data from zircons separated from a Northland ophiolite gabbro yield a mean 206Pb/ 238U age of 31.6 ± 0.2 Ma, providing support for a recently determined 28.3 ± 0.2 Ma SHRIMP age of an associated plagiogranite and ˜ 29-26 Ma 40Ar/ 39Ar ages ( n = 9) of basalts of the ophiolite. Elsewhere, Miocene arc-related calc-alkaline andesite dikes which intrude the ophiolitic rocks contain zircons which yield mean 206Pb/ 238U ages of 20.1 ± 0.2 and 19.8 ± 0.2 Ma. The ophiolite gabbro and the andesites both contain rare inherited zircons ranging from 122-104 Ma. The Early Cretaceous zircons in the arc andesites are interpreted as xenocrysts from the Mt. Camel basement terrane through which magmas of the Northland Miocene arc lavas erupted. The inherited zircons in the ophiolite gabbros suggest that a small fraction of this basement was introduced into the suboceanic mantle by subduction and mixed with mantle melts during ophiolite formation. We postulate that the tholeiitic suite of the ophiolite represents the crustal segment of SSZ lithosphere (SSZL) generated in the southern South Fiji Basin (SFB) at a northeast-dipping subduction zone that was initiated at about 35 Ma. The subduction zone nucleated along a pre-existing transform boundary separating circa 45-20 Ma oceanic lithosphere to the north and west of the Northland Peninsula from nascent back arc basin lithosphere of the SFB. Construction of the SSZL propagated southward along the transform boundary as the SFB continued to unzip to the southeast. After subduction of a large portion of oceanic lithosphere by about 26 Ma and collision of the SSZL with New Zealand, compression between the Australian Plate and the Pacific Plate was taken up along a new southwest-dipping subduction zone behind the SSZL. Renewed volcanism began in the oceanic forearc at 25 Ma producing boninitic-like, SSZ and within-plate alkalic and calc-alkaline rocks. Rocks of these types temporally overlap ophiolite emplacement and subsequent Miocene continental arc construction.

Eocene extensional exhumation of basement and arc rocks along southwesternmost Peru, Central Andes.

NASA Astrophysics Data System (ADS)

Noury, Mélanie; Bernet, Matthias; Sempéré, Thierry

2014-05-01

The overthickened crust of the current Central Andes is commonly viewed as the result of tectonic shortening. However, in the present-day terrestrial forearc and arc of southwesternmost Peru, crustal thickness increases from 30 km along the coastline to >60 km below the active arc, whereas the upper crust exhibits little to no evidence of crustal shortening and, in constrast, many extensional features. How (and when) crustal overthickness was acquired in this region is thus little understood. Because crustal overthickening often results in extensional collapse and/or significant erosion, here we address this issue through a regional-scale study of exhumation using fission-track thermochronology. The limited fission-track data previously available in the area suggested that exhumation began during the Mesozoic. In this study, we present new apatite and zircon fission-track data obtained along the current terrestrial forearc of southwesternmost Peru. This relatively restricted area presents the interest of providing extensive outcrops of Precambrian to Ordovician basement and Early Jurassic to Late Cretaceous arc plutons. In order to compare the chronology of exhumation of these units, we performed extensive sampling for fission-track dating, as well as structural mapping. Our results indicate that the basement rocks and Jurassic plutons that crop out in the Arequipa region, where the crust is now >50 km-thick, experienced a rapid cooling through the 240-110°C temperature range between ~65 and ~35 Ma. This period of rapid exhumation coincided in time with the accumulation of terrestrial forearc deposits (the Lower Moquegua Group), that exhibit many syn-sedimentary extensional features and are bounded by conspicuous normal faults, specifically along the region where intense activity of the main arc between ~90 and ~60 Ma had led to voluminous magma emplacement. This close succession of (1) intense magmatic activity and (2) regional-scale exhumation associated with extensional basins leads us to propose that arc magmatism between ~90 and ~60 Ma was productive enough to significantly thicken the crust, resulting in its subsequent extensional collapse between ~60 and ~35 Ma.

Discovery of a Triassic magmatic arc source for the Permo-Triassic Karakaya subduction complex, NW Turkey

NASA Astrophysics Data System (ADS)

Ayda Ustaömer, Petek; Ustaömer, Timur; Gerdes, Axel; Robertson, Alastair H. F.; Zulauf, Gernold

2014-05-01

The Permo-Triassic Karakaya Complex is well explained by northward subduction of Palaeotethys but until now no corresponding magmatic arc has been identified in the region. With the aim of determining the compositions and ages of the source units, ten sandstone samples were collected from the mappably distinct Ortaoba, Hodul, Kendirli and Orhanlar Units. Zircon grains were extracted from these sandstones and >1300 were dated by the U-Pb method and subsequently analysed for the Lu-Hf isotopic compositions by LA-MC-ICPMS at Goethe University, Frankfurt. The U-Pb-Hf isotope systematics are indicative of two different sediment provenances. The first, represented by the Ortaoba, Hodul and Kendirli Units, is dominated by igneous rocks of Triassic (250-220 Ma), Early Carboniferous-Early Permian (290-340 Ma) and Early to Mid-Devonian (385-400 Ma) ages. The second provenance, represented by the Orhanlar Unit, is indicative of derivation from a peri-Gondwanan terrane. In case of the first provenance, the Devonian and Carboniferous source rocks exibit intermediate eHf(t) values (-11 to -3), consistent with the formation at a continental margin where juvenile mantle-derived magmas mixed with (recycled) old crust having Palaeoproterozoic Hf model ages. In contrast, the Triassic arc magma exhibits higher eHf(t) values (-6 to +6), consistent with the mixing of juvenile mantle-derived melts with (recycled) old crust perhaps somewhat rejuvanated during the Cadomian period. We have therefore identified a Triassic magmatic arc as predicted by the interpretation of the Karakaya Complex as an accretionary complex related to northward subduction (Carboniferous and Devonian granites are already well documented in NW Turkey). Possible explanations for the lack of any outcrop of the source magmatic arc are that it was later subducted or the Karakaya Complex was displaced laterally from its source arc (both post 220 Ma). Strike-slip displacement (driven by oblique subduction?) can also explain the presence of two different sandstone source areas as indicated by the combined U-Pb-Hf isotope and supporting petrographic data. This study was supported by TUBITAK, Project no: 111R015

Arctigenin Treatment Protects against Brain Damage through an Anti-Inflammatory and Anti-Apoptotic Mechanism after Needle Insertion

PubMed Central

Song, Jie; Li, Na; Xia, Yang; Gao, Zhong; Zou, Sa-feng; Kong, Liang; Yao, Ying-Jia; Jiao, Ya-Nan; Yan, Yu-Hui; Li, Shao-Heng; Tao, Zhen-Yu; Lian, Guan; Yang, Jing-Xian; Kang, Ting-Guo

2016-01-01

Convection enhanced delivery (CED) infuses drugs directly into brain tissue. Needle insertion is required and results in a stab wound injury (SWI). Subsequent secondary injury involves the release of inflammatory and apoptotic cytokines, which have dramatic consequences on the integrity of damaged tissue, leading to the evolution of a pericontusional-damaged area minutes to days after in the initial injury. The present study investigated the capacity for arctigenin (ARC) to prevent secondary brain injury and the determination of the underlying mechanism of action in a mouse model of SWI that mimics the process of CED. After CED, mice received a gavage of ARC from 30 min to 14 days. Neurological severity scores (NSS) and wound closure degree were assessed after the injury. Histological analysis and immunocytochemistry were used to evaluated the extent of brain damage and neuroinflammation. Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) was used to detect universal apoptosis. Enzyme-linked immunosorbent assays (ELISA) was used to test the inflammatory cytokines (tumor necrosis factor (TNF)-α, interleukin (IL)-6 and IL-10) and lactate dehydrogenase (LDH) content. Gene levels of inflammation (TNF-α, IL-6, and IL-10) and apoptosis (Caspase-3, Bax and Bcl-2) were detected by reverse transcription-polymerase chain reaction (RT-PCR). Using these, we analyzed ARC’s efficacy and mechanism of action. Results: ARC treatment improved neurological function by reducing brain water content and hematoma and accelerating wound closure relative to untreated mice. ARC treatment reduced the levels of TNF-α and IL-6 and the number of allograft inflammatory factor (IBA)- and myeloperoxidase (MPO)-positive cells and increased the levels of IL-10. ARC-treated mice had fewer TUNEL+ apoptotic neurons and activated caspase-3-positive neurons surrounding the lesion than controls, indicating increased neuronal survival. Conclusions: ARC treatment confers neuroprotection of brain tissue through anti-inflammatory and anti-apoptotic effects in a mouse model of SWI. These results suggest a new strategy for promoting neuronal survival and function after CED to improve long-term patient outcome. PMID:27445818

Hyperphagia induced by sucrose: relation to circulating and CSF glucose and corticosterone and orexigenic peptides in the arcuate nucleus.

PubMed

Gaysinskaya, V A; Karatayev, O; Shuluk, J; Leibowitz, S F

2011-01-01

Sucrose-rich diets compared to starch-rich diets are known to stimulate overeating under chronic conditions. The present study in normal-weight rats established an acute "preload-to-test meal" paradigm for demonstrating sucrose-induced hyperphagia and investigating possible mechanisms that mediate this behavioral phenomenon. In this acute paradigm, the rats were first given a small (15 kcal) sucrose preload (30% sucrose) for 30 min compared to an equicaloric, starch preload (25% starch with 5% sucrose) and then allowed to freely consume a subsequent test meal of lab chow. The sucrose preload, when compared to a starch preload equal in energy density and palatability, consistently increased food intake in the subsequent test meal occurring between 60 and 120 min after the end of the preload. Measurements of hormones, metabolites and hypothalamic peptides immediately preceding this hyperphagia revealed marked differences between the sucrose vs starch groups that could contribute to the increase in food intake. Whereas the sucrose group compared to the starch group immediately after the preload (at 10 min) had elevated levels of glucose in serum and cerebrospinal fluid (CSF) along with reduced expressions of neuropeptide Y (NPY) and agouti-related protein (AgRP) in the arcuate nucleus (ARC), the subsequent effects (at 30-60 min) just preceding the test meal hyperphagia were the reverse. Along with lower levels of glucose, they included markedly elevated serum and CSF levels of corticosterone and mRNA levels of NPY and AgRP in the ARC. In addition to establishing an animal model for sucrose-induced hyperphagia, these results demonstrate peripheral and central mechanisms that may mediate this behavioral phenomenon. Copyright © 2010 Elsevier Inc. All rights reserved.

HYPERPHAGIA INDUCED BY SUCROSE: RELATION TO CIRCULATING AND CSF GLUCOSE AND CORTICOSTERONE AND OREXIGENIC PEPTIDES IN THE ARCUATE NUCLEUS

PubMed Central

Gaysinskaya, V. A.; Karatayev, O.; Shuluk, J.; Leibowitz, S. F.

2010-01-01

Sucrose-rich diets compared to starch-rich diets are known to stimulate overeating under chronic conditions. The present study in normal-weight rats established an acute “preload-to-test meal” paradigm for demonstrating sucrose-induced hyperphagia and investigating possible mechanisms that mediate this behavioral phenomenon. In this acute paradigm, the rats were first given a small (15 kcals) sucrose preload (30% sucrose) for 30 min compared to an equicaloric, starch preload (25% starch with 5% sucrose) and then allowed to freely consume a subsequent test meal of lab chow. The sucrose preload, when compared to a starch preload equal in energy density and palatability, consistently increased food intake in the subsequent test meal occurring between 60–120 min after the end of the preload. Measurements of hormones, metabolites and hypothalamic peptides immediately preceding this hyperphagia revealed marked differences between the sucrose vs starch groups that could contribute to the increase in food intake. Whereas the sucrose group compared to starch group immediately after the preload (at 10 min) had elevated levels of glucose in serum and cerebrospinal fluid (CSF) along with reduced expression of neuropeptide Y (NPY) and agouti-related protein (AgRP) in the arcuate nucleus (ARC), the subsequent effects (at 30–60 min) just preceding the test meal hyperphagia were the reverse. Along with lower levels of glucose, they included markedly elevated serum and CSF levels of corticosterone and mRNA levels of NPY and AgRP in the ARC. In addition to establishing an animal model for sucrose-induced hyperphagia, these results demonstrate peripheral and central mechanisms that may mediate this behavioral phenomenon. PMID:21036188

Lightning Pin Injection Test: MOSFETS in "ON" State

NASA Technical Reports Server (NTRS)

Ely, Jay J.; Nguyen, Truong X.; Szatkowski, George N.; Koppen, Sandra V.; Mielnik, John J.; Vaughan, Roger K.; Saha, Sankalita; Wysocki, Philip F.; Celaya, Jose R.

2011-01-01

The test objective was to evaluate MOSFETs for induced fault modes caused by pin-injecting a standard lightning waveform into them while operating. Lightning Pin-Injection testing was performed at NASA LaRC. Subsequent fault-mode and aging studies were performed by NASA ARC researchers using the Aging and Characterization Platform for semiconductor components. This report documents the test process and results, to provide a basis for subsequent lightning tests. The ultimate IVHM goal is to apply prognostic and health management algorithms using the features extracted during aging to allow calculation of expected remaining useful life. A survey of damage assessment techniques based upon inspection is provided, and includes data for optical microscope and X-ray inspection. Preliminary damage assessments based upon electrical parameters are also provided.

Physics of Intense Electron Current Sources for Helicity Injection

NASA Astrophysics Data System (ADS)

Hinson, E. T.; Barr, J. L.; Bongard, M. W.; Burke, M. G.; Fonck, R. J.; Lewicki, B. T.; Perry, J. M.; Redd, A. J.; Winz, G. R.

2014-10-01

DC helicity injection (HI) for non-solenoidal ST startup requires sources of current at the tokamak edge. Since the rate of HI scales with injection voltage, understanding of the physics setting injector impedance is necessary for a predictive model of the HI rate and subsequent growth of Ip. In Pegasus, arc plasma sources are used for current injection. They operate immersed in tokamak edge plasma, and are biased at ~1-2 kV with respect to the vessel to draw current densities J ~ 1 kA/cm2 from an arc plasma cathode. Prior to tokamak formation, impedance data manifests two regimes, one at low current (< 1 kA) with I ~V 3 / 2 , and a higher current mode where I ~V 1 / 2 holds. The impedance in the I ~V 3 / 2 regime is consistent with an electrostatic double layer. Current in the I ~V 1 / 2 regime is linear in arc gas fueling rate, suggesting a space-charge limit set by nedge. In the presence of tokamak plasmas, voltage oscillations of the order 100s of volts are measured during MHD relaxation activity. These fluctuations occur at the characteristic frequencies of the n = 1 and n = 0 MHD activity observed on magnetic probes, and are suggestive of dynamic activity found in LHI simulations in NIMROD. Advanced injector design techniques have allowed higher voltage operation. These include staged shielding to prevent external arcing, and shaped cathodes, which minimize the onset and material damage due to cathode spot formation. Work supported by US DOE Grant DE-FG02-96ER54375.

Geochronology of the Thompson Creek Mo Deposit: Evidence for the Formation of Arc-related Mo Deposits

NASA Astrophysics Data System (ADS)

Lawrence, C. D.; Coleman, D. S.; Stein, H. J.

2016-12-01

The Thompson Creek Mo deposit in central ID, has been categorized as an arc-related Mo deposit due to the location, grade of Mo, and relative lack of enrichments in F, Rb, and Nb, compared to the Climax-type Mo deposits. Geochronology from this arc-related deposit provides an opportunity to compare and contrast magmatism, and mineralization to that in Climax-type deposits. Distinct pulses of magmatism were required to form the Thompson Creek Mo deposit, which is consistent with recent geochronology from Climax-type deposits. Molybdenite Re-Os geochronology from five veins requires at least three pulses of magmatism and mineralization between 89.39 +/- 0.37 and 88.47 +/- 0.16 Ma. Zircon U-Pb ages from these mineralized samples overlap with molybdenite mineralization, but show a much wider range (91.01 +/- 0.37 to 87.27 +/- 0.69). Previous work from Climax-type Mo deposits suggest a correlation between a super eruption, and the subsequent rapid (<1 Ma) onset, and completion of Mo mineralizing intrusions. The longer life (3-4 Ma) for the Thompson Creek Mo deposit suggests that the mineralizing intrusions for arc-related Mo deposits may not need to have as high [Mo] as the Climax-type deposits. This study also finds a shift in the source of magmatism from the pre- to syn-mineralizing intrusions. Zircons from pre-mineralizing intrusions have much higher (15-60 pg) concentrations of radiogenic Pb than zircons from mineralized intrusions, which all have less than 15 pg, though whole rock [U] are similar.

India-Asia convergence: Insights from burial and exhumation of the Xigaze fore-arc basin, south Tibet

NASA Astrophysics Data System (ADS)

Li, Guangwei; Kohn, Barry; Sandiford, Mike; Xu, Zhiqin

2017-05-01

The composite fore-arc/syncollisional Xigaze basin in south Tibet preserves a key record of India-Asia collision. New apatite fission track and zircon (U-Th)/He data from an N-S transect across the preserved fore-arc basin sequence near Xigaze show a consistent northward Late Cretaceous to middle Miocene younging trend, while coexisting apatite (U-Th-Sm)/He ages are all Miocene. Corresponding detrital zircon U-Pb data are also reported for constraining the Cretaceous depositional ages of the Xigaze basin sequence in the region. Thermal history modeling indicates that the basin experienced northward propagating episodic exhumation, along with a northward migration of the depocenter and a pre-existing Cenozoic syncollisional basin sequence which had been removed. In the southern part, fore-arc exhumation commenced in the Late Cretaceous ( 89 ± 2 Ma). Following transition to a syncollisional basin in the Paleocene, sedimentation in the central and northern Xigaze basin continued until the latest Eocene ( 34 ± 4 Ma). Ongoing folding and thrusting (e.g., Great Counter Thrusts) caused by progressive plate convergence during late Oligocene-early Miocene time resulted in regional uplift and considerable basin denudation, which fed two fluvial basins along its northern and southern flanks and exposed the basement ophiolite. Subsequent incision of the Yarlung River resulted in Miocene cooling in the region. Different episodes in the exhumation history of the Xigaze basin, caused by thrusting of an accretionary wedge and ophiolitic basement, can be linked to changes in India-Asia convergence rates and the changing subduction pattern of the Indian and Neo-Tethyan slabs.

Marky: a tool supporting annotation consistency in multi-user and iterative document annotation projects.

PubMed

Pérez-Pérez, Martín; Glez-Peña, Daniel; Fdez-Riverola, Florentino; Lourenço, Anália

2015-02-01

Document annotation is a key task in the development of Text Mining methods and applications. High quality annotated corpora are invaluable, but their preparation requires a considerable amount of resources and time. Although the existing annotation tools offer good user interaction interfaces to domain experts, project management and quality control abilities are still limited. Therefore, the current work introduces Marky, a new Web-based document annotation tool equipped to manage multi-user and iterative projects, and to evaluate annotation quality throughout the project life cycle. At the core, Marky is a Web application based on the open source CakePHP framework. User interface relies on HTML5 and CSS3 technologies. Rangy library assists in browser-independent implementation of common DOM range and selection tasks, and Ajax and JQuery technologies are used to enhance user-system interaction. Marky grants solid management of inter- and intra-annotator work. Most notably, its annotation tracking system supports systematic and on-demand agreement analysis and annotation amendment. Each annotator may work over documents as usual, but all the annotations made are saved by the tracking system and may be further compared. So, the project administrator is able to evaluate annotation consistency among annotators and across rounds of annotation, while annotators are able to reject or amend subsets of annotations made in previous rounds. As a side effect, the tracking system minimises resource and time consumption. Marky is a novel environment for managing multi-user and iterative document annotation projects. Compared to other tools, Marky offers a similar visually intuitive annotation experience while providing unique means to minimise annotation effort and enforce annotation quality, and therefore corpus consistency. Marky is freely available for non-commercial use at http://sing.ei.uvigo.es/marky. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Is the Juice Worth the Squeeze? Costs and Benefits of Multiple Human Annotators for Clinical Text De-identification.

PubMed

Carrell, David S; Cronkite, David J; Malin, Bradley A; Aberdeen, John S; Hirschman, Lynette

2016-08-05

Clinical text contains valuable information but must be de-identified before it can be used for secondary purposes. Accurate annotation of personally identifiable information (PII) is essential to the development of automated de-identification systems and to manual redaction of PII. Yet the accuracy of annotations may vary considerably across individual annotators and annotation is costly. As such, the marginal benefit of incorporating additional annotators has not been well characterized. This study models the costs and benefits of incorporating increasing numbers of independent human annotators to identify the instances of PII in a corpus. We used a corpus with gold standard annotations to evaluate the performance of teams of annotators of increasing size. Four annotators independently identified PII in a 100-document corpus consisting of randomly selected clinical notes from Family Practice clinics in a large integrated health care system. These annotations were pooled and validated to generate a gold standard corpus for evaluation. Recall rates for all PII types ranged from 0.90 to 0.98 for individual annotators to 0.998 to 1.0 for teams of three, when meas-ured against the gold standard. Median cost per PII instance discovered during corpus annotation ranged from $ 0.71 for an individual annotator to $ 377 for annotations discovered only by a fourth annotator. Incorporating a second annotator into a PII annotation process reduces unredacted PII and improves the quality of annotations to 0.99 recall, yielding clear benefit at reasonable cost; the cost advantages of annotation teams larger than two diminish rapidly.

Active learning reduces annotation time for clinical concept extraction.

PubMed

Kholghi, Mahnoosh; Sitbon, Laurianne; Zuccon, Guido; Nguyen, Anthony

2017-10-01

To investigate: (1) the annotation time savings by various active learning query strategies compared to supervised learning and a random sampling baseline, and (2) the benefits of active learning-assisted pre-annotations in accelerating the manual annotation process compared to de novo annotation. There are 73 and 120 discharge summary reports provided by Beth Israel institute in the train and test sets of the concept extraction task in the i2b2/VA 2010 challenge, respectively. The 73 reports were used in user study experiments for manual annotation. First, all sequences within the 73 reports were manually annotated from scratch. Next, active learning models were built to generate pre-annotations for the sequences selected by a query strategy. The annotation/reviewing time per sequence was recorded. The 120 test reports were used to measure the effectiveness of the active learning models. When annotating from scratch, active learning reduced the annotation time up to 35% and 28% compared to a fully supervised approach and a random sampling baseline, respectively. Reviewing active learning-assisted pre-annotations resulted in 20% further reduction of the annotation time when compared to de novo annotation. The number of concepts that require manual annotation is a good indicator of the annotation time for various active learning approaches as demonstrated by high correlation between time rate and concept annotation rate. Active learning has a key role in reducing the time required to manually annotate domain concepts from clinical free text, either when annotating from scratch or reviewing active learning-assisted pre-annotations. Copyright © 2017 Elsevier B.V. All rights reserved.

Corpus annotation for mining biomedical events from literature

PubMed Central

Kim, Jin-Dong; Ohta, Tomoko; Tsujii, Jun'ichi

2008-01-01

Background Advanced Text Mining (TM) such as semantic enrichment of papers, event or relation extraction, and intelligent Question Answering have increasingly attracted attention in the bio-medical domain. For such attempts to succeed, text annotation from the biological point of view is indispensable. However, due to the complexity of the task, semantic annotation has never been tried on a large scale, apart from relatively simple term annotation. Results We have completed a new type of semantic annotation, event annotation, which is an addition to the existing annotations in the GENIA corpus. The corpus has already been annotated with POS (Parts of Speech), syntactic trees, terms, etc. The new annotation was made on half of the GENIA corpus, consisting of 1,000 Medline abstracts. It contains 9,372 sentences in which 36,114 events are identified. The major challenges during event annotation were (1) to design a scheme of annotation which meets specific requirements of text annotation, (2) to achieve biology-oriented annotation which reflect biologists' interpretation of text, and (3) to ensure the homogeneity of annotation quality across annotators. To meet these challenges, we introduced new concepts such as Single-facet Annotation and Semantic Typing, which have collectively contributed to successful completion of a large scale annotation. Conclusion The resulting event-annotated corpus is the largest and one of the best in quality among similar annotation efforts. We expect it to become a valuable resource for NLP (Natural Language Processing)-based TM in the bio-medical domain. PMID:18182099

From vein precipitates to deformation and fluid rock interaction within a SSZ: Insights from the Izu-Bonin-Mariana fore arc

NASA Astrophysics Data System (ADS)

Micheuz, Peter; Quandt, Dennis; Kurz, Walter

2017-04-01

International Ocean Discovery Program (IODP) expeditions 352 and 351 drilled through oceanic crust of the Philippine Sea plate. The two study areas are located near the outer Izu-Bonin-Mariana (IBM) fore arc and in the Amami Sankaku Basin. The primary objective was to improve our understanding of supra-subduction zones (SSZ) and the process of subduction initiation. The recovered drill cores during IODP expedition 352 represent approximately 50 Ma old fore arc basalts (FAB) and boninites revealing an entire volcanic sequence of a SSZ. Expedition 351 drilled FAB like oceanic crust similar in age to the FABs of expedition 352. In this study we present data on vein microstructures, geochemical data and isotopic signatures of vein precipitates to give new insights into fluid flow and precipitation processes and deformation within the Izu-Bonin fore arc. Veins formed predominantly as a consequence of hydrofracturing resulting in the occurrence of branched vein systems and brecciated samples. Along these hydrofractures the amount of altered host rock fragments varies and locally alters the host rock completely to zeolites and carbonates. Subordinately extensional veins released after the formation of the host rocks. Cross-cutting relationships of different vein types point to multiple fracturing events subsequently filled with minerals originating from a fluid with isotopic seawater signature. Based on vein precipitates, their morphology and their growth patterns four vein types have been defined. Major vein components are (Mg-) calcite and various zeolites determined by Raman spectra and electron microprobe analyses. Zeolites result from alteration of volcanic glass during interaction with a seawaterlike fluid. Type I veins which are characterized by micritic infill represent neptunian dykes. They predominantly occur in the upper levels of drill cores being the result of an initial volume change subsequently to crystallization of the host rocks. Type II veins are characterized by blocky carbonates and idiomorphic to blocky zeolites. Blocky carbonates locally exhibit zonation patterns. Type III and type IV veins are both assumed to be extensional veins. Type III is characterized by syntaxial growth and elongate blocky carbonate minerals. They predominantly occur as asymmetric syntaxial veins, locally exhibiting more than one crack-seal event. Type IV veins are defined as antitaxial fibrous carbonates. Type II veins commonly show deformation microstructures like twinning (type I/II twins), slightly curved twins, and subgrain boundaries indicative of incipient plastic deformation. Based on these observations differential stresses around 50 MPa were needed to deform vein minerals, presumably related to IBM fore arc extension due to the retreat of the subducted Pacific plate. We acknowledge financial support by the Austrian Research Fund (P27982-N29) to W. Kurz

Synthesis of nanowires and nanoparticles of cubic aluminium nitride

NASA Astrophysics Data System (ADS)

Balasubramanian, C.; Godbole, V. P.; Rohatgi, V. K.; Das, A. K.; Bhoraskar, S. V.

2004-03-01

Nanostructures of cubic aluminium nitride were synthesized by DC arc-plasma-induced melting of aluminium in a nitrogen-argon ambient. The material flux ejected from the molten aluminium surface was found to react with nitrogen under highly non-equilibrium conditions and subsequently condense on a water-cooled surface to yield a mixture of nanowires and nanoparticles of crystalline cubic aluminium nitride. Both x-ray diffraction and electron diffraction measurements revealed that the as-synthesized nitrides adopted the cubic phase. Fourier transform infrared spectroscopy was used to understand the bonding configuration. Microstructural features of the synthesized material were best studied by transmission electron microscopy. From these analyses cubic aluminium nitride was found to be the dominating phase for both nanowires and nanoparticles synthesized at low currents. The typical particle size distribution was found to range over 15-80 nm, whereas the wires varied from 30 to 100 nm in diameter and 500 to 700 nm in length, depending upon the process parameters such as arc current and the nitrogen pressure. The reaction products inside the plasma zone were also obtained theoretically by minimization of free energy and the favourable zone temperature necessary for the formation of aluminium nitride was found to be {\\sim } 6000 K. Results are discussed in view of the highly non-equilibrium conditions that prevail during the arc-plasma synthesis.

The Effects Of Micro Arc Oxidation Of Gamma Titanium Aluminide Surfaces On Osteoblast Adhesion And Differentiation

PubMed Central

Santiago-Medina, Pricilla; Sundaram, Paul A.; Diffoot-Carlo, Nanette

2014-01-01

The adhesion and proliferation of human fetal osteoblasts, hFOB 1.19, on micro arc oxidized (MAO) gamma titanium aluminide (γTiAl) surfaces were examined in vitro. Cells were seeded on MAO treated γTiAl disks and incubated for 3 days at 33.5°C and subsequently for 7 days at 39.5°C. Samples were then analyzed by Scanning Electron Microscopy (SEM) and the Alkaline Phosphatase Assay (ALP) to evaluate cell adhesion and differentiation, respectively. Similar Ti-6Al-4V alloy samples were used for comparison. Untreated γTiAl and Ti-6Al-4V disks, to study the effect of micro arc oxidation and glass coverslips as cell growth controls were also incubated concurrently. The ALP Assay results, at 10 days post seeding, showed significant differences in cell differentiation, with p values < 0.05 between MAO γTiAl and MAO Ti-6Al-4V with respect to the corresponding untreated alloys. While SEM images showed that hFOB 1.19 cells adhered and proliferated on all MAO and untreated surfaces, as well as on glass coverslips at 10 days post seeding, cell differentiation, determined by the ALP assay, was significantly higher for the MAO alloys. PMID:24577944

Hubble space telescope observations and geometric models of compact multipolar planetary nebulae

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

Hsia, Chih-Hao; Chau, Wayne; Zhang, Yong

2014-05-20

We report high angular resolution Hubble Space Telescope observations of 10 compact planetary nebulae (PNs). Many interesting internal structures, including multipolar lobes, arcs, two-dimensional rings, tori, and halos, are revealed for the first time. These results suggest that multipolar structures are common among PNs, and these structures develop early in their evolution. From three-dimensional geometric models, we have determined the intrinsic dimensions of the lobes. Assuming the lobes are the result of interactions between later-developed fast winds and previously ejected asymptotic giant branch winds, the geometric structures of these PNs suggest that there are multiple phases of fast winds separatedmore » by temporal variations and/or directional changes. A scenario of evolution from lobe-dominated to cavity-dominated stages is presented. The results reported here will provide serious constraints on any dynamical models of PNs.« less

The magnetic field and turbulence of the cosmic web measured using a brilliant fast radio burst.

PubMed

Ravi, V; Shannon, R M; Bailes, M; Bannister, K; Bhandari, S; Bhat, N D R; Burke-Spolaor, S; Caleb, M; Flynn, C; Jameson, A; Johnston, S; Keane, E F; Kerr, M; Tiburzi, C; Tuntsov, A V; Vedantham, H K

2016-12-09

Fast radio bursts (FRBs) are millisecond-duration events thought to originate beyond the Milky Way galaxy. Uncertainty surrounding the burst sources, and their propagation through intervening plasma, has limited their use as cosmological probes. We report on a mildly dispersed (dispersion measure 266.5 ± 0.1 parsecs per cubic centimeter), exceptionally intense (120 ± 30 janskys), linearly polarized, scintillating burst (FRB 150807) that we directly localize to 9 square arc minutes. On the basis of a low Faraday rotation (12.0 ± 0.7 radians per square meter), we infer negligible magnetization in the circum-burst plasma and constrain the net magnetization of the cosmic web along this sightline to <21 nanogauss, parallel to the line-of-sight. The burst scintillation suggests weak turbulence in the ionized intergalactic medium. Copyright © 2016, American Association for the Advancement of Science.

Characterization and genome functional analysis of a novel metamitron-degrading strain Rhodococcus sp. MET via both triazinone and phenyl rings cleavage

NASA Astrophysics Data System (ADS)

Fang, Hua; Xu, Tianheng; Cao, Duantao; Cheng, Longyin; Yu, Yunlong

2016-08-01

A novel bacterium capable of utilizing metamitron as the sole source of carbon and energy was isolated from contaminated soil and identified as Rhodococcus sp. MET based on its morphological characteristics, BIOLOG GP2 microplate profile, and 16S rDNA phylogeny. Genome sequencing and functional annotation of the isolate MET showed a 6,340,880 bp genome with a 62.47% GC content and 5,987 protein-coding genes. In total, 5,907 genes were annotated with the COG, GO, KEGG, Pfam, Swiss-Prot, TrEMBL, and nr databases. The degradation rate of metamitron by the isolate MET obviously increased with increasing substrate concentrations from 1 to 10 mg/l and subsequently decreased at 100 mg/l. The optimal pH and temperature for metamitron biodegradation were 7.0 and 20-30 °C, respectively. Based on genome annotation of the metamitron degradation genes and the metabolites detected by HPLC-MS/MS, the following metamitron biodegradation pathways were proposed: 1) Metamitron was transformed into 2-(3-hydrazinyl-2-ethyl)-hydrazono-2-phenylacetic acid by triazinone ring cleavage and further mineralization; 2) Metamitron was converted into 3-methyl-4-amino-6(2-hydroxy-muconic acid)-1,2,4-triazine-5(4H)-one by phenyl ring cleavage and further mineralization. The coexistence of diverse mineralization pathways indicates that our isolate may effectively bioremediate triazinone herbicide-contaminated soils.

The variant call format and VCFtools.

PubMed

Danecek, Petr; Auton, Adam; Abecasis, Goncalo; Albers, Cornelis A; Banks, Eric; DePristo, Mark A; Handsaker, Robert E; Lunter, Gerton; Marth, Gabor T; Sherry, Stephen T; McVean, Gilean; Durbin, Richard

2011-08-01

The variant call format (VCF) is a generic format for storing DNA polymorphism data such as SNPs, insertions, deletions and structural variants, together with rich annotations. VCF is usually stored in a compressed manner and can be indexed for fast data retrieval of variants from a range of positions on the reference genome. The format was developed for the 1000 Genomes Project, and has also been adopted by other projects such as UK10K, dbSNP and the NHLBI Exome Project. VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API. http://vcftools.sourceforge.net

DOGMA: domain-based transcriptome and proteome quality assessment.

PubMed

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

2016-09-01

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

BioGPS and MyGene.info: organizing online, gene-centric information.

PubMed

Wu, Chunlei; Macleod, Ian; Su, Andrew I

2013-01-01

Fast-evolving technologies have enabled researchers to easily generate data at genome scale, and using these technologies to compare biological states typically results in a list of candidate genes. Researchers are then faced with the daunting task of prioritizing these candidate genes for follow-up studies. There are hundreds, possibly even thousands, of web-based gene annotation resources available, but it quickly becomes impractical to manually access and review all of these sites for each gene in a candidate gene list. BioGPS (http://biogps.org) was created as a centralized gene portal for aggregating distributed gene annotation resources, emphasizing community extensibility and user customizability. BioGPS serves as a convenient tool for users to access known gene-centric resources, as well as a mechanism to discover new resources that were previously unknown to the user. This article describes updates to BioGPS made after its initial release in 2008. We summarize recent additions of features and data, as well as the robust user activity that underlies this community intelligence application. Finally, we describe MyGene.info (http://mygene.info) and related web services that provide programmatic access to BioGPS.

Big data analytics in immunology: a knowledge-based approach.

PubMed

Zhang, Guang Lan; Sun, Jing; Chitkushev, Lou; Brusic, Vladimir

2014-01-01

With the vast amount of immunological data available, immunology research is entering the big data era. These data vary in granularity, quality, and complexity and are stored in various formats, including publications, technical reports, and databases. The challenge is to make the transition from data to actionable knowledge and wisdom and bridge the knowledge gap and application gap. We report a knowledge-based approach based on a framework called KB-builder that facilitates data mining by enabling fast development and deployment of web-accessible immunological data knowledge warehouses. Immunological knowledge discovery relies heavily on both the availability of accurate, up-to-date, and well-organized data and the proper analytics tools. We propose the use of knowledge-based approaches by developing knowledgebases combining well-annotated data with specialized analytical tools and integrating them into analytical workflow. A set of well-defined workflow types with rich summarization and visualization capacity facilitates the transformation from data to critical information and knowledge. By using KB-builder, we enabled streamlining of normally time-consuming processes of database development. The knowledgebases built using KB-builder will speed up rational vaccine design by providing accurate and well-annotated data coupled with tailored computational analysis tools and workflow.

Advanced two-layer level set with a soft distance constraint for dual surfaces segmentation in medical images

NASA Astrophysics Data System (ADS)

Ji, Yuanbo; van der Geest, Rob J.; Nazarian, Saman; Lelieveldt, Boudewijn P. F.; Tao, Qian

2018-03-01

Anatomical objects in medical images very often have dual contours or surfaces that are highly correlated. Manually segmenting both of them by following local image details is tedious and subjective. In this study, we proposed a two-layer region-based level set method with a soft distance constraint, which not only regularizes the level set evolution at two levels, but also imposes prior information on wall thickness in an effective manner. By updating the level set function and distance constraint functions alternatingly, the method simultaneously optimizes both contours while regularizing their distance. The method was applied to segment the inner and outer wall of both left atrium (LA) and left ventricle (LV) from MR images, using a rough initialization from inside the blood pool. Compared to manual annotation from experience observers, the proposed method achieved an average perpendicular distance (APD) of less than 1mm for the LA segmentation, and less than 1.5mm for the LV segmentation, at both inner and outer contours. The method can be used as a practical tool for fast and accurate dual wall annotations given proper initialization.

Developmental Trajectories of Compensatory Exercise and Fasting Behavior across the Middle School Years

PubMed Central

Davis, Heather A.; Guller, Leila; Smith, Gregory T.

2016-01-01

Compensatory exercise and fasting behavior, in the absence of binge eating and purging, appear to be important eating disorder behaviors that are associated with dysfunction, but little is known about these behaviors in youth. We studied the trajectories of their development in non-binge eating and non-purging girls during early adolescence. Using a longitudinal design, we assessed 564 girls six times over the three years of middle school (grades 6 through 8) and developed trajectories specifying different developmental patterns in relation to the behaviors. Prior to this period, when the girls were in 5th grade (elementary school), we assessed risk factors to predict girls’ subsequent trajectory group membership. Compensatory exercise trajectory groups included a non-engagement group, a group that increased in the behavior, and a group that decreased in the behavior. There were two fasting trajectory groups, one consistently engaging in the behavior and the other consistently not. Elementary school levels of depression, eating expectancies, and thinness expectancies predicted subsequent trajectory group membership. Risk for compensatory exercise and fasting should be evaluated as early as in 5th grade. Targeted interventions should focus on girls in late elementary school or middle school, as this appears to be a critical developmental and maintenance period for compensatory exercise and fasting behavior. PMID:27544806

Effects on the efficiency of activated carbon on exposure to welding fumes

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

Ghosh, D.

1995-02-01

It is the intention of this paper to document that certain types of welding fumes have little or no effect on the effectiveness of the carbon filter air filtration efficiency when directly exposed to a controlled amount of welding fumes for a short-term period. The welding processes studied were restricted to shielded metal arc welding (SMAW), flux cored arc welding (FCAW), gas tungsten arc welding (GTAW) and gas metal arc welding (GMAW) processes. Contrary to the SMAW and FCAW processes, the GTAW (or TIG) and the GMAW (or MIG) welding processes do not require the use of flux as partmore » of the overall process. Credit was taken for these processes occurring in inert gas environments and producing minimal amount of smoke. It was concluded that a study involving the SMAW process would also envelop the effects of the TIG and MIG welding processes. The quantity of welding fumes generated during the arc welding process is a function of the particular process, the size and type of electrode, welding machine amperage, and operator proficiency. For this study, the amount of welding for specific testing was equated to the amount of welding normally conducted during plant unit outages. Different welding electrodes were also evaluated, and the subsequent testing was limited to an E7018 electrode which was judged to be representative of all carbon and stainless steel electrodes commonly used at the site. The effect of welding fumes on activated charcoal was tested using a filtration unit complete with prefilters, upstream and downstream high efficiency particulate air (HEPA) filters, and a carbon adsorber section. The complete system was field tested in accordance with ANSI N510 standards prior to exposing the filters and the adsorber bed to welding fumes. The carbon samples were tested at an established laboratory using ASTM D3803-1989 standards.« less

The physiology and biomechanics of competitive swimming.

PubMed

Troup, J P

1999-04-01

Fast swimming, either in the pool, in open water swimming, or in water polo and synchronized swimming, requires maximizing the efficiencies with which the human body can move through a liquid medium. A multitude of factors can affect the ability to swim fast as well as the final outcome. Physiology and biomechanics are the present tools used by sports scientists to determine which factors are important to fast swimming and, subsequently, to determine how the swimmer may maximize these factors to improve performance.

Orthogonal fast spherical Bessel transform on uniform grid

NASA Astrophysics Data System (ADS)

Serov, Vladislav V.

2017-07-01

We propose an algorithm for the orthogonal fast discrete spherical Bessel transform on a uniform grid. Our approach is based upon the spherical Bessel transform factorization into the two subsequent orthogonal transforms, namely the fast Fourier transform and the orthogonal transform founded on the derivatives of the discrete Legendre orthogonal polynomials. The method utility is illustrated by its implementation for the problem of a two-atomic molecule in a time-dependent external field simulating the one utilized in the attosecond streaking technique.

Modeling loosely annotated images using both given and imagined annotations

NASA Astrophysics Data System (ADS)

Tang, Hong; Boujemaa, Nozha; Chen, Yunhao; Deng, Lei

2011-12-01

In this paper, we present an approach to learn latent semantic analysis models from loosely annotated images for automatic image annotation and indexing. The given annotation in training images is loose due to: 1. ambiguous correspondences between visual features and annotated keywords; 2. incomplete lists of annotated keywords. The second reason motivates us to enrich the incomplete annotation in a simple way before learning a topic model. In particular, some ``imagined'' keywords are poured into the incomplete annotation through measuring similarity between keywords in terms of their co-occurrence. Then, both given and imagined annotations are employed to learn probabilistic topic models for automatically annotating new images. We conduct experiments on two image databases (i.e., Corel and ESP) coupled with their loose annotations, and compare the proposed method with state-of-the-art discrete annotation methods. The proposed method improves word-driven probability latent semantic analysis (PLSA-words) up to a comparable performance with the best discrete annotation method, while a merit of PLSA-words is still kept, i.e., a wider semantic range.

Young Children's Fast Mapping and Generalization of Words, Facts, and Pictograms

ERIC Educational Resources Information Center

Deak, Gedeon O.; Toney, Alexis J.

2013-01-01

To test general and specific processes of symbol learning, 4- and 5-year-old children learned three kinds of abstract associates for novel objects: words, facts, and pictograms. To test fast mapping (i.e., one-trial learning) and subsequent learning, comprehension was tested after each of four exposures. Production was also tested, as was…

Children's Executive Function and High-Calorie, Low-Nutrient Food Intake: Mediating Effects of Child-Perceived Adult Fast Food Intake

ERIC Educational Resources Information Center

Tate, Eleanor B.; Unger, Jennifer B.; Chou, Chih-Ping; Spruijt-Metz, Donna; Pentz, Mary Ann; Riggs, Nathaniel R.

2015-01-01

Objective: This study tested the relationships among child executive function (EF), child-perceived parent fast food intake, and child self-reported subsequent consumption of high-calorie, low-nutrient (HCLN) food. Design: One year and 6-month longitudinal observation from a larger randomized controlled trial. Setting. Southern California…

BioCatalogue: a universal catalogue of web services for the life sciences

PubMed Central

Bhagat, Jiten; Tanoh, Franck; Nzuobontane, Eric; Laurent, Thomas; Orlowski, Jerzy; Roos, Marco; Wolstencroft, Katy; Aleksejevs, Sergejs; Stevens, Robert; Pettifer, Steve; Lopez, Rodrigo; Goble, Carole A.

2010-01-01

The use of Web Services to enable programmatic access to on-line bioinformatics is becoming increasingly important in the Life Sciences. However, their number, distribution and the variable quality of their documentation can make their discovery and subsequent use difficult. A Web Services registry with information on available services will help to bring together service providers and their users. The BioCatalogue (http://www.biocatalogue.org/) provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Services in the BioCatalogue can be described and searched in multiple ways based upon their technical types, bioinformatics categories, user tags, service providers or data inputs and outputs. They are also subject to constant monitoring, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. The system is accessible via a human-readable ‘Web 2.0’-style interface and a programmatic Web Service interface. The BioCatalogue follows a community approach in which all services can be registered, browsed and incrementally documented with annotations by any member of the scientific community. PMID:20484378

BioCatalogue: a universal catalogue of web services for the life sciences.

PubMed

Bhagat, Jiten; Tanoh, Franck; Nzuobontane, Eric; Laurent, Thomas; Orlowski, Jerzy; Roos, Marco; Wolstencroft, Katy; Aleksejevs, Sergejs; Stevens, Robert; Pettifer, Steve; Lopez, Rodrigo; Goble, Carole A

2010-07-01

The use of Web Services to enable programmatic access to on-line bioinformatics is becoming increasingly important in the Life Sciences. However, their number, distribution and the variable quality of their documentation can make their discovery and subsequent use difficult. A Web Services registry with information on available services will help to bring together service providers and their users. The BioCatalogue (http://www.biocatalogue.org/) provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Services in the BioCatalogue can be described and searched in multiple ways based upon their technical types, bioinformatics categories, user tags, service providers or data inputs and outputs. They are also subject to constant monitoring, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. The system is accessible via a human-readable 'Web 2.0'-style interface and a programmatic Web Service interface. The BioCatalogue follows a community approach in which all services can be registered, browsed and incrementally documented with annotations by any member of the scientific community.

Complexity of Gene Expression Evolution after Duplication: Protein Dosage Rebalancing

PubMed Central

Rogozin, Igor B.

2014-01-01

Ongoing debates about functional importance of gene duplications have been recently intensified by a heated discussion of the “ortholog conjecture” (OC). Under the OC, which is central to functional annotation of genomes, orthologous genes are functionally more similar than paralogous genes at the same level of sequence divergence. However, a recent study challenged the OC by reporting a greater functional similarity, in terms of gene ontology (GO) annotations and expression profiles, among within-species paralogs compared to orthologs. These findings were taken to indicate that functional similarity of homologous genes is primarily determined by the cellular context of the genes, rather than evolutionary history. Subsequent studies suggested that the OC appears to be generally valid when applied to mammalian evolution but the complete picture of evolution of gene expression also has to incorporate lineage-specific aspects of paralogy. The observed complexity of gene expression evolution after duplication can be explained through selection for gene dosage effect combined with the duplication-degeneration-complementation model. This paper discusses expression divergence of recent duplications occurring before functional divergence of proteins encoded by duplicate genes. PMID:25197576

ChemScreener: A Distributed Computing Tool for Scaffold based Virtual Screening.

PubMed

Karthikeyan, Muthukumarasamy; Pandit, Deepak; Vyas, Renu

2015-01-01

In this work we present ChemScreener, a Java-based application to perform virtual library generation combined with virtual screening in a platform-independent distributed computing environment. ChemScreener comprises a scaffold identifier, a distinct scaffold extractor, an interactive virtual library generator as well as a virtual screening module for subsequently selecting putative bioactive molecules. The virtual libraries are annotated with chemophore-, pharmacophore- and toxicophore-based information for compound prioritization. The hits selected can then be further processed using QSAR, docking and other in silico approaches which can all be interfaced within the ChemScreener framework. As a sample application, in this work scaffold selectivity, diversity, connectivity and promiscuity towards six important therapeutic classes have been studied. In order to illustrate the computational power of the application, 55 scaffolds extracted from 161 anti-psychotic compounds were enumerated to produce a virtual library comprising 118 million compounds (17 GB) and annotated with chemophore, pharmacophore and toxicophore based features in a single step which would be non-trivial to perform with many standard software tools today on libraries of this size.

TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes

PubMed Central

Leroy, Philippe; Guilhot, Nicolas; Sakai, Hiroaki; Bernard, Aurélien; Choulet, Frédéric; Theil, Sébastien; Reboux, Sébastien; Amano, Naoki; Flutre, Timothée; Pelegrin, Céline; Ohyanagi, Hajime; Seidel, Michael; Giacomoni, Franck; Reichstadt, Mathieu; Alaux, Michael; Gicquello, Emmanuelle; Legeai, Fabrice; Cerutti, Lorenzo; Numa, Hisataka; Tanaka, Tsuyoshi; Mayer, Klaus; Itoh, Takeshi; Quesneville, Hadi; Feuillet, Catherine

2012-01-01

In support of the international effort to obtain a reference sequence of the bread wheat genome and to provide plant communities dealing with large and complex genomes with a versatile, easy-to-use online automated tool for annotation, we have developed the TriAnnot pipeline. Its modular architecture allows for the annotation and masking of transposable elements, the structural, and functional annotation of protein-coding genes with an evidence-based quality indexing, and the identification of conserved non-coding sequences and molecular markers. The TriAnnot pipeline is parallelized on a 712 CPU computing cluster that can run a 1-Gb sequence annotation in less than 5 days. It is accessible through a web interface for small scale analyses or through a server for large scale annotations. The performance of TriAnnot was evaluated in terms of sensitivity, specificity, and general fitness using curated reference sequence sets from rice and wheat. In less than 8 h, TriAnnot was able to predict more than 83% of the 3,748 CDS from rice chromosome 1 with a fitness of 67.4%. On a set of 12 reference Mb-sized contigs from wheat chromosome 3B, TriAnnot predicted and annotated 93.3% of the genes among which 54% were perfectly identified in accordance with the reference annotation. It also allowed the curation of 12 genes based on new biological evidences, increasing the percentage of perfect gene prediction to 63%. TriAnnot systematically showed a higher fitness than other annotation pipelines that are not improved for wheat. As it is easily adaptable to the annotation of other plant genomes, TriAnnot should become a useful resource for the annotation of large and complex genomes in the future. PMID:22645565

Carbohydrate-rich breakfast attenuates glycaemic, insulinaemic and ghrelin response to ad libitum lunch relative to morning fasting in lean adults.

PubMed

Chowdhury, Enhad A; Richardson, Judith D; Tsintzas, Kostas; Thompson, Dylan; Betts, James A

2015-07-14

Breakfast omission is associated with obesity and CVD/diabetes, but the acute effects of extended morning fasting upon subsequent energy intake and metabolic/hormonal responses have received less attention. In a randomised cross-over design, thirty-five lean men (n 14) and women (n 21) extended their overnight fast or ingested a typical carbohydrate-rich breakfast in quantities relative to RMR (i.e. 1963 (sd 238) kJ), before an ad libitum lunch 3 h later. Blood samples were obtained hourly throughout the day until 3 h post-lunch, with subjective appetite measures assessed. Lunch intake was greater following extended fasting (640 (sd 1042) kJ, P< 0.01) but incompletely compensated for the omitted breakfast, with total intake lower than the breakfast trial (3887 (sd 1326) v. 5213 (sd 1590) kJ, P< 0.001). Systemic concentrations of peptide tyrosine-tyrosine and leptin were greater during the afternoon following breakfast (both P< 0.05) but neither acylated/total ghrelin concentrations were suppressed by the ad libitum lunch in the breakfast trial, remaining greater than the morning fasting trial throughout the afternoon (all P< 0.05). Insulin concentrations were greater during the afternoon in the morning fasting trial (all P< 0.01). There were no differences between trials in subjective appetite during the afternoon. In conclusion, morning fasting caused incomplete energy compensation at an ad libitum lunch. Breakfast increased some anorectic hormones during the afternoon but paradoxically abolished ghrelin suppression by the second meal. Extending morning fasting until lunch altered subsequent metabolic and hormonal responses but without greater appetite during the afternoon. The present study clarifies the impact of acute breakfast omission and adds novel insights into second-meal metabolism.

EuCAP, a Eukaryotic Community Annotation Package, and its application to the rice genome

PubMed Central

Thibaud-Nissen, Françoise; Campbell, Matthew; Hamilton, John P; Zhu, Wei; Buell, C Robin

2007-01-01

Background Despite the improvements of tools for automated annotation of genome sequences, manual curation at the structural and functional level can provide an increased level of refinement to genome annotation. The Institute for Genomic Research Rice Genome Annotation (hereafter named the Osa1 Genome Annotation) is the product of an automated pipeline and, for this reason, will benefit from the input of biologists with expertise in rice and/or particular gene families. Leveraging knowledge from a dispersed community of scientists is a demonstrated way of improving a genome annotation. This requires tools that facilitate 1) the submission of gene annotation to an annotation project, 2) the review of the submitted models by project annotators, and 3) the incorporation of the submitted models in the ongoing annotation effort. Results We have developed the Eukaryotic Community Annotation Package (EuCAP), an annotation tool, and have applied it to the rice genome. The primary level of curation by community annotators (CA) has been the annotation of gene families. Annotation can be submitted by email or through the EuCAP Web Tool. The CA models are aligned to the rice pseudomolecules and the coordinates of these alignments, along with functional annotation, are stored in the MySQL EuCAP Gene Model database. Web pages displaying the alignments of the CA models to the Osa1 Genome models are automatically generated from the EuCAP Gene Model database. The alignments are reviewed by the project annotators (PAs) in the context of experimental evidence. Upon approval by the PAs, the CA models, along with the corresponding functional annotations, are integrated into the Osa1 Genome Annotation. The CA annotations, grouped by family, are displayed on the Community Annotation pages of the project website , as well as in the Community Annotation track of the Genome Browser. Conclusion We have applied EuCAP to rice. As of July 2007, the structural and/or functional annotation of 1,094 genes representing 57 families have been deposited and integrated into the current gene set. All of the EuCAP components are open-source, thereby allowing the implementation of EuCAP for the annotation of other genomes. EuCAP is available at . PMID:17961238

Clustering analysis of proteins from microbial genomes at multiple levels of resolution.

PubMed

Zaslavsky, Leonid; Ciufo, Stacy; Fedorov, Boris; Tatusova, Tatiana

2016-08-31

Microbial genomes at the National Center for Biotechnology Information (NCBI) represent a large collection of more than 35,000 assemblies. There are several complexities associated with the data: a great variation in sampling density since human pathogens are densely sampled while other bacteria are less represented; different protein families occur in annotations with different frequencies; and the quality of genome annotation varies greatly. In order to extract useful information from these sophisticated data, the analysis needs to be performed at multiple levels of phylogenomic resolution and protein similarity, with an adequate sampling strategy. Protein clustering is used to construct meaningful and stable groups of similar proteins to be used for analysis and functional annotation. Our approach is to create protein clusters at three levels. First, tight clusters in groups of closely-related genomes (species-level clades) are constructed using a combined approach that takes into account both sequence similarity and genome context. Second, clustroids of conservative in-clade clusters are organized into seed global clusters. Finally, global protein clusters are built around the the seed clusters. We propose filtering strategies that allow limiting the protein set included in global clustering. The in-clade clustering procedure, subsequent selection of clustroids and organization into seed global clusters provides a robust representation and high rate of compression. Seed protein clusters are further extended by adding related proteins. Extended seed clusters include a significant part of the data and represent all major known cell machinery. The remaining part, coming from either non-conservative (unique) or rapidly evolving proteins, from rare genomes, or resulting from low-quality annotation, does not group together well. Processing these proteins requires significant computational resources and results in a large number of questionable clusters. The developed filtering strategies allow to identify and exclude such peripheral proteins limiting the protein dataset in global clustering. Overall, the proposed methodology allows the relevant data at different levels of details to be obtained and data redundancy eliminated while keeping biologically interesting variations.

Annotated chemical patent corpus: a gold standard for text mining.

PubMed

Akhondi, Saber A; Klenner, Alexander G; Tyrchan, Christian; Manchala, Anil K; Boppana, Kiran; Lowe, Daniel; Zimmermann, Marc; Jagarlapudi, Sarma A R P; Sayle, Roger; Kors, Jan A; Muresan, Sorel

2014-01-01

Exploring the chemical and biological space covered by patent applications is crucial in early-stage medicinal chemistry activities. Patent analysis can provide understanding of compound prior art, novelty checking, validation of biological assays, and identification of new starting points for chemical exploration. Extracting chemical and biological entities from patents through manual extraction by expert curators can take substantial amount of time and resources. Text mining methods can help to ease this process. To validate the performance of such methods, a manually annotated patent corpus is essential. In this study we have produced a large gold standard chemical patent corpus. We developed annotation guidelines and selected 200 full patents from the World Intellectual Property Organization, United States Patent and Trademark Office, and European Patent Office. The patents were pre-annotated automatically and made available to four independent annotator groups each consisting of two to ten annotators. The annotators marked chemicals in different subclasses, diseases, targets, and modes of action. Spelling mistakes and spurious line break due to optical character recognition errors were also annotated. A subset of 47 patents was annotated by at least three annotator groups, from which harmonized annotations and inter-annotator agreement scores were derived. One group annotated the full set. The patent corpus includes 400,125 annotations for the full set and 36,537 annotations for the harmonized set. All patents and annotated entities are publicly available at www.biosemantics.org.

Annotated Chemical Patent Corpus: A Gold Standard for Text Mining

PubMed Central

Akhondi, Saber A.; Klenner, Alexander G.; Tyrchan, Christian; Manchala, Anil K.; Boppana, Kiran; Lowe, Daniel; Zimmermann, Marc; Jagarlapudi, Sarma A. R. P.; Sayle, Roger; Kors, Jan A.; Muresan, Sorel

2014-01-01

Exploring the chemical and biological space covered by patent applications is crucial in early-stage medicinal chemistry activities. Patent analysis can provide understanding of compound prior art, novelty checking, validation of biological assays, and identification of new starting points for chemical exploration. Extracting chemical and biological entities from patents through manual extraction by expert curators can take substantial amount of time and resources. Text mining methods can help to ease this process. To validate the performance of such methods, a manually annotated patent corpus is essential. In this study we have produced a large gold standard chemical patent corpus. We developed annotation guidelines and selected 200 full patents from the World Intellectual Property Organization, United States Patent and Trademark Office, and European Patent Office. The patents were pre-annotated automatically and made available to four independent annotator groups each consisting of two to ten annotators. The annotators marked chemicals in different subclasses, diseases, targets, and modes of action. Spelling mistakes and spurious line break due to optical character recognition errors were also annotated. A subset of 47 patents was annotated by at least three annotator groups, from which harmonized annotations and inter-annotator agreement scores were derived. One group annotated the full set. The patent corpus includes 400,125 annotations for the full set and 36,537 annotations for the harmonized set. All patents and annotated entities are publicly available at www.biosemantics.org. PMID:25268232

Reliability of hunger-related assessments during 24-hour fasts and their relationship to body composition and subsequent energy compensation.

PubMed

Tinsley, Grant M; Moore, M Lane; Graybeal, Austin J

2018-05-01

Many diets employ regular periods of fasting that extend beyond a typical overnight fast (i.e. intermittent fasting [IF]). Evaluation of acute fasting responses provides information concerning the potential theoretical rationale for IF. The purpose of the present investigation was to assess the test-retest reliability of hunger-related variables during 24-hour fasts and the relationship between these variables and body composition, as well as subsequent energy intake (EI) after fasting. Eleven participants (6 F, 5 M) completed two 24-hour fasts after being provided a 3-day standardized weight-maintenance diet. From 16 to 24 h of fasting, participants were directly observed and provided hourly assessments of hunger, desire to eat (DTE), prospective food consumption (PFC), fullness and energy. After the fast, participants were allowed ad libitum food consumption, and compensation was calculated as EI relative to weight-maintenance energy needs. Test-retest reliability for hunger-related assessments at particular durations of fasting was evaluated using intraclass correlation coefficients (ICC), changes in dependent variables were evaluated using ANOVA with repeated measures, and relationships between variables were explored using bivariate correlations. At 16 h of fasting, the ICCs for all hunger-related assessments were statistically significant (r = 0.67-0.91; p ≤ 0.05). However, as the fast progressed, reliability varied substantially. When averaged across the nine measurements, the ICCs were: 0.81 (fullness), 0.74 (PFC), 0.67 (energy), 0.44 (DTE) and 0.36 (hunger). Body fat percentage was significantly correlated with changes in PFC (r = 0.62, p = 0.04), hunger (r = 0.66, p = 0.03), DTE (r = 0.71, p = 0.02), and fullness (r = -0.63, p = 0.04), but not energy (r = -0.16, p = 0.64). Average EI compensation was only 60% of weight-maintenance needs, but substantial variability was observed (7 to 110% compensation). Compensation was significantly correlated with changes in PFC (r = 0.72, p = 0.01), hunger (r = 0.63, p = 0.04) and DTE (r = 0.60, p = 0.05), but not fullness (r = 0.58, p = 0.06) or energy (r = 0.35, p = 0.29). Compensation and body fat percentage were not correlated (r = 0.03, p = 0.94). The percent of energy intake from fat and protein increased after the fast (29.9 to 37.3% and 13.8 to 16.8%; p < 0.05), while the percent of energy intake from carbohydrate decreased (56.4 to 46.0%; p = 0.02). These results may have implications for IF programs. It is possible that the implementation of multiple "test fasts," in which subjective variables and subsequent energy intake are evaluated, could be used to identify candidates who may be more likely to benefit from an IF program. Copyright © 2018 Elsevier Inc. All rights reserved.

Peptide YY: a potential therapy for obesity.

PubMed

Renshaw, D; Batterham, R L

2005-03-01

Obesity now represents a modern epidemic in western society with major health and economic consequences. Unfortunately, previous pharmacological approaches to the treatment of obesity have been associated with life-threatening side effects and limited efficacy. Over recent years there has been a marked increase in our understanding of the physiological mechanisms that regulate body weight and how these are perturbed in obesity. One therapeutic strategy is to develop drugs which both mimic and enhance the body's own satiety signals. The gut hormone peptide tyrosine tyrosine (PYY), which is released postprandially from the gastrointestinal tract, has recently been shown to be a physiological regulator of food intake. Peripheral administration of PYY reduces feeding in rodents via a mechanism which requires the Y2 receptor and is thought to primarily involve modulation of the hypothalamic arcuate nucleus (ARC) circuitry. In humans a single 90-minute infusion of PYY has been shown to markedly reduce subsequent 24-hour caloric intake in lean, normal-weight and obese subjects. Moreover, obese subjects have been found to have low levels of fasting and postprandial PYY suggesting a role for this hormone in the pathogenesis of obesity. Although studies examining the effects of chronic peripheral administration of PYY to humans are awaited, the results from continuous infusion studies in a number of obese rodent models are encouraging with reductions in food intake, body weight and adiposity observed. Potential therapeutic manipulations based on the PYY system include development of Y2 agonists, exogenously administration of PYY or increased endogenous release from the gastrointestinal tract.

Surfactant-directed synthesis of mesoporous films made single-step by a tandem photosol-gel/photocalcination route

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

De Paz-Simon, Héloïse; Chemtob, Abraham, E-mail: abraham.chemtob@uha.fr; Croutxé-Barghorn, Céline

2014-11-01

In view of their technological impact in materials chemistry, a simplified and more efficient synthetic route to mesoporous films is highly sought. We report, herein, a smart UV-mediated approach coupling in a one-stage process sol-gel photopolymerization and photoinduced template decomposition/ablation to making mesoporous silica films. Performed at room temperature with a solvent-free solution of silicate precursor and amphiphilic poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) block copolymer, the synthesis relies on photoacid generation to induce the fast formation (≈10 min) of mesostructured silica/surfactant domains. Continuation of UV exposure for three additional hours enables subsequent and complete photodegradation of the polyether copolymer, resulting inmore » ordered or disordered mesoporous silica film. One of the most attractive features is that the one-step procedure relies on a continuous illumination provided by the same conventional medium-pressure Hg-Xe arc lamp equipped with a 254 nm reflector to enhance the emission of energetic photons <300 nm. In addition to X-ray diffraction and transmission electron microscopy, time-resolved Fourier transform infrared spectroscopy has proved to be a powerful in situ technique to probe the different chemical transformations accompanying irradiation. Photocalcination strengthens the inorganic network, while allowing to preserve a higher fraction of residual silanol groups compared with thermal calcination. A polyether chain degradation mechanism based on oxygen reactive species-mediated photo-oxidation is proposed.« less

CALUTRON ION SOURCE

DOEpatents

Lofgren, E.J.

1959-02-17

An improvement is described in ion source mechanisms whereby the source structure is better adapted to withstanid the ravages of heat, erosion, and deterioration concomitant with operation of an ion source of the calutron type. A pair of molybdenum plates define the exit opening of the arc chamber and are in thermal contact with the walls of the chamber. These plates are maintained at a reduced temperature by a pair of copper blocks in thermal conducting contact therewith to form subsequent diverging margins for the exit opening.

The 1990 MB: The first Mars Trojan

NASA Technical Reports Server (NTRS)

Bowell, Edward

1991-01-01

Asteroid 1990 MB was discovered during the course of the Mars and Earth-crossing Asteroid and Comet Survey. An orbit based on a 9-day arc and the asteroid's location near Mars L5 longitude led to speculation that it might be in 1:1 resonance with Mars, analogous to the Trojan asteroids of Jupiter. Subsequent observations strengthened the possibility, and later calculations confirmed it. The most recent orbit shows that the asteroid's semimajor axis is very similar to that of Mars.

Evaluating Computational Gene Ontology Annotations.

PubMed

Škunca, Nives; Roberts, Richard J; Steffen, Martin

2017-01-01

Two avenues to understanding gene function are complementary and often overlapping: experimental work and computational prediction. While experimental annotation generally produces high-quality annotations, it is low throughput. Conversely, computational annotations have broad coverage, but the quality of annotations may be variable, and therefore evaluating the quality of computational annotations is a critical concern.In this chapter, we provide an overview of strategies to evaluate the quality of computational annotations. First, we discuss why evaluating quality in this setting is not trivial. We highlight the various issues that threaten to bias the evaluation of computational annotations, most of which stem from the incompleteness of biological databases. Second, we discuss solutions that address these issues, for example, targeted selection of new experimental annotations and leveraging the existing experimental annotations.