Exploration at the Edge of the Solar System: The Pluto-Kuiper Express Mission (Invited)

NASA Astrophysics Data System (ADS)

Terrile, R. J.

1999-09-01

The Pluto-Kuiper Express mission is one component of the Outer Planets/Solar Probe Project which is part of the exploration strategy laid out in the Solar System Exploration Roadmap. The first three missions of this project are the Europa Orbiter, Pluto-Kuiper Express and the Solar Probe. All require challenging new technologies and the ability to operate in deep space and at Jupiter. Use of common management and design approaches, avionics, and mission software is planned to reduce the costs of the three missions. The Pluto-Kuiper Express mission is planned to launch in 2004 and is designed to provide the first reconnaissance of the Solar System's most distant planet, Pluto, and it, moon Charon. A gravity assist from Jupiter will allow an 8-year flight time to Pluto and the possibility of encountering one or more Edgeworth-Kuiper Belt objects after the Pluto encounter. The primary science objectives for the mission include characterizing the global geology and geomorphology of Pluto and Charon, mapping their surface composition and characterizing Pluto's neutral atmosphere and its escape rate. This mission is currently soliciting scientific investigations through a NASA Announcement of Opportunity.

Automated Discovery of Functional Generality of Human Gene Expression Programs

PubMed Central

Gerber, Georg K; Dowell, Robin D; Jaakkola, Tommi S; Gifford, David K

2007-01-01

An important research problem in computational biology is the identification of expression programs, sets of co-expressed genes orchestrating normal or pathological processes, and the characterization of the functional breadth of these programs. The use of human expression data compendia for discovery of such programs presents several challenges including cellular inhomogeneity within samples, genetic and environmental variation across samples, uncertainty in the numbers of programs and sample populations, and temporal behavior. We developed GeneProgram, a new unsupervised computational framework based on Hierarchical Dirichlet Processes that addresses each of the above challenges. GeneProgram uses expression data to simultaneously organize tissues into groups and genes into overlapping programs with consistent temporal behavior, to produce maps of expression programs, which are sorted by generality scores that exploit the automatically learned groupings. Using synthetic and real gene expression data, we showed that GeneProgram outperformed several popular expression analysis methods. We applied GeneProgram to a compendium of 62 short time-series gene expression datasets exploring the responses of human cells to infectious agents and immune-modulating molecules. GeneProgram produced a map of 104 expression programs, a substantial number of which were significantly enriched for genes involved in key signaling pathways and/or bound by NF-κB transcription factors in genome-wide experiments. Further, GeneProgram discovered expression programs that appear to implicate surprising signaling pathways or receptor types in the response to infection, including Wnt signaling and neurotransmitter receptors. We believe the discovered map of expression programs involved in the response to infection will be useful for guiding future biological experiments; genes from programs with low generality scores might serve as new drug targets that exhibit minimal “cross-talk,” and genes from high generality programs may maintain common physiological responses that go awry in disease states. Further, our method is multipurpose, and can be applied readily to novel compendia of biological data. PMID:17696603

NOAA Office of Exploration and Research > Exploration > Ocean and Coastal

Science.gov Websites

Exploration Systematic Exploration Marine Archaeology Ocean and Coastal Mapping Advancing Technology Overview Exploration Marine Archaeology Ocean and Coastal Mapping Exploration Ocean and Coastal Mapping Home About OER Systematic Exploration Marine Archaeology Ocean and Coastal Mapping Advancing Technology Overview Technology

Evaluation of microRNA alignment techniques

PubMed Central

Kaspi, Antony; El-Osta, Assam

2016-01-01

Genomic alignment of small RNA (smRNA) sequences such as microRNAs poses considerable challenges due to their short length (∼21 nucleotides [nt]) as well as the large size and complexity of plant and animal genomes. While several tools have been developed for high-throughput mapping of longer mRNA-seq reads (>30 nt), there are few that are specifically designed for mapping of smRNA reads including microRNAs. The accuracy of these mappers has not been systematically determined in the case of smRNA-seq. In addition, it is unknown whether these aligners accurately map smRNA reads containing sequence errors and polymorphisms. By using simulated read sets, we determine the alignment sensitivity and accuracy of 16 short-read mappers and quantify their robustness to mismatches, indels, and nontemplated nucleotide additions. These were explored in the context of a plant genome (Oryza sativa, ∼500 Mbp) and a mammalian genome (Homo sapiens, ∼3.1 Gbp). Analysis of simulated and real smRNA-seq data demonstrates that mapper selection impacts differential expression results and interpretation. These results will inform on best practice for smRNA mapping and enable more accurate smRNA detection and quantification of expression and RNA editing. PMID:27284164

Acrylamide inhibits cellular differentiation of human neuroblastoma and glioblastoma cells.

PubMed

Chen, Jong-Hang; Chou, Chin-Cheng

2015-08-01

This study explores human neuroblastoma (SH-SY5Y) and human glioblastoma (U-1240 MG) cellular differentiation changes under exposure to acrylamide (ACR). Differentiation of SH-SY5Y and U-1240 MG cells were induced by retinoic acid (RA) and butyric acid (BA), respectively. Morphological observations and MTT assay showed that the induced cellular differentiation and cell proliferation were inhibited by ACR in a time- and dose-dependent manner. ACR co-treatment with RA attenuated SH-SY5Y expressions of neurofilament protein-L (NF-L), microtubule-associated protein 1b (MAP1b; 1.2 to 0.7, p < 0.001), MAP2c (2.2 to 0.8, p < 0.05), and Janus kinase1 (JAK1; 1.9 to 0.6, p < 0.001), while ACR co-treatment with BA attenuated U-1240 MG expressions of glial fibrillary acidic protein (GFAP), MAP1b (1.2 to 0.6, p < 0.001), MAP2c (1.5 to 0.7, p < 0.01), and JAK1 (2.1 to 0.5, p < 0.001), respectively. ACR also decreased the phosphorylation of extracellular-signal-regulated kinases (ERK) and c-Jun N-terminal kinases (JNK) in U-1240 MG cells, while caffeine reversed this suppression of ERK and JNK phosphorylation caused by ACR treatment. These results showed that RA-induced neurogenesis of SH-SY5Y and BA-induced astrogliogenesis of U-1240 MG cells were attenuated by ACR and were associated with down-regulation of MAPs expression and JAK-STAT signaling. Copyright © 2015 Elsevier Ltd. All rights reserved.

Propagation of error from parameter constraints in quantitative MRI: Example application of multiple spin echo T2 mapping.

PubMed

Lankford, Christopher L; Does, Mark D

2018-02-01

Quantitative MRI may require correcting for nuisance parameters which can or must be constrained to independently measured or assumed values. The noise and/or bias in these constraints propagate to fitted parameters. For example, the case of refocusing pulse flip angle constraint in multiple spin echo T 2 mapping is explored. An analytical expression for the mean-squared error of a parameter of interest was derived as a function of the accuracy and precision of an independent estimate of a nuisance parameter. The expression was validated by simulations and then used to evaluate the effects of flip angle (θ) constraint on the accuracy and precision of T⁁2 for a variety of multi-echo T 2 mapping protocols. Constraining θ improved T⁁2 precision when the θ-map signal-to-noise ratio was greater than approximately one-half that of the first spin echo image. For many practical scenarios, constrained fitting was calculated to reduce not just the variance but the full mean-squared error of T⁁2, for bias in θ⁁≲6%. The analytical expression derived in this work can be applied to inform experimental design in quantitative MRI. The example application to T 2 mapping provided specific cases, depending on θ⁁ accuracy and precision, in which θ⁁ measurement and constraint would be beneficial to T⁁2 variance or mean-squared error. Magn Reson Med 79:673-682, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Temporal lobe stimulation reveals anatomic distinction between auditory naming processes.

PubMed

Hamberger, M J; Seidel, W T; Goodman, R R; Perrine, K; McKhann, G M

2003-05-13

Language errors induced by cortical stimulation can provide insight into function(s) supported by the area stimulated. The authors observed that some stimulation-induced errors during auditory description naming were characterized by tip-of-the-tongue responses or paraphasic errors, suggesting expressive difficulty, whereas others were qualitatively different, suggesting receptive difficulty. They hypothesized that these two response types reflected disruption at different stages of auditory verbal processing and that these "subprocesses" might be supported by anatomically distinct cortical areas. To explore the topographic distribution of error types in auditory verbal processing. Twenty-one patients requiring left temporal lobe surgery underwent preresection language mapping using direct cortical stimulation. Auditory naming was tested at temporal sites extending from 1 cm from the anterior tip to the parietal operculum. Errors were dichotomized as either "expressive" or "receptive." The topographic distribution of error types was explored. Sites associated with the two error types were topographically distinct from one another. Most receptive sites were located in the middle portion of the superior temporal gyrus (STG), whereas most expressive sites fell outside this region, scattered along lateral temporal and temporoparietal cortex. Results raise clinical questions regarding the inclusion of the STG in temporal lobe epilepsy surgery and suggest that more detailed cortical mapping might enable better prediction of postoperative language decline. From a theoretical perspective, results carry implications regarding the understanding of structure-function relations underlying temporal lobe mediation of auditory language processing.

Computational genetic neuroanatomy of the developing mouse brain: dimensionality reduction, visualization, and clustering.

PubMed

Ji, Shuiwang

2013-07-11

The structured organization of cells in the brain plays a key role in its functional efficiency. This delicate organization is the consequence of unique molecular identity of each cell gradually established by precise spatiotemporal gene expression control during development. Currently, studies on the molecular-structural association are beginning to reveal how the spatiotemporal gene expression patterns are related to cellular differentiation and structural development. In this article, we aim at a global, data-driven study of the relationship between gene expressions and neuroanatomy in the developing mouse brain. To enable visual explorations of the high-dimensional data, we map the in situ hybridization gene expression data to a two-dimensional space by preserving both the global and the local structures. Our results show that the developing brain anatomy is largely preserved in the reduced gene expression space. To provide a quantitative analysis, we cluster the reduced data into groups and measure the consistency with neuroanatomy at multiple levels. Our results show that the clusters in the low-dimensional space are more consistent with neuroanatomy than those in the original space. Gene expression patterns and developing brain anatomy are closely related. Dimensionality reduction and visual exploration facilitate the study of this relationship.

NOAA Office of Exploration and Research > Exploration > Systematic

Science.gov Websites

Exploration Systematic Exploration Marine Archaeology Ocean and Coastal Mapping Advancing Technology Overview Exploration Marine Archaeology Ocean and Coastal Mapping Exploration Systematic Exploration Home About OER Systematic Exploration Marine Archaeology Ocean and Coastal Mapping Advancing Technology Overview Technology

Metaphorical mapping between raw-cooked food and strangeness-familiarity in Chinese culture.

PubMed

Deng, Xiaohong; Qu, Yuan; Zheng, Huihui; Lu, Yang; Zhong, Xin; Ward, Anne; Li, Zijun

2017-02-01

Previous research has demonstrated metaphorical mappings between physical coldness-warmth and social distance-closeness. Since the concepts of interpersonal warmth are frequently expressed in terms of food-related words in Chinese, the present study sought to explore whether the concept of raw-cooked food could be unconsciously and automatically mapped onto strangeness-familiarity. After rating the nutritive value of raw or cooked foods, participants were presented with morphing movies in which their acquaintances gradually transformed into strangers or strangers gradually morphed into acquaintances, and were asked to stop the movies when the combined images became predominantly target faces. The results demonstrated that unconscious and automatic metaphorical mappings between raw-cooked food and strangeness-familiarity exist. This study provides a foundation for testing whether Chinese people can think about interpersonal familiarity using mental representations of raw-cooked food and supports cognitive metaphor theory from a crosslinguistic perspective.

The pig genome project has plenty to squeal about.

PubMed

Fan, B; Gorbach, D M; Rothschild, M F

2011-01-01

Significant progress on pig genetics and genomics research has been witnessed in recent years due to the integration of advanced molecular biology techniques, bioinformatics and computational biology, and the collaborative efforts of researchers in the swine genomics community. Progress on expanding the linkage map has slowed down, but the efforts have created a higher-resolution physical map integrating the clone map and BAC end sequence. The number of QTL mapped is still growing and most of the updated QTL mapping results are available through PigQTLdb. Additionally, expression studies using high-throughput microarrays and other gene expression techniques have made significant advancements. The number of identified non-coding RNAs is rapidly increasing and their exact regulatory functions are being explored. A publishable draft (build 10) of the swine genome sequence was available for the pig genomics community by the end of December 2010. Build 9 of the porcine genome is currently available with Ensembl annotation; manual annotation is ongoing. These drafts provide useful tools for such endeavors as comparative genomics and SNP scans for fine QTL mapping. A recent community-wide effort to create a 60K porcine SNP chip has greatly facilitated whole-genome association analyses, haplotype block construction and linkage disequilibrium mapping, which can contribute to whole-genome selection. The future 'systems biology' that integrates and optimizes the information from all research levels can enhance the pig community's understanding of the full complexity of the porcine genome. These recent technological advances and where they may lead are reviewed. Copyright © 2011 S. Karger AG, Basel.

Analytic Reflected Lightcurves for Exoplanets

NASA Astrophysics Data System (ADS)

Haggard, Hal M.; Cowan, Nicolas B.

2018-04-01

The disk-integrated reflected brightness of an exoplanet changes as a function of time due to orbital and rotational motion coupled with an inhomogeneous albedo map. We have previously derived analytic reflected lightcurves for spherical harmonic albedo maps in the special case of a synchronously-rotating planet on an edge-on orbit (Cowan, Fuentes & Haggard 2013). In this letter, we present analytic reflected lightcurves for the general case of a planet on an inclined orbit, with arbitrary spin period and non-zero obliquity. We do so for two different albedo basis maps: bright points (δ-maps), and spherical harmonics (Y_l^m-maps). In particular, we use Wigner D-matrices to express an harmonic lightcurve for an arbitrary viewing geometry as a non-linear combination of harmonic lightcurves for the simpler edge-on, synchronously rotating geometry. These solutions will enable future exploration of the degeneracies and information content of reflected lightcurves, as well as fast calculation of lightcurves for mapping exoplanets based on time-resolved photometry. To these ends we make available Exoplanet Analytic Reflected Lightcurves (EARL), a simple open-source code that allows rapid computation of reflected lightcurves.

PExFInS: An Integrative Post-GWAS Explorer for Functional Indels and SNPs

PubMed Central

Cheng, Zhongshan; Chu, Hin; Fan, Yanhui; Li, Cun; Song, You-Qiang; Zhou, Jie; Yuen, Kwok-Yung

2015-01-01

Expression quantitative trait loci (eQTLs) mapping and linkage disequilibrium (LD) analysis have been widely employed to interpret findings of genome-wide association studies (GWAS). With the availability of deep sequencing data of 423 lymphoblastoid cell lines (LCLs) from six global populations and the microarray expression data, we performed eQTL analysis, identified more than 228 K SNP cis-eQTLs and 21 K indel cis-eQTLs and generated a LCL cis-eQTL database. We demonstrate that the percentages of population-shared and population-specific cis-eQTLs are comparable; while indel cis-eQTLs in the population-specific subsection make more contribution to gene expression variations than those in the population-shared subsection. We found cis-eQTLs, especially the population-shared cis-eQTLs are significantly enriched toward transcription start site. Moreover, the National Human Genome Research Institute cataloged GWAS SNPs are enriched for LCL cis-eQTLs. Specifically, 32.8% GWAS SNPs are LCL cis-eQTLs, among which 12.5% can be tagged by indel cis-eQTLs, suggesting the fundamental contribution of indel cis-eQTLs to GWAS association signals. To search for functional indels and SNPs tagging GWAS SNPs, a pipeline Post-GWAS Explorer for Functional Indels and SNPs (PExFInS) has been developed, integrating LD analysis, functional annotation from public databases, cis-eQTL mapping with our LCL cis-eQTL database and other published cis-eQTL datasets. PMID:26612672

QUADrATiC: scalable gene expression connectivity mapping for repurposing FDA-approved therapeutics.

PubMed

O'Reilly, Paul G; Wen, Qing; Bankhead, Peter; Dunne, Philip D; McArt, Darragh G; McPherson, Suzanne; Hamilton, Peter W; Mills, Ken I; Zhang, Shu-Dong

2016-05-04

Gene expression connectivity mapping has proven to be a powerful and flexible tool for research. Its application has been shown in a broad range of research topics, most commonly as a means of identifying potential small molecule compounds, which may be further investigated as candidates for repurposing to treat diseases. The public release of voluminous data from the Library of Integrated Cellular Signatures (LINCS) programme further enhanced the utilities and potentials of gene expression connectivity mapping in biomedicine. We describe QUADrATiC ( http://go.qub.ac.uk/QUADrATiC ), a user-friendly tool for the exploration of gene expression connectivity on the subset of the LINCS data set corresponding to FDA-approved small molecule compounds. It enables the identification of compounds for repurposing therapeutic potentials. The software is designed to cope with the increased volume of data over existing tools, by taking advantage of multicore computing architectures to provide a scalable solution, which may be installed and operated on a range of computers, from laptops to servers. This scalability is provided by the use of the modern concurrent programming paradigm provided by the Akka framework. The QUADrATiC Graphical User Interface (GUI) has been developed using advanced Javascript frameworks, providing novel visualization capabilities for further analysis of connections. There is also a web services interface, allowing integration with other programs or scripts. QUADrATiC has been shown to provide an improvement over existing connectivity map software, in terms of scope (based on the LINCS data set), applicability (using FDA-approved compounds), usability and speed. It offers potential to biological researchers to analyze transcriptional data and generate potential therapeutics for focussed study in the lab. QUADrATiC represents a step change in the process of investigating gene expression connectivity and provides more biologically-relevant results than previous alternative solutions.

Computational genetic neuroanatomy of the developing mouse brain: dimensionality reduction, visualization, and clustering

PubMed Central

2013-01-01

Background The structured organization of cells in the brain plays a key role in its functional efficiency. This delicate organization is the consequence of unique molecular identity of each cell gradually established by precise spatiotemporal gene expression control during development. Currently, studies on the molecular-structural association are beginning to reveal how the spatiotemporal gene expression patterns are related to cellular differentiation and structural development. Results In this article, we aim at a global, data-driven study of the relationship between gene expressions and neuroanatomy in the developing mouse brain. To enable visual explorations of the high-dimensional data, we map the in situ hybridization gene expression data to a two-dimensional space by preserving both the global and the local structures. Our results show that the developing brain anatomy is largely preserved in the reduced gene expression space. To provide a quantitative analysis, we cluster the reduced data into groups and measure the consistency with neuroanatomy at multiple levels. Our results show that the clusters in the low-dimensional space are more consistent with neuroanatomy than those in the original space. Conclusions Gene expression patterns and developing brain anatomy are closely related. Dimensionality reduction and visual exploration facilitate the study of this relationship. PMID:23845024

GEsture: an online hand-drawing tool for gene expression pattern search.

PubMed

Wang, Chunyan; Xu, Yiqing; Wang, Xuelin; Zhang, Li; Wei, Suyun; Ye, Qiaolin; Zhu, Youxiang; Yin, Hengfu; Nainwal, Manoj; Tanon-Reyes, Luis; Cheng, Feng; Yin, Tongming; Ye, Ning

2018-01-01

Gene expression profiling data provide useful information for the investigation of biological function and process. However, identifying a specific expression pattern from extensive time series gene expression data is not an easy task. Clustering, a popular method, is often used to classify similar expression genes, however, genes with a 'desirable' or 'user-defined' pattern cannot be efficiently detected by clustering methods. To address these limitations, we developed an online tool called GEsture. Users can draw, or graph a curve using a mouse instead of inputting abstract parameters of clustering methods. GEsture explores genes showing similar, opposite and time-delay expression patterns with a gene expression curve as input from time series datasets. We presented three examples that illustrate the capacity of GEsture in gene hunting while following users' requirements. GEsture also provides visualization tools (such as expression pattern figure, heat map and correlation network) to display the searching results. The result outputs may provide useful information for researchers to understand the targets, function and biological processes of the involved genes.

Mars Surface Compositional Units and Some Geological Implications from the Mars Express High Resolution Stereo Camera (HRSC)

NASA Astrophysics Data System (ADS)

McCord, T. B.; Combe, J.-P.; Hayne, P. O.

We are investigating the composition of the Martian surface partly by mapping the small spatial variations of water ice and salt minerals using the spectral images provided by the High Resolution Stereo Camera (HRSC). In order to identify the main mineral components, high spectral resolution data from the Observatoire pour la Mineralogie, l'Eau, les Glaces et l'Activite (OMEGA) imaging spectrometer are used. The join analysis of these two dataset makes the most of their respective abilities and, because of that, it requires a close agreement of their calibration [1]. The first part of this work is a comparison of HRSC and OMEGA measurements, exploration of atmosphere effects and checks of calibration. Then, an attempt to detect and map quantitatively at high spatial resolution (1) water ice both at the poles and in equatorial regions and (2) salts minerals is performed by exploring the spectral types evidenced in HRSC color data. For a given region, these two materials do or could represent additional endmember compositional units detectable with HRSC in addition to the basic units so far: 1) dark rock (basalt) and 2) red rock (iron oxide-rich material) [1]. Both materials also have been reported detected by OMEGA, but at much lower spatial resolution than HRSC. An ice mapping of the north polar regions is performed with OMEGA data by using a spectral index calibrated to ice fraction by using a set of linear combinations of various categories of materials with ice. In addition, a linear spectral unmixing model is used on HRSC data. Both ice fraction maps produce similar quantitative results, allowing us to interpret HRSC data at their full spatial resolution. Low-latitude sites are also explored where past but recent glacial activities have been reported as possible evidence of current water-ice. This includes looking for fresh frost and changes with time. The salt detection with HRSC firstly focused on the Candor Chasma area, where salt have been reported by using OMEGA [2]. The present work extends the analysis to other regions in order to constrain better the general geology and climate of Mars. References: [1] McCord T. B., et al. (2006). The Mars Express High Resolution Stereo Camera spectrophotometric data: Characteristics and science analysis, JGR, submitted. [2] Gendrin, A., N. Mangold, J-P. Bibring, Y. Langevin, B. Gondet, F. Poulet, G. Bonello, C. Quantin, J. Mustard, R. Arvidson, S. LeMouelic (2005), Sulfates in Martian layered terrains: The OMEGA/Mars Express View, Science, 307, 1587-1591

Intraoperative Mapping of Expressive Language Cortex Using Passive Real-Time Electrocorticography

DTIC Science & Technology

2016-08-26

lsev ie r .com/ locate /ebcrCase ReportIntraoperative mapping of expressive language cortex using passive real-time electrocorticographyAmiLyn M...case report, we investigated the utility and practicality of passive intraoperative functional mapping of expressive language cortex using high...expressive lan- guage regions. In preparation of tumor resection, the patient underwent multiple functional language mapping procedures. We examined

Autonomous exploration and mapping of unknown environments

NASA Astrophysics Data System (ADS)

Owens, Jason; Osteen, Phil; Fields, MaryAnne

2012-06-01

Autonomous exploration and mapping is a vital capability for future robotic systems expected to function in arbitrary complex environments. In this paper, we describe an end-to-end robotic solution for remotely mapping buildings. For a typical mapping system, an unmanned system is directed to enter an unknown building at a distance, sense the internal structure, and, barring additional tasks, while in situ, create a 2-D map of the building. This map provides a useful and intuitive representation of the environment for the remote operator. We have integrated a robust mapping and exploration system utilizing laser range scanners and RGB-D cameras, and we demonstrate an exploration and metacognition algorithm on a robotic platform. The algorithm allows the robot to safely navigate the building, explore the interior, report significant features to the operator, and generate a consistent map - all while maintaining localization.

Gene expression patterns combined with bioinformatics analysis identify genes associated with cholangiocarcinoma.

PubMed

Li, Chen; Shen, Weixing; Shen, Sheng; Ai, Zhilong

2013-12-01

To explore the molecular mechanisms of cholangiocarcinoma (CC), microarray technology was used to find biomarkers for early detection and diagnosis. The gene expression profiles from 6 patients with CC and 5 normal controls were downloaded from Gene Expression Omnibus and compared. As a result, 204 differentially co-expressed genes (DCGs) in CC patients compared to normal controls were identified using a computational bioinformatics analysis. These genes were mainly involved in coenzyme metabolic process, peptidase activity and oxidation reduction. A regulatory network was constructed by mapping the DCGs to known regulation data. Four transcription factors, FOXC1, ZIC2, NKX2-2 and GCGR, were hub nodes in the network. In conclusion, this study provides a set of targets useful for future investigations into molecular biomarker studies. Copyright © 2013 Elsevier Ltd. All rights reserved.

Global mapping of transposon location.

PubMed

Gabriel, Abram; Dapprich, Johannes; Kunkel, Mark; Gresham, David; Pratt, Stephen C; Dunham, Maitreya J

2006-12-15

Transposable genetic elements are ubiquitous, yet their presence or absence at any given position within a genome can vary between individual cells, tissues, or strains. Transposable elements have profound impacts on host genomes by altering gene expression, assisting in genomic rearrangements, causing insertional mutations, and serving as sources of phenotypic variation. Characterizing a genome's full complement of transposons requires whole genome sequencing, precluding simple studies of the impact of transposition on interindividual variation. Here, we describe a global mapping approach for identifying transposon locations in any genome, using a combination of transposon-specific DNA extraction and microarray-based comparative hybridization analysis. We use this approach to map the repertoire of endogenous transposons in different laboratory strains of Saccharomyces cerevisiae and demonstrate that transposons are a source of extensive genomic variation. We also apply this method to mapping bacterial transposon insertion sites in a yeast genomic library. This unique whole genome view of transposon location will facilitate our exploration of transposon dynamics, as well as defining bases for individual differences and adaptive potential.

Mapping of Brain Activity by Automated Volume Analysis of Immediate Early Genes.

PubMed

Renier, Nicolas; Adams, Eliza L; Kirst, Christoph; Wu, Zhuhao; Azevedo, Ricardo; Kohl, Johannes; Autry, Anita E; Kadiri, Lolahon; Umadevi Venkataraju, Kannan; Zhou, Yu; Wang, Victoria X; Tang, Cheuk Y; Olsen, Olav; Dulac, Catherine; Osten, Pavel; Tessier-Lavigne, Marc

2016-06-16

Understanding how neural information is processed in physiological and pathological states would benefit from precise detection, localization, and quantification of the activity of all neurons across the entire brain, which has not, to date, been achieved in the mammalian brain. We introduce a pipeline for high-speed acquisition of brain activity at cellular resolution through profiling immediate early gene expression using immunostaining and light-sheet fluorescence imaging, followed by automated mapping and analysis of activity by an open-source software program we term ClearMap. We validate the pipeline first by analysis of brain regions activated in response to haloperidol. Next, we report new cortical regions downstream of whisker-evoked sensory processing during active exploration. Last, we combine activity mapping with axon tracing to uncover new brain regions differentially activated during parenting behavior. This pipeline is widely applicable to different experimental paradigms, including animal species for which transgenic activity reporters are not readily available. Copyright © 2016 Elsevier Inc. All rights reserved.

Mapping of brain activity by automated volume analysis of immediate early genes

PubMed Central

Renier, Nicolas; Adams, Eliza L.; Kirst, Christoph; Wu, Zhuhao; Azevedo, Ricardo; Kohl, Johannes; Autry, Anita E.; Kadiri, Lolahon; Venkataraju, Kannan Umadevi; Zhou, Yu; Wang, Victoria X.; Tang, Cheuk Y.; Olsen, Olav; Dulac, Catherine; Osten, Pavel; Tessier-Lavigne, Marc

2016-01-01

Summary Understanding how neural information is processed in physiological and pathological states would benefit from precise detection, localization and quantification of the activity of all neurons across the entire brain, which has not to date been achieved in the mammalian brain. We introduce a pipeline for high speed acquisition of brain activity at cellular resolution through profiling immediate early gene expression using immunostaining and light-sheet fluorescence imaging, followed by automated mapping and analysis of activity by an open-source software program we term ClearMap. We validate the pipeline first by analysis of brain regions activated in response to Haloperidol. Next, we report new cortical regions downstream of whisker-evoked sensory processing during active exploration. Lastly, we combine activity mapping with axon tracing to uncover new brain regions differentially activated during parenting behavior. This pipeline is widely applicable to different experimental paradigms, including animal species for which transgenic activity reporters are not readily available. PMID:27238021

Evaluation of prognostic and predictive value of microtubule associated protein tau in two independent cohorts.

PubMed

Baquero, Maria T; Lostritto, Karen; Gustavson, Mark D; Bassi, Kimberly A; Appia, Franck; Camp, Robert L; Molinaro, Annette M; Harris, Lyndsay N; Rimm, David L

2011-11-02

Microtubule associated proteins (MAPs) endogenously regulate microtubule stabilization and have been reported as prognostic and predictive markers for taxane response. The microtubule stabilizer, MAP-tau, has shown conflicting results. We quantitatively assessed MAP-tau expression in two independent breast cancer cohorts to determine prognostic and predictive value of this biomarker. MAP-tau expression was evaluated in the retrospective Yale University breast cancer cohort (n = 651) using tissue microarrays and also in the TAX 307 cohort, a clinical trial randomized for TAC versus FAC chemotherapy (n = 140), using conventional whole tissue sections. Expression was measured using the AQUA method for quantitative immunofluorescence. Scores were correlated with clinicopathologic variables, survival, and response to therapy. Assessment of the Yale cohort using Cox univariate analysis indicated an improved overall survival (OS) in tumors with a positive correlation between high MAP-tau expression and overall survival (OS) (HR = 0.691, 95% CI = 0.489-0.974; P = 0.004). Kaplan Meier analysis showed 10-year survival for 65% of patients with high MAP-tau expression compared to 52% with low expression (P = .006). In TAX 307, high expression was associated with significantly longer median time to tumor progression (TTP) regardless of treatment arm (33.0 versus 23.4 months, P = 0.010) with mean TTP of 31.2 months. Response rates did not differ by MAP-tau expression (P = 0.518) or by treatment arm (P = 0.584). Quantitative measurement of MAP-tau expression has prognostic value in both cohorts, with high expression associated with longer TTP and OS. Differences by treatment arm or response rate in low versus high MAP-tau groups were not observed, indicating that MAP-tau is not associated with response to taxanes and is not a useful predictive marker for taxane-based chemotherapy.

Digital gene expression analysis of gene expression differences within Brassica diploids and allopolyploids.

PubMed

Jiang, Jinjin; Wang, Yue; Zhu, Bao; Fang, Tingting; Fang, Yujie; Wang, Youping

2015-01-27

Brassica includes many successfully cultivated crop species of polyploid origin, either by ancestral genome triplication or by hybridization between two diploid progenitors, displaying complex repetitive sequences and transposons. The U's triangle, which consists of three diploids and three amphidiploids, is optimal for the analysis of complicated genomes after polyploidization. Next-generation sequencing enables the transcriptome profiling of polyploids on a global scale. We examined the gene expression patterns of three diploids (Brassica rapa, B. nigra, and B. oleracea) and three amphidiploids (B. napus, B. juncea, and B. carinata) via digital gene expression analysis. In total, the libraries generated between 5.7 and 6.1 million raw reads, and the clean tags of each library were mapped to 18547-21995 genes of B. rapa genome. The unambiguous tag-mapped genes in the libraries were compared. Moreover, the majority of differentially expressed genes (DEGs) were explored among diploids as well as between diploids and amphidiploids. Gene ontological analysis was performed to functionally categorize these DEGs into different classes. The Kyoto Encyclopedia of Genes and Genomes analysis was performed to assign these DEGs into approximately 120 pathways, among which the metabolic pathway, biosynthesis of secondary metabolites, and peroxisomal pathway were enriched. The non-additive genes in Brassica amphidiploids were analyzed, and the results indicated that orthologous genes in polyploids are frequently expressed in a non-additive pattern. Methyltransferase genes showed differential expression pattern in Brassica species. Our results provided an understanding of the transcriptome complexity of natural Brassica species. The gene expression changes in diploids and allopolyploids may help elucidate the morphological and physiological differences among Brassica species.

Analyzing gene expression profiles in dilated cardiomyopathy via bioinformatics methods.

PubMed

Wang, Liming; Zhu, L; Luan, R; Wang, L; Fu, J; Wang, X; Sui, L

2016-10-10

Dilated cardiomyopathy (DCM) is characterized by ventricular dilatation, and it is a common cause of heart failure and cardiac transplantation. This study aimed to explore potential DCM-related genes and their underlying regulatory mechanism using methods of bioinformatics. The gene expression profiles of GSE3586 were downloaded from Gene Expression Omnibus database, including 15 normal samples and 13 DCM samples. The differentially expressed genes (DEGs) were identified between normal and DCM samples using Limma package in R language. Pathway enrichment analysis of DEGs was then performed. Meanwhile, the potential transcription factors (TFs) and microRNAs (miRNAs) of these DEGs were predicted based on their binding sequences. In addition, DEGs were mapped to the cMap database to find the potential small molecule drugs. A total of 4777 genes were identified as DEGs by comparing gene expression profiles between DCM and control samples. DEGs were significantly enriched in 26 pathways, such as lymphocyte TarBase pathway and androgen receptor signaling pathway. Furthermore, potential TFs (SP1, LEF1, and NFAT) were identified, as well as potential miRNAs (miR-9, miR-200 family, and miR-30 family). Additionally, small molecules like isoflupredone and trihexyphenidyl were found to be potential therapeutic drugs for DCM. The identified DEGs (PRSS12 and FOXG1), potential TFs, as well as potential miRNAs, might be involved in DCM.

Analyzing gene expression profiles in dilated cardiomyopathy via bioinformatics methods

PubMed Central

Wang, Liming; Zhu, L.; Luan, R.; Wang, L.; Fu, J.; Wang, X.; Sui, L.

2016-01-01

Dilated cardiomyopathy (DCM) is characterized by ventricular dilatation, and it is a common cause of heart failure and cardiac transplantation. This study aimed to explore potential DCM-related genes and their underlying regulatory mechanism using methods of bioinformatics. The gene expression profiles of GSE3586 were downloaded from Gene Expression Omnibus database, including 15 normal samples and 13 DCM samples. The differentially expressed genes (DEGs) were identified between normal and DCM samples using Limma package in R language. Pathway enrichment analysis of DEGs was then performed. Meanwhile, the potential transcription factors (TFs) and microRNAs (miRNAs) of these DEGs were predicted based on their binding sequences. In addition, DEGs were mapped to the cMap database to find the potential small molecule drugs. A total of 4777 genes were identified as DEGs by comparing gene expression profiles between DCM and control samples. DEGs were significantly enriched in 26 pathways, such as lymphocyte TarBase pathway and androgen receptor signaling pathway. Furthermore, potential TFs (SP1, LEF1, and NFAT) were identified, as well as potential miRNAs (miR-9, miR-200 family, and miR-30 family). Additionally, small molecules like isoflupredone and trihexyphenidyl were found to be potential therapeutic drugs for DCM. The identified DEGs (PRSS12 and FOXG1), potential TFs, as well as potential miRNAs, might be involved in DCM. PMID:27737314

Creating and validating cis-regulatory maps of tissue-specific gene expression regulation

PubMed Central

O'Connor, Timothy R.; Bailey, Timothy L.

2014-01-01

Predicting which genomic regions control the transcription of a given gene is a challenge. We present a novel computational approach for creating and validating maps that associate genomic regions (cis-regulatory modules–CRMs) with genes. The method infers regulatory relationships that explain gene expression observed in a test tissue using widely available genomic data for ‘other’ tissues. To predict the regulatory targets of a CRM, we use cross-tissue correlation between histone modifications present at the CRM and expression at genes within 1 Mbp of it. To validate cis-regulatory maps, we show that they yield more accurate models of gene expression than carefully constructed control maps. These gene expression models predict observed gene expression from transcription factor binding in the CRMs linked to that gene. We show that our maps are able to identify long-range regulatory interactions and improve substantially over maps linking genes and CRMs based on either the control maps or a ‘nearest neighbor’ heuristic. Our results also show that it is essential to include CRMs predicted in multiple tissues during map-building, that H3K27ac is the most informative histone modification, and that CAGE is the most informative measure of gene expression for creating cis-regulatory maps. PMID:25200088

Using microarrays to identify positional candidate genes for QTL: the case study of ACTH response in pigs.

PubMed

Jouffe, Vincent; Rowe, Suzanne; Liaubet, Laurence; Buitenhuis, Bart; Hornshøj, Henrik; SanCristobal, Magali; Mormède, Pierre; de Koning, D J

2009-07-16

Microarray studies can supplement QTL studies by suggesting potential candidate genes in the QTL regions, which by themselves are too large to provide a limited selection of candidate genes. Here we provide a case study where we explore ways to integrate QTL data and microarray data for the pig, which has only a partial genome sequence. We outline various procedures to localize differentially expressed genes on the pig genome and link this with information on published QTL. The starting point is a set of 237 differentially expressed cDNA clones in adrenal tissue from two pig breeds, before and after treatment with adrenocorticotropic hormone (ACTH). Different approaches to localize the differentially expressed (DE) genes to the pig genome showed different levels of success and a clear lack of concordance for some genes between the various approaches. For a focused analysis on 12 genes, overlapping QTL from the public domain were presented. Also, differentially expressed genes underlying QTL for ACTH response were described. Using the latest version of the draft sequence, the differentially expressed genes were mapped to the pig genome. This enabled co-location of DE genes and previously studied QTL regions, but the draft genome sequence is still incomplete and will contain many errors. A further step to explore links between DE genes and QTL at the pathway level was largely unsuccessful due to the lack of annotation of the pig genome. This could be improved by further comparative mapping analyses but this would be time consuming. This paper provides a case study for the integration of QTL data and microarray data for a species with limited genome sequence information and annotation. The results illustrate the challenges that must be addressed but also provide a roadmap for future work that is applicable to other non-model species.

Analysis of improved government geological map information for mineral exploration: Incorporating efficiency, productivity, effectiveness, and risk considerations

USGS Publications Warehouse

Bernknopf, R.L.; Wein, A.M.; St-Onge, M. R.; Lucas, S.B.

2007-01-01

This bulletin/professional paper focuses on the value of geoscientific information and knowledge, as provided in published government bedrock geological maps, to the mineral exploration sector. An economic model is developed that uses an attribute- ranking approach to convert geological maps into domains of mineral favourability. Information about known deposits in these (or analogous) favourability domains allow the calculation of exploration search statistics that provide input into measures of exploration efficiency, productivity, effectiveness, risk, and cost stemming from the use of the published geological maps. Two case studies, the Flin Flon Belt (Manitoba and Saskatchewan) and the south Baffin Island area (Nunavut), demonstrate that updated, finer resolution maps can be used to identify more exploration campaign options, and campaigns thats are more efficient, more effective, and less risky than old, coarser resolution maps when used as a guide for mineral exploration. The Flin Flon Belt study illustrates that an updated, coarser resolution bedrock map enables improved mineral exploration efficiency, productivity, and effectiveness by locating 60% more targets and supporting an exploration campaign that is 44% more efficient. Refining the map resolution provides an additional 17% reduction in search effort across all favourable domains and a 55% reduction in search effort in the most favourable domain. The south Baffin Island case study projects a 40% increase in expected targets and a 27% reduction in search effort when the updated, finer resolution map is used in lieu of the old, coarser resolution map. On southern Baffin Island, the economic value of the up dated map ranges from CAN$2.28 million to CAN$15.21 million, which can be compared to the CAN$1.86 million that it cost to produce the map (a multiplier effect of up to eight).

Mapping out the Details: Supporting Struggling Writers' Written Expression with Concept Mapping

ERIC Educational Resources Information Center

Flanagan, Sara M.; Bouck, Emily C.

2015-01-01

Written expression is a key component of the secondary curriculum, but many students struggle to produce effective written expression passages. However, written expression can be supported through prewriting strategies such as concept mapping. Using a counterbalanced group design, 19 secondary students alternated between using paper- or…

Metabolic Genetic Screens Reveal Multidimensional Regulation of Virulence Gene Expression in Listeria monocytogenes and an Aminopeptidase That Is Critical for PrfA Protein Activation.

PubMed

Friedman, Sivan; Linsky, Marika; Lobel, Lior; Rabinovich, Lev; Sigal, Nadejda; Herskovits, Anat A

2017-06-01

Listeria monocytogenes is an environmental saprophyte and intracellular bacterial pathogen. Upon invading mammalian cells, the bacterium senses abrupt changes in its metabolic environment, which are rapidly transduced to regulation of virulence gene expression. To explore the relationship between L. monocytogenes metabolism and virulence, we monitored virulence gene expression dynamics across a library of genetic mutants grown under two metabolic conditions known to activate the virulent state: charcoal-treated rich medium containing glucose-1-phosphate and minimal defined medium containing limiting concentrations of branched-chain amino acids (BCAAs). We identified over 100 distinct mutants that exhibit aberrant virulence gene expression profiles, the majority of which mapped to nonessential metabolic genes. Mutants displayed enhanced, decreased, and early and late virulence gene expression profiles, as well as persistent levels, demonstrating a high plasticity in virulence gene regulation. Among the mutants, one was noteworthy for its particularly low virulence gene expression level and mapped to an X-prolyl aminopeptidase (PepP). We show that this peptidase plays a role in posttranslational activation of the major virulence regulator, PrfA. Specifically, PepP mediates recruitment of PrfA to the cytoplasmic membrane, a step identified as critical for PrfA protein activation. This study establishes a novel step in the complex mechanism of PrfA activation and further highlights the cross regulation of metabolism and virulence. Copyright © 2017 American Society for Microbiology.

Analytic reflected light curves for exoplanets

NASA Astrophysics Data System (ADS)

Haggard, Hal M.; Cowan, Nicolas B.

2018-07-01

The disc-integrated reflected brightness of an exoplanet changes as a function of time due to orbital and rotational motions coupled with an inhomogeneous albedo map. We have previously derived analytic reflected light curves for spherical harmonic albedo maps in the special case of a synchronously rotating planet on an edge-on orbit (Cowan, Fuentes & Haggard). In this paper, we present analytic reflected light curves for the general case of a planet on an inclined orbit, with arbitrary spin period and non-zero obliquity. We do so for two different albedo basis maps: bright points (δ-maps), and spherical harmonics (Y_ l^m-maps). In particular, we use Wigner D-matrices to express an harmonic light curve for an arbitrary viewing geometry as a non-linear combination of harmonic light curves for the simpler edge-on, synchronously rotating geometry. These solutions will enable future exploration of the degeneracies and information content of reflected light curves, as well as fast calculation of light curves for mapping exoplanets based on time-resolved photometry. To these ends, we make available Exoplanet Analytic Reflected Lightcurves, a simple open-source code that allows rapid computation of reflected light curves.

Mapping commuter cycling risk in urban areas.

PubMed

Yiannakoulias, Nikolaos; Bennet, Scott A; Scott, Darren M

2012-03-01

Cycling is becoming an increasingly important transportation option for commuters. Cycling offers exercise opportunities and reduces the burden of motor vehicle travel on society. Mapping the risk of collision between cyclists and motor vehicles in urban areas is important to understanding safe cyclist route opportunities, making informed transportation planning decisions, and exploring patterns of injury epidemiology. To date, many geographic analyses and representations of cyclist risk have not taken the concept of exposure into account. Instead, risk is either expressed as a rate per capita, or as a count of events. Using data associated with the City of Hamilton, Canada, we illustrate a method for mapping commuter cyclist collision risk per distance travelled. This measure can be used to more realistically represent the underlying geography of cycling risk, and provide more geographically and empirically meaningful information to those interested in understanding how cycling safety varies over space. Copyright © 2011 Elsevier Ltd. All rights reserved.

Multiplexed Immunofluorescence Reveals Potential PD-1/PD-L1 Pathway Vulnerabilities in Craniopharyngioma.

PubMed

Coy, Shannon; Rashid, Rumana; Lin, Jia-Ren; Du, Ziming; Donson, Andrew M; Hankinson, Todd C; Foreman, Nicholas K; Manley, Peter E; Kieran, Mark W; Reardon, David A; Sorger, Peter K; Santagata, Sandro

2018-03-02

Craniopharyngiomas are neoplasms of the sellar/parasellar region that are classified into adamantinomatous (ACP) and papillary (PCP) subtypes. Surgical resection of craniopharyngiomas is challenging, and recurrence is common, frequently leading to profound morbidity. BRAF V600E mutations render PCP susceptible to BRAF/MEK inhibitors, but effective targeted therapies are needed for ACP. We explored the feasibility of targeting the PD-1/PD-L1 immune checkpoint pathway in ACP and PCP. We mapped and quantified PD-L1 and PD-1 expression in ACP and PCP resections using immunohistochemistry, immunofluorescence, and RNA in situ hybridization. We used tissue-based cyclic immunofluorescence (t-CyCIF) to map the spatial distribution of immune cells and characterize cell cycle and signaling pathways in ACP tumor cells which intrinsically express PD-1. All ACP (15±14% of cells, n=23, average±S.D.) and PCP (35±22% of cells, n=18) resections expressed PD-L1. In ACP, PD-L1 was predominantly expressed by tumor cells comprising the cyst-lining. In PCP, PD-L1 was highly-expressed by tumor cells surrounding the stromal fibrovascular cores. ACP also exhibited tumor cell-intrinsic PD-1 expression in whorled epithelial cells with nuclear-localized beta-catenin. These cells exhibited evidence of elevated mTOR and MAPK signaling. Profiling of immune populations in ACP and PCP showed a modest density of CD8+ T-cells. ACP exhibit PD-L1 expression in the tumor cyst-lining and intrinsic PD-1 expression in cells proposed to comprise an oncogenic stem-like population. In PCP, proliferative tumor cells express PD-L1 in a continuous band at the stromal-epithelial interface. Targeting PD-L1 and/or PD-1 in both subtypes of craniopharyngioma might therefore be an effective therapeutic strategy.

Strategic Map for Exploring the Ocean-World Enceladus

NASA Technical Reports Server (NTRS)

Sherwood, Brent

2015-01-01

Among the many "ocean worlds" of our solar system, Enceladus appears unique in its combination of astrobiologically relevant, exploration-worthy attributes: extensive liquid-water ocean with high-temperature hydrothermal activity, containing salts and organics expressed predictably into space. The Enceladus south polar plume allows direct access to telltale molecules, ions, isotopes, and potential cytofragments in space. Plume mass spectroscopy and sample return, in situ investigation of surface fallback deposits, direct vent exploration, and eventually oceanographic exploration can all be envisioned. However, building consensus to fund such ambitious exploration hinges on acquiring key new data. A roadmap is essential. It could start with cost-capped onramps: 1) flythrough analysis of the plume, following up on Cassini measurements with modern instruments; 2) sample return of plume material for analysis on Earth. A methodical mission sequence in which each step depends on emergent results from prior missions would push in situ oceanographic exploration into the second half of this century. Even for this scenario, prioritization by the next planetary Decadal Survey would be pivotal.

Strategic map for exploring the ocean-world Enceladus

NASA Astrophysics Data System (ADS)

Sherwood, Brent

2016-09-01

Among the many "ocean worlds" of our solar system, Enceladus appears unique in its combination of astrobiologically relevant and exploration-worthy attributes: extensive liquid-water ocean with active hydrothermal activity, containing salts and organics expressed predictably into space. The Enceladus south polar plume allows direct access to telltale molecules, ions, isotopes, and potential cytofragments in space. Plume mass spectroscopy and sample return, in situ investigation of surface fallback deposits, direct vent exploration, and eventually oceanographic exploration can all be envisioned. However, building consensus to fund such ambitious exploration hinges on acquiring key new data. A roadmap is essential. It could start with cost-capped onramps such as flythrough analysis of the plume, following up on Cassini measurements with modern instruments; and sample return of plume material for analysis on Earth. A methodical mission sequence in which each step depends on emergent results from prior missions would push in situ oceanographic exploration into the second half of this century. Even for this scenario, prioritization by the next planetary Decadal Survey would be pivotal.

Functional reorganization of visual cortex maps after ischemic lesions is accompanied by changes in expression of cytoskeletal proteins and NMDA and GABA(A) receptor subunits.

PubMed

Zepeda, Angelica; Sengpiel, Frank; Guagnelli, Miguel Angel; Vaca, Luis; Arias, Clorinda

2004-02-25

Reorganization of cortical representations after focal visual cortex lesions has been documented. It has been suggested that functional reorganization may rely on cellular mechanisms involving modifications in the excitatory/inhibitory neurotransmission balance and on morphological changes of neurons peripheral to the lesion. We explored functional reorganization of cortical retinotopic maps after a focal ischemic lesion in primary visual cortex of kittens using optical imaging of intrinsic signals. After 1, 2, and 5 weeks postlesion (wPL), we addressed whether functional reorganization correlated in time with changes in the expression of MAP-2, GAP-43, GFAP, GABA(A) receptor subunit alpha1 (GABA(A)alpha1), subunit 1 of the NMDA receptor (NMDAR1), and in neurotransmitter levels at the border of the lesion. Our results show that: (1) retinotopic maps reorganize with time after an ischemic lesion; (2) MAP-2 levels increase gradually from 1wPL to 5wPL; (3) MAP-2 upregulation is associated with an increase in dendritic-like structures surrounding the lesion and a decrease in GFAP-positive cells; (4) GAP-43 levels reach the highest point at 2wPL; (5) NMDAR1 and glutamate contents increase in parallel from 1wPL to 5wPL; (6) GABA(A)alpha1 levels increase from 1wPL to 2wPL but do not change after this time point; and (7) GABA contents remain low from 1wPL to 5wPL. This is a comprehensive study showing for the first time that functional reorganization correlates in time with dendritic sprouting and with changes in the excitatory/inhibitory neurotransmission systems previously proposed to participate in cortical remodeling and suggests mechanisms by which plasticity of cortical representations may occur.

NOAA Office of Exploration and Research > Public Affairs > OER Symposium

Science.gov Websites

Exploration Marine Archaeology Ocean and Coastal Mapping Advancing Technology Overview Technology Initiatives Exploration Overview Targeted Exploration Systematic Exploration Marine Archaeology Ocean and Coastal Mapping

Comparative Transcriptomic Approaches Exploring Contamination Stress Tolerance in Salix sp. Reveal the Importance for a Metaorganismal de Novo Assembly Approach for Nonmodel Plants1[OPEN

PubMed Central

Brereton, Nicholas J. B.; Marleau, Julie; Nissim, Werther Guidi; Labrecque, Michel; Joly, Simon; Pitre, Frederic E.

2016-01-01

Metatranscriptomic study of nonmodel organisms requires strategies that retain the highly resolved genetic information generated from model organisms while allowing for identification of the unexpected. A real-world biological application of phytoremediation, the field growth of 10 Salix cultivars on polluted soils, was used as an exemplar nonmodel and multifaceted crop response well-disposed to the study of gene expression. Sequence reads were assembled de novo to create 10 independent transcriptomes, a global transcriptome, and were mapped against the Salix purpurea 94006 reference genome. Annotation of assembled contigs was performed without a priori assumption of the originating organism. Global transcriptome construction from 3.03 billion paired-end reads revealed 606,880 unique contigs annotated from 1588 species, often common in all 10 cultivars. Comparisons between transcriptomic and metatranscriptomic methodologies provide clear evidence that nonnative RNA can mistakenly map to reference genomes, especially to conserved regions of common housekeeping genes, such as actin, α/β-tubulin, and elongation factor 1-α. In Salix, Rubisco activase transcripts were down-regulated in contaminated trees across all 10 cultivars, whereas thiamine thizole synthase and CP12, a Calvin Cycle master regulator, were uniformly up-regulated. De novo assembly approaches, with unconstrained annotation, can improve data quality; care should be taken when exploring such plant genetics to reduce de facto data exclusion by mapping to a single reference genome alone. Salix gene expression patterns strongly suggest cultivar-wide alteration of specific photosynthetic apparatus and protection of the antenna complexes from oxidation damage in contaminated trees, providing an insight into common stress tolerance strategies in a real-world phytoremediation system. PMID:27002060

Evaluation of prognostic and predictive value of microtubule associated protein tau in two independent cohorts

PubMed Central

2011-01-01

Introduction Microtubule associated proteins (MAPs) endogenously regulate microtubule stabilization and have been reported as prognostic and predictive markers for taxane response. The microtubule stabilizer, MAP-tau, has shown conflicting results. We quantitatively assessed MAP-tau expression in two independent breast cancer cohorts to determine prognostic and predictive value of this biomarker. Methods MAP-tau expression was evaluated in the retrospective Yale University breast cancer cohort (n = 651) using tissue microarrays and also in the TAX 307 cohort, a clinical trial randomized for TAC versus FAC chemotherapy (n = 140), using conventional whole tissue sections. Expression was measured using the AQUA method for quantitative immunofluorescence. Scores were correlated with clinicopathologic variables, survival, and response to therapy. Results Assessment of the Yale cohort using Cox univariate analysis indicated an improved overall survival (OS) in tumors with a positive correlation between high MAP-tau expression and overall survival (OS) (HR = 0.691, 95% CI = 0.489-0.974; P = 0.004). Kaplan Meier analysis showed 10-year survival for 65% of patients with high MAP-tau expression compared to 52% with low expression (P = .006). In TAX 307, high expression was associated with significantly longer median time to tumor progression (TTP) regardless of treatment arm (33.0 versus 23.4 months, P = 0.010) with mean TTP of 31.2 months. Response rates did not differ by MAP-tau expression (P = 0.518) or by treatment arm (P = 0.584). Conclusions Quantitative measurement of MAP-tau expression has prognostic value in both cohorts, with high expression associated with longer TTP and OS. Differences by treatment arm or response rate in low versus high MAP-tau groups were not observed, indicating that MAP-tau is not associated with response to taxanes and is not a useful predictive marker for taxane-based chemotherapy. PMID:21888627

Exploring teacher's perceptions of concept mapping as a teaching strategy in science: An action research approach

NASA Astrophysics Data System (ADS)

Marks Krpan, Catherine Anne

In order to promote science literacy in the classroom, students need opportunities in which they can personalize their understanding of the concepts they are learning. Current literature supports the use of concept maps in enabling students to make personal connections in their learning of science. Because they involve creating explicit connections between concepts, concept maps can assist students in developing metacognitive strategies and assist educators in identifying misconceptions in students' thinking. The literature also notes that concept maps can improve student achievement and recall. Much of the current literature focuses primarily on concept mapping at the secondary and university levels, with limited focus on the elementary panel. The research rarely considers teachers' thoughts and ideas about the concept mapping process. In order to effectively explore concept mapping from the perspective of elementary teachers, I felt that an action research approach would be appropriate. Action research enabled educators to debate issues about concept mapping and test out ideas in their classrooms. It also afforded the participants opportunities to explore their own thinking, reflect on their personal journeys as educators and play an active role in their professional development. In an effort to explore concept mapping from the perspective of elementary educators, an action research group of 5 educators and myself was established and met regularly from September 1999 until June 2000. All of the educators taught in the Toronto area. These teachers were interested in exploring how concept mapping could be used as a learning tool in their science classrooms. In summary, this study explores the journey of five educators and myself as we engaged in collaborative action research. This study sets out to: (1) Explore how educators believe concept mapping can facilitate teaching and student learning in the science classroom. (2) Explore how educators implement concept mapping in their classrooms. (3) Identify challenges educators experience when they implement concept mapping. (4) Explore factors that impact on facilitating collaborative action research. (5) Provide insight into my growth as an action research facilitator.

The Histamine H1 Receptor Participates in the Increased Dorsal Telencephalic Neurogenesis in Embryos from Diabetic Rats.

PubMed

Solís, Karina H; Méndez, Laura I; García-López, Guadalupe; Díaz, Néstor F; Portillo, Wendy; De Nova-Ocampo, Mónica; Molina-Hernández, Anayansi

2017-01-01

Increased neuron telencephalic differentiation during deep cortical layer formation has been reported in embryos from diabetic mice. Transitory histaminergic neurons within the mesencephalon/rhombencephalon are responsible for fetal histamine synthesis during development, fibers from this system arrives to the frontal and parietal cortex at embryo day (E) 15. Histamine is a neurogenic factor for cortical neural stem cells in vitro through H 1 receptor (H 1 R) which is highly expressed during corticogenesis in rats and mice. Furthermore, in utero administration of an H 1 R antagonist, chlorpheniramine, decreases the neuron markers microtubuline associated protein 2 (MAP2) and forkhead box protein 2. Interestingly, in the diabetic mouse model of diabetes induced with streptozotocin, an increase in fetal neurogenesis in terms of MAP2 expression in the telencephalon is reported at E11.5. Because of the reported effects on cortical neuron differentiation of maternal diabetes in one hand and of histamine in the other, here the participation of histamine and H 1 R on the increased dorsal telencephalic neurogenesis was explored. First, the increased neurogenesis in the dorsal telencephalon at E14 in diabetic rats was corroborated by immunohistochemistry and Western blot. Then, changes during corticogenesis in the level of histamine was analyzed by ELISA and in H 1 R expression by qRT-PCR and Western blot and, finally, we tested H 1 R participation in the increased dorsal telencephalic neurogenesis by the systemic administration of chlorpheniramine. Our results showed a significant increase of histamine at E14 and in the expression of the receptor at E12. The administration of chlorpheniramine to diabetic rats at E12 prevented the increased expression of βIII-tubulin and MAP2 mRNAs (neuron markers) and partially reverted the increased level of MAP2 protein at E14, concluding that H 1 R have an important role in the increased neurogenesis within the dorsal telencephalon of embryos from diabetic rats. This study opens new perspective on the participation of HA and H 1 R receptor in early corticogenesis in health and disease.

The Histamine H1 Receptor Participates in the Increased Dorsal Telencephalic Neurogenesis in Embryos from Diabetic Rats

PubMed Central

Solís, Karina H.; Méndez, Laura I.; García-López, Guadalupe; Díaz, Néstor F.; Portillo, Wendy; De Nova-Ocampo, Mónica; Molina-Hernández, Anayansi

2017-01-01

Increased neuron telencephalic differentiation during deep cortical layer formation has been reported in embryos from diabetic mice. Transitory histaminergic neurons within the mesencephalon/rhombencephalon are responsible for fetal histamine synthesis during development, fibers from this system arrives to the frontal and parietal cortex at embryo day (E) 15. Histamine is a neurogenic factor for cortical neural stem cells in vitro through H1 receptor (H1R) which is highly expressed during corticogenesis in rats and mice. Furthermore, in utero administration of an H1R antagonist, chlorpheniramine, decreases the neuron markers microtubuline associated protein 2 (MAP2) and forkhead box protein 2. Interestingly, in the diabetic mouse model of diabetes induced with streptozotocin, an increase in fetal neurogenesis in terms of MAP2 expression in the telencephalon is reported at E11.5. Because of the reported effects on cortical neuron differentiation of maternal diabetes in one hand and of histamine in the other, here the participation of histamine and H1R on the increased dorsal telencephalic neurogenesis was explored. First, the increased neurogenesis in the dorsal telencephalon at E14 in diabetic rats was corroborated by immunohistochemistry and Western blot. Then, changes during corticogenesis in the level of histamine was analyzed by ELISA and in H1R expression by qRT-PCR and Western blot and, finally, we tested H1R participation in the increased dorsal telencephalic neurogenesis by the systemic administration of chlorpheniramine. Our results showed a significant increase of histamine at E14 and in the expression of the receptor at E12. The administration of chlorpheniramine to diabetic rats at E12 prevented the increased expression of βIII-tubulin and MAP2 mRNAs (neuron markers) and partially reverted the increased level of MAP2 protein at E14, concluding that H1R have an important role in the increased neurogenesis within the dorsal telencephalon of embryos from diabetic rats. This study opens new perspective on the participation of HA and H1R receptor in early corticogenesis in health and disease. PMID:29311766

Systematic drug safety evaluation based on public genomic expression (Connectivity Map) data: Myocardial and infectious adverse reactions as application cases

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

Wang, Kejian, E-mail: kejian.wang.bio@gmail.com; Weng, Zuquan; Sun, Liya

Adverse drug reaction (ADR) is of great importance to both regulatory agencies and the pharmaceutical industry. Various techniques, such as quantitative structure–activity relationship (QSAR) and animal toxicology, are widely used to identify potential risks during the preclinical stage of drug development. Despite these efforts, drugs with safety liabilities can still pass through safety checkpoints and enter the market. This situation raises the concern that conventional chemical structure analysis and phenotypic screening are not sufficient to avoid all clinical adverse events. Genomic expression data following in vitro drug treatments characterize drug actions and thus have become widely used in drug repositioning. Inmore » the present study, we explored prediction of ADRs based on the drug-induced gene-expression profiles from cultured human cells in the Connectivity Map (CMap) database. The results showed that drugs inducing comparable ADRs generally lead to similar CMap expression profiles. Based on such ADR-gene expression association, we established prediction models for various ADRs, including severe myocardial and infectious events. Drugs with FDA boxed warnings of safety liability were effectively identified. We therefore suggest that drug-induced gene expression change, in combination with effective computational methods, may provide a new dimension of information to facilitate systematic drug safety evaluation. - Highlights: • Drugs causing common toxicity lead to similar in vitro gene expression changes. • We built a model to predict drug toxicity with drug-specific expression profiles. • Drugs with FDA black box warnings were effectively identified by our model. • In vitro assay can detect severe toxicity in the early stage of drug development.« less

Design and Implementation WebGIS for Improving the Quality of Exploration Decisions at Sin-Quyen Copper Mine, Northern Vietnam

NASA Astrophysics Data System (ADS)

Quang Truong, Xuan; Luan Truong, Xuan; Nguyen, Tuan Anh; Nguyen, Dinh Tuan; Cong Nguyen, Chi

2017-12-01

The objective of this study is to design and implement a WebGIS Decision Support System (WDSS) for reducing uncertainty and supporting to improve the quality of exploration decisions in the Sin-Quyen copper mine, northern Vietnam. The main distinctive feature of the Sin-Quyen deposit is an unusual composition of ores. Computer and software applied to the exploration problem have had a significant impact on the exploration process over the past 25 years, but up until now, no online system has been undertaken. The system was completely built on open source technology and the Open Geospatial Consortium Web Services (OWS). The input data includes remote sensing (RS), Geographical Information System (GIS) and data from drillhole explorations, the drillhole exploration data sets were designed as a geodatabase and stored in PostgreSQL. The WDSS must be able to processed exploration data and support users to access 2-dimensional (2D) or 3-dimensional (3D) cross-sections and map of boreholles exploration data and drill holes. The interface was designed in order to interact with based maps (e.g., Digital Elevation Model, Google Map, OpenStreetMap) and thematic maps (e.g., land use and land cover, administrative map, drillholes exploration map), and to provide GIS functions (such as creating a new map, updating an existing map, querying and statistical charts). In addition, the system provides geological cross-sections of ore bodies based on Inverse Distance Weighting (IDW), nearest neighbour interpolation and Kriging methods (e.g., Simple Kriging, Ordinary Kriging, Indicator Kriging and CoKriging). The results based on data available indicate that the best estimation method (of 23 borehole exploration data sets) for estimating geological cross-sections of ore bodies in Sin-Quyen copper mine is Ordinary Kriging. The WDSS could provide useful information to improve drilling efficiency in mineral exploration and for management decision making.

Application of satellite photographic and MSS data to selected geologic and natural resource problems in Pennsylvania. 1: Lineaments and mineral occurrences in Pennsylvania. 2: Relation of lineaments to sulfide deposits: Bald Eagle Mountain, Centre County, Pennsylvania. 3: Comparison of Skylab and LANDSAT lineaments with joint orientations in north central Pennsylvania

NASA Technical Reports Server (NTRS)

Kowalik, W. S.; Gold, D. P.; Krohn, M. D.

1975-01-01

Those metallic mineral occurrences in Pennsylvania are reported which lie near lineaments mapped from LANDSAT-1 satellite imagery and verified from Skylab photography where available. The lineaments were categorized by degree of expression and type of expression; the mineral occurrences were classified by host rock age, mineralization type, and value. The accompanying tables and figure document the mineral occurrences geographically associated with lineaments and serve as a base for a mineral exploration model.

Web-based metabolic network visualization with a zooming user interface

PubMed Central

2011-01-01

Background Displaying complex metabolic-map diagrams, for Web browsers, and allowing users to interact with them for querying and overlaying expression data over them is challenging. Description We present a Web-based metabolic-map diagram, which can be interactively explored by the user, called the Cellular Overview. The main characteristic of this application is the zooming user interface enabling the user to focus on appropriate granularities of the network at will. Various searching commands are available to visually highlight sets of reactions, pathways, enzymes, metabolites, and so on. Expression data from single or multiple experiments can be overlaid on the diagram, which we call the Omics Viewer capability. The application provides Web services to highlight the diagram and to invoke the Omics Viewer. This application is entirely written in JavaScript for the client browsers and connect to a Pathway Tools Web server to retrieve data and diagrams. It uses the OpenLayers library to display tiled diagrams. Conclusions This new online tool is capable of displaying large and complex metabolic-map diagrams in a very interactive manner. This application is available as part of the Pathway Tools software that powers multiple metabolic databases including Biocyc.org: The Cellular Overview is accessible under the Tools menu. PMID:21595965

Gene networks associated with conditional fear in mice identified using a systems genetics approach

PubMed Central

2011-01-01

Background Our understanding of the genetic basis of learning and memory remains shrouded in mystery. To explore the genetic networks governing the biology of conditional fear, we used a systems genetics approach to analyze a hybrid mouse diversity panel (HMDP) with high mapping resolution. Results A total of 27 behavioral quantitative trait loci were mapped with a false discovery rate of 5%. By integrating fear phenotypes, transcript profiling data from hippocampus and striatum and also genotype information, two gene co-expression networks correlated with context-dependent immobility were identified. We prioritized the key markers and genes in these pathways using intramodular connectivity measures and structural equation modeling. Highly connected genes in the context fear modules included Psmd6, Ube2a and Usp33, suggesting an important role for ubiquitination in learning and memory. In addition, we surveyed the architecture of brain transcript regulation and demonstrated preservation of gene co-expression modules in hippocampus and striatum, while also highlighting important differences. Rps15a, Kif3a, Stard7, 6330503K22RIK, and Plvap were among the individual genes whose transcript abundance were strongly associated with fear phenotypes. Conclusion Application of our multi-faceted mapping strategy permits an increasingly detailed characterization of the genetic networks underlying behavior. PMID:21410935

MAP3K8 (TPL2/COT) affects obesity-induced adipose tissue inflammation without systemic effects in humans and in mice.

PubMed

Ballak, Dov B; van Essen, Peter; van Diepen, Janna A; Jansen, Henry; Hijmans, Anneke; Matsuguchi, Tetsuya; Sparrer, Helmut; Tack, Cees J; Netea, Mihai G; Joosten, Leo A B; Stienstra, Rinke

2014-01-01

Chronic low-grade inflammation in adipose tissue often accompanies obesity, leading to insulin resistance and increasing the risk for metabolic diseases. MAP3K8 (TPL2/COT) is an important signal transductor and activator of pro-inflammatory pathways that has been linked to obesity-induced adipose tissue inflammation. We used human adipose tissue biopsies to study the relationship of MAP3K8 expression with markers of obesity and expression of pro-inflammatory cytokines (IL-1β, IL-6 and IL-8). Moreover, we evaluated obesity-induced adipose tissue inflammation and insulin resistance in mice lacking MAP3K8 and WT mice on a high-fat diet (HFD) for 16 weeks. Individuals with a BMI >30 displayed a higher mRNA expression of MAP3K8 in adipose tissue compared to individuals with a normal BMI. Additionally, high mRNA expression levels of IL-1β, IL-6 and IL-8, but not TNF -α, in human adipose tissue were associated with higher expression of MAP3K8. Moreover, high plasma SAA and CRP did not associate with increased MAP3K8 expression in adipose tissue. Similarly, no association was found for MAP3K8 expression with plasma insulin or glucose levels. Mice lacking MAP3K8 had similar bodyweight gain as WT mice, yet displayed lower mRNA expression levels of IL-1β, IL-6 and CXCL1 in adipose tissue in response to the HFD as compared to WT animals. However, MAP3K8 deficient mice were not protected against HFD-induced adipose tissue macrophage infiltration or the development of insulin resistance. Together, the data in both human and mouse show that MAP3K8 is involved in local adipose tissue inflammation, specifically for IL-1β and its responsive cytokines IL-6 and IL-8, but does not seem to have systemic effects on insulin resistance.

Codon optimisation to improve expression of a Mycobacterium avium ssp. paratuberculosis-specific membrane-associated antigen by Lactobacillus salivarius.

PubMed

Johnston, Christopher; Douarre, Pierre E; Soulimane, Tewfik; Pletzer, Daniel; Weingart, Helge; MacSharry, John; Coffey, Aidan; Sleator, Roy D; O'Mahony, Jim

2013-06-01

Subunit and DNA-based vaccines against Mycobacterium avium ssp. paratuberculosis (MAP) attempt to overcome inherent issues associated with whole-cell formulations. However, these vaccines can be hampered by poor expression of recombinant antigens from a number of disparate hosts. The high G+C content of MAP invariably leads to a codon bias throughout gene expression. To investigate if the codon bias affects recombinant MAP antigen expression, the open reading frame of a MAP-specific antigen MptD (MAP3733c) was codon optimised for expression against a Lactobacillus salivarius host. Of the total 209 codons which constitute MAP3733c, 172 were modified resulting in a reduced G+C content from 61% for the native gene to 32.7% for the modified form. Both genes were placed under the transcriptional control of the PnisA promoter; allowing controlled heterologous expression in L. salivarius. Expression was monitored using fluorescence microscopy and microplate fluorometry via GFP tags translationally fused to the C-termini of the two MptD genes. A > 37-fold increase in expression was observed for the codon-optimised MAP3733synth variant over the native gene. Due to the low cost and improved expression achieved, codon optimisation significantly improves the potential of L. salivarius as an oral vaccine stratagem against Johne's disease. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

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.

The High Resolution Stereo Camera (HRSC): 10 Years of Imaging Mars

NASA Astrophysics Data System (ADS)

Jaumann, R.; Neukum, G.; Tirsch, D.; Hoffmann, H.

2014-04-01

The HRSC Experiment: Imagery is the major source for our current understanding of the geologic evolution of Mars in qualitative and quantitative terms.Imaging is required to enhance our knowledge of Mars with respect to geological processes occurring on local, regional and global scales and is an essential prerequisite for detailed surface exploration. The High Resolution Stereo Camera (HRSC) of ESA's Mars Express Mission (MEx) is designed to simultaneously map the morphology, topography, structure and geologic context of the surface of Mars as well as atmospheric phenomena [1]. The HRSC directly addresses two of the main scientific goals of the Mars Express mission: (1) High-resolution three-dimensional photogeologic surface exploration and (2) the investigation of surface-atmosphere interactions over time; and significantly supports: (3) the study of atmospheric phenomena by multi-angle coverage and limb sounding as well as (4) multispectral mapping by providing high-resolution threedimensional color context information. In addition, the stereoscopic imagery will especially characterize landing sites and their geologic context [1]. The HRSC surface resolution and the digital terrain models bridge the gap in scales between highest ground resolution images (e.g., HiRISE) and global coverage observations (e.g., Viking). This is also the case with respect to DTMs (e.g., MOLA and local high-resolution DTMs). HRSC is also used as cartographic basis to correlate between panchromatic and multispectral stereo data. The unique multi-angle imaging technique of the HRSC supports its stereo capability by providing not only a stereo triplet but also a stereo quintuplet, making the photogrammetric processing very robust [1, 3]. The capabilities for three dimensional orbital reconnaissance of the Martian surface are ideally met by HRSC making this camera unique in the international Mars exploration effort.

Open Touch/Sound Maps: A system to convey street data through haptic and auditory feedback

NASA Astrophysics Data System (ADS)

Kaklanis, Nikolaos; Votis, Konstantinos; Tzovaras, Dimitrios

2013-08-01

The use of spatial (geographic) information is becoming ever more central and pervasive in today's internet society but the most of it is currently inaccessible to visually impaired users. However, access in visual maps is severely restricted to visually impaired and people with blindness, due to their inability to interpret graphical information. Thus, alternative ways of a map's presentation have to be explored, in order to enforce the accessibility of maps. Multiple types of sensory perception like touch and hearing may work as a substitute of vision for the exploration of maps. The use of multimodal virtual environments seems to be a promising alternative for people with visual impairments. The present paper introduces a tool for automatic multimodal map generation having haptic and audio feedback using OpenStreetMap data. For a desired map area, an elevation map is being automatically generated and can be explored by touch, using a haptic device. A sonification and a text-to-speech (TTS) mechanism provide also audio navigation information during the haptic exploration of the map.

Vision-based mapping with cooperative robots

NASA Astrophysics Data System (ADS)

Little, James J.; Jennings, Cullen; Murray, Don

1998-10-01

Two stereo-vision-based mobile robots navigate and autonomously explore their environment safely while building occupancy grid maps of the environment. The robots maintain position estimates within a global coordinate frame using landmark recognition. This allows them to build a common map by sharing position information and stereo data. Stereo vision processing and map updates are done at 3 Hz and the robots move at speeds of 200 cm/s. Cooperative mapping is achieved through autonomous exploration of unstructured and dynamic environments. The map is constructed conservatively, so as to be useful for collision-free path planning. Each robot maintains a separate copy of a shared map, and then posts updates to the common map when it returns to observe a landmark at home base. Issues include synchronization, mutual localization, navigation, exploration, registration of maps, merging repeated views (fusion), centralized vs decentralized maps.

Expression of the mucus adhesion genes Mub and MapA, adhesion-like factor EF-Tu and bacteriocin gene plaA of Lactobacillus plantarum 423, monitored with real-time PCR.

PubMed

Ramiah, K; van Reenen, C A; Dicks, L M T

2007-05-30

Expression of the mucus adhesion genes Mub and MapA, adhesion-like factor EF-Tu and bacteriocin gene plaA by Lactobacillus plantarum 423, grown in the presence of bile, pancreatin and at low pH, was studied by real-time PCR. Mub, MapA and EF-Tu were up-regulated in the presence of mucus, proportional to increasing concentrations. Expression of MapA was up-regulated in the presence of 3.0 g/l bile and 3.0 g/l pancreatin at pH 6.5. Similar results were recorded in the presence of 10.0 g/l bile and 10.0 g/l pancreatin at pH 6.5. Expression of Mub was down-regulated in the presence of bile and pancreatin, whilst the expression of EF-Tu and plaA remained unchanged. Expression of Mub and MapA remained unchanged at pH 4.0, whilst expression of EF-Tu and plaA were up-regulated. Expression of MapA was down-regulated in the presence of 1.0 g/l l-cysteine HCl, suggesting that the gene is regulated by transcription attenuation that involves cysteine.

Exploring Pacific Seamounts through Telepresence Mapping on the NOAA Ship Okeanos Explorer

NASA Astrophysics Data System (ADS)

Lobecker, E.; Malik, M.; Sowers, D.; Kennedy, B. R.

2016-12-01

Telepresence utilizes modern computer networks and a high bandwidth satellite connection to enable remote users to participate virtually in ocean research and exploration cruises. NOAA's Office of Ocean Exploration and Research (OER) has been leveraging telepresence capabilities since the early 2000s. Through telepresence, remote users have provided support for operations planning and execution, troubleshooting hardware and software, and data interpretation during exploratory ocean mapping and remotely operated vehicle missions conducted by OER. The potential for this technology's application to immersive data acquisition and processing during mapping missions, however, has not yet been fully realized. We report the results of the application of telepresence to an 18-day 24 hour / day seafloor mapping expedition with the NOAA Ship Okeanos Explorer. The mapping team was split between shipboard and shore-based mission team members based at the Exploration Command Center at the University of New Hampshire. This cruise represented the third dedicated mapping cruise in a multi-year NOAA Campaign to Address the Pacific monument Science, Technology, and Ocean Needs (CAPSTONE). Cruise objectives included mapping several previously unmapped seamounts in the Wake Atoll Unit of the recently expanded Pacific Remote Islands Marine National Monument, and mapping of prominent seamount, ridge, and fracture zone features during transits. We discuss (1) expanded shore-based data processing of multiple sonar data streams leading to enhanced, rapid, initial site characterization, (2) remote access control of shipboard sonar data acquisition and processing computers, and (3) potential for broadening multidisciplinary applications of ocean mapping cruises including outreach, education, and communications efforts focused on expanding societal cognition and benefits of ocean exploration.

Presence of intestinal Mycobacterium avium subspecies paratuberculosis (MAP) DNA is not associated with altered MMP expression in ulcerative colitis

PubMed Central

2011-01-01

Background Mycobacterium avium subspecies paratuberculosis (MAP) is suspected to be a causative agent in human Crohn's disease (CD). Recent evidence suggests that pathogenic mycobacteria and MAP can induce the expression of Matrix Metalloproteinases (MMP), which are the main proteases in the pathogenesis of mucosal ulcerations in inflammatory bowel disease (IBD). Within this study we assessed the prevalence of intestinal MAP specific DNA in patients with Crohn's disease, ulcerative colitis (UC), and healthy controls. We further analysed regulation patterns of MMPs in mucosal tissues of UC patients with and without intestinal MAP DNA detection. Methods Colonic biopsy samples were obtained from 63 Norwegian and German IBD patients and 21 healthy controls. RNA was quantified by quantitative real-time polymerase chain reaction (PCR) to study MMP gene expression in both pathological and healthy mucosal specimens. The presence of MAP DNA in colonic mucosa was examined using MAP specific PCR. Results MAP DNA was detected in 20% of UC patients and 33% of healthy controls but only in 7% of patients with CD. UC patients treated with corticosteroids exhibited a significantly increased frequency of intestinal MAP DNA compared to those not receiving corticosteroids. Expression of MMP-1, -2, -7, -9, -13, -19, -28 and TNF-α did not differ between UC patients with presence of intestinal MAP DNA compared to those without. MMP-2, MMP-9 and MMP-13 were significantly decreased in UC patients receiving corticosteroids. Conclusions The presence of intestinal MAP specific DNA is not associated with altered MMP expression in UC in vivo. Corticosteroids are associated with increased detection of intestinal MAP DNA and decreased expression of certain MMPs. Frequent detection of MAP DNA in healthy controls might be attributable to the wide environmental distribution of MAP and its presence in the food-chain. PMID:21477272

CAVEman: Standardized anatomical context for biomedical data mapping.

PubMed

Turinsky, Andrei L; Fanea, Elena; Trinh, Quang; Wat, Stephen; Hallgrímsson, Benedikt; Dong, Xiaoli; Shu, Xueling; Stromer, Julie N; Hill, Jonathan W; Edwards, Carol; Grosenick, Brenda; Yajima, Masumi; Sensen, Christoph W

2008-01-01

The authors have created a software system called the CAVEman, for the visual integration and exploration of heterogeneous anatomical and biomedical data. The CAVEman can be applied for both education and research tasks. The main component of the system is a three-dimensional digital atlas of the adult male human anatomy, structured according to the nomenclature of Terminologia Anatomica. The underlying data-indexing mechanism uses standard ontologies to map a range of biomedical data types onto the atlas. The CAVEman system is now used to visualize genetic processes in the context of the human anatomy and to facilitate visual exploration of the data. Through the use of Javatrade mark software, the atlas-based system is portable to virtually any computer environment, including personal computers and workstations. Existing Java tools for biomedical data analysis have been incorporated into the system. The affordability of virtual-reality installations has increased dramatically over the last several years. This creates new opportunities for educational scenarios that model important processes in a patient's body, including gene expression patterns, metabolic activity, the effects of interventions such as drug treatments, and eventually surgical simulations.

Counter Tunnel Exploration, Mapping, and Localization with an Unmanned Ground Vehicle

DTIC Science & Technology

2014-05-01

support terrorist activity. Past robotic tunnel exploration efforts have had limited success in aiding law enforcement to explore and map the suspect...cross-border tunnels. These efforts have made use of adapted explosive ordnance disposal (EOD) or pipe inspection robotic systems that are not ideally... Robotics Enterprise (JGRE) to develop a prototype robotic system for counter-tunnel operations, focusing on exploration, mapping, and characterization of

PdSlt2 Penicillium digitatum mitogen-activated-protein kinase controls sporulation and virulence during citrus fruit infection.

PubMed

de Ramón-Carbonell, Marta; Sánchez-Torres, Paloma

2017-12-01

The Slt2 mitogen-activated protein (MAP) kinase homologue of Penicillium digitatum, the most relevant pathogen-producing citrus green mould decay during postharvest, was identified and explored. The P. digitatum Slt2-MAPK coding gene (PdSlt2) was functionally characterized by homologous gene elimination and transcriptomic evaluation. The absence of PdSlt2 gene resulted in significantly reduced virulence during citrus infection. The ΔPdSlt2 mutants were also defective in asexual reproduction, showing impairment of sporulation during citrus infection. Gene expression analysis revealed that PdSlt2 was highly induced during citrus fruit infection at early stages (1 dpi). Moreover, PdSlt2 deletion altered gene expression profiles. The relative gene expression (RGE) of fungicide resistance- and fungal virulence-related genes showed that PdSlt2 acts as negative regulator of several transporter encoding genes (ABC and MFS transporters) and a positive regulator of two sterol demethylases. This study indicates that PdSlt2 MAPK is functionally preserved in P. digitatum and highlights the relevant role of the PdSlt2 MAP kinase-mediated signalling pathway in regulating diverse genes crucial for infection and asexual reproduction. Copyright © 2017 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

REGULATION OF EPHRIN-A EXPRESSION IN COMPRESSED RETINOCOLLICULAR MAPS

PubMed Central

Tadesse, T.; Cheng, Q.; Xu, M.; Baro, D.J.; Young, L.J.; Pallas, S.L.

2012-01-01

Retinotopic maps can undergo compression and expansion in response to changes in target size, but the mechanism underlying this compensatory process has remained a mystery. The discovery of ephrins as molecular mediators of Sperry’s chemoaffinity process allows a mechanistic approach to this important issue. In Syrian hamsters, neonatal, partial (PT) ablation of posterior superior colliculus (SC) leads to compression of the retinotopic map, independent of neural activity. Graded, repulsive EphA receptor/ephrin-A ligand interactions direct the formation of the retinocollicular map, but whether ephrins might also be involved in map compression is unknown. To examine whether map compression might be directed by changes in the ephrin expression pattern, we compared ephrin-A2 and ephrin-A5 mRNA expression between normal SC and PT SC using in situ hybridization and quantitative real-time PCR. We found that ephrin-A ligand expression in the compressed maps was low anteriorly and high posteriorly, as in normal animals. Consistent with our hypothesis, the steepness of the ephrin gradient increased in the lesioned colliculi. Interestingly, overall levels of ephrin-A2 and -A5 expression declined immediately after neonatal target damage, perhaps promoting axon outgrowth. These data establish a correlation between changes in ephrin-A gradients and map compression, and suggest that ephrin-A expression gradients may be regulated by target size. This in turn could lead to compression of the retinocollicular map onto the reduced target. These findings have important implications for mechanisms of recovery from traumatic brain injury. PMID:23008269

Virtual environment navigation with look-around mode to explore new real spaces by people who are blind.

PubMed

Lahav, Orly; Gedalevitz, Hadas; Battersby, Steven; Brown, David; Evett, Lindsay; Merritt, Patrick

2018-05-01

This paper examines the ability of people who are blind to construct a mental map and perform orientation tasks in real space by using Nintendo Wii technologies to explore virtual environments. The participant explores new spaces through haptic and auditory feedback triggered by pointing or walking in the virtual environments and later constructs a mental map, which can be used to navigate in real space. The study included 10 participants who were congenitally or adventitiously blind, divided into experimental and control groups. The research was implemented by using virtual environments exploration and orientation tasks in real spaces, using both qualitative and quantitative methods in its methodology. The results show that the mode of exploration afforded to the experimental group is radically new in orientation and mobility training; as a result 60% of the experimental participants constructed mental maps that were based on map model, compared with only 30% of the control group participants. Using technology that enabled them to explore and to collect spatial information in a way that does not exist in real space influenced the ability of the experimental group to construct a mental map based on the map model. Implications for rehabilitation The virtual cane system for the first time enables people who are blind to explore and collect spatial information via the look-around mode in addition to the walk-around mode. People who are blind prefer to use look-around mode to explore new spaces, as opposed to the walking mode. Although the look-around mode requires users to establish a complex collecting and processing procedure for the spatial data, people who are blind using this mode are able to construct a mental map as a map model. For people who are blind (as for the sighted) construction of a mental map based on map model offers more flexibility in choosing a walking path in a real space, accounting for changes that occur in the space.

Thread mapping using system-level model for shared memory multicores

NASA Astrophysics Data System (ADS)

Mitra, Reshmi

Exploring thread-to-core mapping options for a parallel application on a multicore architecture is computationally very expensive. For the same algorithm, the mapping strategy (MS) with the best response time may change with data size and thread counts. The primary challenge is to design a fast, accurate and automatic framework for exploring these MSs for large data-intensive applications. This is to ensure that the users can explore the design space within reasonable machine hours, without thorough understanding on how the code interacts with the platform. Response time is related to the cycles per instructions retired (CPI), taking into account both active and sleep states of the pipeline. This work establishes a hybrid approach, based on Markov Chain Model (MCM) and Model Tree (MT) for system-level steady state CPI prediction. It is designed for shared memory multicore processors with coarse-grained multithreading. The thread status is represented by the MCM states. The program characteristics are modeled as the transition probabilities, representing the system moving between active and suspended thread states. The MT model extrapolates these probabilities for the actual application size (AS) from the smaller AS performance. This aspect of the framework, along with, the use of mathematical expressions for the actual AS performance information, results in a tremendous reduction in the CPI prediction time. The framework is validated using an electromagnetics application. The average performance prediction error for steady state CPI results with 12 different MSs is less than 1%. The total run time of model is of the order of minutes, whereas the actual application execution time is in terms of days.

Broad Integration of Expression Maps and Co-Expression Networks Compassing Novel Gene Functions in the Brain

PubMed Central

Okamura-Oho, Yuko; Shimokawa, Kazuro; Nishimura, Masaomi; Takemoto, Satoko; Sato, Akira; Furuichi, Teiichi; Yokota, Hideo

2014-01-01

Using a recently invented technique for gene expression mapping in the whole-anatomy context, termed transcriptome tomography, we have generated a dataset of 36,000 maps of overall gene expression in the adult-mouse brain. Here, using an informatics approach, we identified a broad co-expression network that follows an inverse power law and is rich in functional interaction and gene-ontology terms. Our framework for the integrated analysis of expression maps and graphs of co-expression networks revealed that groups of combinatorially expressed genes, which regulate cell differentiation during development, were present in the adult brain and each of these groups was associated with a discrete cell types. These groups included non-coding genes of unknown function. We found that these genes specifically linked developmentally conserved groups in the network. A previously unrecognized robust expression pattern covering the whole brain was related to the molecular anatomy of key biological processes occurring in particular areas. PMID:25382412

Oil Exploration Mapping

NASA Technical Reports Server (NTRS)

1994-01-01

After concluding an oil exploration agreement with the Republic of Yemen, Chevron International needed detailed geologic and topographic maps of the area. Chevron's remote sensing team used imagery from Landsat and SPOT, combining images into composite views. The project was successfully concluded and resulted in greatly improved base maps and unique topographic maps.

AT1 receptor-mediated uptake of angiotensin II and NHE-3 expression in proximal tubule cells through a microtubule-dependent endocytic pathway.

PubMed

Li, Xiao C; Hopfer, Ulrich; Zhuo, Jia L

2009-11-01

Angiotensin II (ANG II) is taken up by proximal tubule (PT) cells via AT1 (AT1a) receptor-mediated endocytosis, but the underlying cellular mechanisms remain poorly understood. The present study tested the hypothesis that the microtubule- rather than the clathrin-dependent endocytic pathway regulates AT1-mediated uptake of ANG II and ANG II-induced sodium and hydrogen exchanger-3 (NHE-3) expression in PT cells. The expression of AT1 receptors, clathrin light (LC) and heavy chain (HC) proteins, and type 1 microtubule-associated proteins (MAPs; MAP-1A and MAP-1B) in PT cells were knocked down by their respective small interfering (si) RNAs before AT1-mediated FITC-ANG II uptake and ANG II-induced NHE-3 expression were studied. AT1 siRNAs inhibited AT1 expression and blocked ANG II-induced NHE-3 expression in PT cells, as expected (P < 0.01). Clathrin LC or HC siRNAs knocked down their respective proteins by approximately 90% with a peak response at 24 h, and blocked the clathrin-dependent uptake of Alexa Fluor 594-transferrin (P < 0.01). However, neither LC nor HC siRNAs inhibited AT1-mediated uptake of FITC-ANG II or affected ANG II-induced NHE-3 expression. MAP-1A or MAP-1B siRNAs markedly knocked down MAP-1A or MAP-1B proteins in a time-dependent manner with peak inhibitions at 48 h (>76.8%, P < 0.01). MAP protein knockdown resulted in approximately 52% decreases in AT1-mediated FITC-ANG II uptake and approximately 66% decreases in ANG II-induced NHE-3 expression (P < 0.01). These effects were associated with threefold decreases in ANG II-induced MAP kinases ERK 1/2 activation (P < 0.01), but not with altered AT1 expression or clathrin-dependent transferrin uptake. Both losartan and AT1a receptor deletion in mouse PT cells completely abolished the effects of MAP-1A knockdown on ANG II-induced NHE-3 expression and activation of MAP kinases ERK1/2. Our findings suggest that the alternative microtubule-dependent endocytic pathway, rather than the canonical clathrin-dependent pathway, plays an important role in AT1 (AT1a)-mediated uptake of extracellular ANG II and ANG II-induced NHE-3 expression in PT cells.

ZikaBase: An integrated ZIKV- Human Interactome Map database.

PubMed

Gurumayum, Sanathoi; Brahma, Rahul; Naorem, Leimarembi Devi; Muthaiyan, Mathavan; Gopal, Jeyakodi; Venkatesan, Amouda

2018-01-15

Re-emergence of ZIKV has caused infections in more than 1.5 million people. The molecular mechanism and pathogenesis of ZIKV is not well explored due to unavailability of adequate model and lack of publically accessible resources to provide information of ZIKV-Human protein interactome map till today. This study made an attempt to curate the ZIKV-Human interaction proteins from published literatures and RNA-Seq data. 11 direct interaction, 12 associated genes are retrieved from literatures and 3742 Differentially Expressed Genes (DEGs) are obtained from RNA-Seq analysis. The genes have been analyzed to construct the ZIKV-Human Interactome Map. The importance of the study has been illustrated by the enrichment analysis and observed that direct interaction and associated genes are enriched in viral entry into host cell. Also, ZIKV infection modulates 32% signal and 27% immune system pathways. The integrated database, ZikaBase has been developed to help the virology research community and accessible at https://test5.bicpu.edu.in. Copyright © 2017 Elsevier Inc. All rights reserved.

The differential expression of alternatively polyadenylated transcripts is a common stress-induced response mechanism that modulates mammalian mRNA expression in a quantitative and qualitative fashion.

PubMed

Hollerer, Ina; Curk, Tomaz; Haase, Bettina; Benes, Vladimir; Hauer, Christian; Neu-Yilik, Gabriele; Bhuvanagiri, Madhuri; Hentze, Matthias W; Kulozik, Andreas E

2016-09-01

Stress adaptation plays a pivotal role in biological processes and requires tight regulation of gene expression. In this study, we explored the effect of cellular stress on mRNA polyadenylation and investigated the implications of regulated polyadenylation site usage on mammalian gene expression. High-confidence polyadenylation site mapping combined with global pre-mRNA and mRNA expression profiling revealed that stress induces an accumulation of genes with differentially expressed polyadenylated mRNA isoforms in human cells. Specifically, stress provokes a global trend in polyadenylation site usage toward decreased utilization of promoter-proximal poly(A) sites in introns or ORFs and increased utilization of promoter-distal polyadenylation sites in intergenic regions. This extensively affects gene expression beyond regulating mRNA abundance by changing mRNA length and by altering the configuration of open reading frames. Our study highlights the impact of post-transcriptional mechanisms on stress-dependent gene regulation and reveals the differential expression of alternatively polyadenylated transcripts as a common stress-induced mechanism in mammalian cells. © 2016 Hollerer et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Enhanced expression of codon optimized Mycobacterium avium subsp. paratuberculosis antigens in Lactobacillus salivarius.

PubMed

Johnston, Christopher D; Bannantine, John P; Govender, Rodney; Endersen, Lorraine; Pletzer, Daniel; Weingart, Helge; Coffey, Aidan; O'Mahony, Jim; Sleator, Roy D

2014-01-01

It is well documented that open reading frames containing high GC content show poor expression in A+T rich hosts. Specifically, G+C-rich codon usage is a limiting factor in heterologous expression of Mycobacterium avium subsp. paratuberculosis (MAP) proteins using Lactobacillus salivarius. However, re-engineering opening reading frames through synonymous substitutions can offset codon bias and greatly enhance MAP protein production in this host. In this report, we demonstrate that codon-usage manipulation of MAP2121c can enhance the heterologous expression of the major membrane protein (MMP), analogous to the form in which it is produced natively by MAP bacilli. When heterologously over-expressed, antigenic determinants were preserved in synthetic MMP proteins as shown by monoclonal antibody mediated ELISA. Moreover, MMP is a membrane protein in MAP, which is also targeted to the cellular surface of recombinant L. salivarius at levels comparable to MAP. Additionally, we previously engineered MAP3733c (encoding MptD) and show herein that MptD displays the tendency to associate with the cytoplasmic membrane boundary under confocal microscopy and the intracellularly accumulated protein selectively adheres to the MptD-specific bacteriophage fMptD. This work demonstrates there is potential for L. salivarius as a viable antigen delivery vehicle for MAP, which may provide an effective mucosal vaccine against Johne's disease.

Mycobacterium paratuberculosis, Mycobacterium smegmatis, and lipopolysaccharide induce different transcriptional and post-transcriptional regulation of the IRG1 gene in murine macrophages.

PubMed

Basler, Tina; Jeckstadt, Sabine; Valentin-Weigand, Peter; Goethe, Ralph

2006-03-01

Mycobacterium avium subspecies paratuberculosis (MAP) causes a chronic enteritis in ruminants. In addition, MAP is presently the most favored pathogen linked to Crohn's disease. In this study, we were interested in dissecting the molecular mechanisms of macrophage activation or deactivation after infection with MAP. By subtractive hybridization of cDNAs, we identified the immune-responsive gene 1 (IRG1), which was expressed substantially higher in lipopolysaccharide (LPS)-stimulated than in MAP-infected murine macrophage cell lines. A nuclear run-on transcription assay revealed that the IRG1 gene was activated transcriptionally in LPS-stimulated and MAP-infected macrophages with higher expression in LPS-stimulated cells. Analysis of post-transcriptional regulation demonstrated that IRG1 mRNA stability was increased in LPS-stimulated but not in MAP-infected macrophages. Furthermore, IRG1 gene expression of macrophages infected with the nonpathogenic Mycobacterium smegmatis differed from those of LPS-stimulated and MAP-infected macrophages. At 2 h postinfection, M. smegmatis-induced IRG1 gene expression was as low as in MAP-infected, and 8 h postinfection, it increased nearly to the level in LPS-stimulated macrophages. Transient transfection experiments revealed similar IRG1 promoter activities in MAP- and M. smegmatis-infected cells. Northern analysis demonstrated increased IRG1 mRNA stability in M. smegmatis-infected macrophages. IRG1 mRNA stabilization was p38 mitogen-activated protein kinase-independent. Inhibition of protein synthesis revealed that constitutively expressed factors seemed to be responsible for IRG1 mRNA destabilization. Thus, our data demonstrate that transcriptional and post-transcriptional mechanisms are responsible for a differential IRG1 gene expression in murine macrophages treated with LPS, MAP, and M. smegmatis.

Exploring the Middle Ages with the Medieval Map.

ERIC Educational Resources Information Center

Parry, Joseph D.

1998-01-01

Illustrates how medieval maps provide a means for studying the Middle Ages by allowing students to explore the ideology and representations of the medieval world conveyed by the maps. Explains that students also can compare the maps with literature from the same time period to further analyze the representations of the culture. (CMK)

Cross-regulatory interactions between Fgf8 and Shh in the avian frontonasal prominence.

PubMed

Abzhanov, Arhat; Cordero, Dwight R; Sen, Jonaki; Tabin, Clifford J; Helms, Jill A

2007-12-01

The frontonasal prominence of the developing avian embryo contains an organizing center, defined by juxtaposition of the Sonic hedgehog (Shh) and Fibroblast growth factor 8 (Fgf8) expression domains. This molecular interface presages any detectable growth of the frontonasal prominence, and experiments involving transplantation of this boundary epithelium have demonstrated it is a source of dorsal-ventral and rostral-caudal patterning information for the neural crest-derived mesenchyme of the upper beak. We explored the ontogeny of this organizing center by mapping the expression domains of both genes and their receptors and downstream targets. We tested the extent to which Shh and Fgf8 regulate each other's expression in this frontonasal organizer by either blocking or ectopically activating these pathways. Our experiments revealed mutual antagonism between the two molecules, which aids in establishing and maintaining a molecular boundary that subsequently influences patterning and growth of the middle and upper face.

Normal p21Ras/MAP kinase pathway expression and function in PBMC from patients with polycystic ovary disease.

PubMed

Buchs, A; Chagag, P; Weiss, M; Kish, E; Levinson, R; Aharoni, D; Rapoport, M J

2004-04-01

Polycystic ovary disease (PCOD) is associated with insulin resistance and increased prevalence of type II diabetes mellitus (T2DM). The p21Ras/MAP kinase is a major intracellular signaling pathway mediating insulin signaling in insulin responsive tissues. The expression, regulation and function of the p21Ras/MAP kinase pathway in PCOD patients were examined. Peripheral blood mononuclear cells (PBMC) were isolated from ten patients with PCOD and ten controls. The expression of p21Ras and its regulatory proteins; hSOS1 and p120GAP were studied. The basal and phytohemaglutinin (PHA) or insulin stimulated phosphorylation of MAP kinase was determined. Expression of p21Ras, and its regulatory proteins hSOS1 and p120GAP were similar in PCOD patients and controls. Basal, PHA and insulin stimulated phosphorylation of MAP kinase, were also comparable in the two groups as well as their PBMC proliferative response. These data indicate that the expression and overall function of the p21Ras/MAP kinase pathway remain intact in non-diabetic patients with PCOD.

Course transformation: Content, structure and effectiveness analysis

NASA Astrophysics Data System (ADS)

DuHadway, Linda P.

The organization of learning materials is often limited by the systems available for delivery of such material. Currently, the learning management system (LMS) is widely used to distribute course materials. These systems deliver the material in a text-based, linear way. As online education continues to expand and educators seek to increase their effectiveness by adding more effective active learning strategies, these delivery methods become a limitation. This work demonstrates the possibility of presenting course materials in a graphical way that expresses important relations and provides support for manipulating the order of those materials. The ENABLE system gathers data from an existing course, uses text analysis techniques, graph theory, graph transformation, and a user interface to create and present graphical course maps. These course maps are able to express information not currently available in the LMS. Student agents have been developed to traverse these course maps to identify the variety of possible paths through the material. The temporal relations imposed by the current course delivery methods have been replaced by prerequisite relations that express ordering that provides educational value. Reducing the connections to these more meaningful relations allows more possibilities for change. Technical methods are used to explore and calibrate linear and nonlinear models of learning. These methods are used to track mastery of learning material and identify relative difficulty values. Several probability models are developed and used to demonstrate that data from existing, temporally based courses can be used to make predictions about student success in courses using the same material but organized without the temporal limitations. Combined, these demonstrate the possibility of tools and techniques that can support the implementation of a graphical course map that allows varied paths and provides an enriched, more informative interface between the educator, the student, and the learning material. This fundamental change in how course materials are presented and interfaced with has the potential to make educational opportunities available to a broader spectrum of people with diverse abilities and circumstances. The graphical course map can be pivotal in attaining this transition.

Exploring Students' Mapping Behaviors and Interactive Discourses in a Case Diagnosis Problem: Sequential Analysis of Collaborative Causal Map Drawing Processes

ERIC Educational Resources Information Center

Lee, Woon Jee

2012-01-01

The purpose of this study was to explore the nature of students' mapping and discourse behaviors while constructing causal maps to articulate their understanding of a complex, ill-structured problem. In this study, six graduate-level students were assigned to one of three pair groups, and each pair used the causal mapping software program,…

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

Lazkoz, Ruth; Escamilla-Rivera, Celia; Salzano, Vincenzo

Cosmography provides a model-independent way to map the expansion history of the Universe. In this paper we simulate a Euclid-like survey and explore cosmographic constraints from future Baryonic Acoustic Oscillations (BAO) observations. We derive general expressions for the BAO transverse and radial modes and discuss the optimal order of the cosmographic expansion that provides reliable cosmological constraints. Through constraints on the deceleration and jerk parameters, we show that future BAO data have the potential to provide a model-independent check of the cosmic acceleration as well as a discrimination between the standard ΛCDM model and alternative mechanisms of cosmic acceleration.

LPS-induced chemokine expression in both MyD88-dependent and -independent manners is regulated by Cot/Tpl2-ERK axis in macrophages.

PubMed

Bandow, Kenjiro; Kusuyama, Joji; Shamoto, Mitsuo; Kakimoto, Kyoko; Ohnishi, Tomokazu; Matsuguchi, Tetsuya

2012-05-21

LPS signaling is mediated through MyD88-dependent and -independent pathways, activating NF-?B, MAP kinases and IRF3. Cot/Tpl2 is an essential upstream kinase in LPS-mediated activation of ERKs. Here we explore the roles of MyD88 and Cot/Tpl2 in LPS-induced chemokine expression by studying myd88(-/-) and cot/tpl2(-/-) macrophages. Among the nine LPS-responsive chemokines examined, mRNA induction of ccl5, cxcl10, and cxcl13 is mediated through the MyD88-independent pathway. Notably, Cot/Tpl2-ERK signaling axis exerts negative effects on the expression of these three chemokines. In contrast, LPS-induced gene expression of ccl2, ccl7, cxcl2, cxcl3, ccl8, and cxcl9 is mediated in the MyD88-dependent manner. The Cot/Tpl2-ERK axis promotes the expression of the first four and inhibits the expression of the latter two. Thus, LPS induces expression of multiple chemokines through various signaling pathways in macrophages. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

An eQTL Analysis of Partial Resistance to Puccinia hordei in Barley

PubMed Central

Chen, Xinwei; Hackett, Christine A.; Niks, Rients E.; Hedley, Peter E.; Booth, Clare; Druka, Arnis; Marcel, Thierry C.; Vels, Anton; Bayer, Micha; Milne, Iain; Morris, Jenny; Ramsay, Luke; Marshall, David; Cardle, Linda; Waugh, Robbie

2010-01-01

Background Genetic resistance to barley leaf rust caused by Puccinia hordei involves both R genes and quantitative trait loci. The R genes provide higher but less durable resistance than the quantitative trait loci. Consequently, exploring quantitative or partial resistance has become a favorable alternative for controlling disease. Four quantitative trait loci for partial resistance to leaf rust have been identified in the doubled haploid Steptoe (St)/Morex (Mx) mapping population. Further investigations are required to study the molecular mechanisms underpinning partial resistance and ultimately identify the causal genes. Methodology/Principal Findings We explored partial resistance to barley leaf rust using a genetical genomics approach. We recorded RNA transcript abundance corresponding to each probe on a 15K Agilent custom barley microarray in seedlings from St and Mx and 144 doubled haploid lines of the St/Mx population. A total of 1154 and 1037 genes were, respectively, identified as being P. hordei-responsive among the St and Mx and differentially expressed between P. hordei-infected St and Mx. Normalized ratios from 72 distant-pair hybridisations were used to map the genetic determinants of variation in transcript abundance by expression quantitative trait locus (eQTL) mapping generating 15685 eQTL from 9557 genes. Correlation analysis identified 128 genes that were correlated with resistance, of which 89 had eQTL co-locating with the phenotypic quantitative trait loci (pQTL). Transcript abundance in the parents and conservation of synteny with rice allowed us to prioritise six genes as candidates for Rphq11, the pQTL of largest effect, and highlight one, a phospholipid hydroperoxide glutathione peroxidase (HvPHGPx) for detailed analysis. Conclusions/Significance The eQTL approach yielded information that led to the identification of strong candidate genes underlying pQTL for resistance to leaf rust in barley and on the general pathogen response pathway. The dataset will facilitate a systems appraisal of this host-pathogen interaction and, potentially, for other traits measured in this population. PMID:20066049

[A basic research to share Fourier transform near-infrared spectrum information resource].

PubMed

Zhang, Lu-Da; Li, Jun-Hui; Zhao, Long-Lian; Zhao, Li-Li; Qin, Fang-Li; Yan, Yan-Lu

2004-08-01

A method to share the information resource in the database of Fourier transform near-infrared(FTNIR) spectrum information of agricultural products and utilize the spectrum information sufficiently is explored in this paper. Mapping spectrum information from one instrument to another is studied to express the spectrum information accurately between the instruments. Then mapping spectrum information is used to establish a mathematical model of quantitative analysis without including standard samples. The analysis result is that the relative coefficient r is 0.941 and the relative error is 3.28% between the model estimate values and the Kjeldahl's value for the protein content of twenty-two wheat samples, while the relative coefficient r is 0.963 and the relative error is 2.4% for the other model, which is established by using standard samples. It is shown that the spectrum information can be shared by using the mapping spectrum information. So it can be concluded that the spectrum information in one FTNIR spectrum information database can be transformed to another instrument's mapping spectrum information, which makes full use of the information resource in the database of FTNIR spectrum information to realize the resource sharing between different instruments.

Normal form decomposition for Gaussian-to-Gaussian superoperators

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

De Palma, Giacomo; INFN, Pisa; Mari, Andrea

2015-05-15

In this paper, we explore the set of linear maps sending the set of quantum Gaussian states into itself. These maps are in general not positive, a feature which can be exploited as a test to check whether a given quantum state belongs to the convex hull of Gaussian states (if one of the considered maps sends it into a non-positive operator, the above state is certified not to belong to the set). Generalizing a result known to be valid under the assumption of complete positivity, we provide a characterization of these Gaussian-to-Gaussian (not necessarily positive) superoperators in terms ofmore » their action on the characteristic function of the inputs. For the special case of one-mode mappings, we also show that any Gaussian-to-Gaussian superoperator can be expressed as a concatenation of a phase-space dilatation, followed by the action of a completely positive Gaussian channel, possibly composed with a transposition. While a similar decomposition is shown to fail in the multi-mode scenario, we prove that it still holds at least under the further hypothesis of homogeneous action on the covariance matrix.« less

eQTL Mapping Using RNA-seq Data

PubMed Central

Hu, Yijuan

2012-01-01

As RNA-seq is replacing gene expression microarrays to assess genome-wide transcription abundance, gene expression Quantitative Trait Locus (eQTL) studies using RNA-seq have emerged. RNA-seq delivers two novel features that are important for eQTL studies. First, it provides information on allele-specific expression (ASE), which is not available from gene expression microarrays. Second, it generates unprecedentedly rich data to study RNA-isoform expression. In this paper, we review current methods for eQTL mapping using ASE and discuss some future directions. We also review existing works that use RNA-seq data to study RNA-isoform expression and we discuss the gaps between these works and isoform-specific eQTL mapping. PMID:23667399

43 CFR 3482.3 - Mining operations maps.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 43 Public Lands: Interior 2 2011-10-01 2011-10-01 false Mining operations maps. 3482.3 Section... MANAGEMENT, DEPARTMENT OF THE INTERIOR MINERALS MANAGEMENT (3000) COAL EXPLORATION AND MINING OPERATIONS RULES Exploration and Resource Recovery and Protection Plans § 3482.3 Mining operations maps. (a...

Concept Maps Applied to Mars Exploration Public Outreach

NASA Technical Reports Server (NTRS)

Briggs, Geoffrey; Canas, Alberto; Shamma, David; Scargle, Jeffrey; Novak, Joseph

2004-01-01

This paper describes CMEX Mars, an effort in the creation of a comprehensive set of concept maps to describe all aspects of Mars exploration. These concept maps, created using the CmapTools software developed by the Institute for Human and Machine Cognition, are available on the Internet at http:/cmex.arc.nasa.gov/CMEX and are linked among themselves as well as to resources on the Internet. The work described took place mainly between 1998 and 2001 and combined the goals of: 1) developing a library of concept maps for educational outreach while also 2) refining the capabilities of the software used to create the interactive maps and 3) making them available on the Internet. Here we focus on the library of Mars exploration concept maps that has been created.

From samples to populations in retinex models

NASA Astrophysics Data System (ADS)

Gianini, Gabriele

2017-05-01

Some spatial color algorithms, such as Brownian Milano retinex (MI-retinex) and random spray retinex (RSR), are based on sampling. In Brownian MI-retinex, memoryless random walks (MRWs) explore the neighborhood of a pixel and are then used to compute its output. Considering the relative redundancy and inefficiency of MRW exploration, the algorithm RSR replaced the walks by samples of points (the sprays). Recent works point to the fact that a mapping from the sampling formulation to the probabilistic formulation of the corresponding sampling process can offer useful insights into the models, at the same time featuring intrinsically noise-free outputs. The paper continues the development of this concept and shows that the population-based versions of RSR and Brownian MI-retinex can be used to obtain analytical expressions for the outputs of some test images. The comparison of the two analytic expressions from RSR and from Brownian MI-retinex demonstrates not only that the two outputs are, in general, different but also that they depend in a qualitatively different way upon the features of the image.

Convergent evidence from systematic analysis of GWAS revealed genetic basis of esophageal cancer.

PubMed

Gao, Xue-Xin; Gao, Lei; Wang, Jiu-Qiang; Qu, Su-Su; Qu, Yue; Sun, Hong-Lei; Liu, Si-Dang; Shang, Ying-Li

2016-07-12

Recent genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with risk of esophageal cancer (EC). However, investigation of genetic basis from the perspective of systematic biology and integrative genomics remains scarce.In this study, we explored genetic basis of EC based on GWAS data and implemented a series of bioinformatics methods including functional annotation, expression quantitative trait loci (eQTL) analysis, pathway enrichment analysis and pathway grouped network analysis.Two hundred and thirteen risk SNPs were identified, in which 44 SNPs were found to have significantly differential gene expression in esophageal tissues by eQTL analysis. By pathway enrichment analysis, 170 risk genes mapped by risk SNPs were enriched into 38 significant GO terms and 17 significant KEGG pathways, which were significantly grouped into 9 sub-networks by pathway grouped network analysis. The 9 groups of interconnected pathways were mainly involved with muscle cell proliferation, cellular response to interleukin-6, cell adhesion molecules, and ethanol oxidation, which might participate in the development of EC.Our findings provide genetic evidence and new insight for exploring the molecular mechanisms of EC.

Reduced transcript stabilization restricts TNF-alpha expression in RAW264.7 macrophages infected with pathogenic mycobacteria: evidence for an involvement of lipomannan.

PubMed

Basler, Tina; Holtmann, Helmut; Abel, Jens; Eckstein, Torsten; Baumer, Wolfgang; Valentin-Weigand, Peter; Goethe, Ralph

2010-01-01

Despite the critical role that TNF-alpha plays in the containment of mycobacterial infection, the mechanisms involved in regulation of its expression by mycobacteria are poorly defined. We addressed this question by studying MAP, which causes a chronic enteritis in ruminants and is linked to human Crohn's disease. We found that in MAP infected macrophages, TNF-alpha gene expression was substantially lower than in macrophages infected with nonpathogenic MS or stimulated with LPS. TNF-alpha transcriptional one could not fully explain the differential TNF-alpha mRNA expression, suggesting that there must be a substantial contribution by post-transcriptional mechanisms.Accordingly, we found reduced TNF-alpha mRNA stability in MAP-infected macrophages. Further comparison of MAP- and MS-infected macrophages revealed that lower TNF-alpha mRNA stability combined with lower mRNA and protein expression in MAP-infected macrophages correlated with lower p38 MAPK phosphorylation. These findings were independent of viability of MAP and MS. We demonstrate that the major mycobacterial cell-wall lipoglycan LM of MAP and MS induced TNF-alpha mRNA transcription,but only the MS-LM induced p38 MAPK-dependent transcript stabilization. Overall, our data suggest that pathogenic mycobacteria cause weak p38 and TNF-alpha mRNA stabilization as a result of their structural cell-wall components such as LM and thereby, restrict TNF-alpha expression in macrophages.

Three-Dimensional Gene Map of Cancer Cell Types: Structural Entropy Minimisation Principle for Defining Tumour Subtypes

PubMed Central

Li, Angsheng; Yin, Xianchen; Pan, Yicheng

2016-01-01

In this study, we propose a method for constructing cell sample networks from gene expression profiles, and a structural entropy minimisation principle for detecting natural structure of networks and for identifying cancer cell subtypes. Our method establishes a three-dimensional gene map of cancer cell types and subtypes. The identified subtypes are defined by a unique gene expression pattern, and a three-dimensional gene map is established by defining the unique gene expression pattern for each identified subtype for cancers, including acute leukaemia, lymphoma, multi-tissue, lung cancer and healthy tissue. Our three-dimensional gene map demonstrates that a true tumour type may be divided into subtypes, each defined by a unique gene expression pattern. Clinical data analyses demonstrate that most cell samples of an identified subtype share similar survival times, survival indicators and International Prognostic Index (IPI) scores and indicate that distinct subtypes identified by our algorithms exhibit different overall survival times, survival ratios and IPI scores. Our three-dimensional gene map establishes a high-definition, one-to-one map between the biologically and medically meaningful tumour subtypes and the gene expression patterns, and identifies remarkable cells that form singleton submodules. PMID:26842724

ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets

PubMed Central

Brozovic, Matija; Dantec, Christelle; Dardaillon, Justine; Dauga, Delphine; Faure, Emmanuel; Gineste, Mathieu; Louis, Alexandra; Naville, Magali; Nitta, Kazuhiro R; Piette, Jacques; Reeves, Wendy; Scornavacca, Céline; Simion, Paul; Vincentelli, Renaud; Bellec, Maelle; Aicha, Sameh Ben; Fagotto, Marie; Guéroult-Bellone, Marion; Haeussler, Maximilian; Jacox, Edwin; Lowe, Elijah K; Mendez, Mickael; Roberge, Alexis; Stolfi, Alberto; Yokomori, Rui; Cambillau, Christian; Christiaen, Lionel; Delsuc, Frédéric; Douzery, Emmanuel; Dumollard, Rémi; Kusakabe, Takehiro; Nakai, Kenta; Nishida, Hiroki; Satou, Yutaka; Swalla, Billie; Veeman, Michael; Volff, Jean-Nicolas

2018-01-01

Abstract ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy databases, better support for epigenomics datasets, in particular RNA-seq, ChIP-seq and SELEX-seq, and features novel interactive interfaces for existing and novel datatypes. In particular, the cross-species navigation and comparison is enhanced through a novel taxonomy section describing each represented species and through the implementation of interactive phylogenetic gene trees for 60% of tunicate genes. The gene expression section displays the results of RNA-seq experiments for the three major model species of solitary ascidians. Gene expression is controlled by the binding of transcription factors to cis-regulatory sequences. A high-resolution description of the DNA-binding specificity for 131 Ciona robusta (formerly C. intestinalis type A) transcription factors by SELEX-seq is provided and used to map candidate binding sites across the Ciona robusta and Phallusia mammillata genomes. Finally, use of a WashU Epigenome browser enhances genome navigation, while a Genomicus server was set up to explore microsynteny relationships within tunicates and with vertebrates, Amphioxus, echinoderms and hemichordates. PMID:29149270

Regional frontier exploration in Sinu basin, northwestern Colombia

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

Lindberg, F.A.; Ellis, J.M.; Dekker, L.L.

1989-03-01

In 1983, Gulf and Ecopetrol undertook a regional hydrocarbon evaluation of northwestern Colombia, during the course of which much of the Sinu basin was mapped by field geologists aided by low-altitude aerial photographs. Additional seismic and airborne radar data were acquired to assist in developing a regional structural model. The dominant structures of the Sinu basin were produced by westward-vergent thrust faults, which are offset on the order of 10 to 20 km by northwest-southeast-trending compartmental faults. Numerous mud volcanos are surface expressions of overpressured shales, which migrate upward along both thrust and strike-slip faults. Thrust faults are expressed, onmore » the surface, by steep-sided, asymmetrical anticlines, which are separated by broad synclines filled with clastics shed during Tertiary thrusting. The extremely thick section of Tertiary sediments is dominated by shale but contains some potential reservoir sandstones. These resistive sandstones could be accurately mapped on the radar imagery and projected into the subsurface allowing traps to be better defined. Combining field geology with geologic interpretation of aerial photographs and radar images was very effective in developing a regional structural framework of the Sinu basin.« less

Bedrock Geologic Map of New Hampshire, a Digital Representation of Lyons and Others 1997 Map and Ancillary Files

USGS Publications Warehouse

Bennett, Derek S.; Lyons, John B.; Wittkop, Chad A.; Dicken, Connie L.

2006-01-01

The New Hampshire Geological Survey collects data and performs research on the land, mineral, and water resources of the State, and disseminates the findings of such research to the public through maps, reports, and other publications. The Bedrock Geologic Map of New Hampshire, by John B. Lyons, Wallace A. Bothner, Robert H. Moench, and James B. Thompson, was published in paper format by the U.S. Geological Survey (USGS) in 1997. The online version of this CD contains digital datasets of the State map that are intended to assist the professional geologist, land-use planners, water resource professionals, and engineers and to inform the interested layperson. In addition to the bedrock geology, the datasets include geopolitical and hydrologic information, such as political boundaries, quadrangle boundaries, hydrologic units, and water-well data. A more thorough explanation for each of these datasets may be found in the accompanying metadata files. The data are spatially referenced and may be used in a geographic information system (GIS). ArcExplorer, the Environmental Systems Research Institute's (ESRI) free GIS data viewer, is available at http://www.esri.com/software/arcexplorer. ArcExplorer provides basic functions that are needed to harness the power and versatility of the spatial datasets. Additional information on the viewer and other ESRI products may be found on the ArcExplorer website. Although extensive review and revisions of the data have been performed by the USGS and the New Hampshire Geological Survey, these data represent interpretations made by professional geologists using the best available data, and are intended to provide general geologic information. Use of these data at scales larger than 1:250,000 will not provide greater accuracy. The data are not intended to replace site-specific or specific-use investigations. The U.S. Geological Survey, New Hampshire Geological Survey, and State of New Hampshire make no representation or warranty, expressed or implied, regarding the use, accuracy, or completeness of the data presented herein, or from a map printed from these data; nor shall the act of distribution constitute any such warranty. The New Hampshire Geological Survey disclaims any legal responsibility or liability for interpretations made from the map, or decisions based thereon. For more information on New Hampshire Geological Survey programs please visit the State's website at http://des.nh.gov/Geology/. New Hampshire Geographically Referenced Analysis and Information Transfer System (NH GRANIT) provides access to statewide GIS (http://www.granit.unh.edu/). Questions about this CD or about other datasets should be directed to the New Hampshire Department of Environmental Services.

Function does not follow form in gene regulatory circuits.

PubMed

Payne, Joshua L; Wagner, Andreas

2015-08-20

Gene regulatory circuits are to the cell what arithmetic logic units are to the chip: fundamental components of information processing that map an input onto an output. Gene regulatory circuits come in many different forms, distinct structural configurations that determine who regulates whom. Studies that have focused on the gene expression patterns (functions) of circuits with a given structure (form) have examined just a few structures or gene expression patterns. Here, we use a computational model to exhaustively characterize the gene expression patterns of nearly 17 million three-gene circuits in order to systematically explore the relationship between circuit form and function. Three main conclusions emerge. First, function does not follow form. A circuit of any one structure can have between twelve and nearly thirty thousand distinct gene expression patterns. Second, and conversely, form does not follow function. Most gene expression patterns can be realized by more than one circuit structure. And third, multifunctionality severely constrains circuit form. The number of circuit structures able to drive multiple gene expression patterns decreases rapidly with the number of these patterns. These results indicate that it is generally not possible to infer circuit function from circuit form, or vice versa.

The Role of Geologic Mapping in NASA PDSI Planning

NASA Astrophysics Data System (ADS)

Williams, D. A.; Skinner, J. A.; Radebaugh, J.

2017-12-01

Geologic mapping is an investigative process designed to derive the geologic history of planetary objects at local, regional, hemispheric or global scales. Geologic maps are critical products that aid future exploration by robotic spacecraft or human missions, support resource exploration, and provide context for and help guide scientific discovery. Creation of these tools, however, can be challenging in that, relative to their terrestrial counterparts, non-terrestrial planetary geologic maps lack expansive field-based observations. They rely, instead, on integrating diverse data types wth a range of spatial scales and areal coverage. These facilitate establishment of geomorphic and geologic context but are generally limited with respect to identifying outcrop-scale textural details and resolving temporal and spatial changes in depositional environments. As a result, planetary maps should be prepared with clearly defined contact and unit descriptions as well as a range of potential interpretations. Today geologic maps can be made from images obtained during the traverses of the Mars rovers, and for every new planetary object visited by NASA orbital or flyby spacecraft (e.g., Vesta, Ceres, Titan, Enceladus, Pluto). As Solar System Exploration develops and as NASA prepares to send astronauts back to the Moon and on to Mars, the importance of geologic mapping will increase. In this presentation, we will discuss the past role of geologic mapping in NASA's planetary science activities and our thoughts on the role geologic mapping will have in exploration in the coming decades. Challenges that planetary mapping must address include, among others: 1) determine the geologic framework of all Solar System bodies through the systematic development of geologic maps at appropriate scales, 2) develop digital Geographic Information Systems (GIS)-based mapping techniques and standards to assist with communicating map information to the scientific community and public, 3) develop public awareness of the role and application of geologic map-information to the resolution of national issues relevant to planetary science and eventual off-planet resource assessments, 4) use topical science to drive mapping in areas likely to be determined vital to the welfare of endeavors related to planetary science and exploration.

Visibility graphs and symbolic dynamics

NASA Astrophysics Data System (ADS)

Lacasa, Lucas; Just, Wolfram

2018-07-01

Visibility algorithms are a family of geometric and ordering criteria by which a real-valued time series of N data is mapped into a graph of N nodes. This graph has been shown to often inherit in its topology nontrivial properties of the series structure, and can thus be seen as a combinatorial representation of a dynamical system. Here we explore in some detail the relation between visibility graphs and symbolic dynamics. To do that, we consider the degree sequence of horizontal visibility graphs generated by the one-parameter logistic map, for a range of values of the parameter for which the map shows chaotic behaviour. Numerically, we observe that in the chaotic region the block entropies of these sequences systematically converge to the Lyapunov exponent of the time series. Hence, Pesin's identity suggests that these block entropies are converging to the Kolmogorov-Sinai entropy of the physical measure, which ultimately suggests that the algorithm is implicitly and adaptively constructing phase space partitions which might have the generating property. To give analytical insight, we explore the relation k(x) , x ∈ [ 0 , 1 ] that, for a given datum with value x, assigns in graph space a node with degree k. In the case of the out-degree sequence, such relation is indeed a piece-wise constant function. By making use of explicit methods and tools from symbolic dynamics we are able to analytically show that the algorithm indeed performs an effective partition of the phase space and that such partition is naturally expressed as a countable union of subintervals, where the endpoints of each subinterval are related to the fixed point structure of the iterates of the map and the subinterval enumeration is associated with particular ordering structures that we called motifs.

National Assessment of Oil and Gas Project: Areas of Historical Oil and Gas Exploration and Production in the United States

USGS Publications Warehouse

Biewick, Laura

2008-01-01

This report contains maps and associated spatial data showing historical oil and gas exploration and production in the United States. Because of the proprietary nature of many oil and gas well databases, the United States was divided into cells one-quarter square mile and the production status of all wells in a given cell was aggregated. Base-map reference data are included, using the U.S. Geological Survey (USGS) National Map, the USGS and American Geological Institute (AGI) Global GIS, and a World Shaded Relief map service from the ESRI Geography Network. A hardcopy map was created to synthesize recorded exploration data from 1859, when the first oil well was drilled in the U.S., to 2005. In addition to the hardcopy map product, the data have been refined and made more accessible through the use of Geographic Information System (GIS) tools. The cell data are included in a GIS database constructed for spatial analysis via the USGS Internet Map Service or by importing the data into GIS software such as ArcGIS. The USGS internet map service provides a number of useful and sophisticated geoprocessing and cartographic functions via an internet browser. Also included is a video clip of U.S. oil and gas exploration and production through time.

Do residents of food deserts express different food buying preferences compared to residents of food oases? A mixed-methods analysis.

PubMed

Walker, Renee E; Block, Jason; Kawachi, Ichiro

2012-04-10

Many people lack access to food stores that provide healthful food. Neighborhoods with poor supermarket access have been characterized as "food deserts" (as contrast with "food oases"). This study explored factors influencing food buying practices among residents of food deserts versus food oases in the city of Boston, USA. We used the mixed-methods approach of concept mapping, which allows participants to identify, list, and organize their perceptions according to importance. Resulting maps visually illustrate priority areas. Sixty-seven low-income adults completed the concept mapping process that identified 163 unique statements (e.g. relating to affordability, taste, and convenience) that influence food buying practices. Multivariate statistical techniques grouped the 163 statements into 8 clusters or concepts. Results showed that average cluster ratings and rankings were similar between residents of food deserts and food oases. The implication of this study pertains to the importance of community resources and emergency food assistance programs that have served to minimize the burden associated with hunger and poor food access among low-income, urban populations.

Do residents of food deserts express different food buying preferences compared to residents of food oases? A mixed-methods analysis

PubMed Central

2012-01-01

Background Many people lack access to food stores that provide healthful food. Neighborhoods with poor supermarket access have been characterized as “food deserts” (as contrast with “food oases”). This study explored factors influencing food buying practices among residents of food deserts versus food oases in the city of Boston, USA. Methods We used the mixed-methods approach of concept mapping, which allows participants to identify, list, and organize their perceptions according to importance. Resulting maps visually illustrate priority areas. Results Sixty-seven low-income adults completed the concept mapping process that identified 163 unique statements (e.g. relating to affordability, taste, and convenience) that influence food buying practices. Multivariate statistical techniques grouped the 163 statements into 8 clusters or concepts. Results showed that average cluster ratings and rankings were similar between residents of food deserts and food oases. Conclusions The implication of this study pertains to the importance of community resources and emergency food assistance programs that have served to minimize the burden associated with hunger and poor food access among low-income, urban populations. PMID:22490237

miR-188 promotes senescence of lineage-negative bone marrow cells by targeting MAP3K3 expression.

PubMed

Zheng, Yue; Liu, Hua; Kong, Ye

2017-08-01

Lineage-negative bone marrow cells (lin-BMCs) have reparative potential for overcoming endothelial dysfunction and reducing cardiovascular risk. Here, we found that miR-188 is upregulated and mitogen-activated protein kinase kinase kinase 3 (MAP3K3) is downregulated in aged lin-BMCs, whereas their expression is reversed in young lin-BMCs. We identified and confirmed MAP3K3 as a direct target of miR-188. MiR-188 overexpression or MAP3K3 silencing in young lin-BMCs increases p16 and p21 expression, enhances cell senescence, and decreases the ability for cell proliferation, migration, and tube formation. Conversely, miR-188 suppression in aged lin-BMCs yields the opposite results. We further found that MAP3K3 is involved in miR-188-induced promotion of lin-BMC senescence. All data reveal that miR-188 induces lin-BMC senescence by targeting MAP3K3 expression, thus, providing new theoretical basis for the prevention and treatment of cardiovascular diseases. © 2017 Federation of European Biochemical Societies.

An alternative methionine aminopeptidase, MAP-A, is required for nitrogen starvation and high-light acclimation in the cyanobacterium Synechocystis sp. PCC 6803.

PubMed

Drath, Miriam; Baier, Kerstin; Forchhammer, Karl

2009-05-01

Methionine aminopeptidases (MetAPs or MAPs, encoded by map genes) are ubiquitous and pivotal enzymes for protein maturation in all living organisms. Whereas most bacteria harbour only one map gene, many cyanobacterial genomes contain two map paralogues, the genome of Synechocystis sp. PCC 6803 even three. The physiological function of multiple map paralogues remains elusive so far. This communication reports for the first time differential MetAP function in a cyanobacterium. In Synechocystis sp. PCC 6803, the universally conserved mapC gene (sll0555) is predominantly expressed in exponentially growing cells and appears to be a housekeeping gene. By contrast, expression of mapA (slr0918) and mapB (slr0786) genes increases during stress conditions. The mapB paralogue is only transiently expressed, whereas the widely distributed mapA gene appears to be the major MetAP during stress conditions. A mapA-deficient Synechocystis mutant shows a subtle impairment of photosystem II properties even under non-stressed conditions. In particular, the binding site for the quinone Q(B) is affected, indicating specific N-terminal methionine processing requirements of photosystem II components. MAP-A-specific processing becomes essential under certain stress conditions, since the mapA-deficient mutant is severely impaired in surviving conditions of prolonged nitrogen starvation and high light exposure.

Word Learning in Children with Autism Spectrum Disorders

PubMed Central

Luyster, Rhiannon; Lord, Catherine

2010-01-01

Autism Spectrum Disorders (ASD) have been gaining attention, partly as an example of unusual developmental trajectories related to early neurobiological differences. The present investigation addressed the process of learning new words in order to explore mechanisms of language delay and impairment. The sample included 21 typically developing toddlers matched on expressive vocabulary with 21 young children with ASD. Two tasks were administered to teach children a new word and were supplemented by cognitive and diagnostic measures. In most analyses, there were no group differences in performance. Children with ASD did not consistently make mapping errors, even in word learning situations which required the use of social information. These findings indicate that some children with ASD, in developmentally appropriate tasks, are able to use information from social interactions to guide word-object mappings. This result has important implications for our understanding of how children with ASD learn language. PMID:19899931

A synthetic intrabody-based selective and generic inhibitor of GPCR endocytosis

NASA Astrophysics Data System (ADS)

Ghosh, Eshan; Srivastava, Ashish; Baidya, Mithu; Kumari, Punita; Dwivedi, Hemlata; Nidhi, Kumari; Ranjan, Ravi; Dogra, Shalini; Koide, Akiko; Yadav, Prem N.; Sidhu, Sachdev S.; Koide, Shohei; Shukla, Arun K.

2017-12-01

Beta-arrestins (βarrs) critically mediate desensitization, endocytosis and signalling of G protein-coupled receptors (GPCRs), and they scaffold a large number of interaction partners. However, allosteric modulation of their scaffolding abilities and direct targeting of their interaction interfaces to modulate GPCR functions selectively have not been fully explored yet. Here we identified a series of synthetic antibody fragments (Fabs) against different conformations of βarrs from phage display libraries. Several of these Fabs allosterically and selectively modulated the interaction of βarrs with clathrin and ERK MAP kinase. Interestingly, one of these Fabs selectively disrupted βarr-clathrin interaction, and when expressed as an intrabody, it robustly inhibited agonist-induced endocytosis of a broad set of GPCRs without affecting ERK MAP kinase activation. Our data therefore demonstrate the feasibility of selectively targeting βarr interactions using intrabodies and provide a novel framework for fine-tuning GPCR functions with potential therapeutic implications.

Geophysical delineation of Mg-rich ultramafic rocks for mineral carbon sequestration

USGS Publications Warehouse

McCafferty, Anne E.; Van Gosen, Bradley S.; Krevor, Sam C.; Graves, Chris R.

2009-01-01

This presentation covers three general topics: (1) description of a new geologic compilation of the United States that shows the location of magnesium-rich ultramafic rocks in the conterminous United States; (2) conceptual illustration of the potential ways that ultramafic rocks could be used to sequester carbon dioxide; and (3) description of ways to use geophysical data to refine and extend the geologic mapping of ultramafic rocks and to better characterize their mineralogy.The geophysical focus of this research is twofold. First, we illustrate how airborne magnetic data can be used to map the shallow subsurface geometry of ultramafic rocks for the purpose of estimating the volume of rock material available for mineral CO2 sequestration. Secondly, we explore, on a regional to outcrop scale, how magnetic mineralogy, as expressed in magnetic anomalies, may vary with magnesium minerals, which are the primary minerals of interest for CO2 sequestration. 

Adaptation of video game UVW mapping to 3D visualization of gene expression patterns

NASA Astrophysics Data System (ADS)

Vize, Peter D.; Gerth, Victor E.

2007-01-01

Analysis of gene expression patterns within an organism plays a critical role in associating genes with biological processes in both health and disease. During embryonic development the analysis and comparison of different gene expression patterns allows biologists to identify candidate genes that may regulate the formation of normal tissues and organs and to search for genes associated with congenital diseases. No two individual embryos, or organs, are exactly the same shape or size so comparing spatial gene expression in one embryo to that in another is difficult. We will present our efforts in comparing gene expression data collected using both volumetric and projection approaches. Volumetric data is highly accurate but difficult to process and compare. Projection methods use UV mapping to align texture maps to standardized spatial frameworks. This approach is less accurate but is very rapid and requires very little processing. We have built a database of over 180 3D models depicting gene expression patterns mapped onto the surface of spline based embryo models. Gene expression data in different models can easily be compared to determine common regions of activity. Visualization software, both Java and OpenGL optimized for viewing 3D gene expression data will also be demonstrated.

NOAA Office of Exploration and Research > Education > Overview

Science.gov Websites

Exploration Marine Archaeology Ocean and Coastal Mapping Advancing Technology Overview Technology Initiatives Coastal Mapping Advancing Technology Overview Technology Initiatives Science Overview Data Access Overview

Analysis of multiplex gene expression maps obtained by voxelation.

PubMed

An, Li; Xie, Hongbo; Chin, Mark H; Obradovic, Zoran; Smith, Desmond J; Megalooikonomou, Vasileios

2009-04-29

Gene expression signatures in the mammalian brain hold the key to understanding neural development and neurological disease. Researchers have previously used voxelation in combination with microarrays for acquisition of genome-wide atlases of expression patterns in the mouse brain. On the other hand, some work has been performed on studying gene functions, without taking into account the location information of a gene's expression in a mouse brain. In this paper, we present an approach for identifying the relation between gene expression maps obtained by voxelation and gene functions. To analyze the dataset, we chose typical genes as queries and aimed at discovering similar gene groups. Gene similarity was determined by using the wavelet features extracted from the left and right hemispheres averaged gene expression maps, and by the Euclidean distance between each pair of feature vectors. We also performed a multiple clustering approach on the gene expression maps, combined with hierarchical clustering. Among each group of similar genes and clusters, the gene function similarity was measured by calculating the average gene function distances in the gene ontology structure. By applying our methodology to find similar genes to certain target genes we were able to improve our understanding of gene expression patterns and gene functions. By applying the clustering analysis method, we obtained significant clusters, which have both very similar gene expression maps and very similar gene functions respectively to their corresponding gene ontologies. The cellular component ontology resulted in prominent clusters expressed in cortex and corpus callosum. The molecular function ontology gave prominent clusters in cortex, corpus callosum and hypothalamus. The biological process ontology resulted in clusters in cortex, hypothalamus and choroid plexus. Clusters from all three ontologies combined were most prominently expressed in cortex and corpus callosum. The experimental results confirm the hypothesis that genes with similar gene expression maps might have similar gene functions. The voxelation data takes into account the location information of gene expression level in mouse brain, which is novel in related research. The proposed approach can potentially be used to predict gene functions and provide helpful suggestions to biologists.

First results in terrain mapping for a roving planetary explorer

NASA Technical Reports Server (NTRS)

Krotkov, E.; Caillas, C.; Hebert, M.; Kweon, I. S.; Kanade, Takeo

1989-01-01

To perform planetary exploration without human supervision, a complete autonomous rover must be able to model its environment while exploring its surroundings. Researchers present a new algorithm to construct a geometric terrain representation from a single range image. The form of the representation is an elevation map that includes uncertainty, unknown areas, and local features. By virtue of working in spherical-polar space, the algorithm is independent of the desired map resolution and the orientation of the sensor, unlike other algorithms that work in Cartesian space. They also describe new methods to evaluate regions of the constructed elevation maps to support legged locomotion over rough terrain.

NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps

PubMed Central

2013-01-01

Background Molecular biology knowledge can be formalized and systematically represented in a computer-readable form as a comprehensive map of molecular interactions. There exist an increasing number of maps of molecular interactions containing detailed and step-wise description of various cell mechanisms. It is difficult to explore these large maps, to organize discussion of their content and to maintain them. Several efforts were recently made to combine these capabilities together in one environment, and NaviCell is one of them. Results NaviCell is a web-based environment for exploiting large maps of molecular interactions, created in CellDesigner, allowing their easy exploration, curation and maintenance. It is characterized by a combination of three essential features: (1) efficient map browsing based on Google Maps; (2) semantic zooming for viewing different levels of details or of abstraction of the map and (3) integrated web-based blog for collecting community feedback. NaviCell can be easily used by experts in the field of molecular biology for studying molecular entities of interest in the context of signaling pathways and crosstalk between pathways within a global signaling network. NaviCell allows both exploration of detailed molecular mechanisms represented on the map and a more abstract view of the map up to a top-level modular representation. NaviCell greatly facilitates curation, maintenance and updating the comprehensive maps of molecular interactions in an interactive and user-friendly fashion due to an imbedded blogging system. Conclusions NaviCell provides user-friendly exploration of large-scale maps of molecular interactions, thanks to Google Maps and WordPress interfaces, with which many users are already familiar. Semantic zooming which is used for navigating geographical maps is adopted for molecular maps in NaviCell, making any level of visualization readable. In addition, NaviCell provides a framework for community-based curation of maps. PMID:24099179

NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps.

PubMed

Kuperstein, Inna; Cohen, David P A; Pook, Stuart; Viara, Eric; Calzone, Laurence; Barillot, Emmanuel; Zinovyev, Andrei

2013-10-07

Molecular biology knowledge can be formalized and systematically represented in a computer-readable form as a comprehensive map of molecular interactions. There exist an increasing number of maps of molecular interactions containing detailed and step-wise description of various cell mechanisms. It is difficult to explore these large maps, to organize discussion of their content and to maintain them. Several efforts were recently made to combine these capabilities together in one environment, and NaviCell is one of them. NaviCell is a web-based environment for exploiting large maps of molecular interactions, created in CellDesigner, allowing their easy exploration, curation and maintenance. It is characterized by a combination of three essential features: (1) efficient map browsing based on Google Maps; (2) semantic zooming for viewing different levels of details or of abstraction of the map and (3) integrated web-based blog for collecting community feedback. NaviCell can be easily used by experts in the field of molecular biology for studying molecular entities of interest in the context of signaling pathways and crosstalk between pathways within a global signaling network. NaviCell allows both exploration of detailed molecular mechanisms represented on the map and a more abstract view of the map up to a top-level modular representation. NaviCell greatly facilitates curation, maintenance and updating the comprehensive maps of molecular interactions in an interactive and user-friendly fashion due to an imbedded blogging system. NaviCell provides user-friendly exploration of large-scale maps of molecular interactions, thanks to Google Maps and WordPress interfaces, with which many users are already familiar. Semantic zooming which is used for navigating geographical maps is adopted for molecular maps in NaviCell, making any level of visualization readable. In addition, NaviCell provides a framework for community-based curation of maps.

Combining mouse mammary gland gene expression and comparative mapping for the identification of candidate genes for QTL of milk production traits in cattle

PubMed Central

Ron, Micha; Israeli, Galit; Seroussi, Eyal; Weller, Joel I; Gregg, Jeffrey P; Shani, Moshe; Medrano, Juan F

2007-01-01

Background Many studies have found segregating quantitative trait loci (QTL) for milk production traits in different dairy cattle populations. However, even for relatively large effects with a saturated marker map the confidence interval for QTL location by linkage analysis spans tens of map units, or hundreds of genes. Combining mapping and arraying has been suggested as an approach to identify candidate genes. Thus, gene expression analysis in the mammary gland of genes positioned in the confidence interval of the QTL can bridge the gap between fine mapping and quantitative trait nucleotide (QTN) determination. Results We hybridized Affymetrix microarray (MG-U74v2), containing 12,488 murine probes, with RNA derived from mammary gland of virgin, pregnant, lactating and involuting C57BL/6J mice in a total of nine biological replicates. We combined microarray data from two additional studies that used the same design in mice with a total of 75 biological replicates. The same filtering and normalization was applied to each microarray data using GeneSpring software. Analysis of variance identified 249 differentially expressed probe sets common to the three experiments along the four developmental stages of puberty, pregnancy, lactation and involution. 212 genes were assigned to their bovine map positions through comparative mapping, and thus form a list of candidate genes for previously identified QTLs for milk production traits. A total of 82 of the genes showed mammary gland-specific expression with at least 3-fold expression over the median representing all tissues tested in GeneAtlas. Conclusion This work presents a web tool for candidate genes for QTL (cgQTL) that allows navigation between the map of bovine milk production QTL, potential candidate genes and their level of expression in mammary gland arrays and in GeneAtlas. Three out of four confirmed genes that affect QTL in livestock (ABCG2, DGAT1, GDF8, IGF2) were over expressed in the target organ. Thus, cgQTL can be used to determine priority of candidate genes for QTN analysis based on differential expression in the target organ. PMID:17584498

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

Farfour, Mohammed; Yoon, Wang Jung; Yoon-Geun

Defining and understanding hydrocarbon expressions in seismic expression is main concern of geoscientists in oil and gas exploration and production. Over the last decades several mathematical approaches have been developed in this regard. Most of approaches have addressed information in amplitude of seismic data. Recently, more attention has been drawn towards frequency related information in order to extract frequency behaviors of hydrocarbons bearing sediments. Spectrally decomposing seismic data into individual frequencies found to be an excellent tool for investigating geological formations and their pore fluids. To accomplish this, several mathematical approaches have been invoked. Continuous wavelet transform and Short Timemore » Window Fourier transform are widely used techniques for this purpose. This paper gives an overview of some widely used mathematical technique in hydrocarbon reservoir detection and mapping. This is followed by an application on real data from Boonsville field.« less

Integration of NOAA Ship Okeanos Explorer Seafloor Mapping, Little Hercules ROV, and Sentry AUV Data into Ocean Exploration Operations and Public Data Holdings

NASA Astrophysics Data System (ADS)

Lobecker, E.; Malik, M.; Skarke, A. D.; VerPlanck, N.

2012-12-01

Within NOAA's Office of Ocean Exploration and Research, the Okeanos Explorer Program's main tools for preliminary ocean exploration include a Kongsberg EM 302 multibeam sonar (30 kHz), Kongsberg EK 60 singlebeam sonar (18 kHz), and Knudsen subbottom profiler (3.5 kHz chirp). The program devoted multiple expeditions in the Gulf of Mexico and U.S. Atlantic Margin during its 2012 Field Season to confirm and further develop the EM 302 multibeam sonar's water column backscatter data capability to detect gaseous seeps and vents. While mapping in the seafloor and water column in the vicinity of the salt domes of the Northern Gulf of Mexico, the EM 302 detected over two hundred distinct seeps in the water column. Several seeps have been explored in more detail using high definition cameras and lighting systems of the remotely operated vehicle Little Hercules and the camera platform Seirios. This included filming bubbles escaping from the seafloor at the locations determined by the EM 302 data to ground truth EM302 observations and deduce other properties of these gas seeps e.g. gas flux, and effect of these seeps on surrounding ecosystem. These seeps are now a major research focus area by scientists at the University of New Hampshire's Center for Coastal and Ocean Mapping and other academic institutions around the U.S., and the U.S. Bureau of Ocean Energy Management. . While mapping the Blake Ridge and Cape Fear Diapirs, seven distinct seeps were detected, each rising approximately 900 meters from the seafloor in water depths ranging from 2200 to 2500 meters. Several of these seeps were further explored with Woods Hole Oceanographic Institute's Sentry autonomous underwater vehicle, utilizing itsReson 7125 high resolution multibeam, photo imagery, sidescan, subbottom, and various in-situ sensors to characterize the local environment. It is to be noted that very few of these seeps were previously known. Following the Okeanos Explorer Program's paradigm of "Always Exploring", the mapping team collects data not only during focused mapping operations, but also during all transits. Okeanos Explorer data are collected with regard to the Integrated Ocean and Coastal Mapping Center's concept to "map once use many times", which aims to encourage and enable the multidisciplinary use of seafloor mapping data, including by the fields of marine archaeology, hydrographic mapping, extended continental shelf, biology, geology, geophysics, biopharmaceutical, ocean energy and resources, marine managed areas, fisheries, corals, oceanography, hazards modeling and assessments, education and outreach. To this end, all mapping, CTD and meteorology data sets collected by the NOAA Ship Okeanos Explorer are monitored and evaluated in the field for quality control purposes, and are made available through NOAA's public archives within 60 to 90 days of data collection, in useable formats and with associated metadata records. Additionally, all data sets collected by vehicles onboard the ship, including ROVs and AUVs, are made available directly following each cruise via NOAA's public archives.

Mapping Literacy, Mapping Lives: Teachers Exploring the Sociopolitical Context of Literacy and Learning

ERIC Educational Resources Information Center

Ordonez-Jasis, Rosario; Jasis, Pablo

2011-01-01

In this article the authors explore a language and literacy community mapping project carried out by public school teachers in southern California. They chronicle the knowledge produced by teachers about the depth and diversity of language and literacy resources present in the neighborhoods surrounding their various urban school sites. (Contains 6…

MHC class I-associated peptides derive from selective regions of the human genome.

PubMed

Pearson, Hillary; Daouda, Tariq; Granados, Diana Paola; Durette, Chantal; Bonneil, Eric; Courcelles, Mathieu; Rodenbrock, Anja; Laverdure, Jean-Philippe; Côté, Caroline; Mader, Sylvie; Lemieux, Sébastien; Thibault, Pierre; Perreault, Claude

2016-12-01

MHC class I-associated peptides (MAPs) define the immune self for CD8+ T lymphocytes and are key targets of cancer immunosurveillance. Here, the goals of our work were to determine whether the entire set of protein-coding genes could generate MAPs and whether specific features influence the ability of discrete genes to generate MAPs. Using proteogenomics, we have identified 25,270 MAPs isolated from the B lymphocytes of 18 individuals who collectively expressed 27 high-frequency HLA-A,B allotypes. The entire MAP repertoire presented by these 27 allotypes covered only 10% of the exomic sequences expressed in B lymphocytes. Indeed, 41% of expressed protein-coding genes generated no MAPs, while 59% of genes generated up to 64 MAPs, often derived from adjacent regions and presented by different allotypes. We next identified several features of transcripts and proteins associated with efficient MAP production. From these data, we built a logistic regression model that predicts with good accuracy whether a gene generates MAPs. Our results show preferential selection of MAPs from a limited repertoire of proteins with distinctive features. The notion that the MHC class I immunopeptidome presents only a small fraction of the protein-coding genome for monitoring by the immune system has profound implications in autoimmunity and cancer immunology.

MHC class I–associated peptides derive from selective regions of the human genome

PubMed Central

Pearson, Hillary; Granados, Diana Paola; Durette, Chantal; Bonneil, Eric; Courcelles, Mathieu; Rodenbrock, Anja; Laverdure, Jean-Philippe; Côté, Caroline; Thibault, Pierre

2016-01-01

MHC class I–associated peptides (MAPs) define the immune self for CD8+ T lymphocytes and are key targets of cancer immunosurveillance. Here, the goals of our work were to determine whether the entire set of protein-coding genes could generate MAPs and whether specific features influence the ability of discrete genes to generate MAPs. Using proteogenomics, we have identified 25,270 MAPs isolated from the B lymphocytes of 18 individuals who collectively expressed 27 high-frequency HLA-A,B allotypes. The entire MAP repertoire presented by these 27 allotypes covered only 10% of the exomic sequences expressed in B lymphocytes. Indeed, 41% of expressed protein-coding genes generated no MAPs, while 59% of genes generated up to 64 MAPs, often derived from adjacent regions and presented by different allotypes. We next identified several features of transcripts and proteins associated with efficient MAP production. From these data, we built a logistic regression model that predicts with good accuracy whether a gene generates MAPs. Our results show preferential selection of MAPs from a limited repertoire of proteins with distinctive features. The notion that the MHC class I immunopeptidome presents only a small fraction of the protein-coding genome for monitoring by the immune system has profound implications in autoimmunity and cancer immunology. PMID:27841757

Discovery and mapping of single feature polymorphisms in wheat using Affymetrix arrays

PubMed Central

Bernardo, Amy N; Bradbury, Peter J; Ma, Hongxiang; Hu, Shengwa; Bowden, Robert L; Buckler, Edward S; Bai, Guihua

2009-01-01

Background Wheat (Triticum aestivum L.) is a staple food crop worldwide. The wheat genome has not yet been sequenced due to its huge genome size (~17,000 Mb) and high levels of repetitive sequences; the whole genome sequence may not be expected in the near future. Available linkage maps have low marker density due to limitation in available markers; therefore new technologies that detect genome-wide polymorphisms are still needed to discover a large number of new markers for construction of high-resolution maps. A high-resolution map is a critical tool for gene isolation, molecular breeding and genomic research. Single feature polymorphism (SFP) is a new microarray-based type of marker that is detected by hybridization of DNA or cRNA to oligonucleotide probes. This study was conducted to explore the feasibility of using the Affymetrix GeneChip to discover and map SFPs in the large hexaploid wheat genome. Results Six wheat varieties of diverse origins (Ning 7840, Clark, Jagger, Encruzilhada, Chinese Spring, and Opata 85) were analyzed for significant probe by variety interactions and 396 probe sets with SFPs were identified. A subset of 164 unigenes was sequenced and 54% showed polymorphism within probes. Microarray analysis of 71 recombinant inbred lines from the cross Ning 7840/Clark identified 955 SFPs and 877 of them were mapped together with 269 simple sequence repeat markers. The SFPs were randomly distributed within a chromosome but were unevenly distributed among different genomes. The B genome had the most SFPs, and the D genome had the least. Map positions of a selected set of SFPs were validated by mapping single nucleotide polymorphism using SNaPshot and comparing with expressed sequence tags mapping data. Conclusion The Affymetrix array is a cost-effective platform for SFP discovery and SFP mapping in wheat. The new high-density map constructed in this study will be a useful tool for genetic and genomic research in wheat. PMID:19480702

Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs

PubMed Central

Barrera, Leah O.; Li, Zirong; Smith, Andrew D.; Arden, Karen C.; Cavenee, Webster K.; Zhang, Michael Q.; Green, Roland D.; Ren, Bing

2008-01-01

By integrating genome-wide maps of RNA polymerase II (Polr2a) binding with gene expression data and H3ac and H3K4me3 profiles, we characterized promoters with enriched activity in mouse embryonic stem cells (mES) as well as adult brain, heart, kidney, and liver. We identified ∼24,000 promoters across these samples, including 16,976 annotated mRNA 5′ ends and 5153 additional sites validating cap-analysis of gene expression (CAGE) 5′ end data. We showed that promoters with CpG islands are typically non-tissue specific, with the majority associated with Polr2a and the active chromatin modifications in nearly all the tissues examined. By contrast, the promoters without CpG islands are generally associated with Polr2a and the active chromatin marks in a tissue-dependent way. We defined 4396 tissue-specific promoters by adapting a quantitative index of tissue-specificity based on Polr2a occupancy. While there is a general correspondence between Polr2a occupancy and active chromatin modifications at the tissue-specific promoters, a subset of them appear to be persistently marked by active chromatin modifications in the absence of detectable Polr2a binding, highlighting the complexity of the functional relationship between chromatin modification and gene expression. Our results provide a resource for exploring promoter Polr2a binding and epigenetic states across pluripotent and differentiated cell types in mammals. PMID:18042645

Cardiac Fibroblast-Specific Activating Transcription Factor 3 Protects Against Heart Failure by Suppressing MAP2K3-p38 Signaling.

PubMed

Li, Yulin; Li, Zhenya; Zhang, Congcong; Li, Ping; Wu, Yina; Wang, Chunxiao; Bond Lau, Wayne; Ma, Xin-Liang; Du, Jie

2017-05-23

Hypertensive ventricular remodeling is a common cause of heart failure. However, the molecular mechanisms regulating ventricular remodeling remain poorly understood. We used a discovery-driven/nonbiased approach to identify increased activating transcription factor 3 (ATF3) expression in hypertensive heart. We used loss/gain of function approaches to understand the role of ATF3 in heart failure. We also examined the mechanisms through transcriptome, chromatin immunoprecipitation sequencing analysis, and in vivo and in vitro experiments. ATF3 expression increased in murine hypertensive heart and human hypertrophic heart. Cardiac fibroblast cells are the primary cell type expressing high ATF3 levels in response to hypertensive stimuli. ATF3 knockout (ATF3KO) markedly exaggerated hypertensive ventricular remodeling, a state rescued by lentivirus-mediated/miRNA-aided cardiac fibroblast-selective ATF3 overexpression. Conversely, conditional cardiac fibroblast cell-specific ATF3 transgenic overexpression significantly ameliorated ventricular remodeling and heart failure. We identified Map2K3 as a novel ATF3 target. ATF3 binds with the Map2K3 promoter, recruiting HDAC1, resulting in Map2K3 gene-associated histone deacetylation, thereby inhibiting Map2K3 expression. Genetic Map2K3 knockdown rescued the profibrotic/hypertrophic phenotype in ATF3KO cells. Last, we demonstrated that p38 is the downstream molecule of Map2K3 mediating the profibrotic/hypertrophic effects in ATF3KO animals. Inhibition of p38 signaling reduced transforming growth factor-β signaling-related profibrotic and hypertrophic gene expression, and blocked exaggerated cardiac remodeling in ATF3KO cells. Our study provides the first evidence that ATF3 upregulation in cardiac fibroblasts in response to hypertensive stimuli protects the heart by suppressing Map2K3 expression and subsequent p38-transforming growth factor-β signaling. These results suggest that positive modulation of cardiac fibroblast ATF3 may represent a novel therapeutic approach against hypertensive cardiac remodeling. © 2017 American Heart Association, Inc.

Widening ERTS applications

NASA Technical Reports Server (NTRS)

Mercanti, E. P.

1974-01-01

In less than two years of operation ERTS-1 is shown to have successfully completed its experimental mission and to be delivering an ever-increasing roster of benefits. The widening ERTS applications reviewed include air quality and weather modification, aid to oil exploration, ore-deposit exploration, short-lived event observation, flood area assessment and flood-plain mapping, land and water quality assessment, soil association mapping, crop production measurements, wildlife resources, drought and desertification studies, ground-water exploration, watershed surveys, snow and ice monitoring, surface water mapping, and iceberg surveys. Future projects and developments are also briefly reviewed.

Applying satellite technology to energy and mineral exploration

USGS Publications Warehouse

Carter, William D.; Rowan, Lawrence C.

1978-01-01

IGCP Project 143 ("Remote Sensing and Mineral Exploration"), is a worldwide research project designed to make satellite data an operational geological tool along with the geologic pick, hand lens, topographic map, aerial photo and geophysical instruments and data that comprise the exploration package. While remote sensing data will not replace field exploration and mapping, careful study of such data prior to field work should make the effort more efficient.

Identification and Characterization of the miRNA Transcriptome of Ovis aries

PubMed Central

Wei, Caihong; Sheng, Xihui; Ren, Hangxing; Xu, Lingyang; Lu, Jian; Liu, Jiasen; Zhang, Li; Du, Lixin

2013-01-01

The discovery and identification of Ovis aries (sheep) miRNAs will further promote the study of miRNA functions and gene regulatory mechanisms. To explore the microRNAome (miRNAome) of sheep in depth, samples were collected that included eight developmental stages: the longissimus dorsi muscles of Texel fetuses at 70, 85, 100, 120, and 135 days, and the longissimus dorsi muscles of Ujumqin fetuses at 70, 85, 100, 120, and 135 d, and lambs at 0 (birth), 35, and 70 d. These samples covered all of the representative periods of Ovis aries growth and development throughout gestation (about 150 d) and 70 d after birth. Texel and Ujumqin libraries were separately subjected to Solexa deep sequencing; 35,700,772 raw reads were obtained overall. We used ACGT101-miR v4.2 to analyze the sequence data. Following meticulous comparisons with mammalian mature miRNAs, precursor hairpins (pre-miRNAs), and the latest sheep genome, we substantially extended the Ovis aries miRNAome. The list of pre-miRNAs was extended to 2,319, expressing 2,914 mature miRNAs. Among those, 1,879 were genome mapped to unique miRNAs, representing 2,436 genome locations, and 1,754 pre-miRNAs were mapped to chromosomes. Furthermore, the Ovis aries miRNAome was processed using an elaborate bioinformatic analysis that examined multiple end sequence variation in miRNAs, precursors, chromosomal localizations, species-specific expressions, and conservative properties. Taken together, this study provides the most comprehensive and accurate exploration of the sheep miRNAome, and draws conclusions about numerous characteristics of Ovis aries miRNAs, including miRNAs and isomiRs. PMID:23516575

Spatial reconstruction of single-cell gene expression data.

PubMed

Satija, Rahul; Farrell, Jeffrey A; Gennert, David; Schier, Alexander F; Regev, Aviv

2015-05-01

Spatial localization is a key determinant of cellular fate and behavior, but methods for spatially resolved, transcriptome-wide gene expression profiling across complex tissues are lacking. RNA staining methods assay only a small number of transcripts, whereas single-cell RNA-seq, which measures global gene expression, separates cells from their native spatial context. Here we present Seurat, a computational strategy to infer cellular localization by integrating single-cell RNA-seq data with in situ RNA patterns. We applied Seurat to spatially map 851 single cells from dissociated zebrafish (Danio rerio) embryos and generated a transcriptome-wide map of spatial patterning. We confirmed Seurat's accuracy using several experimental approaches, then used the strategy to identify a set of archetypal expression patterns and spatial markers. Seurat correctly localizes rare subpopulations, accurately mapping both spatially restricted and scattered groups. Seurat will be applicable to mapping cellular localization within complex patterned tissues in diverse systems.

Supporting creativity and appreciation of uncertainty in exploring geo-coded public health data.

PubMed

Thew, S L; Sutcliffe, A; de Bruijn, O; McNaught, J; Procter, R; Jarvis, Paul; Buchan, I

2011-01-01

We present a prototype visualisation tool, ADVISES (Adaptive Visualization for e-Science), designed to support epidemiologists and public health practitioners in exploring geo-coded datasets and generating spatial epidemiological hypotheses. The tool is designed to support creative thinking while providing the means for the user to evaluate the validity of the visualization in terms of statistical uncertainty. We present an overview of the application and the results of an evaluation exploring public health researchers' responses to maps as a new way of viewing familiar data, in particular the use of thematic maps with adjoining descriptive statistics and forest plots to support the generation and evaluation of new hypotheses. A series of qualitative evaluations involved one experienced researcher asking 21 volunteers to interact with the system to perform a series of relatively complex, realistic map-building and exploration tasks, using a 'think aloud' protocol, followed by a semi-structured interview The volunteers were academic epidemiologists and UK National Health Service analysts. All users quickly and confidently created maps, and went on to spend substantial amounts of time exploring and interacting with system, generating hypotheses about their maps. Our findings suggest that the tool is able to support creativity and statistical appreciation among public health professionals and epidemiologists building thematic maps. Software such as this, introduced appropriately, could increase the capability of existing personnel for generating public health intelligence.

Overexpression of peptide deformylase in breast, colon, and lung cancers.

PubMed

Randhawa, Harsharan; Chikara, Shireen; Gehring, Drew; Yildirim, Tuba; Menon, Jyotsana; Reindl, Katie M

2013-07-01

Human mitochondrial peptide deformylase (PDF) has been proposed as a novel cancer therapeutic target. However, very little is known about its expression and regulation in human tissues. The purpose of this study was to characterize the expression pattern of PDF in cancerous tissues and to identify mechanisms that regulate its expression. The mRNA expression levels of PDF and methionine aminopeptidase 1D (MAP1D), an enzyme involved in a related pathway with PDF, were determined using tissue panels containing cDNA from patients with various types of cancer (breast, colon, kidney, liver, lung, ovarian, prostate, or thyroid) and human cell lines. Protein levels of PDF were also determined in 2 colon cancer patients via western blotting. Colon cancer cells were treated with inhibitors of ERK, Akt, and mTOR signaling pathways and the resulting effects on PDF and MAP1D mRNA levels were determined by qPCR for colon and lung cancer cell lines. Finally, the effects of a PDF inhibitor, actinonin, on the proliferation of breast, colon, and prostate cell lines were determined using the CyQUANT assay. PDF and MAP1D mRNA levels were elevated in cancer cell lines compared to non-cancer lines. PDF mRNA levels were significantly increased in breast, colon, and lung cancer samples while MAP1D mRNA levels were increased in just colon cancers. The expression of PDF and MAP1D varied with stage in these cancers. Further, PDF protein expression was elevated in colon cancer tissue samples. Inhibition of the MEK/ERK, but not PI3K or mTOR, pathway reduced the expression of PDF and MAP1D in both colon and lung cancer cell lines. Further, inhibition of PDF with actinonin resulted in greater reduction of breast, colon, and prostate cancer cell proliferation than non-cancer cell lines. This is the first report showing that PDF is over-expressed in breast, colon, and lung cancers, and the first evidence that the MEK/ERK pathway plays a role in regulating the expression of PDF and MAP1D. The over-expression of PDF in several cancers and the inhibition of cancer cell growth by a PDF inhibitor suggest this enzyme may act as an oncogene to promote cancer cell proliferation.

Overexpression of peptide deformylase in breast, colon, and lung cancers

PubMed Central

2013-01-01

Background Human mitochondrial peptide deformylase (PDF) has been proposed as a novel cancer therapeutic target. However, very little is known about its expression and regulation in human tissues. The purpose of this study was to characterize the expression pattern of PDF in cancerous tissues and to identify mechanisms that regulate its expression. Methods The mRNA expression levels of PDF and methionine aminopeptidase 1D (MAP1D), an enzyme involved in a related pathway with PDF, were determined using tissue panels containing cDNA from patients with various types of cancer (breast, colon, kidney, liver, lung, ovarian, prostate, or thyroid) and human cell lines. Protein levels of PDF were also determined in 2 colon cancer patients via western blotting. Colon cancer cells were treated with inhibitors of ERK, Akt, and mTOR signaling pathways and the resulting effects on PDF and MAP1D mRNA levels were determined by qPCR for colon and lung cancer cell lines. Finally, the effects of a PDF inhibitor, actinonin, on the proliferation of breast, colon, and prostate cell lines were determined using the CyQUANT assay. Results PDF and MAP1D mRNA levels were elevated in cancer cell lines compared to non-cancer lines. PDF mRNA levels were significantly increased in breast, colon, and lung cancer samples while MAP1D mRNA levels were increased in just colon cancers. The expression of PDF and MAP1D varied with stage in these cancers. Further, PDF protein expression was elevated in colon cancer tissue samples. Inhibition of the MEK/ERK, but not PI3K or mTOR, pathway reduced the expression of PDF and MAP1D in both colon and lung cancer cell lines. Further, inhibition of PDF with actinonin resulted in greater reduction of breast, colon, and prostate cancer cell proliferation than non-cancer cell lines. Conclusions This is the first report showing that PDF is over-expressed in breast, colon, and lung cancers, and the first evidence that the MEK/ERK pathway plays a role in regulating the expression of PDF and MAP1D. The over-expression of PDF in several cancers and the inhibition of cancer cell growth by a PDF inhibitor suggest this enzyme may act as an oncogene to promote cancer cell proliferation. PMID:23815882

ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets.

PubMed

Brozovic, Matija; Dantec, Christelle; Dardaillon, Justine; Dauga, Delphine; Faure, Emmanuel; Gineste, Mathieu; Louis, Alexandra; Naville, Magali; Nitta, Kazuhiro R; Piette, Jacques; Reeves, Wendy; Scornavacca, Céline; Simion, Paul; Vincentelli, Renaud; Bellec, Maelle; Aicha, Sameh Ben; Fagotto, Marie; Guéroult-Bellone, Marion; Haeussler, Maximilian; Jacox, Edwin; Lowe, Elijah K; Mendez, Mickael; Roberge, Alexis; Stolfi, Alberto; Yokomori, Rui; Brown, C Titus; Cambillau, Christian; Christiaen, Lionel; Delsuc, Frédéric; Douzery, Emmanuel; Dumollard, Rémi; Kusakabe, Takehiro; Nakai, Kenta; Nishida, Hiroki; Satou, Yutaka; Swalla, Billie; Veeman, Michael; Volff, Jean-Nicolas; Lemaire, Patrick

2018-01-04

ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy databases, better support for epigenomics datasets, in particular RNA-seq, ChIP-seq and SELEX-seq, and features novel interactive interfaces for existing and novel datatypes. In particular, the cross-species navigation and comparison is enhanced through a novel taxonomy section describing each represented species and through the implementation of interactive phylogenetic gene trees for 60% of tunicate genes. The gene expression section displays the results of RNA-seq experiments for the three major model species of solitary ascidians. Gene expression is controlled by the binding of transcription factors to cis-regulatory sequences. A high-resolution description of the DNA-binding specificity for 131 Ciona robusta (formerly C. intestinalis type A) transcription factors by SELEX-seq is provided and used to map candidate binding sites across the Ciona robusta and Phallusia mammillata genomes. Finally, use of a WashU Epigenome browser enhances genome navigation, while a Genomicus server was set up to explore microsynteny relationships within tunicates and with vertebrates, Amphioxus, echinoderms and hemichordates. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Quantum groups, Yang-Baxter maps and quasi-determinants

NASA Astrophysics Data System (ADS)

Tsuboi, Zengo

2018-01-01

For any quasi-triangular Hopf algebra, there exists the universal R-matrix, which satisfies the Yang-Baxter equation. It is known that the adjoint action of the universal R-matrix on the elements of the tensor square of the algebra constitutes a quantum Yang-Baxter map, which satisfies the set-theoretic Yang-Baxter equation. The map has a zero curvature representation among L-operators defined as images of the universal R-matrix. We find that the zero curvature representation can be solved by the Gauss decomposition of a product of L-operators. Thereby obtained a quasi-determinant expression of the quantum Yang-Baxter map associated with the quantum algebra Uq (gl (n)). Moreover, the map is identified with products of quasi-Plücker coordinates over a matrix composed of the L-operators. We also consider the quasi-classical limit, where the underlying quantum algebra reduces to a Poisson algebra. The quasi-determinant expression of the quantum Yang-Baxter map reduces to ratios of determinants, which give a new expression of a classical Yang-Baxter map.

Expressive map design: OGC SLD/SE++ extension for expressive map styles

NASA Astrophysics Data System (ADS)

Christophe, Sidonie; Duménieu, Bertrand; Masse, Antoine; Hoarau, Charlotte; Ory, Jérémie; Brédif, Mathieu; Lecordix, François; Mellado, Nicolas; Turbet, Jérémie; Loi, Hugo; Hurtut, Thomas; Vanderhaeghe, David; Vergne, Romain; Thollot, Joëlle

2018-05-01

In the context of custom map design, handling more artistic and expressive tools has been identified as a carto-graphic need, in order to design stylized and expressive maps. Based on previous works on style formalization, an approach for specifying the map style has been proposed and experimented for particular use cases. A first step deals with the analysis of inspiration sources, in order to extract `what does make the style of the source', i.e. the salient visual characteristics to be automatically reproduced (textures, spatial arrangements, linear stylization, etc.). In a second step, in order to mimic and generate those visual characteristics, existing and innovative rendering techniques have been implemented in our GIS engine, thus extending the capabilities to generate expressive renderings. Therefore, an extension of the existing cartographic pipeline has been proposed based on the following aspects: 1- extension of the symbolization specifications OGC SLD/SE in order to provide a formalism to specify and reference expressive rendering methods; 2- separate the specification of each rendering method and its parameterization, as metadata. The main contribution has been described in (Christophe et al. 2016). In this paper, we focus firstly on the extension of the cartographic pipeline (SLD++ and metadata) and secondly on map design capabilities which have been experimented on various topographic styles: old cartographic styles (Cassini), artistic styles (watercolor, impressionism, Japanese print), hybrid topographic styles (ortho-imagery & vector data) and finally abstract and photo-realist styles for the geovisualization of costal area. The genericity and interoperability of our approach are promising and have already been tested for 3D visualization.

Angiogenin Expression during Early Human Placental Development; Association with Blood Vessel Formation

PubMed Central

Pavlov, Nadine; Guibourdenche, Jean; Degrelle, Séverine A.; Evain-Brion, Danièle

2014-01-01

The placenta is a transient organ essential for fetal development. During human placental development, chorionic villi grow in coordination with a large capillary network resulting from both vasculogenesis and angiogenesis. Angiogenin is one of the most potent inducers of neovascularisation in experimental models in vivo. We and others have previously mapped angiogenin expression in the human term placenta. Here, we explored angiogenin involvement in early human placental development. We studied, angiogenin expression by in situ hybridisation and/or by RT-PCR in tissues and primary cultured trophoblastic cells and angiogenin cellular distribution by coimmunolabelling with cell markers: CD31 (PECAM-1), vascular endothelial cadherin (VE-cadherin), vascular endothelial growth factor receptor-2 (VEGF-R2), Tie-2, von Willebrand factor, CD34, erythropoeitin receptor (Epo-R), alpha-smooth muscle actin, CD45, cytokeratin 7, and Ki-67. Extravillous and villous cytotrophoblasts, isolated and differentiated in vitro, expressed and secreted angiogenin. Angiogenin was detected in villous trophoblastic layers, and structured and nascent fetal vessels. In decidua, it was expressed by glandular epithelial cells, vascular cells and macrophages. The observed pattern of angiogenin expression is compatible with a role in blood vessel formation and in cross-talk between trophoblasts and endothelial cells. In view of angiogenin properties, we suggest that angiogenin may participate in placental vasculogenesis and organogenesis. PMID:25093183

Endophenotype Network Models: Common Core of Complex Diseases

PubMed Central

Ghiassian, Susan Dina; Menche, Jörg; Chasman, Daniel I.; Giulianini, Franco; Wang, Ruisheng; Ricchiuto, Piero; Aikawa, Masanori; Iwata, Hiroshi; Müller, Christian; Zeller, Tania; Sharma, Amitabh; Wild, Philipp; Lackner, Karl; Singh, Sasha; Ridker, Paul M.; Blankenberg, Stefan; Barabási, Albert-László; Loscalzo, Joseph

2016-01-01

Historically, human diseases have been differentiated and categorized based on the organ system in which they primarily manifest. Recently, an alternative view is emerging that emphasizes that different diseases often have common underlying mechanisms and shared intermediate pathophenotypes, or endo(pheno)types. Within this framework, a specific disease’s expression is a consequence of the interplay between the relevant endophenotypes and their local, organ-based environment. Important examples of such endophenotypes are inflammation, fibrosis, and thrombosis and their essential roles in many developing diseases. In this study, we construct endophenotype network models and explore their relation to different diseases in general and to cardiovascular diseases in particular. We identify the local neighborhoods (module) within the interconnected map of molecular components, i.e., the subnetworks of the human interactome that represent the inflammasome, thrombosome, and fibrosome. We find that these neighborhoods are highly overlapping and significantly enriched with disease-associated genes. In particular they are also enriched with differentially expressed genes linked to cardiovascular disease (risk). Finally, using proteomic data, we explore how macrophage activation contributes to our understanding of inflammatory processes and responses. The results of our analysis show that inflammatory responses initiate from within the cross-talk of the three identified endophenotypic modules. PMID:27278246

Endophenotype Network Models: Common Core of Complex Diseases

NASA Astrophysics Data System (ADS)

Ghiassian, Susan Dina; Menche, Jörg; Chasman, Daniel I.; Giulianini, Franco; Wang, Ruisheng; Ricchiuto, Piero; Aikawa, Masanori; Iwata, Hiroshi; Müller, Christian; Zeller, Tania; Sharma, Amitabh; Wild, Philipp; Lackner, Karl; Singh, Sasha; Ridker, Paul M.; Blankenberg, Stefan; Barabási, Albert-László; Loscalzo, Joseph

2016-06-01

Historically, human diseases have been differentiated and categorized based on the organ system in which they primarily manifest. Recently, an alternative view is emerging that emphasizes that different diseases often have common underlying mechanisms and shared intermediate pathophenotypes, or endo(pheno)types. Within this framework, a specific disease’s expression is a consequence of the interplay between the relevant endophenotypes and their local, organ-based environment. Important examples of such endophenotypes are inflammation, fibrosis, and thrombosis and their essential roles in many developing diseases. In this study, we construct endophenotype network models and explore their relation to different diseases in general and to cardiovascular diseases in particular. We identify the local neighborhoods (module) within the interconnected map of molecular components, i.e., the subnetworks of the human interactome that represent the inflammasome, thrombosome, and fibrosome. We find that these neighborhoods are highly overlapping and significantly enriched with disease-associated genes. In particular they are also enriched with differentially expressed genes linked to cardiovascular disease (risk). Finally, using proteomic data, we explore how macrophage activation contributes to our understanding of inflammatory processes and responses. The results of our analysis show that inflammatory responses initiate from within the cross-talk of the three identified endophenotypic modules.

Expression of Momordica charantia MAP30 and its antitumor effect on bladder cancer cells.

PubMed

Hlin, Hao; Zhi-Guo, Zhang; Cong-Hui, Han; Yan, Zhao; Qing, Liang; Bo, Jiang; Hou-Guang, He; Jun-Jie, Zhang; Pei-Ying, Zhang

2016-06-01

Momordica charantia (MC) is an edible medicinal plant that is known for its diversified biological functions. Momordica Antiviral Protein 30kD (MAP30) is a type I single chain ribosome-inactivating protein (RIP) isolated from the mature fruit and seeds of MC. Since MAP30 content in MC is limited, the study aim was to generate the recombinant MAP30 protein using prokaryotic expression system and determine its apoptotic/growth inhibitory effects on bladder cancer 5637 cells. MAP30 gene was amplified by PCR from MC genomic DNA and identified by sequencing. The target gene was inserted into pET-28a (+) vector and transformed into E. coli BL21 (DE3) cells. Positive clones were selected by PCR. Recombinant protein was efficiently expressed under induction with 1.0 mM Isopropylthio-β-D-galactoside (IPTG) at 30° C for 4 hours. Cytotoxicity studies were performed using MTT assay by treating 5637 bladder cancer cells with 100 µg/mL, 200 µg/mL, and 400 µg/mL concentrations of MAP30 for 24 hours and 48 hours, respectively. Flow cytometry was used to measure the apoptosis of MAP30-treatedcells in time course experiments. Full-length MAP30 gene was successfully expressed in Escherichia coli (E. coli) BL21 strain and MAP30 recombinant protein inhibited the growth of bladder cancer 5637 cells at 200 µg/mL and 400 µg/mL concentrations by inducing apoptosis of target cells in a dose- and time-dependent manner. It was, therefore, concluded that the MAP30 recombinant protein displayed potent antitumor activity in vitro.

Expression of a Recombinant Anti-HIV and Anti-Tumor Protein, MAP30, in Nicotiana tobacum Hairy Roots: A pH-Stable and Thermophilic Antimicrobial Protein.

PubMed

Moghadam, Ali; Niazi, Ali; Afsharifar, Alireza; Taghavi, Seyed Mohsen

2016-01-01

In contrast to conventional antibiotics, which microorganisms can readily evade, it is nearly impossible for a microbial strain that is sensitive to antimicrobial proteins to convert to a resistant strain. Therefore, antimicrobial proteins and peptides that are promising alternative candidates for the control of bacterial infections are under investigation. The MAP30 protein of Momordica charantia is a valuable type I ribosome-inactivating protein (RIP) with anti-HIV and anti-tumor activities. Whereas the antimicrobial activity of some type I RIPs has been confirmed, less attention has been paid to the antimicrobial activity of MAP30 produced in a stable, easily handled, and extremely cost-effective protein-expression system. rMAP30-KDEL was expressed in Nicotiana tobacum hairy roots, and its effect on different microorganisms was investigated. Analysis of the extracted total proteins of transgenic hairy roots showed that rMAP30-KDEL was expressed effectively and that this protein exhibited significant antibacterial activity in a dose-dependent manner. rMAP30-KDEL also possessed thermal and pH stability. Bioinformatic analysis of MAP30 and other RIPs regarding their conserved motifs, amino-acid contents, charge, aliphatic index, GRAVY value, and secondary structures demonstrated that these factors accounted for their thermophilicity. Therefore, RIPs such as MAP30 and its derived peptides might have promising applications as food preservatives, and their analysis might provide useful insights into designing clinically applicable antibiotic agents.

Expression of a Recombinant Anti-HIV and Anti-Tumor Protein, MAP30, in Nicotiana tobacum Hairy Roots: A pH-Stable and Thermophilic Antimicrobial Protein

PubMed Central

Moghadam, Ali; Niazi, Ali; Afsharifar, Alireza; Taghavi, Seyed Mohsen

2016-01-01

In contrast to conventional antibiotics, which microorganisms can readily evade, it is nearly impossible for a microbial strain that is sensitive to antimicrobial proteins to convert to a resistant strain. Therefore, antimicrobial proteins and peptides that are promising alternative candidates for the control of bacterial infections are under investigation. The MAP30 protein of Momordica charantia is a valuable type I ribosome-inactivating protein (RIP) with anti-HIV and anti-tumor activities. Whereas the antimicrobial activity of some type I RIPs has been confirmed, less attention has been paid to the antimicrobial activity of MAP30 produced in a stable, easily handled, and extremely cost-effective protein-expression system. rMAP30-KDEL was expressed in Nicotiana tobacum hairy roots, and its effect on different microorganisms was investigated. Analysis of the extracted total proteins of transgenic hairy roots showed that rMAP30-KDEL was expressed effectively and that this protein exhibited significant antibacterial activity in a dose-dependent manner. rMAP30-KDEL also possessed thermal and pH stability. Bioinformatic analysis of MAP30 and other RIPs regarding their conserved motifs, amino-acid contents, charge, aliphatic index, GRAVY value, and secondary structures demonstrated that these factors accounted for their thermophilicity. Therefore, RIPs such as MAP30 and its derived peptides might have promising applications as food preservatives, and their analysis might provide useful insights into designing clinically applicable antibiotic agents. PMID:27459300

EMAP and EMAGE: a framework for understanding spatially organized data.

PubMed

Baldock, Richard A; Bard, Jonathan B L; Burger, Albert; Burton, Nicolas; Christiansen, Jeff; Feng, Guanjie; Hill, Bill; Houghton, Derek; Kaufman, Matthew; Rao, Jianguo; Sharpe, James; Ross, Allyson; Stevenson, Peter; Venkataraman, Shanmugasundaram; Waterhouse, Andrew; Yang, Yiya; Davidson, Duncan R

2003-01-01

The Edinburgh MouseAtlas Project (EMAP) is a time-series of mouse-embryo volumetric models. The models provide a context-free spatial framework onto which structural interpretations and experimental data can be mapped. This enables collation, comparison, and query of complex spatial patterns with respect to each other and with respect to known or hypothesized structure. The atlas also includes a time-dependent anatomical ontology and mapping between the ontology and the spatial models in the form of delineated anatomical regions or tissues. The models provide a natural, graphical context for browsing and visualizing complex data. The Edinburgh Mouse Atlas Gene-Expression Database (EMAGE) is one of the first applications of the EMAP framework and provides a spatially mapped gene-expression database with associated tools for data mapping, submission, and query. In this article, we describe the underlying principles of the Atlas and the gene-expression database, and provide a practical introduction to the use of the EMAP and EMAGE tools, including use of new techniques for whole body gene-expression data capture and mapping.

Comparison of the theoretical and real-world evolutionary potential of a genetic circuit

NASA Astrophysics Data System (ADS)

Razo-Mejia, M.; Boedicker, J. Q.; Jones, D.; DeLuna, A.; Kinney, J. B.; Phillips, R.

2014-04-01

With the development of next-generation sequencing technologies, many large scale experimental efforts aim to map genotypic variability among individuals. This natural variability in populations fuels many fundamental biological processes, ranging from evolutionary adaptation and speciation to the spread of genetic diseases and drug resistance. An interesting and important component of this variability is present within the regulatory regions of genes. As these regions evolve, accumulated mutations lead to modulation of gene expression, which may have consequences for the phenotype. A simple model system where the link between genetic variability, gene regulation and function can be studied in detail is missing. In this article we develop a model to explore how the sequence of the wild-type lac promoter dictates the fold-change in gene expression. The model combines single-base pair resolution maps of transcription factor and RNA polymerase binding energies with a comprehensive thermodynamic model of gene regulation. The model was validated by predicting and then measuring the variability of lac operon regulation in a collection of natural isolates. We then implement the model to analyze the sensitivity of the promoter sequence to the regulatory output, and predict the potential for regulation to evolve due to point mutations in the promoter region.

Application of a new laser Doppler imaging system in planning and monitoring of surgical flaps

NASA Astrophysics Data System (ADS)

Schlosser, Stefan; Wirth, Raphael; Plock, Jan A.; Serov, Alexandre; Banic, Andrej; Erni, Dominique

2010-05-01

There is a demand for technologies able to assess the perfusion of surgical flaps quantitatively and reliably to avoid ischemic complications. The aim of this study is to test a new high-speed high-definition laser Doppler imaging (LDI) system (FluxEXPLORER, Microvascular Imaging, Lausanne, Switzerland) in terms of preoperative mapping of the vascular supply (perforator vessels) and postoperative flow monitoring. The FluxEXPLORER performs perfusion mapping of an area 9×9 cm with a resolution of 256×256 pixels within 6 s in high-definition imaging mode. The sensitivity and predictability to localize perforators is expressed by the coincidence of preoperatively assessed LDI high flow spots with intraoperatively verified perforators in nine patients. 18 free flaps are monitored before, during, and after total ischemia. 63% of all verified perforators correspond to a high flow spot, and 38% of all high flow spots correspond to a verified perforator (positive predictive value). All perfused flaps reveal a value of above 221 perfusion units (PUs), and all values obtained in the ischemic flaps are beneath 187 PU. In summary, we conclude that the present LDI system can serve as a reliable, fast, and easy-to-handle tool to detect ischemia in free flaps, whereas perforator vessels cannot be detected appropriately.

Utility of high-altitude infrared spectral data in mineral exploration: Application to Northern Patagonia Mountains, Arizona

USGS Publications Warehouse

Berger, B.R.; King, T.V.V.; Morath, L.C.; Phillips, J.D.

2003-01-01

Synoptic views of hydrothermal alteration assemblages are of considerable utility in regional-scale minerals exploration. Recent advances in data acquisition and analysis technologies have greatly enhanced the usefulness of remotely sensed imaging spectroscopy for reliable alteration mineral assemblages mapping. Using NASA's Airborne Visible Infrared Imaging Spectrometer (AVIRIS) sensor, this study mapped large areas of advanced argillic and phyllic-argillic alteration assemblages in the southeastern Santa Rita and northern Patagonia mountains, Arizona. Two concealed porphyry copper deposits have been identified during past exploration, the Red Mountain and Sunnyside deposits, and related published hydrothermal alteration zoning studies allow the comparison of the results obtained from AVIRIS data to the more traditional field mapping approaches. The AVIRIS mapping compares favorably with field-based studies. An analysis of iron-bearing oxide minerals above a concealed supergene chalcocite deposit at Red Mountain also indicates that remotely sensed data can be of value in the interpretation of leached caps above porphyry copper deposits. In conjunction with other types of geophysical data, AVIRIS mineral maps can be used to discriminate different exploration targets within a region.

Four not six: Revealing culturally common facial expressions of emotion.

PubMed

Jack, Rachael E; Sun, Wei; Delis, Ioannis; Garrod, Oliver G B; Schyns, Philippe G

2016-06-01

As a highly social species, humans generate complex facial expressions to communicate a diverse range of emotions. Since Darwin's work, identifying among these complex patterns which are common across cultures and which are culture-specific has remained a central question in psychology, anthropology, philosophy, and more recently machine vision and social robotics. Classic approaches to addressing this question typically tested the cross-cultural recognition of theoretically motivated facial expressions representing 6 emotions, and reported universality. Yet, variable recognition accuracy across cultures suggests a narrower cross-cultural communication supported by sets of simpler expressive patterns embedded in more complex facial expressions. We explore this hypothesis by modeling the facial expressions of over 60 emotions across 2 cultures, and segregating out the latent expressive patterns. Using a multidisciplinary approach, we first map the conceptual organization of a broad spectrum of emotion words by building semantic networks in 2 cultures. For each emotion word in each culture, we then model and validate its corresponding dynamic facial expression, producing over 60 culturally valid facial expression models. We then apply to the pooled models a multivariate data reduction technique, revealing 4 latent and culturally common facial expression patterns that each communicates specific combinations of valence, arousal, and dominance. We then reveal the face movements that accentuate each latent expressive pattern to create complex facial expressions. Our data questions the widely held view that 6 facial expression patterns are universal, instead suggesting 4 latent expressive patterns with direct implications for emotion communication, social psychology, cognitive neuroscience, and social robotics. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Dual Transcriptomic Profiling of Host and Microbiota during Health and Disease in Pediatric Asthma.

PubMed

Pérez-Losada, Marcos; Castro-Nallar, Eduardo; Bendall, Matthew L; Freishtat, Robert J; Crandall, Keith A

2015-01-01

High-throughput sequencing (HTS) analysis of microbial communities from the respiratory airways has heavily relied on the 16S rRNA gene. Given the intrinsic limitations of this approach, airway microbiome research has focused on assessing bacterial composition during health and disease, and its variation in relation to clinical and environmental factors, or other microbiomes. Consequently, very little effort has been dedicated to describing the functional characteristics of the airway microbiota and even less to explore the microbe-host interactions. Here we present a simultaneous assessment of microbiome and host functional diversity and host-microbe interactions from the same RNA-seq experiment, while accounting for variation in clinical metadata. Transcriptomic (host) and metatranscriptomic (microbiota) sequences from the nasal epithelium of 8 asthmatics and 6 healthy controls were separated in silico and mapped to available human and NCBI-NR protein reference databases. Human genes differentially expressed in asthmatics and controls were then used to infer upstream regulators involved in immune and inflammatory responses. Concomitantly, microbial genes were mapped to metabolic databases (COG, SEED, and KEGG) to infer microbial functions differentially expressed in asthmatics and controls. Finally, multivariate analysis was applied to find associations between microbiome characteristics and host upstream regulators while accounting for clinical variation. Our study showed significant differences in the metabolism of microbiomes from asthmatic and non-asthmatic children for up to 25% of the functional properties tested. Enrichment analysis of 499 differentially expressed host genes for inflammatory and immune responses revealed 43 upstream regulators differentially activated in asthma. Microbial adhesion (virulence) and Proteobacteria abundance were significantly associated with variation in the expression of the upstream regulator IL1A; suggesting that microbiome characteristics modulate host inflammatory and immune systems during asthma.

Robustness, evolvability, and the logic of genetic regulation.

PubMed

Payne, Joshua L; Moore, Jason H; Wagner, Andreas

2014-01-01

In gene regulatory circuits, the expression of individual genes is commonly modulated by a set of regulating gene products, which bind to a gene's cis-regulatory region. This region encodes an input-output function, referred to as signal-integration logic, that maps a specific combination of regulatory signals (inputs) to a particular expression state (output) of a gene. The space of all possible signal-integration functions is vast and the mapping from input to output is many-to-one: For the same set of inputs, many functions (genotypes) yield the same expression output (phenotype). Here, we exhaustively enumerate the set of signal-integration functions that yield identical gene expression patterns within a computational model of gene regulatory circuits. Our goal is to characterize the relationship between robustness and evolvability in the signal-integration space of regulatory circuits, and to understand how these properties vary between the genotypic and phenotypic scales. Among other results, we find that the distributions of genotypic robustness are skewed, so that the majority of signal-integration functions are robust to perturbation. We show that the connected set of genotypes that make up a given phenotype are constrained to specific regions of the space of all possible signal-integration functions, but that as the distance between genotypes increases, so does their capacity for unique innovations. In addition, we find that robust phenotypes are (i) evolvable, (ii) easily identified by random mutation, and (iii) mutationally biased toward other robust phenotypes. We explore the implications of these latter observations for mutation-based evolution by conducting random walks between randomly chosen source and target phenotypes. We demonstrate that the time required to identify the target phenotype is independent of the properties of the source phenotype.

Robustness, Evolvability, and the Logic of Genetic Regulation

PubMed Central

Moore, Jason H.; Wagner, Andreas

2014-01-01

In gene regulatory circuits, the expression of individual genes is commonly modulated by a set of regulating gene products, which bind to a gene’s cis-regulatory region. This region encodes an input-output function, referred to as signal-integration logic, that maps a specific combination of regulatory signals (inputs) to a particular expression state (output) of a gene. The space of all possible signal-integration functions is vast and the mapping from input to output is many-to-one: for the same set of inputs, many functions (genotypes) yield the same expression output (phenotype). Here, we exhaustively enumerate the set of signal-integration functions that yield idential gene expression patterns within a computational model of gene regulatory circuits. Our goal is to characterize the relationship between robustness and evolvability in the signal-integration space of regulatory circuits, and to understand how these properties vary between the genotypic and phenotypic scales. Among other results, we find that the distributions of genotypic robustness are skewed, such that the majority of signal-integration functions are robust to perturbation. We show that the connected set of genotypes that make up a given phenotype are constrained to specific regions of the space of all possible signal-integration functions, but that as the distance between genotypes increases, so does their capacity for unique innovations. In addition, we find that robust phenotypes are (i) evolvable, (ii) easily identified by random mutation, and (iii) mutationally biased toward other robust phenotypes. We explore the implications of these latter observations for mutation-based evolution by conducting random walks between randomly chosen source and target phenotypes. We demonstrate that the time required to identify the target phenotype is independent of the properties of the source phenotype. PMID:23373974

Ephrin-B2 Reverse Signaling Is Required for Topography but Not Pattern Formation of Lateral Superior Olivary Inputs to the Inferior Colliculus

PubMed Central

Wallace, Matthew M.; Kavianpour, Sarah M.; Gabriele, Mark L.

2014-01-01

Graded and modular expressions of Eph-ephrins are known to provide positional information for the formation of topographic maps and patterning in the developing nervous system. Previously we have shown that ephrin-B2 is expressed in a continuous gradient across the tonotopic axis of the central nucleus of the inferior colliculus (CNIC), whereas patterns are discontinuous and modular in the lateral cortex of the IC (LCIC). The present study explores the involvement of ephrin-B2 signaling in the development of projections to the CNIC and LCIC arising from the lateral superior olivary nuclei (LSO) prior to hearing onset. Anterograde and retrograde fluorescent tracing methods in neonatal fixed tissue preparations were used to compare topographic mapping and the establishment of LSO layers/modules in wild-type and ephrin-B2lacZ/+ mice (severely compromised reverse signaling). At birth, pioneer LSO axons occupy the ipsilateral IC in both groups but are delayed contralaterally in ephrin-B2lacZ/+ mutants. By the onset of hearing, both wild-type and mutant projections form discernible layers bilaterally in the CNIC and modular arrangements within the ipsilateral LCIC. In contrast, ephrin-B2lacZ/+ mice lack a reliable topography in LSO-IC projections, suggesting that fully functional ephrin-B2 reverse signaling is required for normal projection mapping. Taken together, these ephrin-B2 findings paired with known coexpression of EphA4 suggest the importance of these signaling proteins in establishing functional auditory circuits prior to experience. PMID:23042409

Ephrin-B2 reverse signaling is required for topography but not pattern formation of lateral superior olivary inputs to the inferior colliculus.

PubMed

Wallace, Matthew M; Kavianpour, Sarah M; Gabriele, Mark L

2013-05-01

Graded and modular expressions of Eph-ephrins are known to provide positional information for the formation of topographic maps and patterning in the developing nervous system. Previously we have shown that ephrin-B2 is expressed in a continuous gradient across the tonotopic axis of the central nucleus of the inferior colliculus (CNIC), whereas patterns are discontinuous and modular in the lateral cortex of the IC (LCIC). The present study explores the involvement of ephrin-B2 signaling in the development of projections to the CNIC and LCIC arising from the lateral superior olivary nuclei (LSO) prior to hearing onset. Anterograde and retrograde fluorescent tracing methods in neonatal fixed tissue preparations were used to compare topographic mapping and the establishment of LSO layers/modules in wild-type and ephrin-B2(lacZ/+) mice (severely compromised reverse signaling). At birth, pioneer LSO axons occupy the ipsilateral IC in both groups but are delayed contralaterally in ephrin-B2(lacZ/+) mutants. By the onset of hearing, both wild-type and mutant projections form discernible layers bilaterally in the CNIC and modular arrangements within the ipsilateral LCIC. In contrast, ephrin-B2(lacZ/+) mice lack a reliable topography in LSO-IC projections, suggesting that fully functional ephrin-B2 reverse signaling is required for normal projection mapping. Taken together, these ephrin-B2 findings paired with known coexpression of EphA4 suggest the importance of these signaling proteins in establishing functional auditory circuits prior to experience. Copyright © 2012 Wiley Periodicals, Inc.

The effect of cavernous nerve traction on erectile function in rats

PubMed Central

Chen, Liping; Wang, Tao; Wang, Shaogang; Liu, Jihong

2017-01-01

We performed this study to evaluate the effect of cavernous nerve (CN) traction on erectile function in rats. Thirty-two 8- week-old Sprague–Dawley rats were divided into four groups: control, 1-minute CN traction, 2-minute CN traction, and 2-minute CN crush. CN traction was performed using a glass hook with a tensile force of 0.2 Newton. One month later, the mean arterial pressure (MAP) and intracavernosal pressure (ICP) in response to CN stimulation were measured to assess erectile function. The penis and major pelvic ganglion (MPG) were harvested to explore the expression of neuronal nitric oxide synthase (nNOS) and neurofilament, fibrosis and apoptosis. The ICP/MAP ratio was reduced in the 2-minute CN traction group compared with the control group (P < 0.05). The ICP/MAP ratio in the CN crush group was lower than in the other three groups (P < 0.05, for each). Expression of nNOS in both MPG and dorsal penile nerve was lower in the CN traction group than in the control group, but was higher than in the CN crush group (P < 0.05). Nerve fiber number in the dorsal penile nerve was reduced by 2-minute CN traction (P < 0.05). The ratios of collagen to smooth muscle content and the apoptosis were both increased the in 2-minute CN traction group compared with the control group (P < 0.05). The findings indicate that CN traction is an effective CN injury model and the injury it caused is relatively mild compared with the CN crush model. PMID:28982169

Disease quantification on PET/CT images without object delineation

NASA Astrophysics Data System (ADS)

Tong, Yubing; Udupa, Jayaram K.; Odhner, Dewey; Wu, Caiyun; Fitzpatrick, Danielle; Winchell, Nicole; Schuster, Stephen J.; Torigian, Drew A.

2017-03-01

The derivation of quantitative information from images to make quantitative radiology (QR) clinically practical continues to face a major image analysis hurdle because of image segmentation challenges. This paper presents a novel approach to disease quantification (DQ) via positron emission tomography/computed tomography (PET/CT) images that explores how to decouple DQ methods from explicit dependence on object segmentation through the use of only object recognition results to quantify disease burden. The concept of an object-dependent disease map is introduced to express disease severity without performing explicit delineation and partial volume correction of either objects or lesions. The parameters of the disease map are estimated from a set of training image data sets. The idea is illustrated on 20 lung lesions and 20 liver lesions derived from 18F-2-fluoro-2-deoxy-D-glucose (FDG)-PET/CT scans of patients with various types of cancers and also on 20 NEMA PET/CT phantom data sets. Our preliminary results show that, on phantom data sets, "disease burden" can be estimated to within 2% of known absolute true activity. Notwithstanding the difficulty in establishing true quantification on patient PET images, our results achieve 8% deviation from "true" estimates, with slightly larger deviations for small and diffuse lesions where establishing ground truth becomes really questionable, and smaller deviations for larger lesions where ground truth set up becomes more reliable. We are currently exploring extensions of the approach to include fully automated body-wide DQ, extensions to just CT or magnetic resonance imaging (MRI) alone, to PET/CT performed with radiotracers other than FDG, and other functional forms of disease maps.

Exploring discrepancies between quantitative validation results and the geomorphic plausibility of statistical landslide susceptibility maps

NASA Astrophysics Data System (ADS)

Steger, Stefan; Brenning, Alexander; Bell, Rainer; Petschko, Helene; Glade, Thomas

2016-06-01

Empirical models are frequently applied to produce landslide susceptibility maps for large areas. Subsequent quantitative validation results are routinely used as the primary criteria to infer the validity and applicability of the final maps or to select one of several models. This study hypothesizes that such direct deductions can be misleading. The main objective was to explore discrepancies between the predictive performance of a landslide susceptibility model and the geomorphic plausibility of subsequent landslide susceptibility maps while a particular emphasis was placed on the influence of incomplete landslide inventories on modelling and validation results. The study was conducted within the Flysch Zone of Lower Austria (1,354 km2) which is known to be highly susceptible to landslides of the slide-type movement. Sixteen susceptibility models were generated by applying two statistical classifiers (logistic regression and generalized additive model) and two machine learning techniques (random forest and support vector machine) separately for two landslide inventories of differing completeness and two predictor sets. The results were validated quantitatively by estimating the area under the receiver operating characteristic curve (AUROC) with single holdout and spatial cross-validation technique. The heuristic evaluation of the geomorphic plausibility of the final results was supported by findings of an exploratory data analysis, an estimation of odds ratios and an evaluation of the spatial structure of the final maps. The results showed that maps generated by different inventories, classifiers and predictors appeared differently while holdout validation revealed similar high predictive performances. Spatial cross-validation proved useful to expose spatially varying inconsistencies of the modelling results while additionally providing evidence for slightly overfitted machine learning-based models. However, the highest predictive performances were obtained for maps that explicitly expressed geomorphically implausible relationships indicating that the predictive performance of a model might be misleading in the case a predictor systematically relates to a spatially consistent bias of the inventory. Furthermore, we observed that random forest-based maps displayed spatial artifacts. The most plausible susceptibility map of the study area showed smooth prediction surfaces while the underlying model revealed a high predictive capability and was generated with an accurate landslide inventory and predictors that did not directly describe a bias. However, none of the presented models was found to be completely unbiased. This study showed that high predictive performances cannot be equated with a high plausibility and applicability of subsequent landslide susceptibility maps. We suggest that greater emphasis should be placed on identifying confounding factors and biases in landslide inventories. A joint discussion between modelers and decision makers of the spatial pattern of the final susceptibility maps in the field might increase their acceptance and applicability.

Working towards a clearer and more helpful hazard map: investigating the influence of hazard map design on hazard communication

NASA Astrophysics Data System (ADS)

Thompson, M. A.; Lindsay, J. M.; Gaillard, J.

2015-12-01

Globally, geological hazards are communicated using maps. In traditional hazard mapping practice, scientists analyse data about a hazard, and then display the results on a map for stakeholder and public use. However, this one-way, top-down approach to hazard communication is not necessarily effective or reliable. The messages which people take away will be dependent on the way in which they read, interpret, and understand the map, a facet of hazard communication which has been relatively unexplored. Decades of cartographic studies suggest that variables in the visual representation of data on maps, such as colour and symbology, can have a powerful effect on how people understand map content. In practice, however, there is little guidance or consistency in how hazard information is expressed and represented on maps. Accordingly, decisions are often made based on subjective preference, rather than research-backed principles. Here we present the results of a study in which we explore how hazard map design features can influence hazard map interpretation, and we propose a number of considerations for hazard map design. A series of hazard maps were generated, with each one showing the same probabilistic volcanic ashfall dataset, but using different verbal and visual variables (e.g., different colour schemes, data classifications, probabilistic formats). Following a short pilot study, these maps were used in an online survey of 110 stakeholders and scientists in New Zealand. Participants answered 30 open-ended and multiple choice questions about ashfall hazard based on the different maps. Results suggest that hazard map design can have a significant influence on the messages readers take away. For example, diverging colour schemes were associated with concepts of "risk" and decision-making more than sequential schemes, and participants made more precise estimates of hazard with isarithmic data classifications compared to binned or gradational shading. Based on such findings, we make a number of suggestions for communicating hazard using maps. Most importantly, we emphasise that multiple meanings may be taken away from a map, and this may have important implications in a crisis. We propose that engaging with map audiences in a two-way dialogue in times of peace may help prevent miscommunications in the event of a crisis.

Gonadal Transcriptome Analysis of Male and Female Olive Flounder (Paralichthys olivaceus)

PubMed Central

Fan, Zhaofei; You, Feng; Wang, Lijuan; Weng, Shenda; Wu, Zhihao; Hu, Jinwei; Zou, Yuxia; Tan, Xungang; Zhang, Peijun

2014-01-01

Olive flounder (Paralichthys olivaceus) is an important commercially cultured marine flatfish in China, Korea, and Japan, of which female grows faster than male. In order to explore the molecular mechanism of flounder sex determination and development, we used RNA-seq technology to investigate transcriptomes of flounder gonads. This produced 22,253,217 and 19,777,841 qualified reads from ovary and testes, which were jointly assembled into 97,233 contigs. Among them, 23,223 contigs were mapped to known genes, of which 2,193 were predicted to be differentially expressed in ovary and 887 in testes. According to annotation information, several sex-related biological pathways including ovarian steroidogenesis and estrogen signaling pathways were firstly found in flounder. The dimorphic expression of overall sex-related genes provides further insights into sex determination and gonadal development. Our study also provides an archive for further studies of molecular mechanism of fish sex determination. PMID:25121093

Neutrality and Robustness in Evo-Devo: Emergence of Lateral Inhibition

PubMed Central

Munteanu, Andreea; Solé, Ricard V.

2008-01-01

Embryonic development is defined by the hierarchical dynamical process that translates genetic information (genotype) into a spatial gene expression pattern (phenotype) providing the positional information for the correct unfolding of the organism. The nature and evolutionary implications of genotype–phenotype mapping still remain key topics in evolutionary developmental biology (evo-devo). We have explored here issues of neutrality, robustness, and diversity in evo-devo by means of a simple model of gene regulatory networks. The small size of the system allowed an exhaustive analysis of the entire fitness landscape and the extent of its neutrality. This analysis shows that evolution leads to a class of robust genetic networks with an expression pattern characteristic of lateral inhibition. This class is a repertoire of distinct implementations of this key developmental process, the diversity of which provides valuable clues about its underlying causal principles. PMID:19023404

Students' Ideas about How and Why Chemical Reactions Happen: Mapping the conceptual landscape

NASA Astrophysics Data System (ADS)

Yan, Fan; Talanquer, Vicente

2015-12-01

Research in science education has revealed that many students struggle to understand chemical reactions. Improving teaching and learning about chemical processes demands that we develop a clearer understanding of student reasoning in this area and of how this reasoning evolves with training in the domain. Thus, we have carried out a qualitative study to explore students reasoning about chemical causality and mechanism. Study participants included individuals at different educational levels, from college to graduate school. We identified diverse conceptual modes expressed by students when engaged in the analysis of different types of reactions. Main findings indicate that student reasoning about chemical reactions is influenced by the nature of the process. More advanced students tended to express conceptual modes that were more normative and had more explanatory power, but major conceptual difficulties persisted in their reasoning. The results of our study are relevant to educators interested in conceptual development, learning progressions, and assessment.

Regional mapping of hydrothermally altered igneous rocks along the Urumieh-Dokhtar, Chagai, and Alborz Belts of western Asia using Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) data and Interactive Data Language (IDL) logical operators: a tool for porphyry copper exploration and assessment: Chapter O in Global mineral resource assessment

USGS Publications Warehouse

Mars, John L.; Zientek, M.L.; Hammarstrom, J.M.; Johnson, K.M.; Pierce, F.W.

2014-01-01

The ASTER alteration map and corresponding geologic maps were used to select circular to elliptical patterns of argillic- and phyllic-altered volcanic and intrusive rocks as potential porphyry copper sites. One hundred and seventy eight potential porphyry copper sites were mapped along the UDVB, and 23 sites were mapped along the CVB. The potential sites were selected to assist in further exploration and assessments of undiscovered porphyry copper deposits.

Cellular context–mediated Akt dynamics regulates MAP kinase signaling thresholds during angiogenesis

PubMed Central

Hellesøy, Monica; Lorens, James B.

2015-01-01

The formation of new blood vessels by sprouting angiogenesis is tightly regulated by contextual cues that affect angiogeneic growth factor signaling. Both constitutive activation and loss of Akt kinase activity in endothelial cells impair angiogenesis, suggesting that Akt dynamics mediates contextual microenvironmental regulation. We explored the temporal regulation of Akt in endothelial cells during formation of capillary-like networks induced by cell–cell contact with vascular smooth muscle cells (vSMCs) and vSMC-associated VEGF. Expression of constitutively active Akt1 strongly inhibited network formation, whereas hemiphosphorylated Akt1 epi-alleles with reduced kinase activity had an intermediate inhibitory effect. Conversely, inhibition of Akt signaling did not affect endothelial cell migration or morphogenesis in vSMC cocultures that generate capillary-like structures. We found that endothelial Akt activity is transiently blocked by proteasomal degradation in the presence of SMCs during the initial phase of capillary-like structure formation. Suppressed Akt activity corresponded to the increased endothelial MAP kinase signaling that was required for angiogenic endothelial morphogenesis. These results reveal a regulatory principle by which cellular context regulates Akt protein dynamics, which determines MAP kinase signaling thresholds necessary drive a morphogenetic program during angiogenesis. PMID:26023089

YouGenMap: a web platform for dynamic multi-comparative mapping and visualization of genetic maps

Treesearch

Keith Batesole; Kokulapalan Wimalanathan; Lin Liu; Fan Zhang; Craig S. Echt; Chun Liang

2014-01-01

Comparative genetic maps are used in examination of genome organization, detection of conserved gene order, and exploration of marker order variations. YouGenMap is an open-source web tool that offers dynamic comparative mapping capability of users' own genetic mapping between 2 or more map sets. Users' genetic map data and optional gene annotations are...

Understanding the Cryosphere of Europa Using Imaging Spectroscopy

NASA Astrophysics Data System (ADS)

Blaney, D. L.; Green, R. O.; Hibbitts, C.; Clark, R. N.; Dalton, J. B.; Davies, A. G.; Langevin, Y.; Hedman, M.; Lunine, J. I.; McCord, T. B.; Murchie, S. L.; Paranicas, C.; Seelos, F. P.; Soderblom, J. M.; Diniega, S.

2017-12-01

Europa's surface expresses a complex interplay of geologic processes driven by the ocean beneath the cryosphere that are subsequently modified by the Jovian environment once exposed on the surface. Several recent Earth-based observations of Europa's tenuous atmosphere suggest that there may in fact be active plumes [1,2,3]. However, the frequency and the duration of activity at any specific location cannot be precisely determined by these observations, but could be with spacecraft observations. For instance, recently active areas on Europa from plumes or other processes may result in distinctive spectral signatures on the surface. Possible spectral signatures that may indicate recent activity include: differences in ice grain size or ice crystallinity; the lack of radiolytic signatures (e.g. a deficit in species due to implantation, radiation darkening of salts, degradation of organic compounds); and thermal anomalies. The Mapping Imaging Spectrometer for Europa (MISE) on NASA's Europa Clipper Mission will be able to map these species thus enabling the identification of these deposits and other young and/or least processed areas. These signatures may also enable a relative geochronology for Europa to be developed. For example, recent work by Proctor et al [4] finds that bands of different stratigraphic ages have different spectral features potentially due to radiation effects on the deposits. We will explore borrowing analyses techniques from earth observing missions of the Arctic. On Earth, data from the Airborne Visible / Infrared Imaging Spectrometer Next Generation (AVRIS-NG) (https://avirisng.jpl.nasa.gov/aviris-ng.html) is being used to explore Earth's cryosphere. AVRIS-NG data collected from the Greenland ice sheet and high latitude sea ice is being used to map of key ice properties such as grain size and contaminants. These data and processing approaches will be used to explore and validate imaging spectroscopy approaches which MISE might use on Europa.

Human and Robotic Mission to Small Bodies: Mapping, Planning and Exploration

NASA Technical Reports Server (NTRS)

Neffian, Ara V.; Bellerose, Julie; Beyer, Ross A.; Archinal, Brent; Edwards, Laurence; Lee, Pascal; Colaprete, Anthony; Fong, Terry

2013-01-01

This study investigates the requirements, performs a gap analysis and makes a set of recommendations for mapping products and exploration tools required to support operations and scientific discovery for near- term and future NASA missions to small bodies. The mapping products and their requirements are based on the analysis of current mission scenarios (rendezvous, docking, and sample return) and recommendations made by the NEA Users Team (NUT) in the framework of human exploration. The mapping products that sat- isfy operational, scienti c, and public outreach goals include topography, images, albedo, gravity, mass, density, subsurface radar, mineralogical and thermal maps. The gap analysis points to a need for incremental generation of mapping products from low (flyby) to high-resolution data needed for anchoring and docking, real-time spatial data processing for hazard avoidance and astronaut or robot localization in low gravity, high dynamic environments, and motivates a standard for coordinate reference systems capable of describing irregular body shapes. Another aspect investigated in this study is the set of requirements and the gap analysis for exploration tools that support visualization and simulation of operational conditions including soil interactions, environment dynamics, and communications coverage. Building robust, usable data sets and visualisation/simulation tools is the best way for mission designers and simulators to make correct decisions for future missions. In the near term, it is the most useful way to begin building capabilities for small body exploration without needing to commit to specific mission architectures.

MAP30 promotes apoptosis of U251 and U87 cells by suppressing the LGR5 and Wnt/β-catenin signaling pathway, and enhancing Smac expression

PubMed Central

Jiang, Yilin; Miao, Junjie; Wang, Dongliang; Zhou, Jingru; Liu, Bo; Jiao, Feng; Liang, Jiangfeng; Wang, Yangshuo; Fan, Cungang; Zhang, Qingjun

2018-01-01

Significant antitumor activity of Momordica anti-human immunodeficiency virus protein of 30 kDa (MAP30) purified from Momordica charantia has been the subject of previous research. However, the effective mechanism of MAP30 on malignant glioma cells has not yet been clarified. The aim of the present study was to investigate the effects and mechanism of MAP30 on U87 and U251 cell lines. A Cell Counting Kit-8 assay, wound healing assay and Transwell assay were used to detect the effects on U87 and U251 cells treated with different concentrations of MAP30 (0.5, 1, 2, 4, 8 and 16 µM) over different periods of time. Proliferation, migration and invasion of each cell line were markedly inhibited by MAP30 in a dose- and time-dependent manner. Flow cytometry and fluorescence staining demonstrated that apoptosis increased and the cell cycle was arrested in S-phase in the two investigated cell lines following MAP30 treatment. Western blot analysis demonstrated that leucine-rich-repeat-containing G-protein-coupled receptor 5 (LGR5) expression and key proteins in the Wnt/β-catenin signaling pathway were apparently decreased, whereas second mitochondria-derived activator of caspase (Smac) protein expression significantly increased with MAP30 treatment in the same manner. These results suggest that MAP30 markedly induces apoptosis in U87 and U251 cell lines by suppressing LGR5 and the Wnt/β-catenin signaling pathway, and enhancing Smac expression in a dose- and time-dependent manner. PMID:29556310

Absolute color scale for improved diagnostics with wavefront error mapping.

PubMed

Smolek, Michael K; Klyce, Stephen D

2007-11-01

Wavefront data are expressed in micrometers and referenced to the pupil plane, but current methods to map wavefront error lack standardization. Many use normalized or floating scales that may confuse the user by generating ambiguous, noisy, or varying information. An absolute scale that combines consistent clinical information with statistical relevance is needed for wavefront error mapping. The color contours should correspond better to current corneal topography standards to improve clinical interpretation. Retrospective analysis of wavefront error data. Historic ophthalmic medical records. Topographic modeling system topographical examinations of 120 corneas across 12 categories were used. Corneal wavefront error data in micrometers from each topography map were extracted at 8 Zernike polynomial orders and for 3 pupil diameters expressed in millimeters (3, 5, and 7 mm). Both total aberrations (orders 2 through 8) and higher-order aberrations (orders 3 through 8) were expressed in the form of frequency histograms to determine the working range of the scale across all categories. The standard deviation of the mean error of normal corneas determined the map contour resolution. Map colors were based on corneal topography color standards and on the ability to distinguish adjacent color contours through contrast. Higher-order and total wavefront error contour maps for different corneal conditions. An absolute color scale was produced that encompassed a range of +/-6.5 microm and a contour interval of 0.5 microm. All aberrations in the categorical database were plotted with no loss of clinical information necessary for classification. In the few instances where mapped information was beyond the range of the scale, the type and severity of aberration remained legible. When wavefront data are expressed in micrometers, this absolute scale facilitates the determination of the severity of aberrations present compared with a floating scale, particularly for distinguishing normal from abnormal levels of wavefront error. The new color palette makes it easier to identify disorders. The corneal mapping method can be extended to mapping whole eye wavefront errors. When refraction data are expressed in diopters, the previously published corneal topography scale is suggested.

Dominance and Sexual Dimorphism Pervade the Salix purpurea L. Transcriptome

DOE PAGES

Carlson, Craig H.; Choi, Yongwook; Chan, Agnes P.; ...

2017-09-01

The heritability of gene expression is critical in understanding heterosis and is dependent on allele-specific regulation by local and remote factors in the genome. We used RNA-Seq to test whether variation in gene expression among F 1 and F 2 intraspecific Salix purpurea progeny is attributable to cis- and trans-regulatory divergence. We assessed the mode of inheritance based on gene expression levels and allele-specific expression for F1 and F2 intraspecific progeny in two distinct tissue types: shoot tip and stem internode. In addition, we explored sexually dimorphic patterns of inheritance and regulatory divergence among F 1 progeny individuals. We showmore » that in S. purpurea intraspecific crosses, gene expression inheritance largely exhibits a maternal dominant pattern, regardless of tissue type or pedigree. A significantly greater number of cis- and trans-regulated genes coincided with upregulation of the maternal parent allele in the progeny, irrespective of the magnitude, whereas the paternal allele was higher expressed for genes showing cis × trans or compensatory regulation. Importantly, consistent with previous genetic mapping results for sex in shrub willow, we have delimited sex-biased gene expression to a 2 Mb pericentromeric region on S. purpurea chr15 and further refined the sex determination region. Lastly, altogether, our results offer insight into the inheritance of gene expression in S. purpurea as well as evidence of sexually dimorphic expression which may have contributed to the evolution of dioecy in Salix.« less

Dominance and Sexual Dimorphism Pervade the Salix purpurea L. Transcriptome

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

Carlson, Craig H.; Choi, Yongwook; Chan, Agnes P.

The heritability of gene expression is critical in understanding heterosis and is dependent on allele-specific regulation by local and remote factors in the genome. We used RNA-Seq to test whether variation in gene expression among F 1 and F 2 intraspecific Salix purpurea progeny is attributable to cis- and trans-regulatory divergence. We assessed the mode of inheritance based on gene expression levels and allele-specific expression for F1 and F2 intraspecific progeny in two distinct tissue types: shoot tip and stem internode. In addition, we explored sexually dimorphic patterns of inheritance and regulatory divergence among F 1 progeny individuals. We showmore » that in S. purpurea intraspecific crosses, gene expression inheritance largely exhibits a maternal dominant pattern, regardless of tissue type or pedigree. A significantly greater number of cis- and trans-regulated genes coincided with upregulation of the maternal parent allele in the progeny, irrespective of the magnitude, whereas the paternal allele was higher expressed for genes showing cis × trans or compensatory regulation. Importantly, consistent with previous genetic mapping results for sex in shrub willow, we have delimited sex-biased gene expression to a 2 Mb pericentromeric region on S. purpurea chr15 and further refined the sex determination region. Lastly, altogether, our results offer insight into the inheritance of gene expression in S. purpurea as well as evidence of sexually dimorphic expression which may have contributed to the evolution of dioecy in Salix.« less

New Strategy for Exploration Technology Development: The Human Exploration and Development of Space (HEDS) Exploration/Commercialization Technology Initiative

NASA Technical Reports Server (NTRS)

Mankins, John C.

2000-01-01

In FY 2001, NASA will undertake a new research and technology program supporting the goals of human exploration: the Human Exploration and Development of Space (HEDS) Exploration/Commercialization Technology Initiative (HTCI). The HTCI represents a new strategic approach to exploration technology, in which an emphasis will be placed on identifying and developing technologies for systems and infrastructures that may be common among exploration and commercial development of space objectives. A family of preliminary strategic research and technology (R&T) road maps have been formulated that address "technology for human exploration and development of space (THREADS). These road maps frame and bound the likely content of the HTCL Notional technology themes for the initiative include: (1) space resources development, (2) space utilities and power, (3) habitation and bioastronautics, (4) space assembly, inspection and maintenance, (5) exploration and expeditions, and (6) space transportation. This paper will summarize the results of the THREADS road mapping process and describe the current status and content of the HTCI within that framework. The paper will highlight the space resources development theme within the Initiative and will summarize plans for the coming year.

NOAA Ship Okeanos Explorer 2012 Field Season in the Northern Gulf of Mexico and U.S. Atlantic Continental Margin

NASA Astrophysics Data System (ADS)

Skarke, A. D.; Lobecker, E.; Malik, M.; VerPlanck, N.

2012-12-01

The NOAA Ship Okeanos Explorer, jointly operated by the NOAA Office of Ocean Exploration and Research and the NOAA Office of Marine and Aviation Operations, is America's only federally managed ship dedicated solely to ocean exploration. The 2012 field season was spent exploring the northern Gulf of Mexico and the U.S. Atlantic continental shelf break and slope. In the Gulf of Mexico, mapping and remotely operated vehicle operations focused on the salt domes and canyons offshore Mississippi and Louisiana, and characterized several of the hundreds of seeps that were detected in the water column backscatter data collected with the ship's Kongsberg EM 302 multibeam sonar (30 kHz) during the 2011 field season. A team of NOAA and non-NOAA partners identified priority frontier areas along the continental shelf and slope between North Carolina and Cape Cod, mapping numerous canyons selected for focused mapping exploration in partnership with the North East Fisheries Science Center, the Mid-Atlantic Regional Council on the Ocean (a state level partnership between various states including NY, NJ, DE, MD, and VA), Woods Hole Oceanographic Institution (WHOI) and Virginia Sea Grant. The 2012 mapping efforts built on data collected during the 2011 field season. Okeanos Explorer data were leveraged by NOAA Ship Henry B. Bigelow to conduct towed camera operations to ground truth multibeam backscatter data for deepwater coral habitat assessment. The Blake Ridge and Cape Fear Diapirs offshore North Carolina were a third focus of exploration operations. Seven 900 meter high cold seeps were discovered in the diapir province. Exploration incorporated WHOI's Sentry autonomous underwater vehicle and its full suite of mapping and oceanographic sensors were used to characterize six seep sites. All data collected by Okeanos Explorer are available via the NOAA public archives with metadata records within 60 to 90 days of the end of each cruise.

Molecular-biological analysis of the effect of methamphetamine on the heart in restrained mice.

PubMed

Shinone, Kotaro; Tomita, Masafumi; Inoue, Hiromasa; Nakagawa, Yasuhisa; Ikemura, Mayumi; Nata, Masayuki

2010-03-01

In order to investigate the interaction in the heart between the administration of methamphetamine (MAP) and restraint of the body following it, we administrated MAP intraperitoneally to mice and restrained them, and then determined the level of mRNA expression of 22 genes in the heart using quantitative RT-PCR method. The mRNA expressions of Nfkbiz, Nr4a1 and Dusp1 changed significantly after the administration of MAP, suggesting the induction of an inflammatory condition such as damage to the myocardium. Moreover, the serum concentrations of inflammatory cytokines such as tumor necrosis factor-alpha, interleukin (IL)-1 beta and IL-6 were significantly increased by the administration of MAP. On the other hand, the mRNA expressions of Rgs2 and Rasd1 were changed by both the administration of MAP and body restraint without interaction, which indicated that these insults affected the circulatory system additively or synergistically. From these results, it is likely that the administration of MAP, followed by body restraint, might cause acute myocardial damage due to the direct myocardial toxic effect of MAP, myocardial hypoxia and/or severe hypertension, which is one of the mechanisms for sudden death in MAP abusers who were restrained due to their excited state. (c) 2010. Published by Elsevier Ireland Ltd.

Models for loosely linked gene duplicates suggest lengthy persistence of both copies.

PubMed

O'Hely, Martin; Wockner, Leesa

2007-06-21

Consider the appearance of a duplicate copy of a gene at a locus linked loosely, if at all, to the locus at which the gene is usually found. If all copies of the gene are subject to non-functionalizing mutations, then two fates are possible: loss of functional copies at the duplicate locus (loss of duplicate expression), or loss of functional copies at the original locus (map change). This paper proposes a simple model to address the probability of map change, the time taken for a map change and/or loss of duplicate expression, and considers where in the spectrum between loss of duplicate expression and map change such a duplicate complex is likely to be found. The findings are: the probability of map change is always half the reciprocal of the population size N, the time for a map change to occur is order NlogN generations, and that there is a marked tendency for duplicates to remain near equi-frequency with the gene at the original locus for a large portion of that time. This is in excellent agreement with simulations.

sscMap: an extensible Java application for connecting small-molecule drugs using gene-expression signatures.

PubMed

Zhang, Shu-Dong; Gant, Timothy W

2009-07-31

Connectivity mapping is a process to recognize novel pharmacological and toxicological properties in small molecules by comparing their gene expression signatures with others in a database. A simple and robust method for connectivity mapping with increased specificity and sensitivity was recently developed, and its utility demonstrated using experimentally derived gene signatures. This paper introduces sscMap (statistically significant connections' map), a Java application designed to undertake connectivity mapping tasks using the recently published method. The software is bundled with a default collection of reference gene-expression profiles based on the publicly available dataset from the Broad Institute Connectivity Map 02, which includes data from over 7000 Affymetrix microarrays, for over 1000 small-molecule compounds, and 6100 treatment instances in 5 human cell lines. In addition, the application allows users to add their custom collections of reference profiles and is applicable to a wide range of other 'omics technologies. The utility of sscMap is two fold. First, it serves to make statistically significant connections between a user-supplied gene signature and the 6100 core reference profiles based on the Broad Institute expanded dataset. Second, it allows users to apply the same improved method to custom-built reference profiles which can be added to the database for future referencing. The software can be freely downloaded from http://purl.oclc.org/NET/sscMap.

A synthetic biology approach to the development of transcriptional regulatory models and custom enhancer design☆,☆☆

PubMed Central

Martinez, Carlos A.; Barr, Kenneth; Kim, Ah-Ram; Reinitz, John

2013-01-01

Synthetic biology offers novel opportunities for elucidating transcriptional regulatory mechanisms and enhancer logic. Complex cis-regulatory sequences—like the ones driving expression of the Drosophila even-skipped gene—have proven difficult to design from existing knowledge, presumably due to the large number of protein-protein interactions needed to drive the correct expression patterns of genes in multicellular organisms. This work discusses two novel computational methods for the custom design of enhancers that employ a sophisticated, empirically validated transcriptional model, optimization algorithms, and synthetic biology. These synthetic elements have both utilitarian and academic value, including improving existing regulatory models as well as evolutionary questions. The first method involves the use of simulated annealing to explore the sequence space for synthetic enhancers whose expression output fit a given search criterion. The second method uses a novel optimization algorithm to find functionally accessible pathways between two enhancer sequences. These paths describe a set of mutations wherein the predicted expression pattern does not significantly vary at any point along the path. Both methods rely on a predictive mathematical framework that maps the enhancer sequence space to functional output. PMID:23732772

Variant ribosomal RNA alleles are conserved and exhibit tissue-specific expression

PubMed Central

Parks, Matthew M.; Kurylo, Chad M.; Dass, Randall A.; Bojmar, Linda; Lyden, David; Vincent, C. Theresa; Blanchard, Scott C.

2018-01-01

The ribosome, the integration point for protein synthesis in the cell, is conventionally considered a homogeneous molecular assembly that only passively contributes to gene expression. Yet, epigenetic features of the ribosomal DNA (rDNA) operon and changes in the ribosome’s molecular composition have been associated with disease phenotypes, suggesting that the ribosome itself may possess inherent regulatory capacity. Analyzing whole-genome sequencing data from the 1000 Genomes Project and the Mouse Genomes Project, we find that rDNA copy number varies widely across individuals, and we identify pervasive intra- and interindividual nucleotide variation in the 5S, 5.8S, 18S, and 28S ribosomal RNA (rRNA) genes of both human and mouse. Conserved rRNA sequence heterogeneities map to functional centers of the assembled ribosome, variant rRNA alleles exhibit tissue-specific expression, and ribosomes bearing variant rRNA alleles are present in the actively translating ribosome pool. These findings provide a critical framework for exploring the possibility that the expression of genomically encoded variant rRNA alleles gives rise to physically and functionally heterogeneous ribosomes that contribute to mammalian physiology and human disease. PMID:29503865

Terrain discovery and navigation of a multi-articulated linear robot using map-seeking circuits

NASA Astrophysics Data System (ADS)

Snider, Ross K.; Arathorn, David W.

2006-05-01

A significant challenge in robotics is providing a robot with the ability to sense its environment and then autonomously move while accommodating obstacles. The DARPA Grand Challenge, one of the most visible examples, set the goal of driving a vehicle autonomously for over a hundred miles avoiding obstacles along a predetermined path. Map-Seeking Circuits have shown their biomimetic capability in both vision and inverse kinematics and here we demonstrate their potential usefulness for intelligent exploration of unknown terrain using a multi-articulated linear robot. A robot that could handle any degree of terrain complexity would be useful for exploring inaccessible crowded spaces such as rubble piles in emergency situations, patrolling/intelligence gathering in tough terrain, tunnel exploration, and possibly even planetary exploration. Here we simulate autonomous exploratory navigation by an interaction of terrain discovery using the multi-articulated linear robot to build a local terrain map and exploitation of that growing terrain map to solve the propulsion problem of the robot.

Powerful Identification of Cis-regulatory SNPs in Human Primary Monocytes Using Allele-Specific Gene Expression

PubMed Central

Almlöf, Jonas Carlsson; Lundmark, Per; Lundmark, Anders; Ge, Bing; Maouche, Seraya; Göring, Harald H. H.; Liljedahl, Ulrika; Enström, Camilla; Brocheton, Jessy; Proust, Carole; Godefroy, Tiphaine; Sambrook, Jennifer G.; Jolley, Jennifer; Crisp-Hihn, Abigail; Foad, Nicola; Lloyd-Jones, Heather; Stephens, Jonathan; Gwilliam, Rhian; Rice, Catherine M.; Hengstenberg, Christian; Samani, Nilesh J.; Erdmann, Jeanette; Schunkert, Heribert; Pastinen, Tomi; Deloukas, Panos; Goodall, Alison H.; Ouwehand, Willem H.; Cambien, François; Syvänen, Ann-Christine

2012-01-01

A large number of genome-wide association studies have been performed during the past five years to identify associations between SNPs and human complex diseases and traits. The assignment of a functional role for the identified disease-associated SNP is not straight-forward. Genome-wide expression quantitative trait locus (eQTL) analysis is frequently used as the initial step to define a function while allele-specific gene expression (ASE) analysis has not yet gained a wide-spread use in disease mapping studies. We compared the power to identify cis-acting regulatory SNPs (cis-rSNPs) by genome-wide allele-specific gene expression (ASE) analysis with that of traditional expression quantitative trait locus (eQTL) mapping. Our study included 395 healthy blood donors for whom global gene expression profiles in circulating monocytes were determined by Illumina BeadArrays. ASE was assessed in a subset of these monocytes from 188 donors by quantitative genotyping of mRNA using a genome-wide panel of SNP markers. The performance of the two methods for detecting cis-rSNPs was evaluated by comparing associations between SNP genotypes and gene expression levels in sample sets of varying size. We found that up to 8-fold more samples are required for eQTL mapping to reach the same statistical power as that obtained by ASE analysis for the same rSNPs. The performance of ASE is insensitive to SNPs with low minor allele frequencies and detects a larger number of significantly associated rSNPs using the same sample size as eQTL mapping. An unequivocal conclusion from our comparison is that ASE analysis is more sensitive for detecting cis-rSNPs than standard eQTL mapping. Our study shows the potential of ASE mapping in tissue samples and primary cells which are difficult to obtain in large numbers. PMID:23300628

[Discrimination and homophobia associated to the human immunodeficiency virus epidemic].

PubMed

Orozco-Núñez, Emanuel; Alcalde-Rabanal, Jacqueline Elizabeth; Ruiz-Larios, José Arturo; Sucilla-Pérez, Héctor; García-Cerde, Rodrigo

2015-01-01

To describe a political mapping on discrimination and homophobia associated to human immunodeficiency virus (HIV) in the context of public institutions in Mexico. The political mapping was conducted in six Mexican states. Stakeholders who were involved in HIV actions from public and private sectors were included. Semistructured interviews were applied to explore homophobia and discrimination associated with HIV. Information was systematized using the Policy Maker software, which is a good support for analyzing health policies. Discriminatory and homophobic practices in the public domain occurred, damaging people´s integrity via insults, derision and hate crimes. Most stakeholders expressed a supportive position to prevent discrimination and homophobia and some of them had great influence on policy-making decisions. It was found that state policy frameworks are less specific in addressing these issues. Homophobia and discrimination associated to HIV are still considered problematic in Mexico. Homophobia is a very sensitive issue that requires further attention. Also, an actual execution of governmental authority requires greater enforcement of laws against discrimination and homophobia.

Systems Biology Analysis of Gene Expression during In Vivo Mycobacterium avium paratuberculosis Enteric Colonization Reveals Role for Immune Tolerance

PubMed Central

Khare, Sangeeta; Lawhon, Sara D.; Drake, Kenneth L.; Nunes, Jairo E. S.; Figueiredo, Josely F.; Rossetti, Carlos A.; Gull, Tamara; Everts, Robin E.; Lewin, Harris A.; Galindo, Cristi L.; Garner, Harold R.; Adams, Leslie Garry

2012-01-01

Survival and persistence of Mycobacterium avium subsp. paratuberculosis (MAP) in the intestinal mucosa is associated with host immune tolerance. However, the initial events during MAP interaction with its host that lead to pathogen survival, granulomatous inflammation, and clinical disease progression are poorly defined. We hypothesize that immune tolerance is initiated upon initial contact of MAP with the intestinal Peyer's patch. To test our hypothesis, ligated ileal loops in neonatal calves were infected with MAP. Intestinal tissue RNAs were collected (0.5, 1, 2, 4, 8 and 12 hrs post-infection), processed, and hybridized to bovine gene expression microarrays. By comparing the gene transcription responses of calves infected with the MAP, informative complex patterns of expression were clearly visible. To interpret these complex data, changes in the gene expression were further analyzed by dynamic Bayesian analysis, and genes were grouped into the specific pathways and gene ontology categories to create a holistic model. This model revealed three different phases of responses: i) early (30 min and 1 hr post-infection), ii) intermediate (2, 4 and 8 hrs post-infection), and iii) late (12 hrs post-infection). We describe here the data that include expression profiles for perturbed pathways, as well as, mechanistic genes (genes predicted to have regulatory influence) that are associated with immune tolerance. In the Early Phase of MAP infection, multiple pathways were initiated in response to MAP invasion via receptor mediated endocytosis and changes in intestinal permeability. During the Intermediate Phase, perturbed pathways involved the inflammatory responses, cytokine-cytokine receptor interaction, and cell-cell signaling. During the Late Phase of infection, gene responses associated with immune tolerance were initiated at the level of T-cell signaling. Our study provides evidence that MAP infection resulted in differentially regulated genes, perturbed pathways and specifically modified mechanistic genes contributing to the colonization of Peyer's patch. PMID:22912686

Olympus Mons, Mars: Constraints on Lava Flow Silica Composition

NASA Astrophysics Data System (ADS)

Kirshner, M.; Jurdy, D. M.

2016-12-01

Olympus Mons, Mars, the largest known volcano in our solar system, contains numerous enigmatic lava flow features. Lava tubes have received attention as their final morphologies may offer habitable zones for both native life and human exploration. Such tubes were formed through mechanisms involving several volatile species with significant silica content. Olympus Mons, a shield volcano, might be expected to have flows with silica content similar to that of terrestrial basaltic flows. However, past investigations have estimated a slightly more andesitic composition. Data pertaining to lava tubes such as flow width and slope are collected from the Mars Reconnaissance Orbiter's Context Camera, Mars Odyssey's THEMIS instrument, and Mars Express' HRSC instrument. Compiling this data in GIS software allows for extensive mapping and analysis of Olympus Mons' seemingly inactive flow features. A rheological analysis performed on 62 mapped lava tubes utilizes geometric parameters inferred from mapping. Lava was modeled as a Bingham fluid on an inclined plane, allowing for the derivation of lava yield stress. Percent silica content was calculated for each of the 62 mapped flows using a relationship derived from observations of terrestrial lava yield strengths and corresponding silica composition. Results indicate that lava tube flows across Olympus Mons were on average basaltic in nature, occasionally reaching into the andesitic classification: percent silica content is 51% on average and ranges between roughly 40% and 57%.

Moraxella catarrhalis synthesizes an autotransporter that is an acid phosphatase.

PubMed

Hoopman, Todd C; Wang, Wei; Brautigam, Chad A; Sedillo, Jennifer L; Reilly, Thomas J; Hansen, Eric J

2008-02-01

Moraxella catarrhalis O35E was shown to synthesize a 105-kDa protein that has similarity to both acid phosphatases and autotransporters. The N-terminal portion of the M. catarrhalis acid phosphatase A (MapA) was most similar (the BLAST probability score was 10(-10)) to bacterial class A nonspecific acid phosphatases. The central region of the MapA protein had similarity to passenger domains of other autotransporter proteins, whereas the C-terminal portion of MapA resembled the translocation domain of conventional autotransporters. Cloning and expression of the M. catarrhalis mapA gene in Escherichia coli confirmed the presence of acid phosphatase activity in the MapA protein. The MapA protein was shown to be localized to the outer membrane of M. catarrhalis and was not detected either in the soluble cytoplasmic fraction from disrupted M. catarrhalis cells or in the spent culture supernatant fluid from M. catarrhalis. Use of the predicted MapA translocation domain in a fusion construct with the passenger domain from another predicted M. catarrhalis autotransporter confirmed the translocation ability of this MapA domain. Inactivation of the mapA gene in M. catarrhalis strain O35E reduced the acid phosphatase activity expressed by this organism, and this mutation could be complemented in trans with the wild-type mapA gene. Nucleotide sequence analysis of the mapA gene from six M. catarrhalis strains showed that this protein was highly conserved among strains of this pathogen. Site-directed mutagenesis of a critical histidine residue (H233A) in the predicted active site of the acid phosphatase domain in MapA eliminated acid phosphatase activity in the recombinant MapA protein. This is the first description of an autotransporter protein that expresses acid phosphatase activity.

Moraxella catarrhalis Synthesizes an Autotransporter That Is an Acid Phosphatase▿

PubMed Central

Hoopman, Todd C.; Wang, Wei; Brautigam, Chad A.; Sedillo, Jennifer L.; Reilly, Thomas J.; Hansen, Eric J.

2008-01-01

Moraxella catarrhalis O35E was shown to synthesize a 105-kDa protein that has similarity to both acid phosphatases and autotransporters. The N-terminal portion of the M. catarrhalis acid phosphatase A (MapA) was most similar (the BLAST probability score was 10−10) to bacterial class A nonspecific acid phosphatases. The central region of the MapA protein had similarity to passenger domains of other autotransporter proteins, whereas the C-terminal portion of MapA resembled the translocation domain of conventional autotransporters. Cloning and expression of the M. catarrhalis mapA gene in Escherichia coli confirmed the presence of acid phosphatase activity in the MapA protein. The MapA protein was shown to be localized to the outer membrane of M. catarrhalis and was not detected either in the soluble cytoplasmic fraction from disrupted M. catarrhalis cells or in the spent culture supernatant fluid from M. catarrhalis. Use of the predicted MapA translocation domain in a fusion construct with the passenger domain from another predicted M. catarrhalis autotransporter confirmed the translocation ability of this MapA domain. Inactivation of the mapA gene in M. catarrhalis strain O35E reduced the acid phosphatase activity expressed by this organism, and this mutation could be complemented in trans with the wild-type mapA gene. Nucleotide sequence analysis of the mapA gene from six M. catarrhalis strains showed that this protein was highly conserved among strains of this pathogen. Site-directed mutagenesis of a critical histidine residue (H233A) in the predicted active site of the acid phosphatase domain in MapA eliminated acid phosphatase activity in the recombinant MapA protein. This is the first description of an autotransporter protein that expresses acid phosphatase activity. PMID:18065547

NOAA Office of Ocean Exploration and Research'sOkeanos Explorer Program 2014 Discoveries - U.S. Atlantic Continental Margin and Gulf of Mexico

NASA Astrophysics Data System (ADS)

Lobecker, E.; McKenna, L.; Sowers, D.; Elliott, K.; Kennedy, B.

2014-12-01

NOAA ShipOkeanos Explorer, the only U.S. federal vessel dedicated to global ocean exploration, made several important discoveries in U.S. waters of the North Atlantic Ocean and Gulf of Mexico during the 2014 field season. Based on input received from a broad group ofmarine scientists and resource managers, over 100,000 square kilometers of seafloor and associated water column were systematically explored using advanced mapping sonars. 39 ROV diveswere conducted, leading to new discoveries that will further ourunderstanding of biologic, geologic, and underwater-cultural heritage secrets hidden withinthe oceans. In the Atlantic, season highlights include completion of a multi-year submarine canyons mapping effort of the continental shelf break from North Carolina to the U.S.-Canada maritime border;new information on the ephemerality of recently discovered and geographically extensive cold water seeps; and continued exploration of the New England Seamount chain; and mapping of two potential historically significant World War II wreck sites. In the Gulf of Mexico, season highlights includecompletion of a multi-year mapping effort of the West Florida Escarpment providing new insight into submarine landslides and detachment zones;the discovery of at least two asphalt volcanoes, or 'tar lilies'; range extensions of deep-sea corals; discovery of two potential new species of crinoids; identification of at least 300 potential cold water seeps; and ROV exploration of three historically significant19th century shipwrecks. In both regions, high-resolution mapping led to new insight into the geological context in which deep sea corals develop,while ROV dives provided valuable observations of deep sea coral habitats and their associated organisms, and chemosynthetic habitats. All mapping and ROV data is freely available to the public in usable data formats and maintained in national geophysical and oceanographic data archives.

Serial analysis of gene expression (SAGE) in normal human trabecular meshwork.

PubMed

Liu, Yutao; Munro, Drew; Layfield, David; Dellinger, Andrew; Walter, Jeffrey; Peterson, Katherine; Rickman, Catherine Bowes; Allingham, R Rand; Hauser, Michael A

2011-04-08

To identify the genes expressed in normal human trabecular meshwork tissue, a tissue critical to the pathogenesis of glaucoma. Total RNA was extracted from human trabecular meshwork (HTM) harvested from 3 different donors. Extracted RNA was used to synthesize individual SAGE (serial analysis of gene expression) libraries using the I-SAGE Long kit from Invitrogen. Libraries were analyzed using SAGE 2000 software to extract the 17 base pair sequence tags. The extracted sequence tags were mapped to the genome using SAGE Genie map. A total of 298,834 SAGE tags were identified from all HTM libraries (96,842, 88,126, and 113,866 tags, respectively). Collectively, there were 107,325 unique tags. There were 10,329 unique tags with a minimum of 2 counts from a single library. These tags were mapped to known unique Unigene clusters. Approximately 29% of the tags (orphan tags) did not map to a known Unigene cluster. Thirteen percent of the tags mapped to at least 2 Unigene clusters. Sequence tags from many glaucoma-related genes, including myocilin, optineurin, and WD repeat domain 36, were identified. This is the first time SAGE analysis has been used to characterize the gene expression profile in normal HTM. SAGE analysis provides an unbiased sampling of gene expression of the target tissue. These data will provide new and valuable information to improve understanding of the biology of human aqueous outflow.

Quantitative proteomics revealed partial fungistatic mechanism of ammonia against conidial germination of nematode-trapping fungus Arthrobotrys oligospora ATCC24927.

PubMed

Liu, Tong; Tian, Dong-Wei; Zou, Li-Juan; Liu, Fang-Yu; Can, Qi-Yan; Yang, Jin-Kui; Xu, Jian-Ping; Huang, Xiao-Wei; Xi, Jia-Qin; Zhu, Ming-Liang; Mo, Ming-He; Zhang, Ke-Qin

2018-05-01

Ammonia is one of the fungistatic factors in soil that can suppress conidial germination, but the molecular mechanism underlying the suppression is unknown. In this study, the proteomes of fungistatic conidia, fresh conidia and germinated conidia of Arthrobotrys oligospora ATCC24927 were determined and quantified. The protein expression profile of fungistatic conidia was significantly different from those in the other two conditions. 281 proteins were down expressed in fungistatic conidia and characterized by GO annotation. Gene transcription analysis and inhibition of puromycin (a protein translation inhibitor) on conidial germination suggested that down expression of 33 protein translation related proteins might well result in repression of protein synthesis and inhibition of conidial germination. In addition, 16 down-expressed proteins were mapped to the Ras/mitogen-activated protein (Ras/MAP) regulatory networks which regulate conidial DNA synthesis. The conidial DNA synthesis was found to be definitely inhibited under by ammonia, and function studies of two Ras/MAP proteins by using knock-out strains provided partial evidence that Ras/MAP pathway regulate the conidial germination. These results suggested that down-expression of Ras/MAP related proteins might result in inhibition of DNA synthesis and finally result in inhibition conidial germination. This study revealed partial fungistatic mechanism of ammonia against conidial germination. Copyright © 2018 Elsevier Ltd. All rights reserved.

Effectively identifying regulatory hotspots while capturing expression heterogeneity in gene expression studies

PubMed Central

2014-01-01

Expression quantitative trait loci (eQTL) mapping is a tool that can systematically identify genetic variation affecting gene expression. eQTL mapping studies have shown that certain genomic locations, referred to as regulatory hotspots, may affect the expression levels of many genes. Recently, studies have shown that various confounding factors may induce spurious regulatory hotspots. Here, we introduce a novel statistical method that effectively eliminates spurious hotspots while retaining genuine hotspots. Applied to simulated and real datasets, we validate that our method achieves greater sensitivity while retaining low false discovery rates compared to previous methods. PMID:24708878

Augmented paper maps: Exploring the design space of a mixed reality system

NASA Astrophysics Data System (ADS)

Paelke, Volker; Sester, Monika

Paper maps and mobile electronic devices have complementary strengths and shortcomings in outdoor use. In many scenarios, like small craft sailing or cross-country trekking, a complete replacement of maps is neither useful nor desirable. Paper maps are fail-safe, relatively cheap, offer superior resolution and provide large scale overview. In uses like open-water sailing it is therefore mandatory to carry adequate maps/charts. GPS based mobile devices, on the other hand, offer useful features like automatic positioning and plotting, real-time information update and dynamic adaptation to user requirements. While paper maps are now commonly used in combination with mobile GPS devices, there is no meaningful integration between the two, and the combined use leads to a number of interaction problems and potential safety issues. In this paper we explore the design space of augmented paper maps in which maps are augmented with additional functionality through a mobile device to achieve a meaningful integration between device and map that combines their respective strengths.

Color threshold and ratio of S100 beta, MAP5, NF68/200, GABA & GAD. I. Distribution in inner ear afferents

NASA Technical Reports Server (NTRS)

Fermin, C. D.; Martin, D. S.; Hara, H.

1997-01-01

Afferents of chick embryos (Gallus domesticus) VIIIth nerve were examined at E3, E6, E9, E13, El7, and hatching (NH) for anti-S100 beta, anti-MAP5, anti-GABA, anti-GAD and anti-NF68/200 stain. Different ages were processed together to determine if the distribution of these antibodies changed during synaptogenesis and myelination. Color thresholding showed that saturation of pixels changed for S100 beta only 5%, for NF68/200 10%, and for MAP5, 10%, between E9-NH. Color ratio of NF68/200 over MAP5 was 1.00 at E13 and 0.25 at E16 and NH. S100 beta, GABA and GAD were co-expressed on nerve endings at the edge of the maculae and center of the cristae, whereas hair cells in the center of the maculae expressed either S100 beta or GABA, but not both. S100 beta/NF68/200 shared antigenic sites on the chalices, but NF68/200 expression was higher than S100 beta in the chalices at hatching. MAP5 was expressed in more neurons than NF68/200 at E11, whereas NF68/200 was more abundant than MAP5 at hatching. The results suggest that: 1) the immunoexpression of these neuronal proteins is modulated concomitantly with the establishment of afferent synapses and myelination; 2) S100 beta may serve a neurotrophic function in the chalices where it is co-expressed with the neurotransmitter GABA and its synthesizing enzyme GAD.

--No Title--

Science.gov Websites

and Cuttings Repository Oil & Gas Oil & Gas (Map-Based) Spills (Environmental Events) Tanks Exploration Notice of Intent Uranium Exploration Permit Oil & Gas Approved Oil & Gas Permits Oil and Gas Maps Undergound Injection Control - Class II Well Production/Injection Report Oil & Gas

swimming

Science.gov Websites

and Cuttings Repository Oil & Gas Oil & Gas (Map-Based) Spills (Environmental Events) Tanks Exploration Notice of Intent Uranium Exploration Permit Oil & Gas Approved Oil & Gas Permits Oil and Gas Maps Undergound Injection Control - Class II Well Production/Injection Report Oil & Gas

Topographical mapping of α- and β-keratins on developing chicken skin integuments: Functional interaction and evolutionary perspectives

PubMed Central

Wu, Ping; Ng, Chen Siang; Yan, Jie; Lai, Yung-Chih; Chen, Chih-Kuan; Lai, Yu-Ting; Wu, Siao-Man; Chen, Jiun-Jie; Luo, Weiqi; Widelitz, Randall B.; Li, Wen-Hsiung; Chuong, Cheng-Ming

2015-01-01

Avian integumentary organs include feathers, scales, claws, and beaks. They cover the body surface and play various functions to help adapt birds to diverse environments. These keratinized structures are mainly composed of corneous materials made of α-keratins, which exist in all vertebrates, and β-keratins, which only exist in birds and reptiles. Here, members of the keratin gene families were used to study how gene family evolution contributes to novelty and adaptation, focusing on tissue morphogenesis. Using chicken as a model, we applied RNA-seq and in situ hybridization to map α- and β-keratin genes in various skin appendages at embryonic developmental stages. The data demonstrate that temporal and spatial α- and β-keratin expression is involved in establishing the diversity of skin appendage phenotypes. Embryonic feathers express a higher proportion of β-keratin genes than other skin regions. In feather filament morphogenesis, β-keratins show intricate complexity in diverse substructures of feather branches. To explore functional interactions, we used a retrovirus transgenic system to ectopically express mutant α- or antisense β-keratin forms. α- and β-keratins show mutual dependence and mutations in either keratin type results in disrupted keratin networks and failure to form proper feather branches. Our data suggest that combinations of α- and β-keratin genes contribute to the morphological and structural diversity of different avian skin appendages, with feather-β-keratins conferring more possible composites in building intrafeather architecture complexity, setting up a platform of morphological evolution of functional forms in feathers. PMID:26598683

Galactic and zodiacal light surface brightness measurements with the Atmosphere Explorer satellites

NASA Technical Reports Server (NTRS)

Abreu, V. J.; Hays, P. B.; Yee, J. H.

1982-01-01

Galactic and zodiacal light surface maps based on the Atmosphere Explorer-C, -D, and -E satellite data are presented at 7320, 6300, 5577, 5200, and 4278 A. A procedure used to generate these maps, which involves separation of the individual stars and diffuse starlight from the zodiacal light, is described in detail. The maps can be used in atmospheric emission studies to correct for galactic emissions which contaminate satellite as well as ground-based photometric observations. The zodiacal light maps show enhanced features which are important for understanding the nature of interplanetary dust.

The road ahead: working towards effective clinical translation of myocardial gene therapies

PubMed Central

Katz, Michael G; Fargnoli, Anthony S; Williams, Richard D; Bridges, Charles R

2014-01-01

During the last two decades the fields of molecular and cellular cardiology, and more recently molecular cardiac surgery, have developed rapidly. The concept of delivering cDNA encoding a therapeutic gene to cardiomyocytes using a vector system with substantial cardiac tropism, allowing for long-term expression of a therapeutic protein, has moved from hypothesis to bench to clinical application. However, the clinical results to date are still disappointing. The ideal gene transfer method should be explored in clinically relevant animal models of heart disease to evaluate the relative roles of specific molecular pathways in disease pathogenesis, helping to validate the potential targets for therapeutic intervention. Successful clinical cardiovascular gene therapy also requires the use of nonimmunogenic cardiotropic vectors capable of expressing the requisite amount of therapeutic protein in vivo and in situ. Depending on the desired application either regional or global myocardial gene delivery is required. Cardiac-specific delivery techniques incorporating mapping technologies for regional delivery and highly efficient methodologies for global delivery should improve the precision and specificity of gene transfer to the areas of interest and minimize collateral organ gene expression. PMID:24341816

Recovery from retinal lesions: molecular plasticity mechanisms in visual cortex far beyond the deprived zone.

PubMed

Hu, Tjing-Tjing; Van den Bergh, Gert; Thorrez, Lieven; Heylen, Kevin; Eysel, Ulf T; Arckens, Lutgarde

2011-12-01

In cats with central retinal lesions, deprivation of the lesion projection zone (LPZ) in primary visual cortex (area 17) induces remapping of the cortical topography. Recovery of visually driven cortical activity in the LPZ involves distinct changes in protein expression. Recent observations, about molecular activity changes throughout area 17, challenge the view that its remote nondeprived parts would not be involved in this recovery process. We here investigated the dynamics of the protein expression pattern of remote nondeprived area 17 triggered by central retinal lesions to explore to what extent far peripheral area 17 would contribute to the topographic map reorganization inside the visual cortex. Using functional proteomics, we identified 40 proteins specifically differentially expressed between far peripheral area 17 of control and experimental animals 14 days to 8 months postlesion. Our results demonstrate that far peripheral area 17 is implicated in the functional adaptation to the visual deprivation, involving a meshwork of interacting proteins, operating in diverse pathways. In particular, endocytosis/exocytosis processes appeared to be essential via their intimate correlation with long-term potentiation and neurite outgrowth mechanisms.

GIS prospectivity mapping and 3D modeling validation for potential uranium deposit targets in Shangnan district, China

NASA Astrophysics Data System (ADS)

Xie, Jiayu; Wang, Gongwen; Sha, Yazhou; Liu, Jiajun; Wen, Botao; Nie, Ming; Zhang, Shuai

2017-04-01

Integrating multi-source geoscience information (such as geology, geophysics, geochemistry, and remote sensing) using GIS mapping is one of the key topics and frontiers in quantitative geosciences for mineral exploration. GIS prospective mapping and three-dimensional (3D) modeling can be used not only to extract exploration criteria and delineate metallogenetic targets but also to provide important information for the quantitative assessment of mineral resources. This paper uses the Shangnan district of Shaanxi province (China) as a case study area. GIS mapping and potential granite-hydrothermal uranium targeting were conducted in the study area combining weights of evidence (WofE) and concentration-area (C-A) fractal methods with multi-source geoscience information. 3D deposit-scale modeling using GOCAD software was performed to validate the shapes and features of the potential targets at the subsurface. The research results show that: (1) the known deposits have potential zones at depth, and the 3D geological models can delineate surface or subsurface ore-forming features, which can be used to analyze the uncertainty of the shape and feature of prospectivity mapping at the subsurface; (2) single geochemistry anomalies or remote sensing anomalies at the surface require combining the depth exploration criteria of geophysics to identify potential targets; and (3) the single or sparse exploration criteria zone with few mineralization spots at the surface has high uncertainty in terms of the exploration target.

Deep Interior Mission: Imaging the Interior of Near-Earth Asteroids Using Radio Reflection Tomography

NASA Technical Reports Server (NTRS)

Safaeinili, A.; Asphaug, E.; Rodriquez, E.; Gurrola, E.; Belton, M.; Klaasen, K.; Ostro, S.; Plaut, J.; Yeomans, D.

2005-01-01

Near-Earth asteroids are important exploration targets since they provide clues to the evolution of the solar system. They are also of interest since they present a clear danger to Earth. Our mission objective is to image the internal structure of two NEOs using radio reflection tomography (RRT) in order to explore the record of asteroid origin and impact evolution, and to test the fundamental hypothesis that some NEOs are rubble piles rather than consolidated bodies. Our mission s RRT technique is analogous to doing a CAT scan of the asteroid from orbit. Closely sampled radar echoes are processed to yield volumetric maps of mechanical and compositional boundaries, and to measure interior material dielectric properties. The RRT instrument is a radar that operates at 5 and 15 MHz with two 30-m (tip-to-tip) dipole antennas that are used in a cross-dipole configuration. The radar transmitter and receiver electronics have heritage from JPL's MARSIS contribution to Mars Express, and the antenna is similar to systems used in IMAGE and LACE missions. The 5-MHz channel is designed to penetrate greater than 1 km of basaltic rock, and 15-MHz penetrates a few hundred meters or more. In addition to RRT volumetric imaging, we use redundant color cameras to explore the surface expressions of unit boundaries, in order to relate interior radar imaging to what is observable from spacecraft imaging and from Earth. The camera also yields stereo color imaging for geology and RRT-related compositional analysis. Gravity and high fidelity geodesy are used to explore how interior structure is expressed in shape, density, mass distribution and spin. Ion thruster propulsion is utilized by Deep Interior to enable tomographic radar mapping of multiple asteroids. Within the Discovery AO scheduling parameters we identify two targets, S-type 1999 ND43 (approximately 500 m diameter) and V-type 3908 Nyx (approximately 1 km), asteroids whose compositions bracket the diversity of solar system materials that we are likely to encounter, from undifferentiated to highly evolved. The 5-15 MHz radar is capable of probing more primitive bodies (e.g. comets or C-types) that may be available given other launch schedules. 5 MHz radar easily penetrates, with the required SNR , greater than 1 km of basalt (a good analog for Nyx). Basalt has a greater loss tangent than expected for most asteroids, although iron-rich M-types are probably not appropriate targets. 15 MHz radar penetrates the outer approximately 100 m of rocky 1 km asteroids and the deep interiors of comets. Laboratory studies of the most common NE0 materials expected (S-, C- and V-type meteorite analogs) will commence in 2005.

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

PubMed

Glaab, Enrico; Schneider, Reinhard

2015-07-01

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

A reference genetic linkage map of apomictic Hieracium species based on expressed markers derived from developing ovule transcripts

PubMed Central

Shirasawa, Kenta; Hand, Melanie L.; Henderson, Steven T.; Okada, Takashi; Johnson, Susan D.; Taylor, Jennifer M.; Spriggs, Andrew; Siddons, Hayley; Hirakawa, Hideki; Isobe, Sachiko; Tabata, Satoshi; Koltunow, Anna M. G.

2015-01-01

Background and Aims Apomixis in plants generates clonal progeny with a maternal genotype through asexual seed formation. Hieracium subgenus Pilosella (Asteraceae) contains polyploid, highly heterozygous apomictic and sexual species. Within apomictic Hieracium, dominant genetic loci independently regulate the qualitative developmental components of apomixis. In H. praealtum, LOSS OF APOMEIOSIS (LOA) enables formation of embryo sacs without meiosis and LOSS OF PARTHENOGENESIS (LOP) enables fertilization-independent seed formation. A locus required for fertilization-independent endosperm formation (AutE) has been identified in H. piloselloides. Additional quantitative loci appear to influence the penetrance of the qualitative loci, although the controlling genes remain unknown. This study aimed to develop the first genetic linkage maps for sexual and apomictic Hieracium species using simple sequence repeat (SSR) markers derived from expressed transcripts within the developing ovaries. Methods RNA from microdissected Hieracium ovule cell types and ovaries was sequenced and SSRs were identified. Two different F1 mapping populations were created to overcome difficulties associated with genome complexity and asexual reproduction. SSR markers were analysed within each mapping population to generate draft linkage maps for apomictic and sexual Hieracium species. Key Results A collection of 14 684 Hieracium expressed SSR markers were developed and linkage maps were constructed for Hieracium species using a subset of the SSR markers. Both the LOA and LOP loci were successfully assigned to linkage groups; however, AutE could not be mapped using the current populations. Comparisons with lettuce (Lactuca sativa) revealed partial macrosynteny between the two Asteraceae species. Conclusions A collection of SSR markers and draft linkage maps were developed for two apomictic and one sexual Hieracium species. These maps will support cloning of controlling genes at LOA and LOP loci in Hieracium and should also assist with identification of quantitative loci that affect the expressivity of apomixis. Future work will focus on mapping AutE using alternative populations. PMID:25538115

A qualitative enquiry into OpenStreetMap making

NASA Astrophysics Data System (ADS)

Lin, Yu-Wei

2011-04-01

Based on a case study on the OpenStreetMap community, this paper provides a contextual and embodied understanding of the user-led, user-participatory and user-generated produsage phenomenon. It employs Grounded Theory, Social Worlds Theory, and qualitative methods to illuminate and explores the produsage processes of OpenStreetMap making, and how knowledge artefacts such as maps can be collectively and collaboratively produced by a community of people, who are situated in different places around the world but engaged with the same repertoire of mapping practices. The empirical data illustrate that OpenStreetMap itself acts as a boundary object that enables actors from different social worlds to co-produce the Map through interacting with each other and negotiating the meanings of mapping, the mapping data and the Map itself. The discourses also show that unlike traditional maps that black-box cartographic knowledge and offer a single dominant perspective of cities or places, OpenStreetMap is an embodied epistemic object that embraces different world views. The paper also explores how contributors build their identities as an OpenStreetMaper alongside some other identities they have. Understanding the identity-building process helps to understand mapping as an embodied activity with emotional, cognitive and social repertoires.

Counter tunnel exploration, mapping, and localization with an unmanned ground vehicle

NASA Astrophysics Data System (ADS)

Larson, Jacoby; Okorn, Brian; Pastore, Tracy; Hooper, David; Edwards, Jim

2014-06-01

Covert, cross-border tunnels are a security vulnerability that enables people and contraband to illegally enter the United States. All of these tunnels to-date have been constructed for the purpose of drug smuggling, but they may also be used to support terrorist activity. Past robotic tunnel exploration efforts have had limited success in aiding law enforcement to explore and map the suspect cross-border tunnels. These efforts have made use of adapted explosive ordnance disposal (EOD) or pipe inspection robotic systems that are not ideally suited to the cross-border tunnel environment. The Counter Tunnel project was sponsored by the Office of Secretary of Defense (OSD) Joint Ground Robotics Enterprise (JGRE) to develop a prototype robotic system for counter-tunnel operations, focusing on exploration, mapping, and characterization of tunnels. The purpose of this system is to provide a safe and effective solution for three-dimensional (3D) localization, mapping, and characterization of a tunnel environment. The system is composed of the robotic mobility platform, the mapping sensor payload, and the delivery apparatus. The system is able to deploy and retrieve the robotic mobility platform through a 20-cm-diameter borehole into the tunnel. This requirement posed many challenges in order to design and package the sensor and robotic system to fit through this narrow opening and be able to perform the mission. This paper provides a short description of a few aspects of the Counter Tunnel system such as mobility, perception, and localization, which were developed to meet the unique challenges required to access, explore, and map tunnel environments.

Translation of Bernstein Coefficients Under an Affine Mapping of the Unit Interval

NASA Technical Reports Server (NTRS)

Alford, John A., II

2012-01-01

We derive an expression connecting the coefficients of a polynomial expanded in the Bernstein basis to the coefficients of an equivalent expansion of the polynomial under an affine mapping of the domain. The expression may be useful in the calculation of bounds for multi-variate polynomials.

Enhanced expression of codon optimized Mycobacterium avium subsp. paratuberculosis antigens in Lactobacillus salivarius

USDA-ARS?s Scientific Manuscript database

We have previously identified the mycobacterial high G+C codon usage bias as a limiting factor in heterologous expression of MAP proteins from Lb.salivarius, and demonstrated that codon optimisation of a synthetic coding gene greatly enhances MAP protein production. Here, we effectively demonstrate ...

Functional Implications of Limited Leptin Receptor and Ghrelin Receptor Coexpression in the Brain

PubMed Central

Perello, Mario; Scott, Michael M.; Sakata, Ichiro; Lee, Charlotte E.; Chuang, Jen-Chieh; Osborne-Lawrence, Sherri; Rovinsky, Sherry A.; Elmquist, Joel K.; Zigman, Jeffrey M.

2012-01-01

The hormones leptin and ghrelin act in apposition to one another in the regulation of body weight homeostasis. Interestingly, both leptin receptor expression and ghrelin receptor expression have been observed within many of the same nuclei of the central nervous system (CNS), suggesting that these hormones may act on a common population of neurons to produce changes in food intake and energy expenditure. In the present study we explored the extent of this putative direct leptin and ghrelin interaction in the CNS and addressed the question of whether a loss of ghrelin signaling would affect sensitivity to leptin. Using histological mapping of leptin receptor and ghrelin receptor expression, we found that cells containing both leptin receptors and ghrelin receptors are mainly located in the medial part of the hypothalamic arcuate nucleus. In contrast, coexpression was much less extensive elsewhere in the brain. To assess the functional consequences of this observed receptor distribution, we explored the effect of ghrelin receptor deletion on leptin sensitivity. In particular, the responses of ad libitum-fed, diet-induced obese and fasted mice to the anorectic actions of leptin were examined. Surprisingly, we found that deletion of the ghrelin receptor did not affect the sensitivity to exogenously administrated leptin. Thus, we conclude that ghrelin and leptin act largely on distinct neuronal populations and that ghrelin receptor deficiency does not affect sensitivity to the anorexigenic and body weight-lowering actions of leptin. PMID:21674492

Functional implications of limited leptin receptor and ghrelin receptor coexpression in the brain.

PubMed

Perello, Mario; Scott, Michael M; Sakata, Ichiro; Lee, Charlotte E; Chuang, Jen-Chieh; Osborne-Lawrence, Sherri; Rovinsky, Sherry A; Elmquist, Joel K; Zigman, Jeffrey M

2012-02-01

The hormones leptin and ghrelin act in apposition to one another in the regulation of body weight homeostasis. Interestingly, both leptin receptor expression and ghrelin receptor expression have been observed within many of the same nuclei of the central nervous system (CNS), suggesting that these hormones may act on a common population of neurons to produce changes in food intake and energy expenditure. In the present study we explored the extent of this putative direct leptin and ghrelin interaction in the CNS and addressed the question of whether a loss of ghrelin signaling would affect sensitivity to leptin. Using histological mapping of leptin receptor and ghrelin receptor expression, we found that cells containing both leptin receptors and ghrelin receptors are mainly located in the medial part of the hypothalamic arcuate nucleus. In contrast, coexpression was much less extensive elsewhere in the brain. To assess the functional consequences of this observed receptor distribution, we explored the effect of ghrelin receptor deletion on leptin sensitivity. In particular, the responses of ad libitum-fed, diet-induced obese and fasted mice to the anorectic actions of leptin were examined. Surprisingly, we found that deletion of the ghrelin receptor did not affect the sensitivity to exogenously administrated leptin. Thus, we conclude that ghrelin and leptin act largely on distinct neuronal populations and that ghrelin receptor deficiency does not affect sensitivity to the anorexigenic and body weight-lowering actions of leptin. Copyright © 2011 Wiley-Liss, Inc.

The Future of Web Maps in Next Generation Textbooks

NASA Astrophysics Data System (ADS)

DiBiase, D.; Prasad, S.

2014-12-01

The reformation of the "Object Formerly Known as Textbook" (coined by the Chronicle of Higher Education) toward a digital future is underway. Emerging nextgen texts look less like electronic books ("ebooks") and more like online courseware. In addition to text and illustrations, nextgen textbooks for STEM subjects are likely to combine quizzes, grade management tools, support for social learning, and interactive media including web maps. Web maps are interactive, multi-scale, online maps that enable teachers and learners to explore, interrogate, and mash up the wide variety of map layers available in the cloud. This presentation will show how web maps coupled with interactive quizzes enable students' purposeful explorations and interpretations of spatial patterns related to humankind's interactions with the earth. Attendees will also learn about Esri's offer to donate ArcGIS Online web mapping subscriptions to every U.S. school as part of the President Obama's ConnectED initiative.

Three education modules using EnviroAtlas-Exploration and Discovery Through Maps: Teaching Science with Technology

EPA Science Inventory

Session #1: Exploration and Discovery through Maps: Teaching Science with Technology (elementary school) - EnviroAtlas is a tool developed by the U.S. Environmental Protection Agency and its partners that empowers anyone with the internet to be a highly informed local decision-ma...

The historical development of the magnetic method in exploration

USGS Publications Warehouse

Nabighian, M.N.; Grauch, V.J.S.; Hansen, R.O.; LaFehr, T.R.; Li, Y.; Peirce, J.W.; Phillips, J.D.; Ruder, M.E.

2005-01-01

The magnetic method, perhaps the oldest of geophysical exploration techniques, blossomed after the advent of airborne surveys in World War II. With improvements in instrumentation, navigation, and platform compensation, it is now possible to map the entire crustal section at a variety of scales, from strongly magnetic basement at regional scale to weakly magnetic sedimentary contacts at local scale. Methods of data filtering, display, and interpretation have also advanced, especially with the availability of low-cost, high-performance personal computers and color raster graphics. The magnetic method is the primary exploration tool in the search for minerals. In other arenas, the magnetic method has evolved from its sole use for mapping basement structure to include a wide range of new applications, such as locating intrasedimentary faults, defining subtle lithologic contacts, mapping salt domes in weakly magnetic sediments, and better defining targets through 3D inversion. These new applications have increased the method's utility in all realms of exploration - in the search for minerals, oil and gas, geothermal resources, and groundwater, and for a variety of other purposes such as natural hazards assessment, mapping impact structures, and engineering and environmental studies. ?? 2005 Society of Exploration Geophysicists. All rights reserved.

The Salient Map Analysis for Research and Teaching (SMART) method: Powerful potential as a formative assessment in the biomedical sciences

NASA Astrophysics Data System (ADS)

Cathcart, Laura Anne

This dissertation consists of two studies: 1) development and characterization of the Salient Map Analysis for Research and Teaching (SMART) method as a formative assessment tool and 2) a case study exploring how a paramedic instructor's beliefs about learners affect her utilization of the SMART method and vice versa. The first study explored: How can a novel concept map analysis method be designed as an effective formative assessment tool? The SMART method improves upon existing concept map analysis methods because it does not require hierarchically structured concept maps and it preserves the rich content of the maps instead of reducing each map down to a numerical score. The SMART method is performed by comparing a set of students' maps to each other and to an instructor's map. The resulting composite map depicts, in percentages and highlighted colors, the similarities and differences between all of the maps. Some advantages of the SMART method as a formative assessment tool include its ability to highlight changes across time, problematic or alternative conceptions, and patterns of student responses at a glance. Study two explored: How do a paramedic instructor's beliefs about students and learning affect---and become affected by---her use of the SMART method as a formative assessment tool? This case study of Angel, an expert paramedic instructor, begins to address a gap in the emergency medical services (EMS) education literature, which contains almost no research on teachers or pedagogy. Angel and I worked together as participant co-researchers (Heron & Reason, 1997) exploring the affordances of the SMART method. This study, based on those interactions with Angel, involved using open coding to identify themes (Strauss & Corbin, 1998) from Angel's views of students and use of the SMART method. Angel views learning as a sense-making process. She has a multi-faceted view of her students as novices and invests substantial time trying to understand their concept maps. Not only do these beliefs affect her use of the SMART method; in addition, her beliefs are refined through the use of the SMART method.

ASTER, ALI and Hyperion sensors data for lithological mapping and ore minerals exploration.

PubMed

Beiranvand Pour, Amin; Hashim, Mazlan

2014-01-01

This paper provides a review of the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER), Advanced Land Imager (ALI), and Hyperion data and applications of the data as a tool for ore minerals exploration, lithological and structural mapping. Spectral information extraction from ASTER, ALI, and Hyperion data has great ability to assist geologists in all disciplines to map the distribution and detect the rock units exposed at the earth's surface. The near coincidence of Earth Observing System (EOS)/Terra and Earth Observing One (EO-1) platforms allows acquiring ASTER, ALI, and Hyperion imagery of the same ground areas, resulting accurate information for geological mapping applications especially in the reconnaissance stages of hydrothermal copper and gold exploration, chromite, magnetite, massive sulfide and uranium ore deposits, mineral components of soils and structural interpretation at both regional and district scales. Shortwave length infrared and thermal infrared bands of ASTER have sufficient spectral resolution to map fundamental absorptions of hydroxyl mineral groups and silica and carbonate minerals for regional mapping purposes. Ferric-iron bearing minerals can be discriminated using six unique wavelength bands of ALI spanning the visible and near infrared. Hyperion visible and near infrared bands (0.4 to 1.0 μm) and shortwave infrared bands (0.9 to 2.5 μm) allowed to produce image maps of iron oxide minerals, hydroxyl-bearing minerals, sulfates and carbonates in association with hydrothermal alteration assemblages, respectively. The techniques and achievements reviewed in the present paper can further introduce the efficacy of ASTER, ALI, and Hyperion data for future mineral and lithological mapping and exploration of the porphyry copper, epithermal gold, chromite, magnetite, massive sulfide and uranium ore deposits especially in arid and semi-arid territory.

Mapping Early American History: Beyond What Happened Where

ERIC Educational Resources Information Center

Milson, Andrew J.

2014-01-01

American history demands to be mapped. The stories of exploration, the colonies, the Louisiana Purchase, and so on are incomplete without maps to locate historical places, events, and conflicts. Yet maps can do more for the history teacher than simply illustrating what happened where or what territory was acquired when. Maps also provide clues…

Integrating Concept Mapping and the Learning Cycle To Teach Diffusion and Osmosis Concepts to High School Biology Students.

ERIC Educational Resources Information Center

Odom, Arthur L.; Kelly, Paul V.

2001-01-01

Explores the effectiveness of concept mapping, the learning cycle, expository instruction, and a combination of concept mapping/learning cycle in promoting conceptual understanding of diffusion and osmosis. Concludes that the concept mapping/learning cycle and concept mapping treatment groups significantly outperformed the expository treatment…

The role of MAP kinases in the induction of iNOS expression in neutrophils exposed to NDMA: the involvement transcription factors.

PubMed

Ratajczak-Wrona, W; Jablonska, E; Garley, M; Jablonski, J; Radziwon, P; Iwaniuk, A

2013-01-01

The role of MAP kinases in the activation of AP-1 (c-Jun, c-Fos) and NF-κB p65 engaged in the regulation of iNOS expression in human neutrophils (PMNs) exposed to N-nitrosodimethylamine (NDMA) was analyzed in the study. The study included a group of 20 healthy individuals. Isolated human PMN were incubated in the presence of NDMA. Selective MAP kinases inhibitors were used. The expression of proteins in the cytoplasmic and nuclear fractions was assessed using Western blot method. The results show that NDMA intensifies iNOS, c-Jun, NF-κB p65 and IκB-α expression in the analyzed PMNs. The blocking of the p38 pathway led to lower iNOS expression, and higher expression of c-Jun and c-Fos in the cytoplasmic fraction, and also lower c-Jun expression in the nuclear fraction of PMNs exposed to NDMA. A decrease in iNOS expression in the cytoplasmic fraction, and also c-Jun in both fractions of the examined cells, was observed as a result of JNK pathway inhibition. The blocking of the ERK5 pathway led to higher iNOS, c-Jun and c-Fos expression in the cytoplasmic fraction, and higher c-Jun expression in the nuclear fraction of PMNs exposed to NDMA. The study also demonstrated that blocking of the p38 and JNK pathways resulted in higher expression of NF-κB p65 and IκB-α in the cytoplasmic fraction and their lower expression in the nuclear fraction of these cells. Our data indicate the role of MAP kinases p38 and JNK in the activation of c-Jun and NF-κB p65 transcription factors engaged in the regulation of iNOS expression in human neutrophils exposed to NDMA. However ERK5 kinase is not involved in the regulation of iNOS and NO production by those cells.

Face Generation Using Emotional Regions for Sensibility Robot

NASA Astrophysics Data System (ADS)

Gotoh, Minori; Kanoh, Masayoshi; Kato, Shohei; Kunitachi, Tsutomu; Itoh, Hidenori

We think that psychological interaction is necessary for smooth communication between robots and people. One way to psychologically interact with others is through facial expressions. Facial expressions are very important for communication because they show true emotions and feelings. The ``Ifbot'' robot communicates with people by considering its own ``emotions''. Ifbot has many facial expressions to communicate enjoyment. We developed a method for generating facial expressions based on human subjective judgements mapping Ifbot's facial expressions to its emotions. We first created Ifbot's emotional space to map its facial expressions. We applied a five-layer auto-associative neural network to the space. We then subjectively evaluated the emotional space and created emotional regions based on the results. We generated emotive facial expressions using the emotional regions.

The conceptual maps in the development of the course of biology of tenth degree: An investigation experience action in the classroom

NASA Astrophysics Data System (ADS)

Samo Goyco, Marisol

This investigation describes and combines the qualitative and quantitative methods of nature. The research I have work explore, observe, record and also it describes the experience to consider the education and teaching of the course. This investigation is a research that our students from the biology course, since the constructivist approach identifying and correct mistake. In this investigation there were participating twenty five students of tenth grade from a public school specialized in music. This research includes conceptual maps, computer integration, science programmed, internet, and broadcast and assessment approach. The research of conceptual maps establishes the correct method to perform capture the acknowledgement and attention of the investigators and the students which represents a significant relation between the concepts. Thought the investigator sustains on the cycle spiral of Carr and kemmis (1988) I design every unit considering the previous ideology of the student and elaborating the unit plan. Sustaining Maintain the methodology of the action research. The methodology has response to a new teaching paradigm. Situate as a principal assignment of the professor to contribute in the process of active learning to the students. Also helps to have in this process a reflection in their function or goals. During the research I analyze and wrote the observation and materials. The investigator express in her writing the final findings in every cycle. Also evaluates the map concepts the varied integration of activity and the assessment skills which are used through the socialized discussion. The socialized discussion communicates the participant concepts that should be attended. The students express between their peers and in front of the research of the investigator how they felt in terms of resources and the development of the maps. At the moment of this information I design the next cycle responding to the outstanding needs, this reflection genre a mayor interest in the students for the concept learning, they also demonstrate an active participation in the learning process. The findings demonstrate that the conceptual maps and the resources integration are concepts of development. An outspoken communication with the educators produces advantage for both parts. In this study I suggest to the professor and evaluate their continually practice reducing the stress of educational between students and educators.

Transcription factor profiling reveals molecular choreography and key regulators of human retrotransposon expression

PubMed Central

Sun, Xiaoji; Wang, Xuya; Tang, Zuojian; Grivainis, Mark; Kahler, David; Yun, Chi; Mita, Paolo; Fenyö, David

2018-01-01

Transposable elements (TEs) represent a substantial fraction of many eukaryotic genomes, and transcriptional regulation of these factors is important to determine TE activities in human cells. However, due to the repetitive nature of TEs, identifying transcription factor (TF)-binding sites from ChIP-sequencing (ChIP-seq) datasets is challenging. Current algorithms are focused on subtle differences between TE copies and thus bias the analysis to relatively old and inactive TEs. Here we describe an approach termed “MapRRCon” (mapping repeat reads to a consensus) which allows us to identify proteins binding to TE DNA sequences by mapping ChIP-seq reads to the TE consensus sequence after whole-genome alignment. Although this method does not assign binding sites to individual insertions in the genome, it provides a landscape of interacting TFs by capturing factors that bind to TEs under various conditions. We applied this method to screen TFs’ interaction with L1 in human cells/tissues using ENCODE ChIP-seq datasets and identified 178 of the 512 TFs tested as bound to L1 in at least one biological condition with most of them (138) localized to the promoter. Among these L1-binding factors, we focused on Myc and CTCF, as they play important roles in cancer progression and 3D chromatin structure formation. Furthermore, we explored the transcriptomes of The Cancer Genome Atlas breast and ovarian tumor samples in which a consistent anti-/correlation between L1 and Myc/CTCF expression was observed, suggesting that these two factors may play roles in regulating L1 transcription during the development of such tumors. PMID:29802231

Cognitive maps and attention.

PubMed

Hardt, Oliver; Nadel, Lynn

2009-01-01

Cognitive map theory suggested that exploring an environment and attending to a stimulus should lead to its integration into an allocentric environmental representation. We here report that directed attention in the form of exploration serves to gather information needed to determine an optimal spatial strategy, given task demands and characteristics of the environment. Attended environmental features may integrate into spatial representations if they meet the requirements of the optimal spatial strategy: when learning involves a cognitive mapping strategy, cues with high codability (e.g., concrete objects) will be incorporated into a map, but cues with low codability (e.g., abstract paintings) will not. However, instructions encouraging map learning can lead to the incorporation of cues with low codability. On the other hand, if spatial learning is not map-based, abstract cues can and will be used to encode locations. Since exploration appears to determine what strategy to apply and whether or not to encode a cue, recognition memory for environmental features is independent of whether or not a cue is part of a spatial representation. In fact, when abstract cues were used in a way that was not map-based, or when they were not used for spatial navigation at all, they were nevertheless recognized as familiar. Thus, the relation between exploratory activity on the one hand and spatial strategy and memory on the other appears more complex than initially suggested by cognitive map theory.

Genome contact map explorer: a platform for the comparison, interactive visualization and analysis of genome contact maps

PubMed Central

Kumar, Rajendra; Sobhy, Haitham

2017-01-01

Abstract Hi-C experiments generate data in form of large genome contact maps (Hi-C maps). These show that chromosomes are arranged in a hierarchy of three-dimensional compartments. But to understand how these compartments form and by how much they affect genetic processes such as gene regulation, biologists and bioinformaticians need efficient tools to visualize and analyze Hi-C data. However, this is technically challenging because these maps are big. In this paper, we remedied this problem, partly by implementing an efficient file format and developed the genome contact map explorer platform. Apart from tools to process Hi-C data, such as normalization methods and a programmable interface, we made a graphical interface that let users browse, scroll and zoom Hi-C maps to visually search for patterns in the Hi-C data. In the software, it is also possible to browse several maps simultaneously and plot related genomic data. The software is openly accessible to the scientific community. PMID:28973466

Cis-regulatory changes in Kit ligand expression and parallel evolution of pigmentation in sticklebacks and humans

PubMed Central

Miller, Craig T.; Beleza, Sandra; Pollen, Alex A.; Schluter, Dolph; Kittles, Rick A.; Shriver, Mark D.; Kingsley, David M.

2010-01-01

SUMMARY Dramatic pigmentation changes have evolved within most vertebrate groups, including fish and humans. Here we use genetic crosses in sticklebacks to investigate the parallel origin of pigmentation changes in natural populations. High-resolution mapping and expression experiments show that light gills and light ventrums map to a divergent regulatory allele of the Kit ligand (Kitlg) gene. The divergent allele reduces expression in gill and skin tissue, and is shared by multiple derived freshwater populations with reduced pigmentation. In humans, Europeans and East Asians also share derived alleles at the KITLG locus. Strong signatures of selection map to regulatory regions surrounding the gene, and admixture mapping shows that the KITLG genomic region has a significant effect on human skin color. These experiments suggest that regulatory changes in Kitlg contribute to natural variation in vertebrate pigmentation, and that similar genetic mechanisms may underlie rapid evolutionary change in fish and humans. PMID:18083106

Spatial reconstruction of single-cell gene expression

PubMed Central

Satija, Rahul; Farrell, Jeffrey A.; Gennert, David; Schier, Alexander F.; Regev, Aviv

2015-01-01

Spatial localization is a key determinant of cellular fate and behavior, but spatial RNA assays traditionally rely on staining for a limited number of RNA species. In contrast, single-cell RNA-seq allows for deep profiling of cellular gene expression, but established methods separate cells from their native spatial context. Here we present Seurat, a computational strategy to infer cellular localization by integrating single-cell RNA-seq data with in situ RNA patterns. We applied Seurat to spatially map 851 single cells from dissociated zebrafish (Danio rerio) embryos, inferring a transcriptome-wide map of spatial patterning. We confirmed Seurat’s accuracy using several experimental approaches, and used it to identify a set of archetypal expression patterns and spatial markers. Additionally, Seurat correctly localizes rare subpopulations, accurately mapping both spatially restricted and scattered groups. Seurat will be applicable to mapping cellular localization within complex patterned tissues in diverse systems. PMID:25867923

Porcine MAP3K5 analysis: molecular cloning, characterization, tissue expression pattern, and copy number variations associated with residual feed intake.

PubMed

Pu, L; Zhang, L C; Zhang, J S; Song, X; Wang, L G; Liang, J; Zhang, Y B; Liu, X; Yan, H; Zhang, T; Yue, J W; Li, N; Wu, Q Q; Wang, L X

2016-08-12

Mitogen-activated protein kinase kinase kinase 5 (MAP3K5) is essential for apoptosis, proliferation, differentiation, and immune responses, and is a candidate marker for residual feed intake (RFI) in pig. We cloned the full-length cDNA sequence of porcine MAP3K5 by rapid-amplification of cDNA ends. The 5451-bp gene contains a 5'-untranslated region (UTR) (718 bp), a coding region (3738 bp), and a 3'-UTR (995 bp), and encodes a peptide of 1245 amino acids, which shares 97, 99, 97, 93, 91, and 84% sequence identity with cattle, sheep, human, mouse, chicken, and zebrafish MAP3K5, respectively. The deduced MAP3K5 protein sequence contains two conserved domains: a DUF4071 domain and a protein kinase domain. Phylogenetic analysis showed that porcine MAP3K5 forms a separate branch to vicugna and camel MAP3K5. Tissue expression analysis using real-time quantitative polymerase chain reaction (qRT-PCR) revealed that MAP3K5 was expressed in the heart, liver, spleen, lung, kidney, muscle, fat, pancrea, ileum, and stomach tissues. Copy number variation was detected for porcine MAP3K5 and validated by qRT-PCR. Furthermore, a significant increase in average copy number was detected in the low RFI group when compared to the high RFI group in a Duroc pig population. These results provide useful information regarding the influence of MAP3K5 on RFI in pigs.

A molecular atlas of the developing ectoderm defines neural, neural crest, placode, and nonneural progenitor identity in vertebrates.

PubMed

Plouhinec, Jean-Louis; Medina-Ruiz, Sofía; Borday, Caroline; Bernard, Elsa; Vert, Jean-Philippe; Eisen, Michael B; Harland, Richard M; Monsoro-Burq, Anne H

2017-10-01

During vertebrate neurulation, the embryonic ectoderm is patterned into lineage progenitors for neural plate, neural crest, placodes and epidermis. Here, we use Xenopus laevis embryos to analyze the spatial and temporal transcriptome of distinct ectodermal domains in the course of neurulation, during the establishment of cell lineages. In order to define the transcriptome of small groups of cells from a single germ layer and to retain spatial information, dorsal and ventral ectoderm was subdivided along the anterior-posterior and medial-lateral axes by microdissections. Principal component analysis on the transcriptomes of these ectoderm fragments primarily identifies embryonic axes and temporal dynamics. This provides a genetic code to define positional information of any ectoderm sample along the anterior-posterior and dorsal-ventral axes directly from its transcriptome. In parallel, we use nonnegative matrix factorization to predict enhanced gene expression maps onto early and mid-neurula embryos, and specific signatures for each ectoderm area. The clustering of spatial and temporal datasets allowed detection of multiple biologically relevant groups (e.g., Wnt signaling, neural crest development, sensory placode specification, ciliogenesis, germ layer specification). We provide an interactive network interface, EctoMap, for exploring synexpression relationships among genes expressed in the neurula, and suggest several strategies to use this comprehensive dataset to address questions in developmental biology as well as stem cell or cancer research.

A molecular atlas of the developing ectoderm defines neural, neural crest, placode, and nonneural progenitor identity in vertebrates

PubMed Central

Borday, Caroline; Bernard, Elsa; Vert, Jean-Philippe; Eisen, Michael B.; Harland, Richard M.

2017-01-01

During vertebrate neurulation, the embryonic ectoderm is patterned into lineage progenitors for neural plate, neural crest, placodes and epidermis. Here, we use Xenopus laevis embryos to analyze the spatial and temporal transcriptome of distinct ectodermal domains in the course of neurulation, during the establishment of cell lineages. In order to define the transcriptome of small groups of cells from a single germ layer and to retain spatial information, dorsal and ventral ectoderm was subdivided along the anterior-posterior and medial-lateral axes by microdissections. Principal component analysis on the transcriptomes of these ectoderm fragments primarily identifies embryonic axes and temporal dynamics. This provides a genetic code to define positional information of any ectoderm sample along the anterior-posterior and dorsal-ventral axes directly from its transcriptome. In parallel, we use nonnegative matrix factorization to predict enhanced gene expression maps onto early and mid-neurula embryos, and specific signatures for each ectoderm area. The clustering of spatial and temporal datasets allowed detection of multiple biologically relevant groups (e.g., Wnt signaling, neural crest development, sensory placode specification, ciliogenesis, germ layer specification). We provide an interactive network interface, EctoMap, for exploring synexpression relationships among genes expressed in the neurula, and suggest several strategies to use this comprehensive dataset to address questions in developmental biology as well as stem cell or cancer research. PMID:29049289

Landsat analysis for uranium exploration in Northeast Turkey

USGS Publications Warehouse

Lee, Keenan

1983-01-01

No uranium deposits are known in the Trabzon, Turkey region, and consequently, exploration criteria have not been defined. Nonetheless, by analogy with uranium deposits studied elsewhere, exploration guides are suggested to include dense concentrations of linear features, lineaments -- especially with northwest trend, acidic plutonic rocks, and alteration indicated by limonite. A suite of digitally processed images of a single Landsat scene served as the image base for mapping 3,376 linear features. Analysis of the linear feature data yielded two statistically significant trends, which in turn defined two sets of strong lineaments. Color composite images were used to map acidic plutonic rocks and areas of surficial limonitic materials. The Landsat interpretation yielded a map of these exploration guides that may be used to evaluate relative uranium potential. One area in particular shows a high coincidence of favorable indicators.

TRAM (Transcriptome Mapper): database-driven creation and analysis of transcriptome maps from multiple sources

PubMed Central

2011-01-01

Background Several tools have been developed to perform global gene expression profile data analysis, to search for specific chromosomal regions whose features meet defined criteria as well as to study neighbouring gene expression. However, most of these tools are tailored for a specific use in a particular context (e.g. they are species-specific, or limited to a particular data format) and they typically accept only gene lists as input. Results TRAM (Transcriptome Mapper) is a new general tool that allows the simple generation and analysis of quantitative transcriptome maps, starting from any source listing gene expression values for a given gene set (e.g. expression microarrays), implemented as a relational database. It includes a parser able to assign univocal and updated gene symbols to gene identifiers from different data sources. Moreover, TRAM is able to perform intra-sample and inter-sample data normalization, including an original variant of quantile normalization (scaled quantile), useful to normalize data from platforms with highly different numbers of investigated genes. When in 'Map' mode, the software generates a quantitative representation of the transcriptome of a sample (or of a pool of samples) and identifies if segments of defined lengths are over/under-expressed compared to the desired threshold. When in 'Cluster' mode, the software searches for a set of over/under-expressed consecutive genes. Statistical significance for all results is calculated with respect to genes localized on the same chromosome or to all genome genes. Transcriptome maps, showing differential expression between two sample groups, relative to two different biological conditions, may be easily generated. We present the results of a biological model test, based on a meta-analysis comparison between a sample pool of human CD34+ hematopoietic progenitor cells and a sample pool of megakaryocytic cells. Biologically relevant chromosomal segments and gene clusters with differential expression during the differentiation toward megakaryocyte were identified. Conclusions TRAM is designed to create, and statistically analyze, quantitative transcriptome maps, based on gene expression data from multiple sources. The release includes FileMaker Pro database management runtime application and it is freely available at http://apollo11.isto.unibo.it/software/, along with preconfigured implementations for mapping of human, mouse and zebrafish transcriptomes. PMID:21333005

Identification of human candidate genes for male infertility by digital differential display.

PubMed

Olesen, C; Hansen, C; Bendsen, E; Byskov, A G; Schwinger, E; Lopez-Pajares, I; Jensen, P K; Kristoffersson, U; Schubert, R; Van Assche, E; Wahlstroem, J; Lespinasse, J; Tommerup, N

2001-01-01

Evidence for the importance of genetic factors in male fertility is accumulating. In the literature and the Mendelian Cytogenetics Network database, 265 cases of infertile males with balanced reciprocal translocations have been described. The candidacy for infertility of 14 testis-expressed transcripts (TETs) were examined by comparing their chromosomal mapping position to the position of balanced reciprocal translocation breakpoints found in the 265 infertile males. The 14 TETs were selected by using digital differential display (electronic subtraction) to search for apparently testis-specific transcripts in the TIGR database. The testis specificity of the 14 TETs was further examined by reverse transcription-polymerase chain reaction (RT-PCR) on adult and fetal tissues showing that four TETs (TET1 to TET4) were testis-expressed only, six TETs (TET5 to TET10) appeared to be differentially expressed and the remaining four TETs (TET11 to TET14) were ubiquitously expressed. Interestingly, the two tesis expressed-only transcripts, TET1 and TET2, mapped to chromosomal regions where seven and six translocation breakpoints have been reported in infertile males respectively. Furthermore, one ubiquitously, but predominantly testis-expressed, transcript, TET11, mapped to 1p32-33, where 13 translocation breakpoints have been found in infertile males. Interestingly, the mouse mutation, skeletal fusions with sterility, sks, maps to the syntenic region in the mouse genome. Another transcript, TET7, was the human homologue of rat Tpx-1, which functions in the specific interaction of spermatogenic cells with Sertoli cells. TPX-1 maps to 6p21 where three cases of chromosomal breakpoints in infertile males have been reported. Finally, TET8 was a novel transcript which in the fetal stage is testis-specific, but in the adult is expressed in multiple tissues, including testis. We named this novel transcript fetal and adult testis-expressed transcript (FATE).

Hippocampal synapsin I, growth-associated protein-43, and microtubule-associated protein-2 immunoreactivity in learned helplessness rats and antidepressant-treated rats.

PubMed

Iwata, M; Shirayama, Y; Ishida, H; Kawahara, R

2006-09-01

Learned helplessness rats are thought to be an animal model of depression. To study the role of synapse plasticity in depression, we examined the effects of learned helplessness and antidepressant treatments on synapsin I (a marker of presynaptic terminals), growth-associated protein-43 (GAP-43; a marker of growth cones), and microtubule-associated protein-2 (MAP-2; a marker of dendrites) in the hippocampus by immunolabeling. (1) Learned helplessness rats showed significant increases in the expression of synapsin I two days after the attainment of learned helplessness, and significant decreases in the protein expression eight days after the achievement of learned helplessness. Subchronic treatment of naïve rats with imipramine or fluvoxamine significantly decreased the expression of synapsin I. (2) Learned helplessness increased the expression of GAP-43 two days and eight days after learned helplessness training. Subchronic treatment of naïve rats with fluvoxamine but not imipramine showed a tendency to decrease the expression of synapsin I. (3) Learned helplessness rats showed increased expression of MAP-2 eight days after the attainment of learned helplessness. Naïve rats subchronically treated with imipramine showed a tendency toward increased expression of MAP-2, but those treated with fluvoxamine did not. These results indicate that the neuroplasticity-related proteins synapsin I, GAP-43, and MAP-2 may play a role in the pathophysiology of depression and the mechanisms of antidepressants.

CARFMAP: A Curated Pathway Map of Cardiac Fibroblasts.

PubMed

Nim, Hieu T; Furtado, Milena B; Costa, Mauro W; Kitano, Hiroaki; Rosenthal, Nadia A; Boyd, Sarah E

2015-01-01

The adult mammalian heart contains multiple cell types that work in unison under tightly regulated conditions to maintain homeostasis. Cardiac fibroblasts are a significant and unique population of non-muscle cells in the heart that have recently gained substantial interest in the cardiac biology community. To better understand this renaissance cell, it is essential to systematically survey what has been known in the literature about the cellular and molecular processes involved. We have built CARFMAP (http://visionet.erc.monash.edu.au/CARFMAP), an interactive cardiac fibroblast pathway map derived from the biomedical literature using a software-assisted manual data collection approach. CARFMAP is an information-rich interactive tool that enables cardiac biologists to explore the large body of literature in various creative ways. There is surprisingly little overlap between the cardiac fibroblast pathway map, a foreskin fibroblast pathway map, and a whole mouse organism signalling pathway map from the REACTOME database. Among the use cases of CARFMAP is a common task in our cardiac biology laboratory of identifying new genes that are (1) relevant to cardiac literature, and (2) differentially regulated in high-throughput assays. From the expression profiles of mouse cardiac and tail fibroblasts, we employed CARFMAP to characterise cardiac fibroblast pathways. Using CARFMAP in conjunction with transcriptomic data, we generated a stringent list of six genes that would not have been singled out using bioinformatics analyses alone. Experimental validation showed that five genes (Mmp3, Il6, Edn1, Pdgfc and Fgf10) are differentially regulated in the cardiac fibroblast. CARFMAP is a powerful tool for systems analyses of cardiac fibroblasts, facilitating systems-level cardiovascular research.

A Children's Oncology Group and TARGET initiative exploring the genetic landscape of Wilms tumor. | Office of Cancer Genomics

Cancer.gov

We performed genome-wide sequencing and analyzed mRNA and miRNA expression, DNA copy number, and DNA methylation in 117 Wilms tumors, followed by targeted sequencing of 651 Wilms tumors. In addition to genes previously implicated in Wilms tumors (WT1, CTNNB1, AMER1, DROSHA, DGCR8, XPO5, DICER1, SIX1, SIX2, MLLT1, MYCN, and TP53), we identified mutations in genes not previously recognized as recurrently involved in Wilms tumors, the most frequent being BCOR, BCORL1, NONO, MAX, COL6A3, ASXL1, MAP3K4, and ARID1A.

Remote sensing as a mineral prospecting technique

NASA Technical Reports Server (NTRS)

Meneses, P. R. (Principal Investigator)

1984-01-01

Remote sensing and its application as an alternative technique to mineral resource exploration are reviewed. Emphasis is given here to the analysis of the three basic attributes of remote sensing, i.e., spatial attributes related to regional structural mapping, spectral attributes related to rock discrimination and seasonal attributes related to geobotanic anomalies mapping, all of which are employed in mineral exploration. Special emphasis is given to new developments of the Thematic Mapper of the LANDSAT-5, principally with reference to the application of the bands 1.6 and 2.2 microns to map hydrothermally altered rocks and the band of red and blue shift to geobotanical anomalies mapping.

Color Shaded-Relief and Surface-Classification Maps of the Fish Creek Area, Harrison Bay Quadrangle, Northern Alaska

USGS Publications Warehouse

Mars, John L.; Garrity, Christopher P.; Houseknecht, David W.; Amoroso, Lee; Meares, Donald C.

2007-01-01

Introduction The northeastern part of the National Petroleum Reserve in Alaska (NPRA) has become an area of active petroleum exploration during the past five years. Recent leasing and exploration drilling in the NPRA requires the U.S. Bureau of Land Management (BLM) to manage and monitor a variety of surface activities that include seismic surveying, exploration drilling, oil-field development drilling, construction of oil-production facilities, and construction of pipelines and access roads. BLM evaluates a variety of permit applications, environmental impact studies, and other documents that require rapid compilation and analysis of data pertaining to surface and subsurface geology, hydrology, and biology. In addition, BLM must monitor these activities and assess their impacts on the natural environment. Timely and accurate completion of these land-management tasks requires elevation, hydrologic, geologic, petroleum-activity, and cadastral data, all integrated in digital formats at a higher resolution than is currently available in nondigital (paper) formats. To support these land-management tasks, a series of maps was generated from remotely sensed data in an area of high petroleum-industry activity (fig. 1). The maps cover an area from approximately latitude 70?00' N. to 70?30' N. and from longitude 151?00' W. to 153?10' W. The area includes the Alpine oil field in the east, the Husky Inigok exploration well (site of a landing strip) in the west, many of the exploration wells drilled in NPRA since 2000, and the route of a proposed pipeline to carry oil from discovery wells in NPRA to the Alpine oil field. This map area is referred to as the 'Fish Creek area' after a creek that flows through the region. The map series includes (1) a color shaded-relief map based on 5-m-resolution data (sheet 1), (2) a surface-classification map based on 30-m-resolution data (sheet 2), and (3) a 5-m-resolution shaded relief-surface classification map that combines the shaded-relief and surface-classification data (sheet 3). Remote sensing datasets that were used to compile the maps include Landsat 7 Enhanced Thematic Mapper+ (ETM+), and interferometric synthetic aperture radar (IFSAR) data. In addition, a 1:250,000-scale geologic map of the Harrison Bay quadrangle, Alaska (Carter and Galloway, 1985, 2005) was used in conjunction with ETM+ and IFSAR data.

Maps & minds : mapping through the ages

USGS Publications Warehouse

,

1984-01-01

Throughout time, maps have expressed our understanding of our world. Human affairs have been influenced strongly by the quality of maps available to us at the major turning points in our history. "Maps & Minds" traces the ebb and flow of a few central ideas in the mainstream of mapping. Our expanding knowledge of our cosmic neighborhood stems largely from a small number of simple but grand ideas, vigorously pursued.

Evaluation of phenoxybenzamine in the CFA model of pain following gene expression studies and connectivity mapping.

PubMed

Chang, Meiping; Smith, Sarah; Thorpe, Andrew; Barratt, Michael J; Karim, Farzana

2010-09-16

We have previously used the rat 4 day Complete Freund's Adjuvant (CFA) model to screen compounds with potential to reduce osteoarthritic pain. The aim of this study was to identify genes altered in this model of osteoarthritic pain and use this information to infer analgesic potential of compounds based on their own gene expression profiles using the Connectivity Map approach. Using microarrays, we identified differentially expressed genes in L4 and L5 dorsal root ganglia (DRG) from rats that had received intraplantar CFA for 4 days compared to matched, untreated control animals. Analysis of these data indicated that the two groups were distinguishable by differences in genes important in immune responses, nerve growth and regeneration. This list of differentially expressed genes defined a "CFA signature". We used the Connectivity Map approach to identify pharmacologic agents in the Broad Institute Build02 database that had gene expression signatures that were inversely related ('negatively connected') with our CFA signature. To test the predictive nature of the Connectivity Map methodology, we tested phenoxybenzamine (an alpha adrenergic receptor antagonist) - one of the most negatively connected compounds identified in this database - for analgesic activity in the CFA model. Our results indicate that at 10 mg/kg, phenoxybenzamine demonstrated analgesia comparable to that of Naproxen in this model. Evaluation of phenoxybenzamine-induced analgesia in the current study lends support to the utility of the Connectivity Map approach for identifying compounds with analgesic properties in the CFA model.

Animation of Mapped Photo Collections for Storytelling

NASA Astrophysics Data System (ADS)

Fujita, Hideyuki; Arikawa, Masatoshi

Our research goal is to facilitate the sharing of stories with digital photographs. Some map websites now collect stories associated with peoples' relationships to places. Users map collections of places and include their intangible emotional associations with each location along with photographs, videos, etc. Though this framework of mapping stories is important, it is not sufficiently expressive to communicate stories in a narrative fashion. For example, when the number of the mapped collections of places is particularly large, it is neither easy for viewers to interpret the map nor is it easy for the creator to express a story as a series of events in the real world. This is because each narrative, in the form of a sequence of textual narratives, a sequence of photographs, a movie, or audio is mapped to just one point. As a result, it is up to the viewer to decide which points on the map must be read, and in what order. The conventional framework is fairly suitable for mapping and expressing fragments or snapshots of a whole story and not for conveying the whole story as a narrative using the entire map as the setting. We therefore propose a new framework, Spatial Slideshow, for mapping personal photo collections and representing them as stories such as route guidances, sightseeing guidances, historical topics, fieldwork records, personal diaries, and so on. It is a fusion of personal photo mapping and photo storytelling. Each story is conveyed through a sequence of mapped photographs, presented as a synchronized animation of a map and an enhanced photo slideshow. The main technical novelty of this paper is a method for creating three-dimensional animations of photographs that induce the visual effect of motion from photo to photo. We believe that the proposed framework may have considerable significance in facilitating the grassroots development of spatial content driven by visual communication concerning real-world locations or events.

Exploration of a Capability-Focused Aerospace System of Systems Architecture Alternative with Bilayer Design Space, Based on RST-SOM Algorithmic Methods

PubMed Central

Li, Zhifei; Qin, Dongliang

2014-01-01

In defense related programs, the use of capability-based analysis, design, and acquisition has been significant. In order to confront one of the most challenging features of a huge design space in capability based analysis (CBA), a literature review of design space exploration was first examined. Then, in the process of an aerospace system of systems design space exploration, a bilayer mapping method was put forward, based on the existing experimental and operating data. Finally, the feasibility of the foregoing approach was demonstrated with an illustrative example. With the data mining RST (rough sets theory) and SOM (self-organized mapping) techniques, the alternative to the aerospace system of systems architecture was mapping from P-space (performance space) to C-space (configuration space), and then from C-space to D-space (design space), respectively. Ultimately, the performance space was mapped to the design space, which completed the exploration and preliminary reduction of the entire design space. This method provides a computational analysis and implementation scheme for large-scale simulation. PMID:24790572

The Primordial Inflation Polarization ExploreR (PIPER)

NASA Astrophysics Data System (ADS)

Gandilo, Natalie; Ade, Peter; Benford, Dominic; Bennett, Charles; Chuss, David; Datta, Rahul; Dotson, Jessie; Essinger-Hileman, Thomas; Fixsen, Dale; Halpern, Mark; Hilton, Gene; Hinshaw, Gary; Irwin, Kent; Jhabvala, Christine; Kimball, Mark; Kogut, Al; Lowe, Luke; McMahon, Jeff; Miller, Timothy; Mirel, Paul; Moseley, Samuel Harvey; Pawlyk, Samuel; Rodriguez, Samelys; Sharp, Elmer; Shirron, Peter; Staguhn, Johannes G.; Sullivan, Dan; Switzer, Eric; Taraschi, Peter; Tucker, Carole; Walts, Alexander; Wollack, Edward

2018-01-01

The Primordial Inflation Polarization ExploreR (PIPER) is a balloon-borne telescope designed to map the large scale polarization of the Cosmic Microwave Background as well as the polarized emission from galactic dust at 200, 270, 350, and 600 GHz, with 21, 15, 14, and 14 arcminutes of angular resolution respectively. PIPER uses twin telescopes with Variable-delay Polarization Modulators to simultaneously map Stokes I, Q, U and V. Cold optics and the lack of a warm window allow the instrument to achieve background limited sensitivity, with mapping speed approximately 10 times faster than a similar instrument with a single ambient-temperature mirror. Over the course of 8 conventional balloon flights from the Northern and Southern hemisphere, PIPER will map 85% of the sky, measuring the B-mode polarization spectrum from the reionization bump to l~300, and placing an upper limit on the tensor-to-scalar ratio of r<0.007. An engineering flight is planned for October 2017 from Fort Sumner, New Mexico, and the first science flight is planned for June 2018 from Palestine, Texas.

Exploration of a capability-focused aerospace system of systems architecture alternative with bilayer design space, based on RST-SOM algorithmic methods.

PubMed

Li, Zhifei; Qin, Dongliang; Yang, Feng

2014-01-01

In defense related programs, the use of capability-based analysis, design, and acquisition has been significant. In order to confront one of the most challenging features of a huge design space in capability based analysis (CBA), a literature review of design space exploration was first examined. Then, in the process of an aerospace system of systems design space exploration, a bilayer mapping method was put forward, based on the existing experimental and operating data. Finally, the feasibility of the foregoing approach was demonstrated with an illustrative example. With the data mining RST (rough sets theory) and SOM (self-organized mapping) techniques, the alternative to the aerospace system of systems architecture was mapping from P-space (performance space) to C-space (configuration space), and then from C-space to D-space (design space), respectively. Ultimately, the performance space was mapped to the design space, which completed the exploration and preliminary reduction of the entire design space. This method provides a computational analysis and implementation scheme for large-scale simulation.

Mapping texts through dimensionality reduction and visualization techniques for interactive exploration of document collections

NASA Astrophysics Data System (ADS)

de Andrade Lopes, Alneu; Minghim, Rosane; Melo, Vinícius; Paulovich, Fernando V.

2006-01-01

The current availability of information many times impair the tasks of searching, browsing and analyzing information pertinent to a topic of interest. This paper presents a methodology to create a meaningful graphical representation of documents corpora targeted at supporting exploration of correlated documents. The purpose of such an approach is to produce a map from a document body on a research topic or field based on the analysis of their contents, and similarities amongst articles. The document map is generated, after text pre-processing, by projecting the data in two dimensions using Latent Semantic Indexing. The projection is followed by hierarchical clustering to support sub-area identification. The map can be interactively explored, helping to narrow down the search for relevant articles. Tests were performed using a collection of documents pre-classified into three research subject classes: Case-Based Reasoning, Information Retrieval, and Inductive Logic Programming. The map produced was capable of separating the main areas and approaching documents by their similarity, revealing possible topics, and identifying boundaries between them. The tool can deal with the exploration of inter-topics and intra-topic relationship and is useful in many contexts that need deciding on relevant articles to read, such as scientific research, education, and training.

Identification of prostate cancer modifier pathways using parental strain expression mapping

PubMed Central

Xu, Qing; Majumder, Pradip K.; Ross, Kenneth; Shim, Yeonju; Golub, Todd R.; Loda, Massimo; Sellers, William R.

2007-01-01

Inherited genetic risk factors play an important role in cancer. However, other than the Mendelian fashion cancer susceptibility genes found in familial cancer syndromes, little is known about risk modifiers that control individual susceptibility. Here we developed a strategy, parental strain expression mapping, that utilizes the homogeneity of inbred mice and genome-wide mRNA expression analyses to directly identify candidate germ-line modifier genes and pathways underlying phenotypic differences among murine strains exposed to transgenic activation of AKT1. We identified multiple candidate modifier pathways and, specifically, the glycolysis pathway as a candidate negative modulator of AKT1-induced proliferation. In keeping with the findings in the murine models, in multiple human prostate expression data set, we found that enrichment of glycolysis pathways in normal tissues was associated with decreased rates of cancer recurrence after prostatectomy. Together, these data suggest that parental strain expression mapping can directly identify germ-line modifier pathways of relevance to human disease. PMID:17978178

Exact protein distributions for stochastic models of gene expression using partitioning of Poisson processes.

PubMed

Pendar, Hodjat; Platini, Thierry; Kulkarni, Rahul V

2013-04-01

Stochasticity in gene expression gives rise to fluctuations in protein levels across a population of genetically identical cells. Such fluctuations can lead to phenotypic variation in clonal populations; hence, there is considerable interest in quantifying noise in gene expression using stochastic models. However, obtaining exact analytical results for protein distributions has been an intractable task for all but the simplest models. Here, we invoke the partitioning property of Poisson processes to develop a mapping that significantly simplifies the analysis of stochastic models of gene expression. The mapping leads to exact protein distributions using results for mRNA distributions in models with promoter-based regulation. Using this approach, we derive exact analytical results for steady-state and time-dependent distributions for the basic two-stage model of gene expression. Furthermore, we show how the mapping leads to exact protein distributions for extensions of the basic model that include the effects of posttranscriptional and posttranslational regulation. The approach developed in this work is widely applicable and can contribute to a quantitative understanding of stochasticity in gene expression and its regulation.

Exact protein distributions for stochastic models of gene expression using partitioning of Poisson processes

NASA Astrophysics Data System (ADS)

Pendar, Hodjat; Platini, Thierry; Kulkarni, Rahul V.

2013-04-01

Stochasticity in gene expression gives rise to fluctuations in protein levels across a population of genetically identical cells. Such fluctuations can lead to phenotypic variation in clonal populations; hence, there is considerable interest in quantifying noise in gene expression using stochastic models. However, obtaining exact analytical results for protein distributions has been an intractable task for all but the simplest models. Here, we invoke the partitioning property of Poisson processes to develop a mapping that significantly simplifies the analysis of stochastic models of gene expression. The mapping leads to exact protein distributions using results for mRNA distributions in models with promoter-based regulation. Using this approach, we derive exact analytical results for steady-state and time-dependent distributions for the basic two-stage model of gene expression. Furthermore, we show how the mapping leads to exact protein distributions for extensions of the basic model that include the effects of posttranscriptional and posttranslational regulation. The approach developed in this work is widely applicable and can contribute to a quantitative understanding of stochasticity in gene expression and its regulation.

Graded and discontinuous EphA-ephrinB expression patterns in the developing auditory brainstem

PubMed Central

Wallace, Matthew M.; Harris, J. Aaron; Brubaker, Donald Q.; Klotz, Caitlyn A.; Gabriele, Mark L.

2016-01-01

Eph-ephrin interactions guide topographic mapping and pattern formation in a variety of systems. In contrast to other sensory pathways, their precise role in the assembly of central auditory circuits remains poorly understood. The auditory midbrain, or inferior colliculus (IC) is an intriguing structure for exploring guidance of patterned projections as adjacent subdivisions exhibit distinct organizational features. The central nucleus of the IC (CNIC) and deep aspects of its neighboring lateral cortex (LCIC, Layer 3) are tonotopically-organized and receive layered inputs from primarily downstream auditory sources. While less is known about more superficial aspects of the LCIC, its inputs are multimodal, lack a clear tonotopic order, and appear discontinuous, terminating in modular, patch/matrix-like distributions. Here we utilize X-Gal staining approaches in lacZ mutant mice (ephrin-B2, -B3, and EphA4) to reveal EphA-ephrinB expression patterns in the nascent IC during the period of projection shaping that precedes hearing onset. We also report early postnatal protein expression in the cochlear nuclei, the superior olivary complex, the nuclei of the lateral lemniscus, and relevant midline structures. Continuous ephrin-B2 and EphA4 expression gradients exist along frequency axes of the CNIC and LCIC Layer 3. In contrast, more superficial LCIC localization is not graded, but confined to a series of discrete ephrin-B2 and EphA4-positive Layer 2 modules. While heavily expressed in the midline, much of the auditory brainstem is devoid of ephrin-B3, including the CNIC, LCIC Layer 2 modular fields, the dorsal nucleus of the lateral lemniscus (DNLL), as well as much of the superior olivary complex and cochlear nuclei. Ephrin-B3 LCIC expression appears complementary to that of ephrin-B2 and EphA4, with protein most concentrated in presumptive extramodular zones. Described tonotopic gradients and seemingly complementary modular/extramodular patterns suggest Eph-ephrin guidance in establishing juxtaposed continuous and discrete neural maps in the developing IC prior to experience. PMID:26906676

Graded and discontinuous EphA-ephrinB expression patterns in the developing auditory brainstem.

PubMed

Wallace, Matthew M; Harris, J Aaron; Brubaker, Donald Q; Klotz, Caitlyn A; Gabriele, Mark L

2016-05-01

Eph-ephrin interactions guide topographic mapping and pattern formation in a variety of systems. In contrast to other sensory pathways, their precise role in the assembly of central auditory circuits remains poorly understood. The auditory midbrain, or inferior colliculus (IC) is an intriguing structure for exploring guidance of patterned projections as adjacent subdivisions exhibit distinct organizational features. The central nucleus of the IC (CNIC) and deep aspects of its neighboring lateral cortex (LCIC, Layer 3) are tonotopically-organized and receive layered inputs from primarily downstream auditory sources. While less is known about more superficial aspects of the LCIC, its inputs are multimodal, lack a clear tonotopic order, and appear discontinuous, terminating in modular, patch/matrix-like distributions. Here we utilize X-Gal staining approaches in lacZ mutant mice (ephrin-B2, -B3, and EphA4) to reveal EphA-ephrinB expression patterns in the nascent IC during the period of projection shaping that precedes hearing onset. We also report early postnatal protein expression in the cochlear nuclei, the superior olivary complex, the nuclei of the lateral lemniscus, and relevant midline structures. Continuous ephrin-B2 and EphA4 expression gradients exist along frequency axes of the CNIC and LCIC Layer 3. In contrast, more superficial LCIC localization is not graded, but confined to a series of discrete ephrin-B2 and EphA4-positive Layer 2 modules. While heavily expressed in the midline, much of the auditory brainstem is devoid of ephrin-B3, including the CNIC, LCIC Layer 2 modular fields, the dorsal nucleus of the lateral lemniscus (DNLL), as well as much of the superior olivary complex and cochlear nuclei. Ephrin-B3 LCIC expression appears complementary to that of ephrin-B2 and EphA4, with protein most concentrated in presumptive extramodular zones. Described tonotopic gradients and seemingly complementary modular/extramodular patterns suggest Eph-ephrin guidance in establishing juxtaposed continuous and discrete neural maps in the developing IC prior to experience. Copyright © 2016 Elsevier B.V. All rights reserved.

[Cloning of human CD45 gene and its expression in Hela cells].

PubMed

Li, Jie; Xu, Tianyu; Wu, Lulin; Zhang, Liyun; Lu, Xiao; Zuo, Daming; Chen, Zhengliang

2015-11-01

To clone human CD45 gene PTPRC and establish Hela cells overexpressing recombinant human CD45 protein. The intact cDNA encoding human CD45 amplified using RT-PCR from the total RNA extracted from peripheral blood mononuclear cells (PBMCs) of a healthy donor was cloned into pMD-18T vector. The CD45 cDNA fragment amplified from the pMD-18T-CD45 by PCR was inserted to the coding region of the PcDNA3.1-3xflag vector, and the resultant recombinant expression vector PcDNA3.1-3xflag-CD45 was transfected into Hela cells. The expression of CD45 in Hela cells was detected by flow cytometry and Western blotting, and the phosphastase activity of CD45 was quantified using an alkaline phosphatase assay kit. The cDNA fragment of about 3 900 bp was amplified from human PBMCs and cloned into pMD-18T vector. The recombinant expression vector PcDNA3.1-3xflag-CD45 was constructed, whose restriction maps and sequence were consistent with those expected. The expression of CD45 in transfected Hela cells was detected by flow cytometry and Western blotting, and the expressed recombinant CD45 protein in Hela cells showed a phosphastase activity. The cDNA of human CD45 was successfully cloned and effectively expressed in Hela cells, which provides a basis for further exploration of the functions of CD45.

Activities for Plate Tectonics using GeoMapApp

NASA Astrophysics Data System (ADS)

Goodwillie, A. M.

2016-12-01

The concept of plate tectonics is a fundamental component of our understanding of how Earth works yet authentic, high-quality geoscience data related to plate tectonics may not be readily available to all students. To compound matters, when data is accessible, students may not possess the skills or resources necessary to explore and analyse it. As a result, much emphasis at federal and state level is now placed upon encouraging students to work with more data and more technology more often and more rigourously. Easy-to-use digital platforms offer much potential for promoting inquiry-based learning at all levels of education. GeoMapApp is one such tool. Developed at Columbia University's Lamont-Doherty Earth Observatory, GeoMapApp (http://www.geomapapp.org) is a free resource that integrates a wide range of research-grade geoscience data in one intuitive map-based interface. Simple strategies for data manipulation, visualisation and presentation allow uses to explore the data in meaningful ways. Layering and transparency capabilities further allow learners to use GeoMapApp to compare multiple data sets at once, and high-impact Save Session functionality allows a GeoMapApp project to be saved for sharing or later use. In this presentation, activities related to plate tectonics will be highlighted. One GeoMapApp activity helps students investigate plate boundaries by exploring earthquake and volcano locations. Another requires students to calculate the rate of seafloor spreading using crustal age data in various ocean basins. A third uses the GeoMapApp layering technique to explore the influence of geological forces in shaping the landscape. Each activity shown can be done by students on an individual basis, as pairs, or as groups. Educators report that student use of GeoMapApp fosters an increased sense of data "ownership" amongst students, promotes STEM skills, and provides them with access to authentic research-grade geoscience data using the same cutting-edge technological tool used by researchers.

Characterization of Mitogen-Activated Protein Kinase Expression in Nucleus Accumbens and Hippocampus of Rats Subjected to Food Selection in the Cafeteria Diet Protocol.

PubMed

Sarro-Ramírez, Andrea; Sánchez, Daniel; Tejeda-Padrón, Alma; Buenfil-Canto, Linda Vianey; Valladares-García, Jorge; Pacheco-Pantoja, Elda; Arias-Carrión, Oscar; Murillo-Rodríguez, Eric

2016-01-01

Obesity is a world-wide health problem that requires different experimental perspectives to understand the onset of this disease, including the neurobiological basis of food selection. From a molecular perspective, obesity has been related with activity of several endogenous molecules, including the mitogenactivated protein kinases (MAP-K). The aim of this study was to characterize MAP-K expression in hedonic and learning and memory brain-associated areas such as nucleus accumbens (AcbC) and hippocampus (HIPP) after food selection. We show that animals fed with cafeteria diet during 14 days displayed an increase in p38 MAP-K activity in AcbC if chose cheese. Conversely, a diminution was observed in animals that preferred chocolate in AcbC. Also, a decrease of p38 MAP-K phosphorylation was found in HIPP in rats that selected either cheese or chocolate. Our data demonstrate a putative role of MAP-K expression in food selection. These findings advance our understanding of neuromolecular basis engaged in obesity.

MARs Tools for Interactive ANalysis (MARTIAN): Google Maps Tools for Visual Exploration of Geophysical Modeling on Mars

NASA Astrophysics Data System (ADS)

Dimitrova, L. L.; Haines, M.; Holt, W. E.; Schultz, R. A.; Richard, G.; Haines, A. J.

2006-12-01

Interactive maps of surface-breaking faults and stress models on Mars provide important tools to engage undergraduate students, educators, and scientists with current geological and geophysical research. We have developed a map based on the Google Maps API -- an Internet based tool combining DHTML and AJAX, -- which allows very large maps to be viewed over the World Wide Web. Typically, small portions of the maps are downloaded as needed, rather than the entire image at once. This set-up enables relatively fast access for users with low bandwidth. Furthermore, Google Maps provides an extensible interactive interface making it ideal for visualizing multiple data sets at the user's choice. The Google Maps API works primarily with data referenced to latitudes and longitudes, which is then mapped in Mercator projection only. We have developed utilities for general cylindrical coordinate systems by converting these coordinates into equivalent Mercator projection before including them on the map. The MARTIAN project is available at http://rock.geo.sunysb.edu/~holt/Mars/MARTIAN/. We begin with an introduction to the Martian surface using a topography model. Faults from several datasets are classified by type (extension vs. compression) and by time epoch. Deviatoric stresses due to gravitational potential energy differences, calculated from the topography and crustal thickness, can be overlain. Several quantitative measures for the fit of the stress field to the faults are also included. We provide introductory text and exercises spanning a range of topics: how are faults identified, what stress is and how it relates to faults, what gravitational potential energy is and how variations in it produce stress, how the models are created, and how these models can be evaluated and interpreted. The MARTIAN tool is used at Stony Brook University in GEO 310: Introduction to Geophysics, a class geared towards junior and senior geosciences majors. Although this project is in its early stages, high school and college teachers, as well as researchers have expressed interest in using and extending these tools for visualizing and interacting with data on Earth and other planetary bodies.

30 CFR 784.23 - Operation plan: Maps and plans.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 30 Mineral Resources 3 2010-07-01 2010-07-01 false Operation plan: Maps and plans. 784.23 Section... PLAN § 784.23 Operation plan: Maps and plans. Each application shall contain maps and plans as follows... INTERIOR SURFACE COAL MINING AND RECLAMATION OPERATIONS PERMITS AND COAL EXPLORATION SYSTEMS UNDER...

43 CFR 3482.3 - Mining operations maps.

Code of Federal Regulations, 2012 CFR

2012-10-01

... and up-to-date maps of the mine, drawn to scales acceptable to the authorized officer. Before a mine... boundary lines; surface buildings; dip of the coal bed(s); true north; map scale; map explanation; location...; geologic conditions as determined from outcrops, drill holes, exploration, or mining; any unusual geologic...

43 CFR 3482.3 - Mining operations maps.

Code of Federal Regulations, 2013 CFR

2013-10-01

... and up-to-date maps of the mine, drawn to scales acceptable to the authorized officer. Before a mine... boundary lines; surface buildings; dip of the coal bed(s); true north; map scale; map explanation; location...; geologic conditions as determined from outcrops, drill holes, exploration, or mining; any unusual geologic...

43 CFR 3482.3 - Mining operations maps.

Code of Federal Regulations, 2014 CFR

2014-10-01

... and up-to-date maps of the mine, drawn to scales acceptable to the authorized officer. Before a mine... boundary lines; surface buildings; dip of the coal bed(s); true north; map scale; map explanation; location...; geologic conditions as determined from outcrops, drill holes, exploration, or mining; any unusual geologic...

Fine mapping of regulatory loci for mammalian gene expression using radiation hybrids

PubMed Central

Park, Christopher C; Ahn, Sangtae; Bloom, Joshua S; Lin, Andy; Wang, Richard T; Wu, Tongtong; Sekar, Aswin; Khan, Arshad H; Farr, Christine J; Lusis, Aldons J; Leahy, Richard M; Lange, Kenneth; Smith, Desmond J

2010-01-01

We mapped regulatory loci for nearly all protein-coding genes in mammals using comparative genomic hybridization and expression array measurements from a panel of mouse–hamster radiation hybrid cell lines. The large number of breaks in the mouse chromosomes and the dense genotyping of the panel allowed extremely sharp mapping of loci. As the regulatory loci result from extra gene dosage, we call them copy number expression quantitative trait loci, or ceQTLs. The −2log10P support interval for the ceQTLs was <150 kb, containing an average of <2–3 genes. We identified 29,769 trans ceQTLs with −log10P > 4, including 13 hotspots each regulating >100 genes in trans. Further, this work identifies 2,761 trans ceQTLs harboring no known genes, and provides evidence for a mode of gene expression autoregulation specific to the X chromosome. PMID:18362883

Grid Visualization Tool

NASA Technical Reports Server (NTRS)

Chouinard, Caroline; Fisher, Forest; Estlin, Tara; Gaines, Daniel; Schaffer, Steven

2005-01-01

The Grid Visualization Tool (GVT) is a computer program for displaying the path of a mobile robotic explorer (rover) on a terrain map. The GVT reads a map-data file in either portable graymap (PGM) or portable pixmap (PPM) format, representing a gray-scale or color map image, respectively. The GVT also accepts input from path-planning and activity-planning software. From these inputs, the GVT generates a map overlaid with one or more rover path(s), waypoints, locations of targets to be explored, and/or target-status information (indicating success or failure in exploring each target). The display can also indicate different types of paths or path segments, such as the path actually traveled versus a planned path or the path traveled to the present position versus planned future movement along a path. The program provides for updating of the display in real time to facilitate visualization of progress. The size of the display and the map scale can be changed as desired by the user. The GVT was written in the C++ language using the Open Graphics Library (OpenGL) software. It has been compiled for both Sun Solaris and Linux operating systems.

Facial Expression Generation from Speaker's Emotional States in Daily Conversation

NASA Astrophysics Data System (ADS)

Mori, Hiroki; Ohshima, Koh

A framework for generating facial expressions from emotional states in daily conversation is described. It provides a mapping between emotional states and facial expressions, where the former is represented by vectors with psychologically-defined abstract dimensions, and the latter is coded by the Facial Action Coding System. In order to obtain the mapping, parallel data with rated emotional states and facial expressions were collected for utterances of a female speaker, and a neural network was trained with the data. The effectiveness of proposed method is verified by a subjective evaluation test. As the result, the Mean Opinion Score with respect to the suitability of generated facial expression was 3.86 for the speaker, which was close to that of hand-made facial expressions.

Temporal analysis and spatial mapping of Lymantria dispar nuclear polyhedrosis virus transcripts and in vitro translation polypeptides

Treesearch

James M. Slavicek

1991-01-01

Genomic expression of the Lymantriu dispar multinucleocapsid nuclear polyhedrosis virus (LdMNPV) was studied. Viral specific transcripts expressed in cell culture at various times from 2 through 72 h postinfection were identified and their genomic origins mapped through Northern analysis. Sixty-five distinct transcripts were identified in this...

SEAFLOOR EXPLORATION AND CHARACTERIZATION: PREREQUISITE TO OCEAN SPACE UTILIZATION.

USGS Publications Warehouse

Hill, Gary; Lockwood, Millington

1987-01-01

A historical survey of US bathymetric mapping is presented up through the major mapping project begun in response to the 1983, establishment of an Exclusive Economic Zone (EEZ), 200 nautical miles seaward. The EEZ extends sovereign rights for the purposes of exploring, exploiting, conserving, and managing natural resources in the coastal ocean. This new area is approximately 3. 4 million square nautical miles or about 1. 3 times the total US land area. To characterize the resources within it, the US National Oceanic and Atmospheric Administration (NOAA) and the US Geological Survey (USGS) are undertaking systematic mapping programs of the EEZ. NOAA's effort includes detailed bathymetric mapping of the seabed. The USGS is using a wide-swath side-scan sonar system to map the EEZ seafloor on a reconaissance scale.

MOPED 2.5—An Integrated Multi-Omics Resource: Multi-Omics Profiling Expression Database Now Includes Transcriptomics Data

PubMed Central

Montague, Elizabeth; Stanberry, Larissa; Higdon, Roger; Janko, Imre; Lee, Elaine; Anderson, Nathaniel; Choiniere, John; Stewart, Elizabeth; Yandl, Gregory; Broomall, William; Kolker, Natali

2014-01-01

Abstract Multi-omics data-driven scientific discovery crucially rests on high-throughput technologies and data sharing. Currently, data are scattered across single omics repositories, stored in varying raw and processed formats, and are often accompanied by limited or no metadata. The Multi-Omics Profiling Expression Database (MOPED, http://moped.proteinspire.org) version 2.5 is a freely accessible multi-omics expression database. Continual improvement and expansion of MOPED is driven by feedback from the Life Sciences Community. In order to meet the emergent need for an integrated multi-omics data resource, MOPED 2.5 now includes gene relative expression data in addition to protein absolute and relative expression data from over 250 large-scale experiments. To facilitate accurate integration of experiments and increase reproducibility, MOPED provides extensive metadata through the Data-Enabled Life Sciences Alliance (DELSA Global, http://delsaglobal.org) metadata checklist. MOPED 2.5 has greatly increased the number of proteomics absolute and relative expression records to over 500,000, in addition to adding more than four million transcriptomics relative expression records. MOPED has an intuitive user interface with tabs for querying different types of omics expression data and new tools for data visualization. Summary information including expression data, pathway mappings, and direct connection between proteins and genes can be viewed on Protein and Gene Details pages. These connections in MOPED provide a context for multi-omics expression data exploration. Researchers are encouraged to submit omics data which will be consistently processed into expression summaries. MOPED as a multi-omics data resource is a pivotal public database, interdisciplinary knowledge resource, and platform for multi-omics understanding. PMID:24910945

Identification and Characterization of Genes Required for Early Myxococcus xanthus Developmental Gene Expression

PubMed Central

Guo, Dongchuan; Wu, Yun; Kaplan, Heidi B.

2000-01-01

Starvation and cell density regulate the developmental expression of Myxococcus xanthus gene 4521. Three classes of mutants allow expression of this developmental gene during growth on nutrient agar, such that colonies of strains containing a Tn5 lac Ω4521 fusion are Lac+. One class of these mutants inactivates SasN, a negative regulator of 4521 expression; another class activates SasS, a sensor kinase-positive regulator of 4521 expression; and a third class blocks lipopolysaccharide (LPS) O-antigen biosynthesis. To identify additional positive regulators of 4521 expression, 11 Lac− TnV.AS transposon insertion mutants were isolated from a screen of 18,000 Lac+ LPS O-antigen mutants containing Tn5 lac Ω4521 (Tcr). Ten mutations identified genes that could encode positive regulators of 4521 developmental expression based on their ability to abolish 4521 expression during development in the absence of LPS O antigen and in an otherwise wild-type background. Eight of these mutations mapped to the sasB locus, which encodes the known 4521 regulators SasS and SasN. One mapped to sasS, whereas seven identified new genes. Three mutations mapped to a gene encoding an NtrC-like response regulator homologue, designated sasR, and four others mapped to a gene designated sasP. One mutation, designated ssp10, specifically suppressed the LPS O-antigen defect; the ssp10 mutation had no effect on 4521 expression in an otherwise wild-type background but reduced 4521 developmental expression in the absence of LPS O antigen to a level close to that of the parent strain. All of the mutations except those in sasP conferred defects during growth and development. These data indicate that a number of elements are required for 4521 developmental expression and that most of these are necessary for normal growth and fruiting body development. PMID:10913090

Microtubule-associated protein 1S-related autophagy inhibits apoptosis of intestinal epithelial cells via Wnt/β-catenin signaling in Crohn's disease.

PubMed

Bai, Wenxia; Bai, Jian'an; Li, Yanhai; Tian, Delong; Shi, Ruihua

2017-04-08

Many autophagy-related genes, to our knowledge, have been identified as Crohn's disease (CD) polymorphic sites by genomic wide studies. As a novel member of the microtubule-associated protein 1 (MAP1) family, MAP1S is a microtubule-binding proteins involved in autophagy. However, its expression and potential functions in CD have not been understood. For the first time, we discovered the up-regulated MAP1S and autophagy level (indicated by LC3-Ⅱ/LC3-Ⅰ) in inflamed epithelium among CD patients. Similarly, in TNBS-induced murine colitis model, MAP1S expression was obviously increased. Meanwhile, we found the co-location of MAP1S and active-caspase 3 which acted as "apoptotic executor" which might indicate the basis of their co-efficient. At the cellular level, MAP1S silencing inhibited starvation-induced over-expression of active-caspase 3 partially via Wnt/β-catenin signaling activation in HCT-116 cells. Finally, we demonstrated that IWP-2, an inhibitor of the Wnt/β-catenin signaling, reversed the down-regulation of active-caspase 3 induced by MAP1S siRNA in HCT-116 cells. Taken together, our results suggested that MAP1S were up-regulated among CD patients and MAP1S-related autophagy inhibits apoptosis of intestinal epithelial cells (IECs) through Wnt/β-catenin signaling pathway which might play a vital role in the protection of intestinal mucosal barrier and inhibition the progression of CD. Copyright © 2017 Elsevier Inc. All rights reserved.

Mapping Inner Space: Learning and Teaching Visual Mapping. Second Edition.

ERIC Educational Resources Information Center

Margulies, Nancy

More than 10 years ago, when "Mapping Inner Space" was first published, a few teachers were using this creative technique and teaching it to their students. Today mapping is widely used in schools, universities, and the corporate world, as well. This second edition of the book explores a variety of mapping styles and also takes a fresh look at the…

Charting the Land of Flowers: Exploration and Mapmaking in Spanish Florida

ERIC Educational Resources Information Center

Kite-Powell, Rodney

2013-01-01

Produced by cartographers of many nations over the course of six centuries, maps detailing Florida and the North American continent tell tales of exploration, conflict, and change. Before 1492, Europeans were unaware of what existed on the other side of the Atlantic Ocean. That reality is illustrated quite well on two maps that show the…

D Modelling and Mapping for Virtual Exploration of Underwater Archaeology Assets

NASA Astrophysics Data System (ADS)

Liarokapis, F.; Kouřil, P.; Agrafiotis, P.; Demesticha, S.; Chmelík, J.; Skarlatos, D.

2017-02-01

This paper investigates immersive technologies to increase exploration time in an underwater archaeological site, both for the public, as well as, for researchers and scholars. Focus is on the Mazotos shipwreck site in Cyprus, which is located 44 meters underwater. The aim of this work is two-fold: (a) realistic modelling and mapping of the site and (b) an immersive virtual reality visit. For 3D modelling and mapping optical data were used. The underwater exploration is composed of a variety of sea elements including: plants, fish, stones, and artefacts, which are randomly positioned. Users can experience an immersive virtual underwater visit in Mazotos shipwreck site and get some information about the shipwreck and its contents for raising their archaeological knowledge and cultural awareness.

Validation of Innovative Exploration Technologies for Newberry Volcano: Drill Site Location Map 2010

DOE Data Explorer

Jaffe, Todd

2012-01-01

Newberry seeks to explore "blind" (no surface evidence) convective hydrothermal systems associated with a young silicic pluton on the flanks of Newberry Volcano. This project will employ a combination of innovative and conventional techniques to identify the location of subsurface geothermal fluids associated with the hot pluton. Newberry project drill site location map 2010. Once the exploration mythology is validated, it can be applied throughout the Cascade Range and elsewhere to locate and develop “blind” geothermal resources.

A reference genetic linkage map of apomictic Hieracium species based on expressed markers derived from developing ovule transcripts.

PubMed

Shirasawa, Kenta; Hand, Melanie L; Henderson, Steven T; Okada, Takashi; Johnson, Susan D; Taylor, Jennifer M; Spriggs, Andrew; Siddons, Hayley; Hirakawa, Hideki; Isobe, Sachiko; Tabata, Satoshi; Koltunow, Anna M G

2015-03-01

Apomixis in plants generates clonal progeny with a maternal genotype through asexual seed formation. Hieracium subgenus Pilosella (Asteraceae) contains polyploid, highly heterozygous apomictic and sexual species. Within apomictic Hieracium, dominant genetic loci independently regulate the qualitative developmental components of apomixis. In H. praealtum, LOSS OF APOMEIOSIS (LOA) enables formation of embryo sacs without meiosis and LOSS OF PARTHENOGENESIS (LOP) enables fertilization-independent seed formation. A locus required for fertilization-independent endosperm formation (AutE) has been identified in H. piloselloides. Additional quantitative loci appear to influence the penetrance of the qualitative loci, although the controlling genes remain unknown. This study aimed to develop the first genetic linkage maps for sexual and apomictic Hieracium species using simple sequence repeat (SSR) markers derived from expressed transcripts within the developing ovaries. RNA from microdissected Hieracium ovule cell types and ovaries was sequenced and SSRs were identified. Two different F1 mapping populations were created to overcome difficulties associated with genome complexity and asexual reproduction. SSR markers were analysed within each mapping population to generate draft linkage maps for apomictic and sexual Hieracium species. A collection of 14 684 Hieracium expressed SSR markers were developed and linkage maps were constructed for Hieracium species using a subset of the SSR markers. Both the LOA and LOP loci were successfully assigned to linkage groups; however, AutE could not be mapped using the current populations. Comparisons with lettuce (Lactuca sativa) revealed partial macrosynteny between the two Asteraceae species. A collection of SSR markers and draft linkage maps were developed for two apomictic and one sexual Hieracium species. These maps will support cloning of controlling genes at LOA and LOP loci in Hieracium and should also assist with identification of quantitative loci that affect the expressivity of apomixis. Future work will focus on mapping AutE using alternative populations. © The Author 2014. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Systems Analysis of Early Host Gene Expression Provides Clues for Transient Mycobacterium avium ssp avium vs. Persistent Mycobacterium avium ssp paratuberculosis Intestinal Infections

PubMed Central

Khare, Sangeeta; Drake, Kenneth L.; Lawhon, Sara D.; Nunes, Jairo E. S.; Figueiredo, Josely F.; Rossetti, Carlos A.; Gull, Tamara; Everts, Robin E.; Lewin, Harris. A.; Adams, Leslie Garry

2016-01-01

It has long been a quest in ruminants to understand how two very similar mycobacterial species, Mycobacterium avium ssp. paratuberculosis (MAP) and Mycobacterium avium ssp. avium (MAA) lead to either a chronic persistent infection or a rapid-transient infection, respectively. Here, we hypothesized that when the host immune response is activated by MAP or MAA, the outcome of the infection depends on the early activation of signaling molecules and host temporal gene expression. To test our hypothesis, ligated jejuno-ileal loops including Peyer’s patches in neonatal calves were inoculated with PBS, MAP, or MAA. A temporal analysis of the host transcriptome profile was conducted at several times post-infection (0.5, 1, 2, 4, 8 and 12 hours). When comparing the transcriptional responses of calves infected with the MAA versus MAP, discordant patterns of mucosal expression were clearly evident, and the numbers of unique transcripts altered were moderately less for MAA-infected tissue than were mucosal tissues infected with the MAP. To interpret these complex data, changes in the gene expression were further analyzed by dynamic Bayesian analysis. Bayesian network modeling identified mechanistic genes, gene-to-gene relationships, pathways and Gene Ontologies (GO) biological processes that are involved in specific cell activation during infection. MAP and MAA had significant different pathway perturbation at 0.5 and 12 hours post inoculation. Inverse processes were observed between MAP and MAA response for epithelial cell proliferation, negative regulation of chemotaxis, cell-cell adhesion mediated by integrin and regulation of cytokine-mediated signaling. MAP inoculated tissue had significantly lower expression of phagocytosis receptors such as mannose receptor and complement receptors. This study reveals that perturbation of genes and cellular pathways during MAP infection resulted in host evasion by mucosal membrane barrier weakening to access entry in the ileum, inhibition of Ca signaling associated with decreased phagosome-lysosome fusion as well as phagocytosis inhibition, bias toward Th2 cell immune response accompanied by cell recruitment, cell proliferation and cell differentiation; leading to persistent infection. Contrarily, MAA infection was related to cellular responses associated with activation of molecular pathways that release chemicals and cytokines involved with containment of infection and a strong bias toward Th1 immune response, resulting in a transient infection. PMID:27653506

Systems Analysis of Early Host Gene Expression Provides Clues for Transient Mycobacterium avium ssp avium vs. Persistent Mycobacterium avium ssp paratuberculosis Intestinal Infections.

PubMed

Khare, Sangeeta; Drake, Kenneth L; Lawhon, Sara D; Nunes, Jairo E S; Figueiredo, Josely F; Rossetti, Carlos A; Gull, Tamara; Everts, Robin E; Lewin, Harris A; Adams, Leslie Garry

It has long been a quest in ruminants to understand how two very similar mycobacterial species, Mycobacterium avium ssp. paratuberculosis (MAP) and Mycobacterium avium ssp. avium (MAA) lead to either a chronic persistent infection or a rapid-transient infection, respectively. Here, we hypothesized that when the host immune response is activated by MAP or MAA, the outcome of the infection depends on the early activation of signaling molecules and host temporal gene expression. To test our hypothesis, ligated jejuno-ileal loops including Peyer's patches in neonatal calves were inoculated with PBS, MAP, or MAA. A temporal analysis of the host transcriptome profile was conducted at several times post-infection (0.5, 1, 2, 4, 8 and 12 hours). When comparing the transcriptional responses of calves infected with the MAA versus MAP, discordant patterns of mucosal expression were clearly evident, and the numbers of unique transcripts altered were moderately less for MAA-infected tissue than were mucosal tissues infected with the MAP. To interpret these complex data, changes in the gene expression were further analyzed by dynamic Bayesian analysis. Bayesian network modeling identified mechanistic genes, gene-to-gene relationships, pathways and Gene Ontologies (GO) biological processes that are involved in specific cell activation during infection. MAP and MAA had significant different pathway perturbation at 0.5 and 12 hours post inoculation. Inverse processes were observed between MAP and MAA response for epithelial cell proliferation, negative regulation of chemotaxis, cell-cell adhesion mediated by integrin and regulation of cytokine-mediated signaling. MAP inoculated tissue had significantly lower expression of phagocytosis receptors such as mannose receptor and complement receptors. This study reveals that perturbation of genes and cellular pathways during MAP infection resulted in host evasion by mucosal membrane barrier weakening to access entry in the ileum, inhibition of Ca signaling associated with decreased phagosome-lysosome fusion as well as phagocytosis inhibition, bias toward Th2 cell immune response accompanied by cell recruitment, cell proliferation and cell differentiation; leading to persistent infection. Contrarily, MAA infection was related to cellular responses associated with activation of molecular pathways that release chemicals and cytokines involved with containment of infection and a strong bias toward Th1 immune response, resulting in a transient infection.

Meta-Analyses of Dehalococcoides mccartyi Strain 195 Transcriptomic Profiles Identify a Respiration Rate-Related Gene Expression Transition Point and Interoperon Recruitment of a Key Oxidoreductase Subunit

PubMed Central

Mansfeldt, Cresten B.; Rowe, Annette R.; Heavner, Gretchen L. W.; Zinder, Stephen H.

2014-01-01

A cDNA-microarray was designed and used to monitor the transcriptomic profile of Dehalococcoides mccartyi strain 195 (in a mixed community) respiring various chlorinated organics, including chloroethenes and 2,3-dichlorophenol. The cultures were continuously fed in order to establish steady-state respiration rates and substrate levels. The organization of array data into a clustered heat map revealed two major experimental partitions. This partitioning in the data set was further explored through principal component analysis. The first two principal components separated the experiments into those with slow (1.6 ± 0.6 μM Cl−/h)- and fast (22.9 ± 9.6 μM Cl−/h)-respiring cultures. Additionally, the transcripts with the highest loadings in these principal components were identified, suggesting that those transcripts were responsible for the partitioning of the experiments. By analyzing the transcriptomes (n = 53) across experiments, relationships among transcripts were identified, and hypotheses about the relationships between electron transport chain members were proposed. One hypothesis, that the hydrogenases Hup and Hym and the formate dehydrogenase-like oxidoreductase (DET0186-DET0187) form a complex (as displayed by their tight clustering in the heat map analysis), was explored using a nondenaturing protein separation technique combined with proteomic sequencing. Although these proteins did not migrate as a single complex, DET0112 (an FdhB-like protein encoded in the Hup operon) was found to comigrate with DET0187 rather than with the catalytic Hup subunit DET0110. On closer inspection of the genome annotations of all Dehalococcoides strains, the DET0185-to-DET0187 operon was found to lack a key subunit, an FdhB-like protein. Therefore, on the basis of the transcriptomic, genomic, and proteomic evidence, the place of the missing subunit in the DET0185-to-DET0187 operon is likely filled by recruiting a subunit expressed from the Hup operon (DET0112). PMID:25063656

The Depositional and Erosional History of Northwestern Aeolis Mons, Gale Crater, Mars: Insights from Detailed 1:2K Geologic Mapping

NASA Astrophysics Data System (ADS)

Edgar, L. A.; Calef, F. J., III; Thomson, B. J.

2017-12-01

The Mars Science Laboratory (MSL) Curiosity rover is currently exploring the stratigraphy exposed in Aeolis Mons, the central mound of Gale crater. Gale crater has been the target of numerous remote sensing studies, aimed at understanding the origin and evolution of the mound, informally known as Mt. Sharp. A number of efforts have produced geologic maps of the mound and the MSL traverse path, in order to investigate the stratigraphic relationships between different sedimentary units. However, a scale gap exists between local mapping and stratigraphic analyses of the area explored by Curiosity and regional mapping of Aeolis Mons. As Curiosity explores the northwest flank of Aeolis Mons, there is a critical need for investigations to bridge this gap to enable rover-scale observations to be tied to orbital interpretations. This study is focused on detailed geologic mapping and stratigraphic correlations for the northwest flank of Aeolis Mons, including an area that the Curiosity rover will likely explore. The study region covers a 5.8 x 10 km area from approximately 137.27 to 137.44 °E and -4.70 to -4.82 °N. A 25 cm/pixel mosaic produced from images acquired by the High Resolution Imaging Science Experiment (HiRISE) camera provides a basemap for all mapping, and topographic information is provided by a HiRISE 1 m Digital Terrain Model. Preliminary digital geologic mapping was carried out at a scale of 1:10,000 to provide a framework for detailed geologic mapping efforts. Higher-resolution geologic mapping was then conducted at a scale of 1:2,000, and type localities were identified. As a result of newer, higher-resolution datasets that are now available and more narrowly focused mapping, we identify a number of new geologic units. Erosional remnants of some units point to a substantial erosional history. Collectively, the stratigraphy records diverse sedimentary environments and more variability in the depositional and erosional histories than previously identified. This study helps bridge the gap between previous mapping efforts and detailed rover-scale mapping, and will enable rover observations to be more closely tied to orbital interpretations across the northwest flank of Aeolis Mons.

[Effect of rhynchophylline on behaviors of methamphetamine-dependent zebrafish and the mechanism].

PubMed

Chen, Yi-Fei; Peng, Ju; Fang, Miao; Liu, Yi; Nie, Ling-Hui; Mo, Zhi-Xian; Zhu, Ling-Ling

2016-11-20

To observe the effect of rhynchophylline on methamphetamine-dependent zebrafish and explore the possible mechanism. Zebrafish were divided into control group, amphetamine group, low- (50 mg/kg) and high (100 mg/kg)-dose rhynchophylline groups, and ketamine (150 mg/kg) group. Conditioned place preference (CPP) was induced in zebrafish with methamphetamine, and the staying time in the drug box and the tracking map of the zebrafish were observed with Noldus Ethovision XT system. The protein expressions of TH, NR2B and GLUR2 in the brain of zebrafish with CPP were detected with Western blotting. Compared with the control group, zebrafish in methamphetamine group showed significant variations in the staying time and swimming distance in the drug box after conditioning (P<0.05) with obvious alterations of NR2B, TH and GLUR2 expressions in the brain (P<0.05). Treatment of methamphetamine-dependent zebrafish with high-dose rhynchophylline significantly reduced the variations in the staying time and swimming distance in the drug box (P<0.05) and in the expressions of NR2B, TH and GLUR2 in the brain (P<0.05). Rhynchophylline can inhibit methamphetamine dependence in zebrafish, the mechanism of which may involve the expressions of TH, NR2B and GLUR2 proteins in the brain.

Direct Correlation between Motile Behavior and Protein Abundance in Single Cells

PubMed Central

Gillet, Sébastien; Frankel, Nicholas W.; Weibel, Douglas B.

2016-01-01

Understanding how stochastic molecular fluctuations affect cell behavior requires the quantification of both behavior and protein numbers in the same cells. Here, we combine automated microscopy with in situ hydrogel polymerization to measure single-cell protein expression after tracking swimming behavior. We characterized the distribution of non-genetic phenotypic diversity in Escherichia coli motility, which affects single-cell exploration. By expressing fluorescently tagged chemotaxis proteins (CheR and CheB) at different levels, we quantitatively mapped motile phenotype (tumble bias) to protein numbers using thousands of single-cell measurements. Our results disagreed with established models until we incorporated the role of CheB in receptor deamidation and the slow fluctuations in receptor methylation. Beyond refining models, our central finding is that changes in numbers of CheR and CheB affect the population mean tumble bias and its variance independently. Therefore, it is possible to adjust the degree of phenotypic diversity of a population by adjusting the global level of expression of CheR and CheB while keeping their ratio constant, which, as shown in previous studies, confers functional robustness to the system. Since genetic control of protein expression is heritable, our results suggest that non-genetic diversity in motile behavior is selectable, supporting earlier hypotheses that such diversity confers a selective advantage. PMID:27599206

Immunohistochemical comparative analysis of GFAP, MAP - 2, NOGO - A, OLIG - 2 and WT - 1 expression in WHO 2016 classified neuroepithelial tumours and their prognostic value.

PubMed

Schwab, David Emanuel; Lepski, Guilherme; Borchers, Christian; Trautmann, Katrin; Paulsen, Frank; Schittenhelm, Jens

2018-01-01

Immunohistochemistry is routinely used in differential diagnosis of tumours of the central nervous system (CNS). The latest 2016 WHO 2016 revision now includes molecular data such as IDH mutation and 1p/19q codeletion thus restructuring glioma classification. Direct comparative information between commonly used immunohistochemical markers for glial tumours GFAP, MAP - 2, NOGO - A, OLIG - 2 and WT - 1 concerning quality and quantity of expression and their relation to the new molecular markers are lacking. We therefore compared the immunohistochemical staining results of all five antibodies in 34 oligodendrogliomas, 106 ependymomas and 423 astrocytic tumours. GFAP expression was reduced in cases with higher WHO grade, oligodendroglial differentiation and in IDH wildtype diffuse astrocytomas. By contrast MAP - 2 expression was significantly increased in diffuse astrocytomas with IDH mutation, while NOGO - A expression was not associated with any molecular marker. WT - 1 expression was significantly decreased in tumours with IDH mutation and ATRX loss. OLIG - 2 was increased in IDH-mutant grade II astrocytomas and in cases with higher proliferation rate. In univariate survival analysis high WT - 1 expression was significantly associated with worse outcome in diffuse astrocytic tumours (log rank p < 0.0001; n = 211; median time: 280 days vs 562 days). None of the markers was prognostic in multivariate survival analysis. Among the evaluated markers MAP - 2, OLIG - 2 and WT - 1 showed the best potential to separate between glioma entities and can be recommended for a standardized immunohistochemical panel. Copyright © 2017 Elsevier GmbH. All rights reserved.

An expanded maize gene expression atlas based on RNA sequencing and its use to explore root development

DOE PAGES

Stelpflug, Scott C.; Sekhon, Rajandeep S.; Vaillancourt, Brieanne; ...

2015-12-30

Comprehensive and systematic transcriptome profiling provides valuable insight into biological and developmental processes that occur throughout the life cycle of a plant. We have enhanced our previously published microarray-based gene atlas of maize ( Zea mays L.) inbred B73 to now include 79 distinct replicated samples that have been interrogated using RNA sequencing (RNA-seq). The current version of the atlas includes 50 original array-based gene atlas samples, a time-course of 12 stalk and leaf samples postflowering, and an additional set of 17 samples from the maize seedling and adult root system. The entire dataset contains 4.6 billion mapped reads, withmore » an average of 20.5 million mapped reads per biological replicate, allowing for detection of genes with lower transcript abundance. As the new root samples represent key additions to the previously examined tissues, we highlight insights into the root transcriptome, which is represented by 28,894 (73.2%) annotated genes in maize. Additionally, we observed remarkable expression differences across both the longitudinal (four zones) and radial gradients (cortical parenchyma and stele) of the primary root supported by fourfold differential expression of 9353 and 4728 genes, respectively. Among the latter were 1110 genes that encode transcription factors, some of which are orthologs of previously characterized transcription factors known to regulate root development in Arabidopsis thaliana (L.) Heynh., while most are novel, and represent attractive targets for reverse genetics approaches to determine their roles in this important organ. As a result, this comprehensive transcriptome dataset is a powerful tool toward understanding maize development, physiology, and phenotypic diversity.« less

The Carboxyl Terminus of v-Abl Protein Can Augment SH2 Domain Function

PubMed Central

Warren, David; Heilpern, Andrew J.; Berg, Kent; Rosenberg, Naomi

2000-01-01

Abelson murine leukemia virus (Ab-MLV) transforms NIH 3T3 and pre-B cells via expression of the v-Abl tyrosine kinase. Although the enzymatic activity of this molecule is absolutely required for transformation, other regions of the protein are also important for this response. Among these are the SH2 domain, involved in phosphotyrosine-dependent protein-protein interactions, and the long carboxyl terminus, which plays an important role in transformation of hematopoietic cells. Important signals are sent from each of these regions, and transformation is most likely orchestrated by the concerted action of these different parts of the protein. To explore this idea, we compared the ability of the v-Src SH2 domain to substitute for that of v-Abl in the full-length P120 v-Abl protein and in P70 v-Abl, a protein that lacks the carboxyl terminus characteristic of Abl family members. Ab-MLV strains expressing P70/S2 failed to transform NIH 3T3 cells and demonstrated a greatly reduced capacity to mediate signaling events associated with the Ras-dependent mitogen-activated protein (MAP) kinase pathway. In contrast, Ab-MLV strains expressing P120/S2 were indistinguishable from P120 with respect to these features. Analyses of additional mutants demonstrated that the last 162 amino acids of the carboxyl terminus were sufficient to restore transformation. These data demonstrate that an SH2 domain with v-Abl substrate specificity is required for NIH 3T3 transformation in the absence of the carboxyl terminus and suggest that cooperativity between the extreme carboxyl terminus and the SH2 domain facilitates the transmission of transforming signals via the MAP kinase pathway. PMID:10775585

An expanded maize gene expression atlas based on RNA sequencing and its use to explore root development

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

Stelpflug, Scott C.; Sekhon, Rajandeep S.; Vaillancourt, Brieanne

Comprehensive and systematic transcriptome profiling provides valuable insight into biological and developmental processes that occur throughout the life cycle of a plant. We have enhanced our previously published microarray-based gene atlas of maize ( Zea mays L.) inbred B73 to now include 79 distinct replicated samples that have been interrogated using RNA sequencing (RNA-seq). The current version of the atlas includes 50 original array-based gene atlas samples, a time-course of 12 stalk and leaf samples postflowering, and an additional set of 17 samples from the maize seedling and adult root system. The entire dataset contains 4.6 billion mapped reads, withmore » an average of 20.5 million mapped reads per biological replicate, allowing for detection of genes with lower transcript abundance. As the new root samples represent key additions to the previously examined tissues, we highlight insights into the root transcriptome, which is represented by 28,894 (73.2%) annotated genes in maize. Additionally, we observed remarkable expression differences across both the longitudinal (four zones) and radial gradients (cortical parenchyma and stele) of the primary root supported by fourfold differential expression of 9353 and 4728 genes, respectively. Among the latter were 1110 genes that encode transcription factors, some of which are orthologs of previously characterized transcription factors known to regulate root development in Arabidopsis thaliana (L.) Heynh., while most are novel, and represent attractive targets for reverse genetics approaches to determine their roles in this important organ. As a result, this comprehensive transcriptome dataset is a powerful tool toward understanding maize development, physiology, and phenotypic diversity.« less

A high resolution spatiotemporal atlas of gene expression of the developing mouse brain

PubMed Central

Thompson, Carol L.; Ng, Lydia; Menon, Vilas; Martinez, Salvador; Lee, Chang-Kyu; Glattfelder, Katie; Sunkin, Susan M.; Henry, Alex; Lau, Christopher; Dang, Chinh; Garcia-Lopez, Raquel; Martinez-Ferre, Almudena; Pombero, Ana; Rubenstein, John L.R.; Wakeman, Wayne B.; Hohmann, John; Dee, Nick; Sodt, Andrew J.; Young, Rob; Smith, Kimberly; Nguyen, Thuc-Nghi; Kidney, Jolene; Kuan, Leonard; Jeromin, Andreas; Kaykas, Ajamete; Miller, Jeremy; Page, Damon; Orta, Geri; Bernard, Amy; Riley, Zackery; Smith, Simon; Wohnoutka, Paul; Hawrylycz, Mike; Puelles, Luis; Jones, Allan R.

2015-01-01

SUMMARY To provide a temporal framework for the genoarchitecture of brain development, in situ hybridization data were generated for embryonic and postnatal mouse brain at 7 developmental stages for ~2100 genes, processed with an automated informatics pipeline and manually annotated. This resource comprises 434,946 images, 7 reference atlases, an ontogenetic ontology, and tools to explore co-expression of genes across neurodevelopment. Gene sets coinciding with developmental phenomena were identified. A temporal shift in the principles governing the molecular organization of the brain was detected, with transient neuromeric, plate-based organization of the brain present at E11.5 and E13.5. Finally, these data provided a transcription factor code that discriminates brain structures and identifies the developmental age of a tissue, providing a foundation for eventual genetic manipulation or tracking of specific brain structures over development. The resource is available as the Allen Developing Mouse Brain Atlas (developingmouse.brain-map.org). PMID:24952961

Comparing Tactile Maps and Haptic Digital Representations of a Maritime Environment

ERIC Educational Resources Information Center

Simonnet, Mathieu; Vieilledent, Steephane; Jacobson, R. Daniel; Tisseau, Jacques

2011-01-01

A map exploration and representation exercise was conducted with participants who were totally blind. Representations of maritime environments were presented either with a tactile map or with a digital haptic virtual map. We assessed the knowledge of spatial configurations using a triangulation technique. The results revealed that both types of…

Using Ecological Asset Mapping to Investigate Pre-Service Teachers' Cultural Assets

ERIC Educational Resources Information Center

Borrero, Noah; Yeh, Christine

2016-01-01

We examined the impact of a pedagogical strategy, ecological asset mapping, on 19 pre-service teachers' self-exploration, development of respect for others, and critical examination of social injustice. Data were analyzed from participants' ecological asset maps and essays describing the experience of completing and sharing the maps. The analysis…

NOAA Office of Exploration and Research > About OER > Organization > Map of

Science.gov Websites

About OER Overview Organization Guiding Documents Organizational Structure Map of Staff and Affiliate Overview Website & Social Media News Room OER Symposium Guiding Documents Organizational Structure Map About OER Overview Organization Guiding Documents Organizational Structure Map of Staff and Affiliate

2',5'-Dihydroxychalcone down-regulates endothelial connexin43 gap junctions and affects MAP kinase activation.

PubMed

Lee, Yi-Nan; Yeh, Hung-I; Tian, Tin-Yi; Lu, Wen-Wei; Ko, Yu-Shien; Tsai, Cheng-Ho

2002-09-30

We examined the effect of 2',5'-dihydroxychalcone on connexin43 (Cx43) expression and gap-junctional communication in human umbilical vein endothelial cells (HUVEC). The result showed that expression of Cx43 is rapidly reduced by 2',5'-dihydroxychalcone in a dose-dependent manner, Concomitantly, the communication function, determined by fluorescence recovery after photobleaching (FRAP), is decreased. We further investigated whether the mitogen-activated protein (MAP) kinase and the degradation pathway of gap junctions are involved in these processes. Although the change of Cx43 is not affected by the level of fetal calf serum (FCS) used in the medium, activation of MAP kinase varies, depending on the FCS level. At a low level (0.5%), the chalcone inhibits the activation, like PD98059, a specific inhibitor of MAP kinase kinase. However, at a high level (20%), MAP kinase is activated. On the other hand, the chalcone's down-regulating effect on Cx43, while is totally blocked by protease inhibitors leupeptin and N-acetyl-leucyl-norleucinal (ALLN), persists in the presence of PD98059, We concluded that 2',5'-dihydroxychalcone down-regulates Cx43 expression and gap-junctional communication in the HUVEC via enhancement of the proteolysis pathway, and this compound possesses dual effects on MAP kinase activation.

A network approach of gene co-expression in the zea mays/Aspergillus flavus pathosystem to map host/pathogen interaction pathways

USDA-ARS?s Scientific Manuscript database

A gene co-expression network was generated using a dual RNA-seq study with the fungal pathogen A. flavus and its plant host Z. mays during the initial 3 days of infection. The analysis deciphered novel pathways and mapped genes of interest in both organisms during the infection. This network reveal...

Mycobacterium avium subspecies induce differential expression of pro-inflammatory mediators in a murine macrophage model: evidence for enhanced pathogenicity of Mycobacterium avium subspecies paratuberculosis.

PubMed

Basler, Tina; Geffers, Robert; Weiss, Siegfried; Valentin-Weigand, Peter; Goethe, Ralph

2008-01-01

Mycobacterium avium subspecies (ssp.) paratuberculosis (MAP) is the etiological agent of paratuberculosis, a chronic, non-treatable granulomatous enteritis of ruminants. MAP is the only mycobacterium affecting the intestinal tract, which is of interest since it is presently the most favoured pathogen linked to Crohn's disease (CD) in humans due to its frequent detection in CD tissues. MAP is genetically closely related to other M. avium ssp. such as M. avium ssp. avium (MAA) and M. avium ssp. hominissuis (MAH) which can cause mycobacteriosis in animals and immunocompromised humans. We have recently shown that murine macrophage cell lines represent suitable systems to analyse M. avium ssp. patho-mechanisms and could show that MAP, but not MAA, specifically inhibited the antigen-specific stimulatory capacity for CD4(+) T-cells. In the present study, we compared gene expression profiles of murine RAW264.7 macrophages in response to infections with MAP or MAA using murine high-density oligonucleotide Affymetrix microarrays. A comparison of MAP and MAA infection revealed 17 differentially expressed genes. They were expressed at a much lower level in MAP-infected macrophages than in MAA-infected macrophages. Among these were the genes for IL-1beta, IL-1alpha, CXCL2, PTGS2 (COX2), lipocalin (LCN2) and TNF, which are important pro-inflammatory factors. The microarray data were confirmed for selected genes by quantitative real-time reverse transcription PCR and, by protein array analyses and ELISA. Similar to MAA, infection with MAH also showed robust induction of IL-1beta, CXCL2, COX2, LCN2 and TNF. Taken together, our results from M. avium ssp.-infected murine macrophages provide evidence that MAP in contrast to MAA and MAH specifically suppresses the pro-inflammatory defence mechanisms of infected macrophages.

Angiotensin II regulation of neuromodulation: downstream signaling mechanism from activation of mitogen-activated protein kinase.

PubMed

Lu, D; Yang, H; Raizada, M K

1996-12-01

Angiotensin II (Ang II) stimulates expression of tyrosine hydroxylase and norepinephrine transporter genes in brain neurons; however, the signal-transduction mechanism is not clearly defined. This study was conducted to determine the involvement of the mitogen-activated protein (MAP) kinase signaling pathway in Ang II stimulation of these genes. MAP kinase was localized in the perinuclear region of the neuronal soma. Ang II caused activation of MAP kinase and its subsequent translocation from the cytoplasmic to nuclear compartment, both effects being mediated by AT1 receptor subtype. Ang II also stimulated SRE- and AP1-binding activities and fos gene expression and its translocation in a MAP kinase-dependent process. These observations are the first demonstration of a downstream signaling pathway involving MAP kinase in Ang II-mediated neuromodulation in noradrenergic neurons.

TSEMA: interactive prediction of protein pairings between interacting families

PubMed Central

Izarzugaza, José M. G.; Juan, David; Pons, Carles; Ranea, Juan A. G.; Valencia, Alfonso; Pazos, Florencio

2006-01-01

An entire family of methodologies for predicting protein interactions is based on the observed fact that families of interacting proteins tend to have similar phylogenetic trees due to co-evolution. One application of this concept is the prediction of the mapping between the members of two interacting protein families (which protein within one family interacts with which protein within the other). The idea is that the real mapping would be the one maximizing the similarity between the trees. Since the exhaustive exploration of all possible mappings is not feasible for large families, current approaches use heuristic techniques which do not ensure the best solution to be found. This is why it is important to check the results proposed by heuristic techniques and to manually explore other solutions. Here we present TSEMA, the server for efficient mapping assessment. This system calculates an initial mapping between two families of proteins based on a Monte Carlo approach and allows the user to interactively modify it based on performance figures and/or specific biological knowledge. All the explored mappings are graphically shown over a representation of the phylogenetic trees. The system is freely available at . Standalone versions of the software behind the interface are available upon request from the authors. PMID:16845017

The expression ratio of Map7/B2M is prognostic for survival in patients with stage II colon cancer.

PubMed

Blum, Craig; Graham, Amanda; Yousefzadeh, Matt; Shrout, Jessica; Benjamin, Katie; Krishna, Murli; Hoda, Raza; Hoda, Rana; Cole, David J; Garrett-Mayer, Elizabeth; Reed, Carolyn; Wallace, Michael; Mitas, Michael

2008-09-01

Colorectal cancer (CRC) is the second most frequent cause of cancer-related death in the United States. To determine whether certain molecular markers might be prognostic for survival, we measured by quantitative real-time RT-PCR the expression levels of 15 previously studied genes that are known to be up-regulated or down-regulated in the progression of epithelial cancers. The tumor samples were extracted from formalin-fixed paraffin-embedded primary tissues derived from patients with Stage II CRC who developed disease recurrence within two years (n=10), or were disease-free for at least 4 years (n=12). We were able to determine, by AUC curve analysis, that the ratio of microtubule associated protein 7 (Map7)/B2M was predictive of outcome in our sample set. Further, using Kaplan-Meier survival analysis, we observed significantly different curves as a function of marker positivity for the Map7/B2M (p=0.0001; HR=11) expression ratio. This suggests that the expression ratio of Map7/B2M may serve as a valuable prognostic marker in patients with Stage II colon cancer, and potentially guide therapeutic decision making.

The expression ratio of Map7/B2M is prognostic for survival in patients with stage II colon cancer

PubMed Central

BLUM, CRAIG; GRAHAM, AMANDA; YOUSEFZADEH, MATT; SHROUT, JESSICA; BENJAMIN, KATIE; KRISHNA, MURLI; HODA, RAZA; HODA, RANA; COLE, DAVID J.; GARRETT-MAYER, ELIZABETH; REED, CAROLYN; WALLACE, MICHAEL; MITAS, MICHAEL

2012-01-01

Colorectal cancer (CRC) is the second most frequent cause of cancer-related death in the United States. To determine whether certain molecular markers might be prognostic for survival, we measured by quantitative real-time RT-PCR the expression levels of 15 previously studied genes that are known to be up-regulated or down-regulated in the progression of epithelial cancers. The tumor samples were extracted from formalin-fixed paraffin-embedded primary tissues derived from patients with Stage II CRC who developed disease recurrence within two years (n=10), or were disease-free for at least 4 years (n=12). We were able to determine, by AUC curve analysis, that the ratio of microtubule associated protein 7 (Map7)/B2M was predictive of outcome in our sample set. Further, using Kaplan-Meier survival analysis, we observed significantly different curves as a function of marker positivity for the Map7/B2M (p=0.0001; HR=11) expression ratio. This suggests that the expression ratio of Map7/B2M may serve as a valuable prognostic marker in patients with Stage II colon cancer, and potentially guide therapeutic decision making. PMID:18695889

Candidate genes that have facilitated freshwater adaptation by palaemonid prawns in the genus Macrobrachium: identification and expression validation in a model species (M. koombooloomba).

PubMed

Rahi, Md Lifat; Amin, Shorash; Mather, Peter B; Hurwood, David A

2017-01-01

The endemic Australian freshwater prawn, Macrobrachium koombooloomba , provides a model for exploring genes involved with freshwater adaptation because it is one of the relatively few Macrobrachium species that can complete its entire life cycle in freshwater. The present study was conducted to identify potential candidate genes that are likely to contribute to effective freshwater adaptation by M. koombooloomba using a transcriptomics approach. De novo assembly of 75 bp paired end 227,564,643 high quality Illumina raw reads from 6 different cDNA libraries revealed 125,917 contigs of variable lengths (200-18,050 bp) with an N50 value of 1597. In total, 31,272 (24.83%) of the assembled contigs received significant blast hits, of which 27,686 and 22,560 contigs were mapped and functionally annotated, respectively. CEGMA (Core Eukaryotic Genes Mapping Approach) based transcriptome quality assessment revealed 96.37% completeness. We identified 43 different potential genes that are likely to be involved with freshwater adaptation in M. koombooloomba . Identified candidate genes included: 25 genes for osmoregulation, five for cell volume regulation, seven for stress tolerance, three for body fluid (haemolymph) maintenance, eight for epithelial permeability and water channel regulation, nine for egg size control and three for larval development. RSEM (RNA-Seq Expectation Maximization) based abundance estimation revealed that 6,253, 5,753 and 3,795 transcripts were expressed (at TPM value ≥10) in post larvae, juveniles and adults, respectively. Differential gene expression (DGE) analysis showed that 15 genes were expressed differentially in different individuals but these genes apparently were not involved with freshwater adaptation but rather were involved in growth, development and reproductive maturation. The genomic resources developed here will be useful for better understanding the molecular basis of freshwater adaptation in Macrobrachium prawns and other crustaceans more broadly.

Candidate genes that have facilitated freshwater adaptation by palaemonid prawns in the genus Macrobrachium: identification and expression validation in a model species (M. koombooloomba)

PubMed Central

Amin, Shorash; Mather, Peter B.; Hurwood, David A.

2017-01-01

Background The endemic Australian freshwater prawn, Macrobrachium koombooloomba, provides a model for exploring genes involved with freshwater adaptation because it is one of the relatively few Macrobrachium species that can complete its entire life cycle in freshwater. Methods The present study was conducted to identify potential candidate genes that are likely to contribute to effective freshwater adaptation by M. koombooloomba using a transcriptomics approach. De novo assembly of 75 bp paired end 227,564,643 high quality Illumina raw reads from 6 different cDNA libraries revealed 125,917 contigs of variable lengths (200–18,050 bp) with an N50 value of 1597. Results In total, 31,272 (24.83%) of the assembled contigs received significant blast hits, of which 27,686 and 22,560 contigs were mapped and functionally annotated, respectively. CEGMA (Core Eukaryotic Genes Mapping Approach) based transcriptome quality assessment revealed 96.37% completeness. We identified 43 different potential genes that are likely to be involved with freshwater adaptation in M. koombooloomba. Identified candidate genes included: 25 genes for osmoregulation, five for cell volume regulation, seven for stress tolerance, three for body fluid (haemolymph) maintenance, eight for epithelial permeability and water channel regulation, nine for egg size control and three for larval development. RSEM (RNA-Seq Expectation Maximization) based abundance estimation revealed that 6,253, 5,753 and 3,795 transcripts were expressed (at TPM value ≥10) in post larvae, juveniles and adults, respectively. Differential gene expression (DGE) analysis showed that 15 genes were expressed differentially in different individuals but these genes apparently were not involved with freshwater adaptation but rather were involved in growth, development and reproductive maturation. Discussion The genomic resources developed here will be useful for better understanding the molecular basis of freshwater adaptation in Macrobrachium prawns and other crustaceans more broadly. PMID:28194319

Navigational Style Influences Eye Movement Pattern during Exploration and Learning of an Environmental Map

PubMed Central

Piccardi, Laura; De Luca, Maria; Nori, Raffaella; Palermo, Liana; Iachini, Fabiana; Guariglia, Cecilia

2016-01-01

During navigation people may adopt three different spatial styles (i.e., Landmark, Route, and Survey). Landmark style (LS) people are able to recall familiar landmarks but cannot combine them with directional information; Route style (RS) people connect landmarks to each other using egocentric information about direction; Survey style (SS) people use a map-like representation of the environment. SS individuals generally navigate better than LS and RS people. Fifty-one college students (20 LS; 17 RS, and 14 SS) took part in the experiment. The spatial cognitive style (SCS) was assessed by means of the SCS test; participants then had to learn a schematic map of a city, and after 5 min had to recall the path depicted on it. During the learning and delayed recall phases, eye-movements were recorded. Our intent was to investigate whether there is a peculiar way to explore an environmental map related to the individual’s spatial style. Results support the presence of differences in the strategy used by the three spatial styles for learning the path and its delayed recall. Specifically, LS individuals produced a greater number of fixations of short duration, while the opposite eye movement pattern characterized SS individuals. Moreover, SS individuals showed a more spread and comprehensive explorative pattern of the map, while LS individuals focused their exploration on the path and related targets. RS individuals showed a pattern of exploration at a level of proficiency between LS and SS individuals. We discuss the clinical and anatomical implications of our data. PMID:27445735

Using GeoMapApp in the Classroom

NASA Astrophysics Data System (ADS)

Goodwillie, A. M.

2017-12-01

The GeoMapApp tool has been updated with enhanced functionality that is useful in the classroom. Hosted as a service of the IEDA Facility at Columbia University, GeoMapApp (http://www.geomapapp.org) is a free resource that integrates a wide range of research-grade geoscience data in one intuitive map-based interface. It includes earthquake and volcano data, geological maps, plate tectonic data sets, and a high-resolution topography/bathymetry base map. Users can also import and analyse their own data files. Layering and transparency capabilities allow users to compare multiple data sets at once. The GeoMapApp interface presents data in its proper geospatial context, helping students more easily gain insight and understanding from the data. Simple tools for data manipulation allow students to analyse the data in different ways such as generating profiles and producing visualisations for reports. The new Save Session capability is designed to assist in the classroom: The educator saves a pre-loaded state of GeoMapApp. When shared with the class, the saved session file allows students to open GeoMapApp with exactly the same data sets loaded and the same display parameters chosen thus freeing up valuable time in which students can explore the data. In this presentation, activities related to plate tectonics will be highlighted. One activity helps students investigate plate boundaries by exploring earthquake and volcano locations. Another requires students to calculate the rate of seafloor spreading using crustal age data in various ocean basins. A third uses the GeoMapApp layering technique to explore the influence of geological forces in shaping the landscape. Educators report that using GeoMapApp in the classroom lowers the barriers to data accessibility for students; fosters an increased sense of data "ownership" - GeoMapApp presents the same data in the same tool used by researchers; allows engagement with authentic geoscience data; promotes STEM skills and exposure.

Evaluating SPLASH-2 Applications Using MapReduce

NASA Astrophysics Data System (ADS)

Zhu, Shengkai; Xiao, Zhiwei; Chen, Haibo; Chen, Rong; Zhang, Weihua; Zang, Binyu

MapReduce has been prevalent for running data-parallel applications. By hiding other non-functionality parts such as parallelism, fault tolerance and load balance from programmers, MapReduce significantly simplifies the programming of large clusters. Due to the mentioned features of MapReduce above, researchers have also explored the use of MapReduce on other application domains, such as machine learning, textual retrieval and statistical translation, among others.

Occupancy Grid Map Merging Using Feature Maps

DTIC Science & Technology

2010-11-01

each robot begins exploring at different starting points, once two robots can communicate, they send their odometry data, LIDAR observations, and maps...robots [11]. Moreover, it is relevant to mention that significant success has been achieved in solving SLAM problems when using hybrid maps [12...represents the environment by parametric features. Our method is capable of representing a LIDAR scanned environment map in a parametric fashion. In general

A qualitative study on using concept maps in problem-based learning.

PubMed

Chan, Zenobia C Y

2017-05-01

The visual arts, including concept maps, have been shown to be effective tools for facilitating student learning. However, the use of concept maps in nursing education has been under-explored. The aim of this study was to explore how students develop concept maps and what these concept maps consist of, and their views on the use of concept maps as a learning activity in a PBL class. A qualitative approach consisting of an analysis of the contents of the concept maps and interviews with students. The study was conducted in a school of nursing in a university in Hong Kong. A total of 38 students who attended the morning session (20 students) and afternoon session (18 students) respectively of a nursing problem-based learning class. The students in both the morning and afternoon classes were allocated into four groups (4-5 students per group). Each group was asked to draw two concept maps based on a given scenario, and then to participate in a follow-up interview. Two raters individually assessed the concept maps, and then discussed their views with each other. Among the concept maps that were drawn, four were selected. Their four core features of those maps were: a) the integration of informative and artistic elements; b) the delivery of sensational messages; c) the use of images rather than words; and d) three-dimensional and movable. Both raters were concerned about how informative the presentation was, the composition of the elements, and the ease of comprehension, and appreciated the three-dimensional presentation and effective use of images. From the results of the interview, the pros and cons of using concept maps were discerned. This study demonstrated how concept maps could be implemented in a PBL class to boost the students' creativity and to motivate them to learn. This study suggests the use of concept maps as an initiative to motivate student to learn, participate actively, and nurture their creativity. To conclude, this study explored an alternative way for students to make presentations and pioneered the use of art-based concept maps to facilitate student learning. Copyright © 2017 Elsevier Ltd. All rights reserved.

Proteomic analysis to investigate color changes of chilled beef longissimus steaks held under carbon monoxide and high oxygen packaging.

PubMed

Yang, Xiaoyin; Wu, Shuang; Hopkins, David L; Liang, Rongrong; Zhu, Lixian; Zhang, Yimin; Luo, Xin

2018-08-01

This study investigated the proteome basis for color stability variations in beef steaks packaged under two modified atmosphere packaging (MAP) methods: HiOx-MAP (80% O 2 /20% CO 2 ) and CO-MAP (0.4% CO/30% CO 2 /69.6% N 2 ) during 15 days of storage. The color stability, pH, and sarcoplasmic proteome analysis of steaks were evaluated on days 0, 5, 10 and 15 of storage. Proteomic results revealed that the differential expression of the sarcoplasmic proteome during storage contributed to the variations in meat color stability between the two MAP methods. Compared with HiOx-MAP steaks, some glycolytic and energy metabolic enzymes important in NADH regeneration and antioxidant processes, antioxidant peroxiredoxins (thioredoxin-dependent peroxide reductase, peroxiredoxin-2, peroxiredoxin-6) and protein DJ-1 were more abundant in CO-MAP steaks. The over-expression of these proteins could induce CO-MAP steaks to maintain high levels of metmyoglobin reducing activity and oxygen consumption rate, resulting in CO-MAP steaks exhibiting better color stability than HiOx-MAP steaks during storage. Copyright © 2018 Elsevier Ltd. All rights reserved.

Synchrotron radiation based STXM analysis and micro-XRF mapping of differential expression of extracellular thiol groups by Acidithiobacillus ferrooxidans grown on Fe(2+) and S(0).

PubMed

Xia, Jin-Lan; Liu, Hong-Chang; Nie, Zhen-Yuan; Peng, An-An; Zhen, Xiang-Jun; Yang, Yun; Zhang, Xiu-Li

2013-09-01

The differential expression of extracellular thiol groups by Acidithiobacillus ferrooxidans grown on substrates Fe(2+) and S(0) was investigated by using synchrotron radiation based scanning transmission X-ray microscopy (STXM) imaging and microbeam X-ray fluorescence (μ-XRF) mapping. The extracellular thiol groups (SH) were first alkylated by iodoacetic acid forming Protein-SCH2COOH and then the P-SCH2COOH was marked by calcium ions forming P-SCH2COOCa. The STXM imaging and μ-XRF mapping of SH were based on analysis of SCH2COO-bonded Ca(2+). The results indicated that the thiol group content of A. ferrooxidans grown on S(0) is 3.88 times to that on Fe(2+). Combined with selective labeling of SH by Ca(2+), the STXM imaging and μ-XRF mapping provided an in situ and rapid analysis of differential expression of extracellular thiol groups. © 2013.

Graded levels of FGF protein span the midbrain and can instruct graded induction and repression of neural mapping labels

PubMed Central

Chen, Yao; Mohammadi, Moosa; Flanagan, John G.

2009-01-01

Summary Graded guidance labels are widely used in neural map formation, but it is not well understood which potential strategy leads to their graded expression. In midbrain tectal map development, FGFs can induce an entire midbrain, but their protein distribution is unclear, nor is it known whether they may act instructively to produce graded gene expression. Using a receptor-alkaline phosphatase fusion probe, we find a long-range posterior>anterior FGF protein gradient spanning the midbrain. Heparan sulfate proteoglycan (HSPG) is required for this gradient. To test whether graded FGF concentrations can instruct graded gene expression, a quantitative tectal explant assay was developed. Engrailed-2 and ephrin-As, normally in posterior>anterior tectal gradients, showed graded upregulation. Moreover, EphAs, normally in anterior>posterior countergradients, showed coordinately graded downregulation. These results provide a mechanism to establish graded mapping labels, and more generally provide a developmental strategy to coordinately induce a structure and pattern its cell properties in gradients. PMID:19555646

Gene-Based Single Nucleotide Polymorphism Markers for Genetic and Association Mapping in Common Bean

PubMed Central

2012-01-01

Background In common bean, expressed sequence tags (ESTs) are an underestimated source of gene-based markers such as insertion-deletions (Indels) or single-nucleotide polymorphisms (SNPs). However, due to the nature of these conserved sequences, detection of markers is difficult and portrays low levels of polymorphism. Therefore, development of intron-spanning EST-SNP markers can be a valuable resource for genetic experiments such as genetic mapping and association studies. Results In this study, a total of 313 new gene-based markers were developed at target genes. Intronic variation was deeply explored in order to capture more polymorphism. Introns were putatively identified after comparing the common bean ESTs with the soybean genome, and the primers were designed over intron-flanking regions. The intronic regions were evaluated for parental polymorphisms using the single strand conformational polymorphism (SSCP) technique and Sequenom MassARRAY system. A total of 53 new marker loci were placed on an integrated molecular map in the DOR364 × G19833 recombinant inbred line (RIL) population. The new linkage map was used to build a consensus map, merging the linkage maps of the BAT93 × JALO EEP558 and DOR364 × BAT477 populations. A total of 1,060 markers were mapped, with a total map length of 2,041 cM across 11 linkage groups. As a second application of the generated resource, a diversity panel with 93 genotypes was evaluated with 173 SNP markers using the MassARRAY-platform and KASPar technology. These results were coupled with previous SSR evaluations and drought tolerance assays carried out on the same individuals. This agglomerative dataset was examined, in order to discover marker-trait associations, using general linear model (GLM) and mixed linear model (MLM). Some significant associations with yield components were identified, and were consistent with previous findings. Conclusions In short, this study illustrates the power of intron-based markers for linkage and association mapping in common bean. The utility of these markers is discussed in relation with the usefulness of microsatellites, the molecular markers by excellence in this crop. PMID:22734675

Digital Humanities: Envisioning a Collaborative Tool for Mapping, Evaluating, and Sharing Reconstructed Colonial American Parcel Maps

ERIC Educational Resources Information Center

Ruvane, Mary Brent

2012-01-01

The use of GIS technology for the humanities has opened up new avenues for visually exploring and asking questions of our nation's historical record. The potential to harness new knowledge with tools designed to capture and preserve geographic links to the artifacts of our past is within our grasp. This research explores the common information…

A high-density transcript linkage map with 1,845 expressed genes positioned by microarray-based Single Feature Polymorphisms (SFP) in Eucalyptus

PubMed Central

2011-01-01

Background Technological advances are progressively increasing the application of genomics to a wider array of economically and ecologically important species. High-density maps enriched for transcribed genes facilitate the discovery of connections between genes and phenotypes. We report the construction of a high-density linkage map of expressed genes for the heterozygous genome of Eucalyptus using Single Feature Polymorphism (SFP) markers. Results SFP discovery and mapping was achieved using pseudo-testcross screening and selective mapping to simultaneously optimize linkage mapping and microarray costs. SFP genotyping was carried out by hybridizing complementary RNA prepared from 4.5 year-old trees xylem to an SFP array containing 103,000 25-mer oligonucleotide probes representing 20,726 unigenes derived from a modest size expressed sequence tags collection. An SFP-mapping microarray with 43,777 selected candidate SFP probes representing 15,698 genes was subsequently designed and used to genotype SFPs in a larger subset of the segregating population drawn by selective mapping. A total of 1,845 genes were mapped, with 884 of them ordered with high likelihood support on a framework map anchored to 180 microsatellites with average density of 1.2 cM. Using more probes per unigene increased by two-fold the likelihood of detecting segregating SFPs eventually resulting in more genes mapped. In silico validation showed that 87% of the SFPs map to the expected location on the 4.5X draft sequence of the Eucalyptus grandis genome. Conclusions The Eucalyptus 1,845 gene map is the most highly enriched map for transcriptional information for any forest tree species to date. It represents a major improvement on the number of genes previously positioned on Eucalyptus maps and provides an initial glimpse at the gene space for this global tree genome. A general protocol is proposed to build high-density transcript linkage maps in less characterized plant species by SFP genotyping with a concurrent objective of reducing microarray costs. HIgh-density gene-rich maps represent a powerful resource to assist gene discovery endeavors when used in combination with QTL and association mapping and should be especially valuable to assist the assembly of reference genome sequences soon to come for several plant and animal species. PMID:21492453

A search for stratiform massive-sulfide exploration targets in Appalachian Devonian rocks; a case study using computer-assisted attribute-coincidence mapping

USGS Publications Warehouse

Wedow, Helmuth

1983-01-01

The empirical model for sediment-associated, stratiform, exhalative, massive-sulfide deposits presented by D. Large in 1979 and 1980 has been redesigned to permit its use in a computer-assisted search for exploration-target areas in Devonian rocks of the Appalachian region using attribute-coincidence mapping (ACM). Some 36 gridded-data maps and selected maps derived therefrom were developed to show the orthogonal patterns, using the 7-1/2 minute quadrangle as an information cell, of geologic data patterns relevant to the empirical model. From these map and data files, six attribute-coincidence maps were prepared to illustrate both variation in the application of ACM techniques and the extent of possible significant exploration-target areas. As a result of this preliminary work in ACM, four major (and some lesser) exploration-target areas needing further study and analysis have been defined as follows: 1) in western and central New York in the outcrop area of lowermost Upper Devonian rocks straddling the Clarendon-Linden fault; 2) in western Virginia and eastern West Virginia in an area largely coincident with the well-known 'Oriskany' Mn-Fe ores; 3) an area in West Virginia, Maryland, and Virginia along and nearby the trend of the Alabama-New York lineament of King and Zietz approximately between 38- and 40-degrees N. latitude; and 4) an area in northeastern Ohio overlying an area coincident with a significant thickness of Silurian salt and high modern seismic activity. Some lesser, smaller areas suggested by relatively high coincidence may also be worthy of further study.

Remote sensing strategies for global resource exploration and environmental management

NASA Astrophysics Data System (ADS)

Henderson, Frederick B.

Since 1972, satellite remote sensing, when integrated with other exploration techniques, has demonstrated operational exploration and engineering cost savings and reduced exploration risks through improved geological mapping. Land and ocean remote sensing satellite systems under development for the 1990's by the United States, France, Japan, Canada, ESA, Russia, China, and others, will significantly increase our ability to explore for, develop, and manage energy and mineral resources worldwide. A major difference between these systems is the "Open Skies" and "Non-Discriminatory Access to Data" policies as have been practiced by the U.S. and France and the restrictive nationalistic data policies as have been practiced by Russia and India. Global exploration will use satellite remote sensing to better map regional structural and basin-like features that control the distribution of energy and mineral resources. Improved sensors will better map lithologic and stratigraphic units and identify alteration effects in rocks, soils, and vegetation cover indicative of undiscovered subsurface resources. These same sensors will also map and monitor resource development. The use of satellite remote sensing data will grow substantially through increasing integration with other geophysical, geochemical, and geologic data using improved geographic information systems (GIS). International exploration will focus on underdeveloped countries rather than on mature exploration areas such as the United States, Europe, and Japan. Energy and mineral companies and government agencies in these countries and others will utilize available remote sensing data to acquire economic intelligence on global resources. If the "Non-Discriminatory Access to Data" principle is observed by satellite producing countries, exploration will remain competitive "on the ground". In this manner, remote sensing technology will continue to be developed to better explore for and manage the world's needed resources. If, however, satellite producing countries follow the Russian and Indian lead and restrict civil satellite data as tools of their national security and economic policies, remote sensing technology may become internationally competitive in space, redundant, prohibitively expensive, and generally unavailable to the world community.

Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria

PubMed Central

Farasat, Iman; Kushwaha, Manish; Collens, Jason; Easterbrook, Michael; Guido, Matthew; Salis, Howard M

2014-01-01

Developing predictive models of multi-protein genetic systems to understand and optimize their behavior remains a combinatorial challenge, particularly when measurement throughput is limited. We developed a computational approach to build predictive models and identify optimal sequences and expression levels, while circumventing combinatorial explosion. Maximally informative genetic system variants were first designed by the RBS Library Calculator, an algorithm to design sequences for efficiently searching a multi-protein expression space across a > 10,000-fold range with tailored search parameters and well-predicted translation rates. We validated the algorithm's predictions by characterizing 646 genetic system variants, encoded in plasmids and genomes, expressed in six gram-positive and gram-negative bacterial hosts. We then combined the search algorithm with system-level kinetic modeling, requiring the construction and characterization of 73 variants to build a sequence-expression-activity map (SEAMAP) for a biosynthesis pathway. Using model predictions, we designed and characterized 47 additional pathway variants to navigate its activity space, find optimal expression regions with desired activity response curves, and relieve rate-limiting steps in metabolism. Creating sequence-expression-activity maps accelerates the optimization of many protein systems and allows previous measurements to quantitatively inform future designs. PMID:24952589

An Automated Pipeline for Engineering Many-Enzyme Pathways: Computational Sequence Design, Pathway Expression-Flux Mapping, and Scalable Pathway Optimization.

PubMed

Halper, Sean M; Cetnar, Daniel P; Salis, Howard M

2018-01-01

Engineering many-enzyme metabolic pathways suffers from the design curse of dimensionality. There are an astronomical number of synonymous DNA sequence choices, though relatively few will express an evolutionary robust, maximally productive pathway without metabolic bottlenecks. To solve this challenge, we have developed an integrated, automated computational-experimental pipeline that identifies a pathway's optimal DNA sequence without high-throughput screening or many cycles of design-build-test. The first step applies our Operon Calculator algorithm to design a host-specific evolutionary robust bacterial operon sequence with maximally tunable enzyme expression levels. The second step applies our RBS Library Calculator algorithm to systematically vary enzyme expression levels with the smallest-sized library. After characterizing a small number of constructed pathway variants, measurements are supplied to our Pathway Map Calculator algorithm, which then parameterizes a kinetic metabolic model that ultimately predicts the pathway's optimal enzyme expression levels and DNA sequences. Altogether, our algorithms provide the ability to efficiently map the pathway's sequence-expression-activity space and predict DNA sequences with desired metabolic fluxes. Here, we provide a step-by-step guide to applying the Pathway Optimization Pipeline on a desired multi-enzyme pathway in a bacterial host.

The hydrocarbon accumulations mapping in crystalline rocks by mobile geophysical methods

NASA Astrophysics Data System (ADS)

Nesterenko, A.

2013-05-01

Sedimentary-migration origin theory of hydrocarbons dominates nowadays. However, a significant amount of hydrocarbon deposits were discovered in the crystalline rocks, which corroborates the theory of non-organic origin of hydrocarbons. During the solving of problems of oil and gas exploration in crystalline rocks and arrays so-called "direct" methods can be used. These methods include geoelectric methods of forming short-pulsed electromagnetic field (FSPEF) and vertical electric-resonance sounding (VERS) (FSPEF-VERS express-technology). Use of remote Earth sounding (RES) methods is also actual. These mobile technologies are extensively used during the exploration of hydrocarbon accumulations in crystalline rocks, including those within the Ukrainian crystalline shield. The results of explorations Four anomalous geoelectric zones of "gas condensate reservoir" type were quickly revealed as a result of reconnaissance prospecting works (Fig. 1). DTA "Obukhovychi". Anomaly was traced over a distance of 4 km. Approximate area is 12.0 km2. DTA"Korolevskaya". Preliminary established size of anomalous zone is 10.0 km2. The anomalous polarized layers of gas and gas-condensate type were determined. DTA "Olizarovskaya". Approximate size of anomaly is about 56.0 km2. This anomaly is the largest and the most intense. DTA "Druzhba". Preliminary estimated size of anomaly is 16.0 km2. Conclusions Long experience of a successful application of non-classical geoelectric methods for the solving of variety of practical tasks allow one to state their contribution to the development of a new paradigm of geophysical researches. Simultaneous usage of the remote sensing data processing and interpretation method and FSPEF and VERS technologies can essentially optimize and speed up geophysical work. References 1. S.P. Levashov. Detection and mapping of anomalies of "hydrocarbon deposit" type in the fault zones of crystalline arrays by geoelectric methods. / S.P. Levashov, N.A. Yakymchuk, I.N. Korchagin, V.V. Prilukov, J.N. Yakymchuk / / Oil. Gas. Novations. - 2011/4. - P. 10-17. Introduction. (in Russian); Fig. 1. The map of "gas condensate reservoir" type anomalous geoelectric zones on the area of human settlements Malin: 1 - a scale of the intensity of anomalous response, 2 - the zones of tectonic disturbances.

Spirit's Express Route to 'Columbia Hills'

NASA Technical Reports Server (NTRS)

2004-01-01

This map illustrates the Mars Exploration Rover Spirit's position as of sol 112 (April 26, 2004), near the crater called 'Missoula.' Like a train on a tight schedule, Spirit will make regular stops along the way to its ultimate destination, the 'Columbia Hills.' At each stop, or 'station,' the rover will briefly analyze the area's rocks and soils. Each tick mark on the rover's route represents one sol's worth of travel, or about 60 to 70 meters (200 to 230 feet). Rover planners estimate that Spirit will reach the hills around mid-June. Presently, the rover is stopped at a site called 'Plains Station.'

The color thermal data show how well different surface features hold onto heat. Red indicates warmth; blue indicates coolness. Areas with higher temperatures are more likely to be rocky, as rocks absorb heat. Lower temperatures denote small particles and fewer rocks. During its traverse, Spirit will document the causes of these temperature variations.

The map comprises data from the camera on NASA's Mars Global Surveyor orbiter and the thermal emission imaging system on NASA's Mars Odyssey orbiter.

Spirit's Express Route to 'Columbia Hills'

NASA Technical Reports Server (NTRS)

2004-01-01

This map illustrates the Mars Exploration Rover Spirit's position as of sol 112 (April 26, 2004), near the crater called 'Missoula.' Like a train on a tight schedule, Spirit will make regular stops along the way to its ultimate destination, the 'Columbia Hills.' At each stop, or 'station,' the rover will briefly analyze the area's rocks and soils. Each tick mark on the rover's route represents one sol's worth of travel, or about 60 to 70 meters (200 to 230 feet). Rover planners estimate that Spirit will reach the hills around mid-June. Presently, the rover is stopped at a site called 'Plains Station.'

The color thermal data show how well different surface features hold onto heat. Red indicates a higher thermal inertia associated with rocky terrain (cooler in the day, warmer at night); blue indicates a lower thermal inertia associated with smaller particles and fewer rocks (warmer at night, cooler in the day). During its traverse, Spirit will document the causes of these thermal variations.

The map comprises data from the camera on NASA's Mars Global Surveyor orbiter and the thermal emission imaging system on NASA's Mars Odyssey orbiter.

A map of human PRDM9 binding provides evidence for novel behaviors of PRDM9 and other zinc-finger proteins in meiosis

PubMed Central

Noor, Nudrat; Bitoun, Emmanuelle; Tumian, Afidalina; Imbeault, Michael; Chapman, J Ross; Aricescu, A Radu

2017-01-01

PRDM9 binding localizes almost all meiotic recombination sites in humans and mice. However, most PRDM9-bound loci do not become recombination hotspots. To explore factors that affect binding and subsequent recombination outcomes, we mapped human PRDM9 binding sites in a transfected human cell line and measured PRDM9-induced histone modifications. These data reveal varied DNA-binding modalities of PRDM9. We also find that human PRDM9 frequently binds promoters, despite their low recombination rates, and it can activate expression of a small number of genes including CTCFL and VCX. Furthermore, we identify specific sequence motifs that predict consistent, localized meiotic recombination suppression around a subset of PRDM9 binding sites. These motifs strongly associate with KRAB-ZNF protein binding, TRIM28 recruitment, and specific histone modifications. Finally, we demonstrate that, in addition to binding DNA, PRDM9's zinc fingers also mediate its multimerization, and we show that a pair of highly diverged alleles preferentially form homo-multimers. PMID:29072575

Feasibility of Representing a Danish Microbiology Model Using FHIR.

PubMed

Andersen, Mie Vestergaard; Kristensen, Ida Hvass; Larsen, Malene Møller; Pedersen, Claus Hougaard; Gøeg, Kirstine Rosenbeck; Pape-Haugaard, Louise B

2017-01-01

Achieving interoperability in health is a challenge and requires standardization. The newly developed HL7 standard: Fast Healthcare Interoperability Resources (FHIR) promises both flexibility and interoperability. This study investigates the feasibility of expressing a Danish microbiology message model content in FHIR to explore whether complex in-use legacy models can be migrated and what challenges this may pose. The Danish microbiology message model (the DMM) is used as a case to illustrate challenges and opportunities accosted with applying the FHIR standard. Mapping of content from DMM to FHIR was done as close as possible to the DMM to minimize migration costs except when the structure of the content did not fit into FHIR. From the DMM a total of 183 elements were mapped to FHIR. 75 (40.9%) elements were modeled as existing FHIR elements and 96 (52.5%) elements were modeled as extensions and 12 (6.6%) elements were deemed unnecessary because of build-in FHIR characteristics. In this study, it was possible to represent the content of a Danish message model using HL7 FHIR.

Identification of differentially expressed genes in cucumber (Cucumis sativus L.) root under waterlogging stress by digital gene expression profile.

PubMed

Qi, Xiao-Hua; Xu, Xue-Wen; Lin, Xiao-Jian; Zhang, Wen-Jie; Chen, Xue-Hao

2012-03-01

High-throughput tag-sequencing (Tag-seq) analysis based on the Solexa Genome Analyzer platform was applied to analyze the gene expression profiling of cucumber plant at 5 time points over a 24h period of waterlogging treatment. Approximately 5.8 million total clean sequence tags per library were obtained with 143013 distinct clean tag sequences. Approximately 23.69%-29.61% of the distinct clean tags were mapped unambiguously to the unigene database, and 53.78%-60.66% of the distinct clean tags were mapped to the cucumber genome database. Analysis of the differentially expressed genes revealed that most of the genes were down-regulated in the waterlogging stages, and the differentially expressed genes mainly linked to carbon metabolism, photosynthesis, reactive oxygen species generation/scavenging, and hormone synthesis/signaling. Finally, quantitative real-time polymerase chain reaction using nine genes independently verified the tag-mapped results. This present study reveals the comprehensive mechanisms of waterlogging-responsive transcription in cucumber. Copyright © 2011 Elsevier Inc. All rights reserved.

Transposon Variants and Their Effects on Gene Expression in Arabidopsis

PubMed Central

Wang, Xi; Weigel, Detlef; Smith, Lisa M.

2013-01-01

Transposable elements (TEs) make up the majority of many plant genomes. Their transcription and transposition is controlled through siRNAs and epigenetic marks including DNA methylation. To dissect the interplay of siRNA–mediated regulation and TE evolution, and to examine how TE differences affect nearby gene expression, we investigated genome-wide differences in TEs, siRNAs, and gene expression among three Arabidopsis thaliana accessions. Both TE sequence polymorphisms and presence of linked TEs are positively correlated with intraspecific variation in gene expression. The expression of genes within 2 kb of conserved TEs is more stable than that of genes next to variant TEs harboring sequence polymorphisms. Polymorphism levels of TEs and closely linked adjacent genes are positively correlated as well. We also investigated the distribution of 24-nt-long siRNAs, which mediate TE repression. TEs targeted by uniquely mapping siRNAs are on average farther from coding genes, apparently because they more strongly suppress expression of adjacent genes. Furthermore, siRNAs, and especially uniquely mapping siRNAs, are enriched in TE regions missing in other accessions. Thus, targeting by uniquely mapping siRNAs appears to promote sequence deletions in TEs. Overall, our work indicates that siRNA–targeting of TEs may influence removal of sequences from the genome and hence evolution of gene expression in plants. PMID:23408902

MAP18 regulates the direction of pollen tube growth in Arabidopsis by modulating F-actin organization.

PubMed

Zhu, Lei; Zhang, Yan; Kang, Erfang; Xu, Qiangyi; Wang, Miaoying; Rui, Yue; Liu, Baoquan; Yuan, Ming; Fu, Ying

2013-03-01

For fertilization to occur in plants, the pollen tube must be guided to enter the ovule via the micropyle. Previous reports have implicated actin filaments, actin binding proteins, and the tip-focused calcium gradient as key contributors to polar growth of pollen tubes; however, the regulation of directional pollen tube growth is largely unknown. We reported previously that Arabidopsis thaliana MICROTUBULE-ASSOCIATED PROTEIN18 (MAP18) contributes to directional cell growth and cortical microtubule organization. The preferential expression of MAP18 in pollen and in pollen tubes suggests that MAP18 also may function in pollen tube growth. In this study, we demonstrate that MAP18 functions in pollen tubes by influencing actin organization, rather than microtubule assembly. In vitro biochemical results indicate that MAP18 exhibits Ca(2+)-dependent filamentous (F)-actin-severing activity. Abnormal expression of MAP18 in map18 and MAP18 OX plants was associated with disorganization of the actin cytoskeleton in the tube apex, resulting in aberrant pollen tube growth patterns and morphologies, inaccurate micropyle targeting, and fewer fertilization events. Experiments with MAP18 mutants created by site-directed mutagenesis suggest that F-actin-severing activity is essential to the effects of MAP18 on pollen tube growth direction. Our study demonstrates that in Arabidopsis, MAP18 guides the direction of pollen tube growth by modulating actin filaments.

Exploration Gap Assessment (FY13 Update)

DOE Data Explorer

Dan Getman

2013-09-30

This submission contains an update to the previous Exploration Gap Assessment funded in 2012, which identify high potential hydrothermal areas where critical data are needed (gap analysis on exploration data). The uploaded data are contained in two data files for each data category: A shape (SHP) file containing the grid, and a data file (CSV) containing the individual layers that intersected with the grid. This CSV can be joined with the map to retrieve a list of datasets that are available at any given site. A grid of the contiguous U.S. was created with 88,000 10-km by 10-km grid cells, and each cell was populated with the status of data availability corresponding to five data types: 1. well data 2. geologic maps 3. fault maps 4. geochemistry data 5. geophysical data

Environment exploration and SLAM experiment research based on ROS

NASA Astrophysics Data System (ADS)

Li, Zhize; Zheng, Wei

2017-11-01

Robots need to get the information of surrounding environment by means of map learning. SLAM or navigation based on mobile robots is developing rapidly. ROS (Robot Operating System) is widely used in the field of robots because of the convenient code reuse and open source. Numerous excellent algorithms of SLAM or navigation are ported to ROS package. hector_slam is one of them that can set up occupancy grid maps on-line fast with low computation resources requiring. Its characters above make the embedded handheld mapping system possible. Similarly, hector_navigation also does well in the navigation field. It can finish path planning and environment exploration by itself using only an environmental sensor. Combining hector_navigation with hector_slam can realize low cost environment exploration, path planning and slam at the same time

A 3,000-loci transcription map of chromosome 3B unravels the structural and functional features of gene islands in hexaploid wheat.

PubMed

Rustenholz, Camille; Choulet, Frédéric; Laugier, Christel; Safár, Jan; Simková, Hana; Dolezel, Jaroslav; Magni, Federica; Scalabrin, Simone; Cattonaro, Federica; Vautrin, Sonia; Bellec, Arnaud; Bergès, Hélène; Feuillet, Catherine; Paux, Etienne

2011-12-01

To improve our understanding of the organization and regulation of the wheat (Triticum aestivum) gene space, we established a transcription map of a wheat chromosome (3B) by hybridizing a newly developed wheat expression microarray with bacterial artificial chromosome pools from a new version of the 3B physical map as well as with cDNA probes derived from 15 RNA samples. Mapping data for almost 3,000 genes showed that the gene space spans the whole chromosome 3B with a 2-fold increase of gene density toward the telomeres due to an increase in the number of genes in islands. Comparative analyses with rice (Oryza sativa) and Brachypodium distachyon revealed that these gene islands are composed mainly of genes likely originating from interchromosomal gene duplications. Gene Ontology and expression profile analyses for the 3,000 genes located along the chromosome revealed that the gene islands are enriched significantly in genes sharing the same function or expression profile, thereby suggesting that genes in islands acquired shared regulation during evolution. Only a small fraction of these clusters of cofunctional and coexpressed genes was conserved with rice and B. distachyon, indicating a recent origin. Finally, genes with the same expression profiles in remote islands (coregulation islands) were identified suggesting long-distance regulation of gene expression along the chromosomes in wheat.

Mapping correspondence between facial mimicry and emotion recognition in healthy subjects.

PubMed

Ponari, Marta; Conson, Massimiliano; D'Amico, Nunzia Pina; Grossi, Dario; Trojano, Luigi

2012-12-01

We aimed at verifying the hypothesis that facial mimicry is causally and selectively involved in emotion recognition. For this purpose, in Experiment 1, we explored the effect of tonic contraction of muscles in upper or lower half of participants' face on their ability to recognize emotional facial expressions. We found that the "lower" manipulation specifically impaired recognition of happiness and disgust, the "upper" manipulation impaired recognition of anger, while both manipulations affected recognition of fear; recognition of surprise and sadness were not affected by either blocking manipulations. In Experiment 2, we verified whether emotion recognition is hampered by stimuli in which an upper or lower half-face showing an emotional expression is combined with a neutral half-face. We found that the neutral lower half-face interfered with recognition of happiness and disgust, whereas the neutral upper half impaired recognition of anger; recognition of fear and sadness was impaired by both manipulations, whereas recognition of surprise was not affected by either manipulation. Taken together, the present findings support simulation models of emotion recognition and provide insight into the role of mimicry in comprehension of others' emotional facial expressions. PsycINFO Database Record (c) 2012 APA, all rights reserved.

CellLineNavigator: a workbench for cancer cell line analysis

PubMed Central

Krupp, Markus; Itzel, Timo; Maass, Thorsten; Hildebrandt, Andreas; Galle, Peter R.; Teufel, Andreas

2013-01-01

The CellLineNavigator database, freely available at http://www.medicalgenomics.org/celllinenavigator, is a web-based workbench for large scale comparisons of a large collection of diverse cell lines. It aims to support experimental design in the fields of genomics, systems biology and translational biomedical research. Currently, this compendium holds genome wide expression profiles of 317 different cancer cell lines, categorized into 57 different pathological states and 28 individual tissues. To enlarge the scope of CellLineNavigator, the database was furthermore closely linked to commonly used bioinformatics databases and knowledge repositories. To ensure easy data access and search ability, a simple data and an intuitive querying interface were implemented. It allows the user to explore and filter gene expression, focusing on pathological or physiological conditions. For a more complex search, the advanced query interface may be used to query for (i) differentially expressed genes; (ii) pathological or physiological conditions; or (iii) gene names or functional attributes, such as Kyoto Encyclopaedia of Genes and Genomes pathway maps. These queries may also be combined. Finally, CellLineNavigator allows additional advanced analysis of differentially regulated genes by a direct link to the Database for Annotation, Visualization and Integrated Discovery (DAVID) Bioinformatics Resources. PMID:23118487

The influence of uncertain map features on risk beliefs and perceived ambiguity for maps of modeled cancer risk from air pollution

PubMed Central

Myers, Jeffrey D.

2012-01-01

Maps are often used to convey information generated by models, for example, modeled cancer risk from air pollution. The concrete nature of images, such as maps, may convey more certainty than warranted for modeled information. Three map features were selected to communicate the uncertainty of modeled cancer risk: (a) map contours appeared in or out of focus, (b) one or three colors were used, and (c) a verbal-relative or numeric risk expression was used in the legend. Study aims were to assess how these features influenced risk beliefs and the ambiguity of risk beliefs at four assigned map locations that varied by risk level. We applied an integrated conceptual framework to conduct this full factorial experiment with 32 maps that varied by the three dichotomous features and four risk levels; 826 university students participated. Data was analyzed using structural equation modeling. Unfocused contours and the verbal-relative risk expression generated more ambiguity than their counterparts. Focused contours generated stronger risk beliefs for higher risk levels and weaker beliefs for lower risk levels. Number of colors had minimal influence. The magnitude of risk level, conveyed using incrementally darker shading, had a substantial dose-response influence on the strength of risk beliefs. Personal characteristics of prior beliefs and numeracy also had substantial influences. Bottom-up and top-down information processing suggest why iconic visual features of incremental shading and contour focus had the strongest visual influences on risk beliefs and ambiguity. Variations in contour focus and risk expression show promise for fostering appropriate levels of ambiguity. PMID:22985196

CsMAP34, a teleost MAP with dual role: A promoter of MASP-assisted complement activation and a regulator of immune cell activity.

PubMed

Li, Mo-Fei; Li, Jun; Sun, Li

2016-12-23

In teleost fish, the immune functions of mannan-binding lectin (MBL) associated protein (MAP) and MBL associated serine protease (MASP) are scarcely investigated. In the present study, we examined the biological properties both MAP (CsMAP34) and MASP (CsMASP1) molecules from tongue sole (Cynoglossus semilaevis). We found that CsMAP34 and CsMASP1 expressions occurred in nine different tissues and were upregulated by bacterial challenge. CsMAP34 protein was detected in blood, especially during bacterial infection. Recombinant CsMAP34 (rCsMAP34) bound C. semilaevis MBL (rCsBML) when the latter was activated by bacteria, while recombinant CsMASP1 (rCsMASP1) bound activated rCsBML only in the presence of rCsMAP34. rCsMAP34 stimulated the hemolytic and bactericidal activities of serum complement, whereas anti-CsMAP34 antibody blocked complement activities. Knockdown of CsMASP1 in C. semilaevis resulted in significant inhibition of complement activities. Furthermore, rCsMAP34 interacted directly with peripheral blood leukocytes (PBL) and enhanced the respiratory burst, acid phosphatase activity, chemotactic activity, and gene expression of PBL. These results indicate for the first time that a teleost MAP acts one hand as a regulator that promotes the lectin pathway of complement activation via its ability to recruit MBL to MASP, and other hand as a modulator of immune cell activity.

Wind Maps | Geospatial Data Science | NREL

Science.gov Websites

Wind Maps Wind Maps Wind Prospector This GIS application supports resource assessment and data exploration for wind development. This collection of wind maps and assessments details the wind resource in Geospatial Data Science Team. National Wind Resource Assessment The national wind resource assessment was

Florida Error Maps. A Resource Book for Teachers of Florida Geography.

ERIC Educational Resources Information Center

Allen, Rodney F.; And Others

Fifteen maps of Florida, each containing errors to be corrected by students, are presented for use in teaching Florida geography. Among the error maps included are Florida's borders today, the rivers of Florida, cities in the Grapefruit League, and Florida's European explorers. Teachers are encouraged to reproduce the maps and students to use the…

Effects of Multidimensional Concept Maps on Fourth Graders' Learning in Web-Based Computer Course

ERIC Educational Resources Information Center

Huang, Hwa-Shan; Chiou, Chei-Chang; Chiang, Heien-Kun; Lai, Sung-Hsi; Huang, Chiun-Yen; Chou, Yin-Yu

2012-01-01

This study explores the effect of multidimensional concept mapping instruction on students' learning performance in a web-based computer course. The subjects consisted of 103 fourth graders from an elementary school in central Taiwan. They were divided into three groups: multidimensional concept map (MCM) instruction group, Novak concept map (NCM)…

Teachers' Perceptions of Esri Story Maps as Effective Teaching Tools

ERIC Educational Resources Information Center

Strachan, Caitlin; Mitchell, Jerry

2014-01-01

The current study explores teachers' perceptions of Esri Story Maps as effective teaching tools. Story Maps are a relatively new web application created using Esri's cloud-based GIS platform, ArcGIS Online. They combine digitized, dynamic web maps with other story elements to help the creator effectively convey a message. The relative ease…

Mapping Mixed Methods Research: Methods, Measures, and Meaning

ERIC Educational Resources Information Center

Wheeldon, J.

2010-01-01

This article explores how concept maps and mind maps can be used as data collection tools in mixed methods research to combine the clarity of quantitative counts with the nuance of qualitative reflections. Based on more traditional mixed methods approaches, this article details how the use of pre/post concept maps can be used to design qualitative…

EnGeoMAP - geological applications within the EnMAP hyperspectral satellite science program

NASA Astrophysics Data System (ADS)

Boesche, N. K.; Mielke, C.; Rogass, C.; Guanter, L.

2016-12-01

Hyperspectral investigations from near field to space substantially contribute to geological exploration and mining monitoring of raw material and mineral deposits. Due to their spectral characteristics, large mineral occurrences and minefields can be identified from space and the spatial distribution of distinct proxy minerals be mapped. In the frame of the EnMAP hyperspectral satellite science program a mineral and elemental mapping tool was developed - the EnGeoMAP. It contains a basic mineral mapping and a rare earth element mapping approach. This study shows the performance of EnGeoMAP based on simulated EnMAP data of the rare earth element bearing Mountain Pass Carbonatite Complex, USA, and the Rodalquilar and Lomilla Calderas, Spain, which host the economically relevant gold-silver, lead-zinc-silver-gold and alunite deposits. The mountain pass image data was simulated on the basis of AVIRIS Next Generation images, while the Rodalquilar data is based on HyMap images. The EnGeoMAP - Base approach was applied to both images, while the mountain pass image data were additionally analysed using the EnGeoMAP - REE software tool. The results are mineral and elemental maps that serve as proxies for the regional lithology and deposit types. The validation of the maps is based on chemical analyses of field samples. Current airborne sensors meet the spatial and spectral requirements for detailed mineral mapping and future hyperspectral space borne missions will additionally provide a large coverage. For those hyperspectral missions, EnGeoMAP is a rapid data analysis tool that is provided to spectral geologists working in mineral exploration.

Jules Verne Voyager, Jr: An Interactive Map Tool for Teaching Plate Tectonics

NASA Astrophysics Data System (ADS)

Hamburger, M. W.; Meertens, C. M.

2010-12-01

We present an interactive, web-based map utility that can make new geological and geophysical results accessible to a large number and variety of users. The tool provides a user-friendly interface that allows users to access a variety of maps, satellite images, and geophysical data at a range of spatial scales. The map tool, dubbed 'Jules Verne Voyager, Jr.', allows users to interactively create maps of a variety of study areas around the world. The utility was developed in collaboration with the UNAVCO Consortium for study of global-scale tectonic processes. Users can choose from a variety of base maps (including "Face of the Earth" and "Earth at Night" satellite imagery mosaics, global topography, geoid, sea-floor age, strain rate and seismic hazard maps, and others), add a number of geographic and geophysical overlays (coastlines, political boundaries, rivers and lakes, earthquake and volcano locations, stress axes, etc.), and then superimpose both observed and model velocity vectors representing a compilation of 2933 GPS geodetic measurements from around the world. A remarkable characteristic of the geodetic compilation is that users can select from some 21 plates' frames of reference, allowing a visual representation of both 'absolute' plate motion (in a no-net rotation reference frame) and relative motion along all of the world's plate boundaries. The tool allows users to zoom among at least three map scales. The map tool can be viewed at http://jules.unavco.org/VoyagerJr/Earth. A more detailed version of the map utility, developed in conjunction with the EarthScope initiative, focuses on North America geodynamics, and provides more detailed geophysical and geographic information for the United States, Canada, and Mexico. The ‘EarthScope Voyager’ can be accessed at http://jules.unavco.org/VoyagerJr/EarthScope. Because the system uses pre-constructed gif images and overlays, the system can rapidly create and display maps to a large number of users simultaneously and does not require any special software installation on users' systems. In addition, a javascript-based educational interface, dubbed "Exploring our Dynamic Planet", incorporates the map tool, explanatory material, background scientific material, and curricular activities that encourage users to explore Earth processes using the Jules Verne Voyager, Jr. tool. Exploring our Dynamic Planet can be viewed at http://www.dpc.ucar.edu/VoyagerJr/. Because of its flexibility, the map utilities can be used for hands-on exercises exploring plate interaction in a range of academic settings, from high school science classes to entry-level undergraduate to graduate-level tectonics courses.

MicroRNA 27a-3p Regulates Antimicrobial Responses of Murine Macrophages Infected by Mycobacterium avium subspecies paratuberculosis by Targeting Interleukin-10 and TGF-β-Activated Protein Kinase 1 Binding Protein 2

PubMed Central

Hussain, Tariq; Zhao, Deming; Shah, Syed Zahid Ali; Wang, Jie; Yue, Ruichao; Liao, Yi; Sabir, Naveed; Yang, Lifeng; Zhou, Xiangmei

2018-01-01

Mycobacterium avium subspecies paratuberculosis (MAP) persistently survive and replicate in mononuclear phagocytic cells by adopting various strategies to subvert host immune response. Interleukin-10 (IL-10) upregulation via inhibition of macrophage bactericidal activity is a critical step for MAP survival and pathogenesis within the host cell. Mitogen-activated protein kinase p38 signaling cascade plays a crucial role in the elevation of IL-10 and progression of MAP pathogenesis. The contribution of microRNAs (miRNAs) and their influence on the activation of macrophages during MAP pathogenesis are still unclear. In the current study, we found that miRNA-27a-3p (miR-27a) expression is downregulated during MAP infection both in vivo and in vitro. Moreover, miR-27a is also downregulated in toll-like receptor 2 (TLR2)-stimulated murine macrophages (RAW264.7 and bone marrow-derived macrophage). ELISA and real-time qRT-PCR results confirm that overexpression of miR-27a inhibited MAP-induced IL-10 production in macrophages and upregulated pro-inflammatory cytokines, while miR-27a inhibitor counteracted these effects. Luciferase reporter assay results revealed that IL-10 and TGF-β-activated protein kinase 1 binding protein 2 (TAB 2) are potential targets of miR-27a. In addition, we demonstrated that miR-27a negatively regulates TAB 2 expression and diminishes TAB 2-dependent p38/JNK phosphorylation, ultimately downregulating IL-10 expression in MAP-infected macrophages. Furthermore, overexpression of miR-27a significantly inhibited the intracellular survival of MAP in infected macrophages. Our data show that miR-27a augments antimicrobial activities of macrophages and inhibits the expression of IL-10, demonstrating that miR-27a regulates protective innate immune responses during MAP infection and can be exploited as a novel therapeutic target in the control of intracellular pathogens, including paratuberculosis. PMID:29375563

Interacting steps with finite-range interactions: Analytical approximation and numerical results

NASA Astrophysics Data System (ADS)

Jaramillo, Diego Felipe; Téllez, Gabriel; González, Diego Luis; Einstein, T. L.

2013-05-01

We calculate an analytical expression for the terrace-width distribution P(s) for an interacting step system with nearest- and next-nearest-neighbor interactions. Our model is derived by mapping the step system onto a statistically equivalent one-dimensional system of classical particles. The validity of the model is tested with several numerical simulations and experimental results. We explore the effect of the range of interactions q on the functional form of the terrace-width distribution and pair correlation functions. For physically plausible interactions, we find modest changes when next-nearest neighbor interactions are included and generally negligible changes when more distant interactions are allowed. We discuss methods for extracting from simulated experimental data the characteristic scale-setting terms in assumed potential forms.

ERTS-1 imagery as an aid to the understanding of the regional setting of base metal deposits in the North West Cape Province, South Africa. [mineral exploration

NASA Technical Reports Server (NTRS)

Viljoen, R. P.

1974-01-01

A number of base metal finds have recently focussed attention on the North Western Cape Province of South Africa as an area of great potential mineral wealth. From the point of view of competitive mineral exploration it was essential that an insight into the regional geological controls of the base metal mineralization of the area be obtained as rapidly as possible. Conventional methods of producing a suitable regional geological map were considered to be too time-consuming and ERTS-1 imagery was consequently examined. This imagery has made a significant contribution in the compilation of a suitable map on which to base further mineral exploration programmes. The time involved in the compilation of maps of this nature was found to be only a fraction of the time necessary for the production of similar maps using other methods. ERTS imagery is therefore considered to be valuable in producing accurate regional maps in areas where little or no geological data are available, or in areas of poor access. Furthermore, these images have great potential for rapidly defining the regional extent of metallogenic provinces.

Magician Simulator. A Realistic Simulator for Heterogenous Teams of Autonomous Robots

DTIC Science & Technology

2011-01-18

IMU, and LIDAR systems for identifying and tracking mobile OOI at long range (>20m), providing early warnings and allowing neutralization from a... LIDAR and Computer Vision template-based feature tracking approaches. Mapping was solved through Multi-Agent particle-filter based Simultaneous...Locali- zation and Mapping ( SLAM ). Our system contains two maps, a physical map and an influence map (location of hostile OOI, explored and unexplored

Developing of 10-year EEZ seafloor mapping and research program

USGS Publications Warehouse

Lockwood, M.; Hill, G.W.

1988-01-01

The intent of expanding the exploration already begun on the outer continental shelf to the frontier of the EEZ (Exclusive Economic Zone) is to determine the "characteristics' and resource potential of this region. To coordinate this exploration, a Joint Office for Mapping and Research (JOMAR) has been established by the US Geological Survey (in the Department of the Interior) and the National Oceanic and Atmospheric Administration (in the Department of Commerce). JOMAR's main purpose is to help direct and coordinate ongoing and planned seafloor related activities in the EEZ and prepare a 10-year plan for mapping and research. -from Authors

Endothelial protein kinase MAP4K4 promotes vascular inflammation and atherosclerosis

PubMed Central

Roth Flach, Rachel J.; Skoura, Athanasia; Matevossian, Anouch; Danai, Laura V.; Zheng, Wei; Cortes, Christian; Bhattacharya, Samit K.; Aouadi, Myriam; Hagan, Nana; Yawe, Joseph C.; Vangala, Pranitha; Menendez, Lorena Garcia; Cooper, Marcus P.; Fitzgibbons, Timothy P.; Buckbinder, Leonard; Czech, Michael P.

2015-01-01

Signalling pathways that control endothelial cell (EC) permeability, leukocyte adhesion and inflammation are pivotal for atherosclerosis initiation and progression. Here we demonstrate that the Sterile-20-like mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4), which has been implicated in inflammation, is abundantly expressed in ECs and in atherosclerotic plaques from mice and humans. On the basis of endothelial-specific MAP4K4 gene silencing and gene ablation experiments in Apoe−/− mice, we show that MAP4K4 in ECs markedly promotes Western diet-induced aortic macrophage accumulation and atherosclerotic plaque development. Treatment of Apoe−/− and Ldlr−/− mice with a selective small-molecule MAP4K4 inhibitor also markedly reduces atherosclerotic lesion area. MAP4K4 silencing in cultured ECs attenuates cell surface adhesion molecule expression while reducing nuclear localization and activity of NFκB, which is critical for promoting EC activation and atherosclerosis. Taken together, these results reveal that MAP4K4 is a key signalling node that promotes immune cell recruitment in atherosclerosis. PMID:26688060

TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal.

PubMed

Newton, Yulia; Novak, Adam M; Swatloski, Teresa; McColl, Duncan C; Chopra, Sahil; Graim, Kiley; Weinstein, Alana S; Baertsch, Robert; Salama, Sofie R; Ellrott, Kyle; Chopra, Manu; Goldstein, Theodore C; Haussler, David; Morozova, Olena; Stuart, Joshua M

2017-11-01

Vast amounts of molecular data are being collected on tumor samples, which provide unique opportunities for discovering trends within and between cancer subtypes. Such cross-cancer analyses require computational methods that enable intuitive and interactive browsing of thousands of samples based on their molecular similarity. We created a portal called TumorMap to assist in exploration and statistical interrogation of high-dimensional complex "omics" data in an interactive and easily interpretable way. In the TumorMap, samples are arranged on a hexagonal grid based on their similarity to one another in the original genomic space and are rendered with Google's Map technology. While the important feature of this public portal is the ability for the users to build maps from their own data, we pre-built genomic maps from several previously published projects. We demonstrate the utility of this portal by presenting results obtained from The Cancer Genome Atlas project data. Cancer Res; 77(21); e111-4. ©2017 AACR . ©2017 American Association for Cancer Research.

TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal

PubMed Central

Newton, Yulia; Novak, Adam M.; Swatloski, Teresa; McColl, Duncan C.; Chopra, Sahil; Graim, Kiley; Weinstein, Alana S.; Baertsch, Robert; Salama, Sofie R.; Ellrott, Kyle; Chopra, Manu; Goldstein, Theodore C.; Haussler, David; Morozova, Olena; Stuart, Joshua M.

2017-01-01

Vast amounts of molecular data are being collected on tumor samples, which provide unique opportunities for discovering trends within and between cancer subtypes. Such cross-cancer analyses require computational methods that enable intuitive and interactive browsing of thousands of samples based on their molecular similarity. We created a portal called TumorMap to assist in exploration and statistical interrogation of high-dimensional complex “omics” data in an interactive and easily interpretable way. In the TumorMap, samples are arranged on a hexagonal grid based on their similarity to one another in the original genomic space and are rendered with Google’s Map technology. While the important feature of this public portal is the ability for the users to build maps from their own data, we pre-built genomic maps from several previously published projects. We demonstrate the utility of this portal by presenting results obtained from The Cancer Genome Atlas project data. PMID:29092953

Genetic validation of whole-transcriptome sequencing for mapping expression affected by cis-regulatory variation.

PubMed

Babak, Tomas; Garrett-Engele, Philip; Armour, Christopher D; Raymond, Christopher K; Keller, Mark P; Chen, Ronghua; Rohl, Carol A; Johnson, Jason M; Attie, Alan D; Fraser, Hunter B; Schadt, Eric E

2010-08-13

Identifying associations between genotypes and gene expression levels using microarrays has enabled systematic interrogation of regulatory variation underlying complex phenotypes. This approach has vast potential for functional characterization of disease states, but its prohibitive cost, given hundreds to thousands of individual samples from populations have to be genotyped and expression profiled, has limited its widespread application. Here we demonstrate that genomic regions with allele-specific expression (ASE) detected by sequencing cDNA are highly enriched for cis-acting expression quantitative trait loci (cis-eQTL) identified by profiling of 500 animals in parallel, with up to 90% agreement on the allele that is preferentially expressed. We also observed widespread noncoding and antisense ASE and identified several allele-specific alternative splicing variants. Monitoring ASE by sequencing cDNA from as little as one sample is a practical alternative to expression genetics for mapping cis-acting variation that regulates RNA transcription and processing.

Molecular mechanisms of pathogenesis in hepatocellular carcinoma revealed by RNA‑sequencing.

PubMed

Liu, Yao; Yang, Zhe; Du, Feng; Yang, Qiao; Hou, Jie; Yan, Xiaohong; Geng, Yi; Zhao, Yaning; Wang, Hua

2017-11-01

The present study aimed to explore the underlying molecular mechanisms of hepatocellular carcinoma (HCC). RNA‑sequencing profiles GSM629264 and GSM629265, from the GSE25599 data set, were downloaded from the Gene Expression Omnibus database and processed by quality evaluation. GSM629264 and GSM629265 were from HCC and adjacent non‑cancerous tissues, respectively. TopHat software was used for alignment analysis, followed by the detection of novel splicing sites. In addition, the Cufflinks software package was used to analyze gene expressions, and the Cuffdiff program was used to screen for differently expressed genes (DEGs) and differentially expressed splicing variants. Gene ontology functional enrichment and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses of DEGs were also performed. Transcription factors (TFs) and microRNAs (miRNAs) that regulate DEGs were identified, and a protein‑protein interaction (PPI) network was constructed. The hub node in the PPI network was obtained, and the TFs and miRNAs that regulated the hub node were further predicted. The quality of the sequencing data met the standards for analysis, and the clean reads were ~65%. Most sequencing reads mapped into coding sequence exons (CDS_exons), whereas other reads mapped into exon 3' untranslated regions (UTR_Exons), 5'UTR_Exons and Introns. Upregulated and downregulated DEGs between HCC and adjacent non‑cancerous tissues were screened. Genes of differentially expressed splicing variants were identified, including vesicle‑associated membrane protein 4, phosphatidylinositol glycan anchor biosynthesis class C, protein disulfide isomerase family A member 4 and growth arrest specific 5. Screened DEGs were enriched in the complement pathway. In the PPI network, ubiquitin C (UBC) was the hub node. UBC was predicted to be regulated by several TFs, including specificity protein 1 (SP1), FBJ murine osteosarcoma viral oncogene homolog (FOS), proto‑oncogene c‑JUN (JUN), FOS‑like antigen 2 (FOSL2) and SWI/SNF‑related, matrix‑associated, actin‑dependent regulator of chromatin, subfamily A, member 4 (SMARCA4), and several miRNAs, including miR‑30 and miR‑181. Results from the present study demonstrated that UBC, SP1, FOS, JUN, FOSL2, SMARCA4, miR‑30 and miR‑181 may participate in the development of HCC.

Hybrid incompatibility arises in a sequence-based bioenergetic model of transcription factor binding.

PubMed

Tulchinsky, Alexander Y; Johnson, Norman A; Watt, Ward B; Porter, Adam H

2014-11-01

Postzygotic isolation between incipient species results from the accumulation of incompatibilities that arise as a consequence of genetic divergence. When phenotypes are determined by regulatory interactions, hybrid incompatibility can evolve even as a consequence of parallel adaptation in parental populations because interacting genes can produce the same phenotype through incompatible allelic combinations. We explore the evolutionary conditions that promote and constrain hybrid incompatibility in regulatory networks using a bioenergetic model (combining thermodynamics and kinetics) of transcriptional regulation, considering the bioenergetic basis of molecular interactions between transcription factors (TFs) and their binding sites. The bioenergetic parameters consider the free energy of formation of the bond between the TF and its binding site and the availability of TFs in the intracellular environment. Together these determine fractional occupancy of the TF on the promoter site, the degree of subsequent gene expression and in diploids, and the degree of dominance among allelic interactions. This results in a sigmoid genotype-phenotype map and fitness landscape, with the details of the shape determining the degree of bioenergetic evolutionary constraint on hybrid incompatibility. Using individual-based simulations, we subjected two allopatric populations to parallel directional or stabilizing selection. Misregulation of hybrid gene expression occurred under either type of selection, although it evolved faster under directional selection. Under directional selection, the extent of hybrid incompatibility increased with the slope of the genotype-phenotype map near the derived parental expression level. Under stabilizing selection, hybrid incompatibility arose from compensatory mutations and was greater when the bioenergetic properties of the interaction caused the space of nearly neutral genotypes around the stable expression level to be wide. F2's showed higher hybrid incompatibility than F1's to the extent that the bioenergetic properties favored dominant regulatory interactions. The present model is a mechanistically explicit case of the Bateson-Dobzhansky-Muller model, connecting environmental selective pressure to hybrid incompatibility through the molecular mechanism of regulatory divergence. The bioenergetic parameters that determine expression represent measurable properties of transcriptional regulation, providing a predictive framework for empirical studies of how phenotypic evolution results in epistatic incompatibility at the molecular level in hybrids. Copyright © 2014 by the Genetics Society of America.

Lead-induced changes of cytoskeletal protein is involved in the pathological basis in mice brain.

PubMed

Ge, Yaming; Chen, Lingli; Sun, Xianghe; Yin, Zhihong; Song, Xiaochao; Li, Chong; Liu, Junwei; An, Zhixing; Yang, Xuefeng; Ning, Hongmei

2018-04-01

Lead poisoning is a geochemical disease. On the other hand, lead is highly carcinogenic and exhibits liver and kidney toxicity. This element can also cross the blood-brain barrier, reduce learning and memory ability and damage the structure of the cerebral cortex and hippocampus. To further investigate the mechanism of lead neurotoxicity, 4-week-old Kunming mice were used to explore the effects of different concentrations of Pb 2+ (0, 2.4, 4.8 and 9.6 mM) for 9 days. In this study, pathological and ultrastructural changes in brain cells of the treated group were related to damages to mitochondria, chromatin and the nucleus. Lead content in blood was tested by atomic absorption spectroscopy, which showed high lead concentrations in the blood with increasing doses of lead. Distribution of lead in nerve cells was analysed by transmission electron microscopy with energy dispersive spectroscopy. Data showed the presence of lead in nucleopores, chromatin and nuclear membrane of nerve cells in the treatment groups, whereas lead content increased with increasing doses of lead acetate. Finally, microtubule-associated protein 2 (MAP2) mRNA and protein expression levels were detected by real-time PCR and Western blotting, which showed a reduction in MAP2 expression with increasing lead doses in the mouse brain. These findings suggest that acute lead poisoning can cause significant dose-dependent toxic effects on mouse brain function and can contribute to better understanding of lead-induced toxicity.

Building a base map with AutoCAD

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

Flarity, S.J.

1989-12-01

The fundamental step in the exploration process is building a base map. Consequently, any serious computer exploration program should be capable of providing base maps. Data used in constructing base maps are available from commercial sources such as Tobin. and Petroleum Information. These data sets include line and well data, the line data being latitude longitude vectors, and the ell data any identifying text information for well and their locations. AutoCAD is a commercial program useful in building base maps. Its features include infinite zoom and pan capability, layering, block definition, text dialog boxes, and a command language, AutoLisp. AutoLispmore » provides more power by allowing the geologist to modify the way the program works. Three AutoLisp routines presented here allow geologists to construct a geologic base map from raw Tobin data. The first program, WELLS.LSP, sets up the map environment for the subsequent programs, WELLADD.LSP and LINEADD.LSP. Welladd.lisp reads the Tobin data and spots the well symbols and the identifying information. Lineadd.lsp performs the same task on line and textural information contained within the data set.« less

A proto-architecture for innate directionally selective visual maps.

PubMed

Adams, Samantha V; Harris, Chris M

2014-01-01

Self-organizing artificial neural networks are a popular tool for studying visual system development, in particular the cortical feature maps present in real systems that represent properties such as ocular dominance (OD), orientation-selectivity (OR) and direction selectivity (DS). They are also potentially useful in artificial systems, for example robotics, where the ability to extract and learn features from the environment in an unsupervised way is important. In this computational study we explore a DS map that is already latent in a simple artificial network. This latent selectivity arises purely from the cortical architecture without any explicit coding for DS and prior to any self-organising process facilitated by spontaneous activity or training. We find DS maps with local patchy regions that exhibit features similar to maps derived experimentally and from previous modeling studies. We explore the consequences of changes to the afferent and lateral connectivity to establish the key features of this proto-architecture that support DS.

Seismic expression of Red Fork channels in Major and Kay Counties, Oklahoma

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

Hanoch, C.A.

1987-08-01

This paper investigates the application of regional seismic to exploration and development Red Fork sands of the Cherokee Group, in Major and Kay Counties, Oklahoma. A computer-aided exploration system (CAEX) was used to justify the subtle seismic expressions with the geological interpretation. Modeling shows that the low-velocity shales are the anomalous rock in the Cherokee package, which is most represented by siltstone and thin sands. Because the Red Fork channel sands were incised into or deposited with laterally time-equivalent siltstones, no strong reflection coefficient is associated with the top of the sands. The objective sands become a seismic anomaly onlymore » when they cut into and replace a low-velocity shale. This knowledge allows mapping the channel thickness by interpreting the shale thickness from seismic data. A group shoot line in Major County, Oklahoma, has been tied to the geologic control, and the channel thicknesses have been interpreted assuming a detectable vertical resolution of 10 ft. A personal computer-based geophysical work station is used to construct velocity logs representative of the geology to produce forward-modeled synthetic seismic sections, and to display, in color, the seismic trace attributes. These synthetic sections are used as tools to compare with and interpret the seismic line and to evaluate the interpretative value of lowest cost, lesser quality data versus reprocessing or new data acquisition.« less

Assessment of a visually guided autonomous exploration robot

NASA Astrophysics Data System (ADS)

Harris, C.; Evans, R.; Tidey, E.

2008-10-01

A system has been developed to enable a robot vehicle to autonomously explore and map an indoor environment using only visual sensors. The vehicle is equipped with a single camera, whose output is wirelessly transmitted to an off-board standard PC for processing. Visual features within the camera imagery are extracted and tracked, and their 3D positions are calculated using a Structure from Motion algorithm. As the vehicle travels, obstacles in its surroundings are identified and a map of the explored region is generated. This paper discusses suitable criteria for assessing the performance of the system by computer-based simulation and practical experiments with a real vehicle. Performance measures identified include the positional accuracy of the 3D map and the vehicle's location, the efficiency and completeness of the exploration and the system reliability. Selected results are presented and the effect of key system parameters and algorithms on performance is assessed. This work was funded by the Systems Engineering for Autonomous Systems (SEAS) Defence Technology Centre established by the UK Ministry of Defence.

Topic Maps e-Learning Portal Development

ERIC Educational Resources Information Center

Olsevicova, Kamila

2006-01-01

Topic Maps, ISO/IEC 13250 standard, are designed to facilitate the organization and navigation of large collections of information objects by creating meta-level perspectives of their underlying concepts and relationships. The underlying structure of concepts and relations is expressed by domain ontologies. The Topics Maps technology can become…

Exploring the Interactive Patterns of Concept Map-Based Online Discussion: A Sequential Analysis of Users' Operations, Cognitive Processing, and Knowledge Construction

ERIC Educational Resources Information Center

Wu, Sheng-Yi; Chen, Sherry Y.; Hou, Huei-Tse

2016-01-01

Concept maps can be used as a cognitive tool to assist learners' knowledge construction. However, in a concept map-based online discussion environment, studies that take into consideration learners' manipulative actions of composing concept maps, cognitive process among learners' discussion, and social knowledge construction at the same time are…

Core Knowledge and the Emergence of Symbols: The Case of Maps

ERIC Educational Resources Information Center

Huang, Yi; Spelke, Elizabeth S.

2015-01-01

Map reading is unique to humans but is present in people of diverse cultures, at ages as young as 4 years old. Here, we explore the nature and sources of this ability and ask both what geometric information young children use in maps and what nonsymbolic systems are associated with their map-reading performance. Four-year-old children were given…

The Effects of Integrating Computer-Based Concept Mapping for Physics Learning in Junior High School

ERIC Educational Resources Information Center

Chang, Cheng-Chieh; Yeh, Ting-Kuang; Shih, Chang-Ming

2016-01-01

It generally is accepted that concept mapping has a noticeable impact on learning. But literatures show the use of concept mapping is not benefit all learners. The present study explored the effects of incorporating computer-based concept mapping in physics instruction. A total of 61 9th-grade students participated in this study. By using a…

An Investigation into the Representation of Geological Maps by 15-16 Year-Old Turkish Students

ERIC Educational Resources Information Center

Dal, Burckin

2010-01-01

This paper explores secondary school students' representations of a geological map. Ninety-two high school students (ninth graders--15- to 16-years-old) participated in the survey in Turkey. The findings indicate that students have only a vague idea of how a geological map is constructed, and how the map is affected by the topography. The…

Concept Mapping in the Humanities to Facilitate Reflection: Externalizing the Relationship between Public and Personal Learning

ERIC Educational Resources Information Center

Kandiko, Camille; Hay, David; Weller, Saranne

2013-01-01

This article discusses how mapping techniques were used in university teaching in a humanities subject. The use of concept mapping was expanded as a pedagogical tool, with a focus on reflective learning processes. Data were collected through a longitudinal study of concept mapping in a university-level Classics course. This was used to explore how…

Integrated Quantitative Transcriptome Maps of Human Trisomy 21 Tissues and Cells

PubMed Central

Pelleri, Maria Chiara; Cattani, Chiara; Vitale, Lorenza; Antonaros, Francesca; Strippoli, Pierluigi; Locatelli, Chiara; Cocchi, Guido; Piovesan, Allison; Caracausi, Maria

2018-01-01

Down syndrome (DS) is due to the presence of an extra full or partial chromosome 21 (Hsa21). The identification of genes contributing to DS pathogenesis could be the key to any rational therapy of the associated intellectual disability. We aim at generating quantitative transcriptome maps in DS integrating all gene expression profile datasets available for any cell type or tissue, to obtain a complete model of the transcriptome in terms of both expression values for each gene and segmental trend of gene expression along each chromosome. We used the TRAM (Transcriptome Mapper) software for this meta-analysis, comparing transcript expression levels and profiles between DS and normal brain, lymphoblastoid cell lines, blood cells, fibroblasts, thymus and induced pluripotent stem cells, respectively. TRAM combined, normalized, and integrated datasets from different sources and across diverse experimental platforms. The main output was a linear expression value that may be used as a reference for each of up to 37,181 mapped transcripts analyzed, related to both known genes and expression sequence tag (EST) clusters. An independent example in vitro validation of fibroblast transcriptome map data was performed through “Real-Time” reverse transcription polymerase chain reaction showing an excellent correlation coefficient (r = 0.93, p < 0.0001) with data obtained in silico. The availability of linear expression values for each gene allowed the testing of the gene dosage hypothesis of the expected 3:2 DS/normal ratio for Hsa21 as well as other human genes in DS, in addition to listing genes differentially expressed with statistical significance. Although a fraction of Hsa21 genes escapes dosage effects, Hsa21 genes are selectively over-expressed in DS samples compared to genes from other chromosomes, reflecting a decisive role in the pathogenesis of the syndrome. Finally, the analysis of chromosomal segments reveals a high prevalence of Hsa21 over-expressed segments over the other genomic regions, suggesting, in particular, a specific region on Hsa21 that appears to be frequently over-expressed (21q22). Our complete datasets are released as a new framework to investigate transcription in DS for individual genes as well as chromosomal segments in different cell types and tissues. PMID:29740474

Mapping-by-sequencing of Ligon-lintless-1 (Li 1 ) reveals a cluster of neighboring genes with correlated expression in developing fibers of Upland cotton (Gossypium hirsutum L.).

PubMed

Thyssen, Gregory N; Fang, David D; Turley, Rickie B; Florane, Christopher; Li, Ping; Naoumkina, Marina

2015-09-01

Mapping-by-sequencing and SNP marker analysis were used to fine map the Ligon-lintless-1 ( Li 1 ) short fiber mutation in tetraploid cotton to a 255-kb region that contains 16 annotated proteins. The Ligon-lintless-1 (Li 1 ) mutant of cotton (Gossypium hirsutum L.) has been studied as a model for cotton fiber development since its identification in 1929; however, the causative mutation has not been identified yet. Here we report the fine genetic mapping of the mutation to a 255-kb region that contains only 16 annotated genes in the reference Gossypium raimondii genome. We took advantage of the incompletely dominant dwarf vegetative phenotype to identify 100 mutants (Li 1 /Li 1 ) and 100 wild-type (li 1 /li 1 ) homozygotes from a mapping population of 2567 F2 plants, which we bulked and deep sequenced. Since only homozygotes were sequenced, we were able to use a high stringency in SNP calling to rapidly narrow down the region harboring the Li 1 locus, and designed subgenome-specific SNP markers to test the population. We characterized the expression of all sixteen genes in the region by RNA sequencing of elongating fibers and by RT-qPCR at seven time points spanning fiber development. One of the most highly expressed genes found in this interval in wild-type fiber cells is 40-fold under-expressed at the day of anthesis (DOA) in the mutant fiber cells.  This gene is a major facilitator superfamily protein, part of the large family of proteins that includes auxin and sugar transporters. Interestingly, nearly all genes in this region were most highly expressed at DOA and showed a high degree of co-expression. Further characterization is required to determine if transport of hormones or carbohydrates is involved in both the dwarf and lintless phenotypes of Li 1 plants.

Expression map of a complete set of gustatory receptor genes in chemosensory organs of Bombyx mori.

PubMed

Guo, Huizhen; Cheng, Tingcai; Chen, Zhiwei; Jiang, Liang; Guo, Youbing; Liu, Jianqiu; Li, Shenglong; Taniai, Kiyoko; Asaoka, Kiyoshi; Kadono-Okuda, Keiko; Arunkumar, Kallare P; Wu, Jiaqi; Kishino, Hirohisa; Zhang, Huijie; Seth, Rakesh K; Gopinathan, Karumathil P; Montagné, Nicolas; Jacquin-Joly, Emmanuelle; Goldsmith, Marian R; Xia, Qingyou; Mita, Kazuei

2017-03-01

Most lepidopteran species are herbivores, and interaction with host plants affects their gene expression and behavior as well as their genome evolution. Gustatory receptors (Grs) are expected to mediate host plant selection, feeding, oviposition and courtship behavior. However, due to their high diversity, sequence divergence and extremely low level of expression it has been difficult to identify precisely a complete set of Grs in Lepidoptera. By manual annotation and BAC sequencing, we improved annotation of 43 gene sequences compared with previously reported Grs in the most studied lepidopteran model, the silkworm, Bombyx mori, and identified 7 new tandem copies of BmGr30 on chromosome 7, bringing the total number of BmGrs to 76. Among these, we mapped 68 genes to chromosomes in a newly constructed chromosome distribution map and 8 genes to scaffolds; we also found new evidence for large clusters of BmGrs, especially from the bitter receptor family. RNA-seq analysis of diverse BmGr expression patterns in chemosensory organs of larvae and adults enabled us to draw a precise organ specific map of BmGr expression. Interestingly, most of the clustered genes were expressed in the same tissues and more than half of the genes were expressed in larval maxillae, larval thoracic legs and adult legs. For example, BmGr63 showed high expression levels in all organs in both larval and adult stages. By contrast, some genes showed expression limited to specific developmental stages or organs and tissues. BmGr19 was highly expressed in larval chemosensory organs (especially antennae and thoracic legs), the single exon genes BmGr53 and BmGr67 were expressed exclusively in larval tissues, the BmGr27-BmGr31 gene cluster on chr7 displayed a high expression level limited to adult legs and the candidate CO 2 receptor BmGr2 was highly expressed in adult antennae, where few other Grs were expressed. Transcriptional analysis of the Grs in B. mori provides a valuable new reference for finding genes involved in plant-insect interactions in Lepidoptera and establishing correlations between these genes and vital insect behaviors like host plant selection and courtship for mating. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Need for new sensors to map lithologic units

USGS Publications Warehouse

Rowan, Lawrence C.; Barringer, Anthony R.

1980-01-01

One of the most important contributions that remote sensing can make to mineral energy explorations to provide data from satellites to augment regional geological mapping. Geologic maps, which show information on the subsurface, are the main basis for formulating models of resource genesis that guide exploration. However, conventional compilation procedures are time-consuming and therefore often slow the pace of exploration, especially in large, inaccessible areas. Landsat Multispectral Scanner (MSS) images have been applied to a wide variety of specific geological problems, including discrimination of lithologic and delineation of previously unrecognized tectonic features. However, these lithologic distinctions are based on brightness, spectral reflectance, and, less commonly, the morphology of the unit, which in the wavelength region of MSS images are only rarely diagnostic of specific mineralogical content. Limonite is the only lithological material that can be identified be analyzing MSS spectral radiance.

New developments in ground probing radar for Earth resource mapping and planetology

NASA Astrophysics Data System (ADS)

Cattermole, P. J.; Junkin, G.; Finkelstein, M. I.; Kingsley, S. P.

1992-07-01

Ground probing radar is a well established technique for locating buried objects and has found application in resource mapping. The development of this technology for the Mars exploration programme has lead to lightweight systems with potential applications for investigating shallow geological structures on Earth, Mars and Venus. Recent advances in ground probing radar technology for planetary exploration include the development of single-antenna systems with improved beam focussing into the ground and a move to lower frequencies which considerably extends the depth penetration in dry ground. These systems are designed for mobility and could form the basis of autonomous mapping systems for terrestrial exploration. Such systems would be particularly valuable for water resource surveying in arid and semi-arid regions, where there is a need to have lightweight instrumentation that can be moved into sometimes inhospitable terrain.

A tool for exploring space-time patterns: an animation user research.

PubMed

Ogao, Patrick J

2006-08-29

Ever since Dr. John Snow (1813-1854) used a case map to identify water well as the source of a cholera outbreak in London in the 1800s, the use of spatio-temporal maps have become vital tools in a wide range of disease mapping and control initiatives. The increasing use of spatio-temporal maps in these life-threatening sectors warrants that they are accurate, and easy to interpret to enable prompt decision making by health experts. Similar spatio-temporal maps are observed in urban growth and census mapping--all critical aspects a of a country's socio-economic development. In this paper, a user test research was carried out to determine the effectiveness of spatio-temporal maps (animation) in exploring geospatial structures encompassing disease, urban and census mapping. Three types of animation were used, namely; passive, interactive and inference-based animation, with the key differences between them being on the level of interactivity and complementary domain knowledge that each offers to the user. Passive animation maintains the view only status. The user has no control over its contents and dynamic variables. Interactive animation provides users with the basic media player controls, navigation and orientation tools. Inference-based animation incorporates these interactive capabilities together with a complementary automated intelligent view that alerts users to interesting patterns, trends or anomalies that may be inherent in the data sets. The test focussed on the role of animation passive and interactive capabilities in exploring space-time patterns by engaging test-subjects in thinking aloud evaluation protocol. The test subjects were selected from a geoinformatics (map reading, interpretation and analysis abilities) background. Every test-subject used each of the three types of animation and their performances for each session assessed. The results show that interactivity in animation is a preferred exploratory tool in identifying, interpreting and providing explanations about observed geospatial phenomena. Also, exploring geospatial data structures using animation is best achieved using provocative interactive tools such as was seen with the inference-based animation. The visual methods employed using the three types of animation are all related and together these patterns confirm the exploratory cognitive structure and processes for visualization tools. The generic types of animation as defined in this paper play a crucial role in facilitating the visualization of geospatial data. These animations can be created and their contents defined based on the user's presentational and exploratory needs. For highly explorative tasks, maintaining a link between the data sets and the animation is crucial to enabling a rich and effective knowledge discovery environment.

A tool for exploring space-time patterns : an animation user research

PubMed Central

Ogao, Patrick J

2006-01-01

Background Ever since Dr. John Snow (1813–1854) used a case map to identify water well as the source of a cholera outbreak in London in the 1800s, the use of spatio-temporal maps have become vital tools in a wide range of disease mapping and control initiatives. The increasing use of spatio-temporal maps in these life-threatening sectors warrants that they are accurate, and easy to interpret to enable prompt decision making by health experts. Similar spatio-temporal maps are observed in urban growth and census mapping – all critical aspects a of a country's socio-economic development. In this paper, a user test research was carried out to determine the effectiveness of spatio-temporal maps (animation) in exploring geospatial structures encompassing disease, urban and census mapping. Results Three types of animation were used, namely; passive, interactive and inference-based animation, with the key differences between them being on the level of interactivity and complementary domain knowledge that each offers to the user. Passive animation maintains the view only status. The user has no control over its contents and dynamic variables. Interactive animation provides users with the basic media player controls, navigation and orientation tools. Inference-based animation incorporates these interactive capabilities together with a complementary automated intelligent view that alerts users to interesting patterns, trends or anomalies that may be inherent in the data sets. The test focussed on the role of animation passive and interactive capabilities in exploring space-time patterns by engaging test-subjects in thinking aloud evaluation protocol. The test subjects were selected from a geoinformatics (map reading, interpretation and analysis abilities) background. Every test-subject used each of the three types of animation and their performances for each session assessed. The results show that interactivity in animation is a preferred exploratory tool in identifying, interpreting and providing explanations about observed geospatial phenomena. Also, exploring geospatial data structures using animation is best achieved using provocative interactive tools such as was seen with the inference-based animation. The visual methods employed using the three types of animation are all related and together these patterns confirm the exploratory cognitive structure and processes for visualization tools. Conclusion The generic types of animation as defined in this paper play a crucial role in facilitating the visualization of geospatial data. These animations can be created and their contents defined based on the user's presentational and exploratory needs. For highly explorative tasks, maintaining a link between the data sets and the animation is crucial to enabling a rich and effective knowledge discovery environment. PMID:16938138

Map3k8 Modulates Monocyte State and Atherogenesis in ApoE-/- Mice.

PubMed

Sanz-Garcia, Carlos; Sánchez, Ángela; Contreras-Jurado, Constanza; Cales, Carmela; Barranquero, Cristina; Muñoz, Marta; Merino, Ramón; Escudero, Paula; Sanz, Maria-Jesús; Osada, Jesús; Aranda, Ana; Alemany, Susana

2017-02-01

Map3k8 (Cot/Tpl2) activates the MKK1/2-ERK1/2, MAPK pathway downstream from interleukin-1R, tumor necrosis factor-αR, NOD-2R (nucleotide-binding oligomerization domain-like 2R), adiponectinR, and Toll-like receptors. Map3k8 plays a key role in innate and adaptive immunity and influences inflammatory processes by modulating the functions of different cell types. However, its role in atherogenesis remains unknown. In this study, we analyzed the role of this kinase in this pathology. We show here that Map3k8 deficiency results in smaller numbers of Ly6C high CD11c low and Ly6C low CD11c high monocytes in ApoE - /- mice fed a high-fat diet (HFD). Map3k8 -/- ApoE -/- monocytes displayed high rates of apoptosis and reduced amounts of Nr4a1, a transcription factor known to modulate apoptosis in Ly6C low CD11c high monocytes. Map3k8 -/- ApoE -/- splenocytes and macrophages showed irregular patterns of cytokine and chemokine expression. Map3k8 deficiency altered cell adhesion and migration in vivo and decreased CCR2 expression, a determinant chemokine receptor for monocyte mobilization, on circulating Ly6C high CD11c low monocytes. Map3k8 -/- ApoE -/- mice fed an HFD showed decreased cellular infiltration in the atherosclerotic plaque, with low lipid content. Lesions had similar size after Map3k8 +/+ ApoE -/- bone marrow transplant into Map3k8 -/- ApoE -/- and Map3k8 +/+ ApoE -/- mice fed an HFD, whereas smaller plaques were observed after the transplantation of bone marrow lacking both ApoE and Map3k8. Map3k8 decreases apoptosis of monocytes and enhances CCR2 expression on Ly6C high CD11c low monocytes of ApoE -/- mice fed an HFD. These findings explain the smaller aortic lesions in ApoE -/- mice with Map3k8 -/- ApoE -/- bone marrow cells fed an HFD, supporting further studies of Map3k8 as an antiatherosclerotic target. © 2016 American Heart Association, Inc.

Significance of aquaporins’ expression in the prognosis of gastric cancer

PubMed Central

Thapa, Saroj; Chetry, Mandika; Huang, Kaiyu; Peng, Yangpei; Wang, Jinsheng; Wang, Jiaoni; Zhou, Yingying; Shen, Yigen; Xue, Yangjing; Ji, Kangting

2018-01-01

Gastric carcinoma is one of the most lethal malignancy at present with leading cause of cancer-related deaths worldwide. Aquaporins (AQPs) are a family of small, integral membrane proteins, which have been evidenced to play a crucial role in cell migration and proliferation of different cancer cells including gastric cancers. However, the aberrant expression of specific AQPs and its correlation to detect predictive and prognostic significance in gastric cancer remains elusive. In the present study, we comprehensively explored immunohistochemistry based map of protein expression profiles in normal tissues, cancer and cell lines from publicly available Human Protein Atlas (HPA) database. Moreover, to improve our understanding of general gastric biology and guide to find novel predictive prognostic gastric cancer biomarker, we also retrieved ‘The Kaplan–Meier plotter’ (KM plotter) online database with specific AQPs mRNA to overall survival (OS) in different clinicopathological features. We revealed that ubiquitous expression of AQPs protein can be effective tools to generate gastric cancer biomarker. Furthermore, high level AQP3, AQP9, and AQP11 mRNA expression were correlated with better OS in all gastric patients, whereas AQP0, AQP1, AQP4, AQP5, AQP6, AQP8, and AQP10 mRNA expression were associated with poor OS. With regard to the clinicopathological features including Laurens classification, clinical stage, human epidermal growth factor receptor 2 (HER2) status, and different treatment strategy, we could illustrate significant role of individual AQP mRNA expression in the prognosis of gastric cancer patients. Thus, our results indicated that AQP’s protein and mRNA expression in gastric cancer patients provide effective role to predict prognosis and act as an essential agent to therapeutic strategy. PMID:29678898

Musical Maps as Narrative Inquiry

ERIC Educational Resources Information Center

Blair, Deborah V.

2007-01-01

This study explores the metaphorical relationship between the process of narrative inquiry and the process of "musical mapping." The creation of musical maps was used as a classroom tool for enabling students' musical understanding while listening to music. As teacher-researcher, I studied my fifth-grade music students as they interacted with…

Analyzing the Effects of Various Concept Mapping Techniques on Learning Achievement under Different Learning Styles

ERIC Educational Resources Information Center

Chiou, Chei-Chang; Lee, Li-Tze; Tien, Li-Chu; Wang, Yu-Min

2017-01-01

This study explored the effectiveness of different concept mapping techniques on the learning achievement of senior accounting students and whether achievements attained using various techniques are affected by different learning styles. The techniques are computer-assisted construct-by-self-concept mapping (CACSB), computer-assisted…

Concept Mapping Improves Metacomprehension Accuracy among 7th Graders

ERIC Educational Resources Information Center

Redford, Joshua S.; Thiede, Keith W.; Wiley, Jennifer; Griffin, Thomas D.

2012-01-01

Two experiments explored concept map construction as a useful intervention to improve metacomprehension accuracy among 7th grade students. In the first experiment, metacomprehension was marginally better for a concept mapping group than for a rereading group. In the second experiment, metacomprehension accuracy was significantly greater for a…

How To Put Your Maps on the Internet.

ERIC Educational Resources Information Center

Allen, David Yehling

Many libraries are creating raster images of paper maps and making them available over the Internet. This presentation provides an overview of imaging technology for map librarians and administrators considering such projects. References in footnotes and the bibliography enable those interested to explore technical questions in depth. There are…

An Interdisciplinary Theme: Topographic Maps and Plate Tectonics

ERIC Educational Resources Information Center

Concannon, James P.; Aulgur, Linda

2011-01-01

This is an interdisciplinary lesson designed for middle school students studying landforms and geological processes. Students create a two-dimensional topographic map from a three-dimensional landform that they create using clay. Students then use other groups' topographic maps to re-create landforms. Following this, students explore some basic…

State Highway Maps: A Route to a Learning Adventure

ERIC Educational Resources Information Center

McDuffie, Thomas E.; Cifelli, Joseph

2006-01-01

Science within the folds of highway maps is explored through a series of hands-on experiences designed to reinforce and extend map-reading skills in grades 6-8. The increasingly sophisticated, standards-related activities include measuring distances between population centers, finding communities named after trees, animals, and geologic features,…

Exploration and Discovery through Maps: Teaching Science with Technology

EPA Science Inventory

Online maps have the power to bring students closer to their local natural environments. EnviroAtlas is an interactive, web-based tool that was designed by the EPA and its partners to provide access to maps that show the status of the local environment and social elements of an ...

Using Concept Maps to Assess Interdisciplinary Integration of Green Engineering Knowledge

ERIC Educational Resources Information Center

Borrego, Maura; Newswander, Chad B.; McNair, Lisa D.; McGinnis, Sean; Paretti, Marie C.

2009-01-01

Engineering education, like many fields, has started to explore the benefits of concept maps as an assessment technique for knowledge integration. Because they allow students to graphically link topics and represent complex interconnections among diverse concepts, we argue that concept maps are particularly appropriate for assessing…

Understanding Our Changing World through Mapping and Geotechnologies

ERIC Educational Resources Information Center

Kerski, Joseph

2008-01-01

People have always been fascinated with investigating their home--the Earth. For centuries, maps have stirred imaginations and inspired explorations of the unknown. Maps are a rich source of information, showing spatial relationships between climate, vegetation, population, landforms, river systems, land use, soils, natural hazards, and much more.…

Peasant friendly plant breeding and the early years of the green revolution in Mexico.

PubMed

Harwood, Jonathan

2009-01-01

Despite their success in boosting cereals production overall, the Green Revolution programs of the 1950s and 1960s were often criticized for failing to achieve their declared aim of alleviating world hunger. Most critics argued that the programs had produced a technology unsuited to the needs of small peasant farmers. This paper explores why such inappropriate technology might have been developed, focusing on the early years of the Rockefeller Foundation's Mexican Agricultural Program (MAP). It shows that some foundation officers as well as agricultural advisors had prior experience of the problems faced by small farmers in the United States and elsewhere. Moreover, the foundation's expressed concern for rural poverty does not appear to have been mere posturing by an organization anxious to be seen as an agent of philanthropy. Furthermore, the program's early work in maize-breeding was well tailored to the conditions of Mexican agriculture. Once the MAP was up and running, however, it became apparent that the task of getting new varieties and cultivation practices to small farmers was going to be difficult. Needing to make some kind of impact quickly, MAP staff chose to concentrate upon projects that were likely to find a rapid uptake. This meant setting aside the needs of peasant farmers to develop high-yielding varieties suited to large commercial farms.

Association between lesion location and language function in adult glioma using voxel-based lesion-symptom mapping.

PubMed

Banerjee, Pia; Leu, Kevin; Harris, Robert J; Cloughesy, Timothy F; Lai, Albert; Nghiemphu, Phioanh L; Pope, Whitney B; Bookheimer, Susan Y; Ellingson, Benjamin M

2015-01-01

Management of language difficulties is an important aspect of clinical care for glioma patients, and accurately identifying the possible language deficits in patients based on lesion location would be beneficial to clinicians. To that end, we examined the relationship between lesion presence and language performance on tests of receptive language and expressive language using a highly specific voxel-based lesion-symptom mapping (VLSM) approach in glioma patients. 98 adults with primary glioma, who were pre-surgical candidates, were administered seven neurocognitive tests within the domains of receptive language and expressive language. The association between language performance and lesion presence was examined using VLSM. Statistical parametric maps were created for each test, and composite maps for both receptive language and expressive language were created to display the significant voxels common to all tests within these language domains. We identified clusters of voxels with a significant relationship between lesion presence and language performance. All tasks were associated with several white matter pathways. The receptive language tasks were additionally all associated with regions primarily within the lateral temporal lobe and medial temporal lobe. In contrast, the expressive language tasks shared little overlap, despite each task being independently associated with large anatomic areas. Our findings identify the key anatomic structures involved in language functioning in adult glioma patients using an innovative lesion analysis technique and suggest that expressive language abilities may be more task-dependent and distributed than receptive language abilities.

Exploring the cellular basis of human disease through a large-scale mapping of deleterious genes to cell types.

PubMed

Cornish, Alex J; Filippis, Ioannis; David, Alessia; Sternberg, Michael J E

2015-09-01

Each cell type found within the human body performs a diverse and unique set of functions, the disruption of which can lead to disease. However, there currently exists no systematic mapping between cell types and the diseases they can cause. In this study, we integrate protein-protein interaction data with high-quality cell-type-specific gene expression data from the FANTOM5 project to build the largest collection of cell-type-specific interactomes created to date. We develop a novel method, called gene set compactness (GSC), that contrasts the relative positions of disease-associated genes across 73 cell-type-specific interactomes to map genes associated with 196 diseases to the cell types they affect. We conduct text-mining of the PubMed database to produce an independent resource of disease-associated cell types, which we use to validate our method. The GSC method successfully identifies known disease-cell-type associations, as well as highlighting associations that warrant further study. This includes mast cells and multiple sclerosis, a cell population currently being targeted in a multiple sclerosis phase 2 clinical trial. Furthermore, we build a cell-type-based diseasome using the cell types identified as manifesting each disease, offering insight into diseases linked through etiology. The data set produced in this study represents the first large-scale mapping of diseases to the cell types in which they are manifested and will therefore be useful in the study of disease systems. Overall, we demonstrate that our approach links disease-associated genes to the phenotypes they produce, a key goal within systems medicine.

The AR Sandbox: Augmented Reality in Geoscience Education

NASA Astrophysics Data System (ADS)

Kreylos, O.; Kellogg, L. H.; Reed, S.; Hsi, S.; Yikilmaz, M. B.; Schladow, G.; Segale, H.; Chan, L.

2016-12-01

The AR Sandbox is a combination of a physical box full of sand, a 3D (depth) camera such as a Microsoft Kinect, a data projector, and a computer running open-source software, creating a responsive and interactive system to teach geoscience concepts in formal or informal contexts. As one or more users shape the sand surface to create planes, hills, or valleys, the 3D camera scans the surface in real-time, the software creates a dynamic topographic map including elevation color maps and contour lines, and the projector projects that map back onto the sand surface such that real and projected features match exactly. In addition, users can add virtual water to the sandbox, which realistically flows over the real surface driven by a real-time fluid flow simulation. The AR Sandbox can teach basic geographic and hydrologic skills and concepts such as reading topographic maps, interpreting contour lines, formation of watersheds, flooding, or surface wave propagation in a hands-on and explorative manner. AR Sandbox installations in more than 150 institutions have shown high audience engagement and long dwell times of often 20 minutes and more. In a more formal context, the AR Sandbox can be used in field trip preparation, and can teach advanced geoscience skills such as extrapolating 3D sub-surface shapes from surface expression, via advanced software features such as the ability to load digital models of real landscapes and guiding users towards recreating them in the sandbox. Blueprints, installation instructions, and the open-source AR Sandbox software package are available at http://arsandbox.org .

Phosphorylated and Nonphosphorylated PfMAP2 Are Localized in the Nucleus, Dependent on the Stage of Plasmodium falciparum Asexual Maturation

PubMed Central

Dahalan, Farah Aida; Sidek, Hasidah Mohd; Murtey, Mogana Das; Embi, Mohammed Noor; Ibrahim, Jamaiah; Fei Tieng, Lim; Zakaria, Nurul Aiezzah

2016-01-01

Plasmodium falciparum mitogen-activated protein (MAP) kinases, a family of enzymes central to signal transduction processes including inflammatory responses, are a promising target for antimalarial drug development. Our study shows for the first time that the P. falciparum specific MAP kinase 2 (PfMAP2) is colocalized in the nucleus of all of the asexual erythrocytic stages of P. falciparum and is particularly elevated in its phosphorylated form. It was also discovered that PfMAP2 is expressed in its highest quantity during the early trophozoite (ring form) stage and significantly reduced in the mature trophozoite and schizont stages. Although the phosphorylated form of the kinase is always more prevalent, its ratio relative to the nonphosphorylated form remained constant irrespective of the parasites' developmental stage. We have also shown that the TSH motif specifically renders PfMAP2 genetically divergent from the other plasmodial MAP kinase activation sites using Neighbour Joining analysis. Furthermore, TSH motif-specific designed antibody is crucial in determining the location of the expression of the PfMAP2 protein. However, by using immunoelectron microscopy, PPfMAP2 were detected ubiquitously in the parasitized erythrocytes. In summary, PfMAP2 may play a far more important role than previously thought and is a worthy candidate for research as an antimalarial. PMID:27525262

Systematic analysis of transcription start sites in avian development.

PubMed

Lizio, Marina; Deviatiiarov, Ruslan; Nagai, Hiroki; Galan, Laura; Arner, Erik; Itoh, Masayoshi; Lassmann, Timo; Kasukawa, Takeya; Hasegawa, Akira; Ros, Marian A; Hayashizaki, Yoshihide; Carninci, Piero; Forrest, Alistair R R; Kawaji, Hideya; Gusev, Oleg; Sheng, Guojun

2017-09-01

Cap Analysis of Gene Expression (CAGE) in combination with single-molecule sequencing technology allows precision mapping of transcription start sites (TSSs) and genome-wide capture of promoter activities in differentiated and steady state cell populations. Much less is known about whether TSS profiling can characterize diverse and non-steady state cell populations, such as the approximately 400 transitory and heterogeneous cell types that arise during ontogeny of vertebrate animals. To gain such insight, we used the chick model and performed CAGE-based TSS analysis on embryonic samples covering the full 3-week developmental period. In total, 31,863 robust TSS peaks (>1 tag per million [TPM]) were mapped to the latest chicken genome assembly, of which 34% to 46% were active in any given developmental stage. ZENBU, a web-based, open-source platform, was used for interactive data exploration. TSSs of genes critical for lineage differentiation could be precisely mapped and their activities tracked throughout development, suggesting that non-steady state and heterogeneous cell populations are amenable to CAGE-based transcriptional analysis. Our study also uncovered a large set of extremely stable housekeeping TSSs and many novel stage-specific ones. We furthermore demonstrated that TSS mapping could expedite motif-based promoter analysis for regulatory modules associated with stage-specific and housekeeping genes. Finally, using Brachyury as an example, we provide evidence that precise TSS mapping in combination with Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-on technology enables us, for the first time, to efficiently target endogenous avian genes for transcriptional activation. Taken together, our results represent the first report of genome-wide TSS mapping in birds and the first systematic developmental TSS analysis in any amniote species (birds and mammals). By facilitating promoter-based molecular analysis and genetic manipulation, our work also underscores the value of avian models in unravelling the complex regulatory mechanism of cell lineage specification during amniote development.

Multilayer apparent magnetization mapping approach and its application in mineral exploration

NASA Astrophysics Data System (ADS)

Guo, L.; Meng, X.; Chen, Z.

2016-12-01

Apparent magnetization mapping is a technique to estimate magnetization distribution in the subsurface from the observed magnetic data. It has been applied for geologic mapping and mineral exploration for decades. Apparent magnetization mapping usually models the magnetic layer as a collection of vertical, juxtaposed prisms in both horizontal directions, whose top and bottom surfaces are assumed to be horizontal or variable-depth, and then inverts or deconvolves the magnetic anomalies in the space or frequency domain to determine the magnetization of each prism. The conventional mapping approaches usually assume that magnetic sources contain no remanent magnetization. However, such assumptions are not always valid in mineral exploration of metallic ores. In this case, the negligence of the remanence will result in large geologic deviation or the occurrence of negative magnetization. One alternate strategy is to transform the observed magnetic anomalies into some quantities that are insensitive or weakly sensitive to the remanence and then subsequently to perform inversion on these quantities, without needing any a priori information about remanent magnetization. Such kinds of quantities include the amplitude of the magnetic total field anomaly (AMA), and the normalized magnetic source strength (NSS). Here, we present a space-domain inversion approach for multilayer magnetization mapping based on the AMA for reducing effects of remanence. In the real world, magnetization usually varies vertically in the subsurface. If we use only one-layer model for mapping, the result is simply vertical superposition of different magnetization distributions. Hence, a multi-layer model for mapping would be a more realistic approach. We test the approach on the real data from a metallic deposit area in North China. The results demonstrated that our approach is feasible and produces considerable magnetization distribution from top layer to bottom layer in the subsurface.

EphrinA5 protein distribution in the developing mouse brain

PubMed Central

2010-01-01

Background EphrinA5 is one of the best-studied members of the Eph-ephrin family of guidance molecules, known to be involved in brain developmental processes. Using in situ hybridization, ephrinA5 mRNA expression has been detected in the retinotectal, the thalamocortical, and the olfactory systems; however, no study focused on the distribution of the protein. Considering that this membrane-anchored molecule may act far from the neuron soma expressing the transcript, it is of a crucial interest to localize ephrinA5 protein to better understand its function. Results Using immunohistochemistry, we found that ephrinA5 protein is highly expressed in the developing mouse brain from E12.5 to E16.5. The olfactory bulb, the cortex, the striatum, the thalamus, and the colliculi showed high intensity of labelling, suggesting its implication in topographic mapping of olfactory, retinocollicular, thalamocortical, corticothalamic and mesostriatal systems. In the olfactory nerve, we found an early ephrinA5 protein expression at E12.5 suggesting its implication in the guidance of primary olfactory neurons into the olfactory bulb. In the thalamus, we detected a dynamic graduated protein expression, suggesting its role in the corticothalamic patterning, whereas ephrinA5 protein expression in the target region of mesencephalic dopaminergic neurones indicated its involvement in the mesostriatal topographic mapping. Following E16.5, the signal faded gradually and was barely detectable at P0, suggesting a main role for ephrinA5 in primary molecular events in topographic map formation. Conclusion Our work shows that ephrinA5 protein is expressed in restrictive regions of the developing mouse brain. This expression pattern points out the potential sites of action of this molecule in the olfactory, retinotectal, thalamocortical, corticothalamic and mesostriatal systems, during development. This study is essential to better understand the role of ephrinA5 during developmental topographic mapping of connections and to further characterise the mechanisms involved in pathway restoration following cell transplantation in the damaged brain. PMID:20738842

A comparative study of RNA-Seq and microarray data analysis on the two examples of rectal-cancer patients and Burkitt Lymphoma cells.

PubMed

Wolff, Alexander; Bayerlová, Michaela; Gaedcke, Jochen; Kube, Dieter; Beißbarth, Tim

2018-01-01

Pipeline comparisons for gene expression data are highly valuable for applied real data analyses, as they enable the selection of suitable analysis strategies for the dataset at hand. Such pipelines for RNA-Seq data should include mapping of reads, counting and differential gene expression analysis or preprocessing, normalization and differential gene expression in case of microarray analysis, in order to give a global insight into pipeline performances. Four commonly used RNA-Seq pipelines (STAR/HTSeq-Count/edgeR, STAR/RSEM/edgeR, Sailfish/edgeR, TopHat2/Cufflinks/CuffDiff)) were investigated on multiple levels (alignment and counting) and cross-compared with the microarray counterpart on the level of gene expression and gene ontology enrichment. For these comparisons we generated two matched microarray and RNA-Seq datasets: Burkitt Lymphoma cell line data and rectal cancer patient data. The overall mapping rate of STAR was 98.98% for the cell line dataset and 98.49% for the patient dataset. Tophat's overall mapping rate was 97.02% and 96.73%, respectively, while Sailfish had only an overall mapping rate of 84.81% and 54.44%. The correlation of gene expression in microarray and RNA-Seq data was moderately worse for the patient dataset (ρ = 0.67-0.69) than for the cell line dataset (ρ = 0.87-0.88). An exception were the correlation results of Cufflinks, which were substantially lower (ρ = 0.21-0.29 and 0.34-0.53). For both datasets we identified very low numbers of differentially expressed genes using the microarray platform. For RNA-Seq we checked the agreement of differentially expressed genes identified in the different pipelines and of GO-term enrichment results. In conclusion the combination of STAR aligner with HTSeq-Count followed by STAR aligner with RSEM and Sailfish generated differentially expressed genes best suited for the dataset at hand and in agreement with most of the other transcriptomics pipelines.

Astrobiology Road Mapping (AstRoMap) - A project within FP7 of the European Commission: First results

NASA Astrophysics Data System (ADS)

Gomez-Gomez, Felipe; Capria, Maria Teresa; Palomba, Ernesto; Walter, Nicolas; Rettberg, Petra; Muller, Christian; Horneck, Gerda

AstRoMap (Astrobiology and Planetary Exploration Road Mapping) is a funded project formulated in the 5th Call of the European Commission FP7 framework. The main objectives of the AstRoMap are: 1. Identify the main astrobiology issues to be addressed by Europe in the next decades in relation with space exploration 2. Identify potential mission concepts that would allow addressing these issues 3. Identify the technology developments required to enable these missions 4. Provide a prioritized roadmap integrating science and technology activities as well as ground-based approach 5. Map scientific knowledge related to astrobiology in Europe To reach those objectives, AstRoMap is executed within the following steps: 1. Community consultation. In order to map the European astrobiology landscape and to provide a collaborative networking platform for this community, the AstRoMap project hosts a database of scientists (European and beyond) interested in astrobiology and planetary exploration (see: http://www.astromap.eu/database.html). It reflects the demography and the research and teaching activities of the astrobiology community, as well as their professional profiles and involvement in astrobiology projects. Considering future aspects of astrobiology in Europe, the need for more astrobiology-dedicated funding programmes at the EU level, especially for cross-disciplinary groups, was stressed. This might eventually lead to the creation of a European laboratory of Astrobiology, or even of a European Astrobiology Institute. 2. Workshops organisation. On the basis of the feedbacks from the community consultation, the potential participants and interesting topics are being identified to take part in the following workshops: 1-. Origin of organic compounds, steps to life; 2. Physico-chemical boundary conditions for habitability 3. Biosignatures as facilitating life detection 4. Origin of the Solar system 3. Astrobiology road-mapping. Based on the results and major conclusions elaborated during the workshops, an astrobiology roadmap will be constructed tailored to the European needs and competences. 4. Education and public outreach. Parallel to the workshop and consultation activities, AstRoMap will provide a comprehensive education and outreach programme and disseminate the progress of AstRoMap through its web site (http://www.astromap.eu).

The shadow map: a general contact definition for capturing the dynamics of biomolecular folding and function.

PubMed

Noel, Jeffrey K; Whitford, Paul C; Onuchic, José N

2012-07-26

Structure-based models (SBMs) are simplified models of the biomolecular dynamics that arise from funneled energy landscapes. We recently introduced an all-atom SBM that explicitly represents the atomic geometry of a biomolecule. While this initial study showed the robustness of the all-atom SBM Hamiltonian to changes in many of the energetic parameters, an important aspect, which has not been explored previously, is the definition of native interactions. In this study, we propose a general definition for generating atomically grained contact maps called "Shadow". The Shadow algorithm initially considers all atoms within a cutoff distance and then, controlled by a screening parameter, discards the occluded contacts. We show that this choice of contact map is not only well behaved for protein folding, since it produces consistently cooperative folding behavior in SBMs but also desirable for exploring the dynamics of macromolecular assemblies since, it distributes energy similarly between RNAs and proteins despite their disparate internal packing. All-atom structure-based models employing Shadow contact maps provide a general framework for exploring the geometrical features of biomolecules, especially the connections between folding and function.

Application of support vector machines for copper potential mapping in Kerman region, Iran

NASA Astrophysics Data System (ADS)

Shabankareh, Mahdi; Hezarkhani, Ardeshir

2017-04-01

The first step in systematic exploration studies is mineral potential mapping, which involves classification of the study area to favorable and unfavorable parts. Support vector machines (SVM) are designed for supervised classification based on statistical learning theory. This method named support vector classification (SVC). This paper describes SVC model, which combine exploration data in the regional-scale for copper potential mapping in Kerman copper bearing belt in south of Iran. Data layers or evidential maps were in six datasets namely lithology, tectonic, airborne geophysics, ferric alteration, hydroxide alteration and geochemistry. The SVC modeling result selected 2220 pixels as favorable zones, approximately 25 percent of the study area. Besides, 66 out of 86 copper indices, approximately 78.6% of all, were located in favorable zones. Other main goal of this study was to determine how each input affects favorable output. For this purpose, the histogram of each normalized input data to its favorable output was drawn. The histograms of each input dataset for favorable output showed that each information layer had a certain pattern. These patterns of SVC results could be considered as regional copper exploration characteristics.

c-Jun controls the efficiency of MAP kinase signaling by transcriptional repression of MAP kinase phosphatases

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

Sprowles, Amy; Robinson, Dan; Wu Yimi

2005-08-15

The mammalian JNK signaling pathway regulates the transcriptional response of cells to environmental stress, including UV irradiation. This signaling pathway is composed of a classical MAP kinase cascade; activation results in phosphorylation of the transcription factor substrates c-Jun and ATF2, and leads to changes in gene expression. The defining components of this pathway are conserved in the fission yeast S. pombe, where the genetic studies have shown that the ability of the JNK homolog Spc1 to be activated in response to UV irradiation is dependent on the presence of the transcription factor substrate Atf1. We have used genetic analysis tomore » define the role of c-Jun in activation of the mammalian JNK signaling pathway. Our results show that optimal activation of JNK requires the presence of its transcription factor substrate c-Jun. Mutational analysis shows that the ability of c-Jun to support efficient activation of JNK requires the ability of Jun to bind DNA, suggesting a transcriptional mechanism. Consistent with this, we show that c-Jun represses the expression of several MAP kinase phosphatases. In the absence of c-Jun, the increased expression of MAP kinase phosphatases leads to impaired activation of the ERK, JNK, and p38 MAP kinases after pathway activation. The results show that one function of c-Jun is to regulate the efficiency of signaling by the ERK, p38, and JNK MAP kinases, a function that is likely to affect cellular responses to many different stimuli.« less

Tumor necrosis factor-alpha stimulation of calcitonin gene-related peptide expression and secretion from rat trigeminal ganglion neurons.

PubMed

Bowen, Elizabeth J; Schmidt, Thomas W; Firm, Christina S; Russo, Andrew F; Durham, Paul L

2006-01-01

Expression of the neuropeptide calcitonin gene-related peptide (CGRP) in trigeminal ganglion is implicated in neurovascular headaches and temporomandibular joint disorders. Elevation of cytokines contributes to the pathology of these diseases. However, a connection between cytokines and CGRP gene expression in trigeminal ganglion nerves has not been established. We have focused on the effects of the cytokine tumor necrosis factor-alpha (TNF-alpha). TNFR1 receptors were found on the majority of CGRP-containing rat trigeminal ganglion neurons. Treatment of cultures with TNF-alpha stimulated CGRP secretion. In addition, the intracellular signaling intermediate from the TNFR1 receptor, ceramide, caused a similar increase in CGRP release. TNF-alpha caused a coordinate increase in CGRP promoter activity. TNF-alpha treatment activated the transcription factor NF-kappaB, as well as the Jun N-terminal kinase (JNK) and p38 mitogen-activated protein (MAP) kinase pathways. The importance of TNF-alpha induction of MAP kinase pathways was demonstrated by inhibiting MAP kinases with pharmacological reagents and gene transfer with an adenoviral vector encoding MAP kinase phosphatase-1 (MKP-1). We propose that selective and regulated inhibition of MAP kinases in trigeminal neurons may be therapeutically beneficial for inflammatory disorders involving elevated CGRP levels.

Tumor necrosis factor-α stimulation of calcitonin gene-related peptide expression and secretion from rat trigeminal ganglion neurons

PubMed Central

Bowen, Elizabeth J.; Schmidt, Thomas W.; Firm, Christina S.; Russo, Andrew F.; Durham, Paul L.

2006-01-01

Expression of the neuropeptide calcitonin gene-related peptide (CGRP) in trigeminal ganglion is implicated in neurovascular headaches and temporomandibular joint disorders. Elevation of cytokines contributes to the pathology of these diseases. However, a connection between cytokines and CGRP gene expression in trigeminal ganglion nerves has not been established. We have focused on the effects of the cytokine tumor necrosis factorα (TNFα). TNFR1 receptors were found on the majority of CGRP-containing rat trigeminal ganglion neurons. Treatment of cultures with TNFα stimulated CGRP secretion. In addition, the intracellular signaling intermediate from the TNFR1 receptor, ceramide, caused a similar increase in CGRP release. TNFα caused a coordinate increase in CGRP promoter activity. TNFα treatment activated the transcription factor NF-κB, as well as the Jun N-terminal kinase (JNK) and p38 mitogen-activated protein (MAP) kinase pathways. The importance of TNFα induction of MAP kinase pathways was demonstrated by inhibiting MAP kinases with pharmacological reagents and gene transfer with an adenoviral vector encoding MAP kinase phosphatase-1 (MKP-1). We propose that selective and regulated inhibition of MAP kinases in trigeminal neurons may be therapeutically beneficial for inflammatory disorders involving elevated CGRP levels. PMID:16277606

Exploring biology with small organic molecules

PubMed Central

Stockwell, Brent R.

2011-01-01

Small organic molecules have proven to be invaluable tools for investigating biological systems, but there is still much to learn from their use. To discover and to use more effectively new chemical tools to understand biology, strategies are needed that allow us to systematically explore ‘biological-activity space’. Such strategies involve analysing both protein binding of, and phenotypic responses to, small organic molecules. The mapping of biological-activity space using small molecules is akin to mapping the stars — uncharted territory is explored using a system of coordinates that describes where each new feature lies. PMID:15602550

Exploration for fossil and nuclear fuels from orbital altitudes

NASA Technical Reports Server (NTRS)

Short, N. M.

1975-01-01

A review of satellite-based photographic (optical and infrared) and microwave exploration and large-area mapping of the earth's surface in the ERTS program. Synoptic cloud-free coverage of large areas has been achieved with planimetric vertical views of the earth's surface useful in compiling close-to-orthographic mosaics. Radar penetration of cloud cover and infrared penetration of forest cover have been successful to some extent. Geological applications include map editing (with corrections in scale and computer processing of images), landforms analysis, structural geology studies, lithological identification, and exploration for minerals and fuels. Limitations of the method are noted.

A genome-scale map of expression for a mouse brain section obtained using voxelation

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

Chin, Mark H.; Geng, Alex B.; Khan, Arshad H.

Gene expression signatures in the mammalian brain hold the key to understanding neural development and neurological diseases. We have reconstructed 2- dimensional images of gene expression for 20,000 genes in a coronal slice of the mouse brain at the level of the striatum by using microarrays in combination with voxelation at a resolution of 1 mm3. Good reliability of the microarray results were confirmed using multiple replicates, subsequent quantitative RT-PCR voxelation, mass spectrometry voxelation and publicly available in situ hybridization data. Known and novel genes were identified with expression patterns localized to defined substructures within the brain. In addition, genesmore » with unexpected patterns were identified and cluster analysis identified a set of genes with a gradient of dorsal/ventral expression not restricted to known anatomical boundaries. The genome-scale maps of gene expression obtained using voxelation will be a valuable tool for the neuroscience community.« less

A Novel Intergenic ETnII-β Insertion Mutation Causes Multiple Malformations in Polypodia Mice

PubMed Central

Lehoczky, Jessica A.; Thomas, Peedikayil E.; Patrie, Kevin M.; Owens, Kailey M.; Villarreal, Lisa M.; Galbraith, Kenneth; Washburn, Joe; Johnson, Craig N.; Gavino, Bryant; Borowsky, Alexander D.; Millen, Kathleen J.; Wakenight, Paul; Law, William; Van Keuren, Margaret L.; Gavrilina, Galina; Hughes, Elizabeth D.; Saunders, Thomas L.; Brihn, Lesil; Nadeau, Joseph H.; Innis, Jeffrey W.

2013-01-01

Mouse early transposon insertions are responsible for ∼10% of spontaneous mutant phenotypes. We previously reported the phenotypes and genetic mapping of Polypodia, (Ppd), a spontaneous, X-linked dominant mutation with profound effects on body plan morphogenesis. Our new data shows that mutant mice are not born in expected Mendelian ratios secondary to loss after E9.5. In addition, we refined the Ppd genetic interval and discovered a novel ETnII-β early transposon insertion between the genes for Dusp9 and Pnck. The ETn inserted 1.6 kb downstream and antisense to Dusp9 and does not disrupt polyadenylation or splicing of either gene. Knock-in mice engineered to carry the ETn display Ppd characteristic ectopic caudal limb phenotypes, showing that the ETn insertion is the Ppd molecular lesion. Early transposons are actively expressed in the early blastocyst. To explore the consequences of the ETn on the genomic landscape at an early stage of development, we compared interval gene expression between wild-type and mutant ES cells. Mutant ES cell expression analysis revealed marked upregulation of Dusp9 mRNA and protein expression. Evaluation of the 5′ LTR CpG methylation state in adult mice revealed no correlation with the occurrence or severity of Ppd phenotypes at birth. Thus, the broad range of phenotypes observed in this mutant is secondary to a novel intergenic ETn insertion whose effects include dysregulation of nearby interval gene expression at early stages of development. PMID:24339789

Perspectives: Gene Expression in Fisheries Management

USGS Publications Warehouse

Nielsen, Jennifer L.; Pavey, Scott A.

2010-01-01

Functional genes and gene expression have been connected to physiological traits linked to effective production and broodstock selection in aquaculture, selective implications of commercial fish harvest, and adaptive changes reflected in non-commercial fish populations subject to human disturbance and climate change. Gene mapping using single nucleotide polymorphisms (SNPs) to identify functional genes, gene expression (analogue microarrays and real-time PCR), and digital sequencing technologies looking at RNA transcripts present new concepts and opportunities in support of effective and sustainable fisheries. Genomic tools have been rapidly growing in aquaculture research addressing aspects of fish health, toxicology, and early development. Genomic technologies linking effects in functional genes involved in growth, maturation and life history development have been tied to selection resulting from harvest practices. Incorporating new and ever-increasing knowledge of fish genomes is opening a different perspective on local adaptation that will prove invaluable in wild fish conservation and management. Conservation of fish stocks is rapidly incorporating research on critical adaptive responses directed at the effects of human disturbance and climate change through gene expression studies. Genomic studies of fish populations can be generally grouped into three broad categories: 1) evolutionary genomics and biodiversity; 2) adaptive physiological responses to a changing environment; and 3) adaptive behavioral genomics and life history diversity. We review current genomic research in fisheries focusing on those that use microarrays to explore differences in gene expression among phenotypes and within or across populations, information that is critically important to the conservation of fish and their relationship to humans.

Assessment of exploration bias in data-driven predictive models and the estimation of undiscovered resources

USGS Publications Warehouse

Coolbaugh, M.F.; Raines, G.L.; Zehner, R.E.

2007-01-01

The spatial distribution of discovered resources may not fully mimic the distribution of all such resources, discovered and undiscovered, because the process of discovery is biased by accessibility factors (e.g., outcrops, roads, and lakes) and by exploration criteria. In data-driven predictive models, the use of training sites (resource occurrences) biased by exploration criteria and accessibility does not necessarily translate to a biased predictive map. However, problems occur when evidence layers correlate with these same exploration factors. These biases then can produce a data-driven model that predicts known occurrences well, but poorly predicts undiscovered resources. Statistical assessment of correlation between evidence layers and map-based exploration factors is difficult because it is difficult to quantify the "degree of exploration." However, if such a degree-of-exploration map can be produced, the benefits can be enormous. Not only does it become possible to assess this correlation, but it becomes possible to predict undiscovered, instead of discovered, resources. Using geothermal systems in Nevada, USA, as an example, a degree-of-exploration model is created, which then is resolved into purely explored and unexplored equivalents, each occurring within coextensive study areas. A weights-of-evidence (WofE) model is built first without regard to the degree of exploration, and then a revised WofE model is calculated for the "explored fraction" only. Differences in the weights between the two models provide a correlation measure between the evidence and the degree of exploration. The data used to build the geothermal evidence layers are perceived to be independent of degree of exploration. Nevertheless, the evidence layers correlate with exploration because exploration has preferred the same favorable areas identified by the evidence patterns. In this circumstance, however, the weights for the "explored" WofE model minimize this bias. Using these revised weights, posterior probability is extrapolated into unexplored areas to estimate undiscovered deposits. ?? International Association for Mathematical Geology 2007.

Mars Global Geologic Mapping Progress and Suggested Geographic-Based Hierarchal Systems for Unit Grouping and Naming

NASA Technical Reports Server (NTRS)

Tanaka, K. L.; Dohm, J. M.; Irwin, R.; Kolb, E. J.; Skinner, J. A., Jr.; Hare, T. M.

2010-01-01

We are in the fourth year of a fiveyear effort to map the global geology of Mars at 1:20M scale using mainly Mars Global Surveyor, Mars Express, and Mars Odyssey image and altimetry datasets. Previously, we reported on details of project management, mapping datasets (local and regional), initial and anticipated mapping approaches, and tactics of map unit delineation and description [1-2]. Last year, we described mapping and unit delineation results thus far, a new unit identified in the northern plains, and remaining steps to complete the map [3].

Segmentation of singularity maps in the context of soil porosity

NASA Astrophysics Data System (ADS)

Martin-Sotoca, Juan J.; Saa-Requejo, Antonio; Grau, Juan; Tarquis, Ana M.

2016-04-01

Geochemical exploration have found with increasingly interests and benefits of using fractal (power-law) models to characterize geochemical distribution, including concentration-area (C-A) model (Cheng et al., 1994; Cheng, 2012) and concentration-volume (C-V) model (Afzal et al., 2011) just to name a few examples. These methods are based on the singularity maps of a measure that at each point define areas with self-similar properties that are shown in power-law relationships in Concentration-Area plots (C-A method). The C-A method together with the singularity map ("Singularity-CA" method) define thresholds that can be applied to segment the map. Recently, the "Singularity-CA" method has been applied to binarize 2D grayscale Computed Tomography (CT) soil images (Martin-Sotoca et al, 2015). Unlike image segmentation based on global thresholding methods, the "Singularity-CA" method allows to quantify the local scaling property of the grayscale value map in the space domain and determinate the intensity of local singularities. It can be used as a high-pass-filter technique to enhance high frequency patterns usually regarded as anomalies when applied to maps. In this work we will put special attention on how to select the singularity thresholds in the C-A plot to segment the image. We will compare two methods: 1) cross point of linear regressions and 2) Wavelets Transform Modulus Maxima (WTMM) singularity function detection. REFERENCES Cheng, Q., Agterberg, F. P. and Ballantyne, S. B. (1994). The separation of geochemical anomalies from background by fractal methods. Journal of Geochemical Exploration, 51, 109-130. Cheng, Q. (2012). Singularity theory and methods for mapping geochemical anomalies caused by buried sources and for predicting undiscovered mineral deposits in covered areas. Journal of Geochemical Exploration, 122, 55-70. Afzal, P., Fadakar Alghalandis, Y., Khakzad, A., Moarefvand, P. and Rashidnejad Omran, N. (2011) Delineation of mineralization zones in porphyry Cu deposits by fractal concentration-volume modeling. Journal of Geochemical Exploration, 108, 220-232. Martín-Sotoca, J. J., Tarquis, A. M., Saa-Requejo, A. and Grau, J. B. (2015). Pore detection in Computed Tomography (CT) soil images through singularity map analysis. Oral Presentation in PedoFract VIII Congress (June, La Coruña - Spain).

Teaching Plate Tectonic Concepts using GeoMapApp Learning Activities

NASA Astrophysics Data System (ADS)

Goodwillie, A. M.; Kluge, S.

2012-12-01

GeoMapApp Learning Activities ( http://serc.carleton.edu/geomapapp/collection.html ) can help educators to expose undergraduate students to a range of earth science concepts using high-quality data sets in an easy-to-use map-based interface called GeoMapApp. GeoMapApp Learning Activities require students to interact with and analyse research-quality geoscience data as a means to explore and enhance their understanding of underlying content and concepts. Each activity is freely available through the SERC-Carleton web site and offers step-by-step student instructions and answer sheets. Also provided are annotated educator versions of the worksheets that include teaching tips, additional content and suggestions for further work. The activities can be used "off-the-shelf". Or, since the educator may require flexibility to tailor the activities, the documents are provided in Word format for easy modification. Examples of activities include one on the concept of seafloor spreading that requires students to analyse global seafloor crustal age data to calculate spreading rates in different ocean basins. Another activity has students explore hot spots using radiometric age dating of rocks along the Hawaiian-Emperor seamount chain. A third focusses upon the interactive use of contours and profiles to help students visualise 3-D topography on 2-D computer screens. A fourth activity provides a study of mass wasting as revealed through geomorphological evidence. The step-by-step instructions and guided inquiry approach reduce the need for teacher intervention whilst boosting the time that students can spend on productive exploration and learning. The activities can be used, for example, in a classroom lab with the educator present and as self-paced assignments in an out-of-class setting. GeoMapApp Learning Activities are funded through the NSF GeoEd program and are aimed at students in the introductory undergraduate, community college and high school levels. The activities are based upon GeoMapApp (http://www.geomapapp.org), a free map-based data exploration and visualisation tool that allows students to access a wide range of geoscience data in a virtual lab-like environment.

Mapping the transcription start points of the Staphylococcus aureus eap, emp, and vwb promoters reveals a conserved octanucleotide sequence that is essential for expression of these genes.

PubMed

Harraghy, Niamh; Homerova, Dagmar; Herrmann, Mathias; Kormanec, Jan

2008-01-01

Mapping the transcription start points of the eap, emp, and vwb promoters revealed a conserved octanucleotide sequence (COS). Deleting this sequence abolished the expression of eap, emp, and vwb. However, electrophoretic mobility shift assays gave no evidence that this sequence was a binding site for SarA or SaeR, known regulators of eap and emp.

Planetary Geologic Mapping Handbook - 2010. Appendix

NASA Technical Reports Server (NTRS)

Tanaka, K. L.; Skinner, J. A., Jr.; Hare, T. M.

2010-01-01

Geologic maps present, in an historical context, fundamental syntheses of interpretations of the materials, landforms, structures, and processes that characterize planetary surfaces and shallow subsurfaces. Such maps also provide a contextual framework for summarizing and evaluating thematic research for a given region or body. In planetary exploration, for example, geologic maps are used for specialized investigations such as targeting regions of interest for data collection and for characterizing sites for landed missions. Whereas most modern terrestrial geologic maps are constructed from regional views provided by remote sensing data and supplemented in detail by field-based observations and measurements, planetary maps have been largely based on analyses of orbital photography. For planetary bodies in particular, geologic maps commonly represent a snapshot of a surface, because they are based on available information at a time when new data are still being acquired. Thus the field of planetary geologic mapping has been evolving rapidly to embrace the use of new data and modern technology and to accommodate the growing needs of planetary exploration. Planetary geologic maps have been published by the U.S. Geological Survey (USGS) since 1962. Over this time, numerous maps of several planetary bodies have been prepared at a variety of scales and projections using the best available image and topographic bases. Early geologic map bases commonly consisted of hand-mosaicked photographs or airbrushed shaded-relief views and geologic linework was manually drafted using mylar bases and ink drafting pens. Map publishing required a tedious process of scribing, color peel-coat preparation, typesetting, and photo-laboratory work. Beginning in the 1990s, inexpensive computing, display capability and user-friendly illustration software allowed maps to be drawn using digital tools rather than pen and ink, and mylar bases became obsolete. Terrestrial geologic maps published by the USGS now are primarily digital products using geographic information system (GIS) software and file formats. GIS mapping tools permit easy spatial comparison, generation, importation, manipulation, and analysis of multiple raster image, gridded, and vector data sets. GIS software has also permitted the development of projectspecific tools and the sharing of geospatial products among researchers. GIS approaches are now being used in planetary geologic mapping as well. Guidelines or handbooks on techniques in planetary geologic mapping have been developed periodically. As records of the heritage of mapping methods and data, these remain extremely useful guides. However, many of the fundamental aspects of earlier mapping handbooks have evolved significantly, and a comprehensive review of currently accepted mapping methodologies is now warranted. As documented in this handbook, such a review incorporates additional guidelines developed in recent years for planetary geologic mapping by the NASA Planetary Geology and Geophysics (PGG) Program's Planetary Cartography and Geologic Mapping Working Group's (PCGMWG) Geologic Mapping Subcommittee (GEMS) on the selection and use of map bases as well as map preparation, review, publication, and distribution. In light of the current boom in planetary exploration and the ongoing rapid evolution of available data for planetary mapping, this handbook is especially timely.

New Geologic Map of the Argyre Region of Mars: Deciphering the Geologic History Through Mars Global Surveyor, Mars Odyssey, and Mars Express Data

NASA Technical Reports Server (NTRS)

Dohm, J. M.; Banks, M.; Buczkowski, D.

2010-01-01

The primary objective of the mapping effort is to produce a geologic map of the Argyre basin and surrounding region at 1:5,000,000 scale in both digital and print formats that will detail the stratigraphic and crosscutting relations among rock materials and landforms (30 deg. S to 65 deg. S, 290 deg. E to 340 deg E). There has not been a detailed geologic map produced of the Argyre region since the Viking-era mapping investigation. The mapping tasks include stratigraphic mapping, crater counting, feature mapping, quantitative landform analysis, and spectroscopic/ stratigraphic investigation feature mapping. The regional geologic mapping investigation includes the Argyre basin floor and rim materials, the transition zone that straddles the Thaumasia plateau, which includes Argyre impactrelated modification, and the southeast margin of the Thaumasia plateau using important new data sets from the Mars Global Surveyor, Mars Odyssey, Mars Express, and Mars Reconnaissance Orbiter. The geologic information unfolded by this new mapping project will be useful to the community for constraining the regional geology, paleohydrology, and paleoclimate, which includes but is not limited to the assessment of: (1) whether the Argyre basin contained lakes, (2) the extent of reported flooding and glaciation, (3) existing interpretations of the origin of the narrow ridges located in the southeast part of the basin floor, and (4) the extent of Argyre-related tectonism and its influence on the surrounding regions.

Revisiting flow maps: a classification and a 3D alternative to visual clutter

NASA Astrophysics Data System (ADS)

Gu, Yuhang; Kraak, Menno-Jan; Engelhardt, Yuri

2018-05-01

Flow maps have long been servicing people in exploring movement by representing origin-destination data (OD data). Due to recent developments in data collecting techniques the amount of movement data is increasing dramatically. With such huge amounts of data, visual clutter in flow maps is becoming a challenge. This paper revisits flow maps, provides an overview of the characteristics of OD data and proposes a classification system for flow maps. For dealing with problems of visual clutter, 3D flow maps are proposed as potential alternative to 2D flow maps.

A gene-signature progression approach to identifying candidate small-molecule cancer therapeutics with connectivity mapping.

PubMed

Wen, Qing; Kim, Chang-Sik; Hamilton, Peter W; Zhang, Shu-Dong

2016-05-11

Gene expression connectivity mapping has gained much popularity recently with a number of successful applications in biomedical research testifying its utility and promise. Previously methodological research in connectivity mapping mainly focused on two of the key components in the framework, namely, the reference gene expression profiles and the connectivity mapping algorithms. The other key component in this framework, the query gene signature, has been left to users to construct without much consensus on how this should be done, albeit it has been an issue most relevant to end users. As a key input to the connectivity mapping process, gene signature is crucially important in returning biologically meaningful and relevant results. This paper intends to formulate a standardized procedure for constructing high quality gene signatures from a user's perspective. We describe a two-stage process for making quality gene signatures using gene expression data as initial inputs. First, a differential gene expression analysis comparing two distinct biological states; only the genes that have passed stringent statistical criteria are considered in the second stage of the process, which involves ranking genes based on statistical as well as biological significance. We introduce a "gene signature progression" method as a standard procedure in connectivity mapping. Starting from the highest ranked gene, we progressively determine the minimum length of the gene signature that allows connections to the reference profiles (drugs) being established with a preset target false discovery rate. We use a lung cancer dataset and a breast cancer dataset as two case studies to demonstrate how this standardized procedure works, and we show that highly relevant and interesting biological connections are returned. Of particular note is gefitinib, identified as among the candidate therapeutics in our lung cancer case study. Our gene signature was based on gene expression data from Taiwan female non-smoker lung cancer patients, while there is evidence from independent studies that gefitinib is highly effective in treating women, non-smoker or former light smoker, advanced non-small cell lung cancer patients of Asian origin. In summary, we introduced a gene signature progression method into connectivity mapping, which enables a standardized procedure for constructing high quality gene signatures. This progression method is particularly useful when the number of differentially expressed genes identified is large, and when there is a need to prioritize them to be included in the query signature. The results from two case studies demonstrate that the approach we have developed is capable of obtaining pertinent candidate drugs with high precision.

Host genetic variation influences gene expression response to rhinovirus infection.

PubMed

Çalışkan, Minal; Baker, Samuel W; Gilad, Yoav; Ober, Carole

2015-04-01

Rhinovirus (RV) is the most prevalent human respiratory virus and is responsible for at least half of all common colds. RV infections may result in a broad spectrum of effects that range from asymptomatic infections to severe lower respiratory illnesses. The basis for inter-individual variation in the response to RV infection is not well understood. In this study, we explored whether host genetic variation is associated with variation in gene expression response to RV infections between individuals. To do so, we obtained genome-wide genotype and gene expression data in uninfected and RV-infected peripheral blood mononuclear cells (PBMCs) from 98 individuals. We mapped local and distant genetic variation that is associated with inter-individual differences in gene expression levels (eQTLs) in both uninfected and RV-infected cells. We focused specifically on response eQTLs (reQTLs), namely, genetic associations with inter-individual variation in gene expression response to RV infection. We identified local reQTLs for 38 genes, including genes with known functions in viral response (UBA7, OAS1, IRF5) and genes that have been associated with immune and RV-related diseases (e.g., ITGA2, MSR1, GSTM3). The putative regulatory regions of genes with reQTLs were enriched for binding sites of virus-activated STAT2, highlighting the role of condition-specific transcription factors in genotype-by-environment interactions. Overall, we suggest that the 38 loci associated with inter-individual variation in gene expression response to RV-infection represent promising candidates for affecting immune and RV-related respiratory diseases.

Transcription Factor Map Alignment of Promoter Regions

PubMed Central

Blanco, Enrique; Messeguer, Xavier; Smith, Temple F; Guigó, Roderic

2006-01-01

We address the problem of comparing and characterizing the promoter regions of genes with similar expression patterns. This remains a challenging problem in sequence analysis, because often the promoter regions of co-expressed genes do not show discernible sequence conservation. In our approach, thus, we have not directly compared the nucleotide sequence of promoters. Instead, we have obtained predictions of transcription factor binding sites, annotated the predicted sites with the labels of the corresponding binding factors, and aligned the resulting sequences of labels—to which we refer here as transcription factor maps (TF-maps). To obtain the global pairwise alignment of two TF-maps, we have adapted an algorithm initially developed to align restriction enzyme maps. We have optimized the parameters of the algorithm in a small, but well-curated, collection of human–mouse orthologous gene pairs. Results in this dataset, as well as in an independent much larger dataset from the CISRED database, indicate that TF-map alignments are able to uncover conserved regulatory elements, which cannot be detected by the typical sequence alignments. PMID:16733547

The Scale of Exploration: Planetary Missions Set in the Context of Tourist Destinations on Earth

NASA Astrophysics Data System (ADS)

Garry, W. B.; Bleacher, L. V.; Bleacher, J. E.; Petro, N. E.; Mest, S. C.; Williams, S. H.

2012-03-01

What if the Apollo astronauts explored Washington, DC, or the Mars Exploration Rovers explored Disney World? We present educational versions of the traverse maps for Apollo and MER missions set in the context of popular tourist destinations on Earth.

The Canadian West Discovered: An Exhibition of Printed Maps from the 16th to Early 20th Century (Glenbow Museum, Calgary, Alberta, Canada, January 26-April 15, 1983).

ERIC Educational Resources Information Center

Javorski, Mary

This document provides historical research from the earliest French experiences on the upper North American peninsula through today. Approximately 50 maps have been provided outlining the evolution of information that has been collected by those who sought to explore the region. Most of these explorers were trading company employees who were hired…

Development and Demonstration of Autonomous Behaviors for Urban Environment Exploration

DTIC Science & Technology

2012-04-01

exploration, mapping, localization, autonomy, lidar , SLAM 1. INTRODUCTION As global conflicts move into more urban settings, unmanned ground vehicles...mounted Hokuyo lidar is paired with a vertically mounted Hokuyo lidar as an inexpensive way for 3D perception of the environment. In addition, a pair...and mapping ( SLAM ) problem do exist,2–4 most have yet to tackle the problem of online SLAM throughout a multi-story building and/or incorporating

Mapping the Infrared Sky Artist Concept

NASA Image and Video Library

2009-11-17

This artist conception shows NASA Wide-field Infrared Survey Explorer mapping the whole sky in infrared. The mission will unveil hundreds of thousands of asteroids, and hundreds of millions of stars and galaxies.

Nasa's Planetary Geologic Mapping Program: Overview

NASA Astrophysics Data System (ADS)

Williams, D. A.

2016-06-01

NASA's Planetary Science Division supports the geologic mapping of planetary surfaces through a distinct organizational structure and a series of research and analysis (R&A) funding programs. Cartography and geologic mapping issues for NASA's planetary science programs are overseen by the Mapping and Planetary Spatial Infrastructure Team (MAPSIT), which is an assessment group for cartography similar to the Mars Exploration Program Assessment Group (MEPAG) for Mars exploration. MAPSIT's Steering Committee includes specialists in geological mapping, who make up the Geologic Mapping Subcommittee (GEMS). I am the GEMS Chair, and with a group of 3-4 community mappers we advise the U.S. Geological Survey Planetary Geologic Mapping Coordinator (Dr. James Skinner) and develop policy and procedures to aid the planetary geologic mapping community. GEMS meets twice a year, at the Annual Lunar and Planetary Science Conference in March, and at the Annual Planetary Mappers' Meeting in June (attendance is required by all NASA-funded geologic mappers). Funding programs under NASA's current R&A structure to propose geological mapping projects include Mars Data Analysis (Mars), Lunar Data Analysis (Moon), Discovery Data Analysis (Mercury, Vesta, Ceres), Cassini Data Analysis (Saturn moons), Solar System Workings (Venus or Jupiter moons), and the Planetary Data Archiving, Restoration, and Tools (PDART) program. Current NASA policy requires all funded geologic mapping projects to be done digitally using Geographic Information Systems (GIS) software. In this presentation we will discuss details on how geologic mapping is done consistent with current NASA policy and USGS guidelines.

Genetic Architecture of Natural Variation in Rice Nonphotochemical Quenching Capacity Revealed by Genome-Wide Association Study

PubMed Central

Wang, Quanxiu; Zhao, Hu; Jiang, Junpeng; Xu, Jiuyue; Xie, Weibo; Fu, Xiangkui; Liu, Chang; He, Yuqing; Wang, Gongwei

2017-01-01

The photoprotective processes conferred by nonphotochemical quenching (NPQ) serve fundamental roles in maintaining plant fitness and sustainable yield. So far, few loci have been reported to be involved in natural variation of NPQ capacity in rice (Oryza sativa), and the extents of variation explored are very limited. Here we conducted a genome-wide association study (GWAS) for NPQ capacity using a diverse worldwide collection of 529 O. sativa accessions. A total of 33 significant association loci were identified. To check the validity of the GWAS signals, three F2 mapping populations with parents selected from the association panel were constructed and assayed. All QTLs detected in mapping populations could correspond to at least one GWAS signal, indicating the GWAS results were quite reliable. OsPsbS1 was repeatedly detected and explained more than 40% of the variation in the whole association population in two years, and demonstrated to be a common major QTL in all three mapping populations derived from inter-group crosses. We revealed 43 single nucleotide polymorphisms (SNPs) and 7 insertions and deletions (InDels) within a 6,997-bp DNA fragment of OsPsbS1, but found no non-synonymous SNPs or InDels in the coding region, indicating the PsbS1 protein sequence is highly conserved. Haplotypes with the 2,674-bp insertion in the promoter region exhibited significantly higher NPQ values and higher expression levels of OsPsbS1. The OsPsbS1 RNAi plants and CRISPR/Cas9 mutants exhibited drastically decreased NPQ values. OsPsbS1 had specific and high-level expression in green tissues of rice. However, we didn't find significant function for OsPsbS2, the other rice PsbS homologue. Manipulation of the significant loci or candidate genes identified may enhance photoprotection and improve photosynthesis and yield in rice. PMID:29081789

Genetic Architecture of Natural Variation in Rice Nonphotochemical Quenching Capacity Revealed by Genome-Wide Association Study.

PubMed

Wang, Quanxiu; Zhao, Hu; Jiang, Junpeng; Xu, Jiuyue; Xie, Weibo; Fu, Xiangkui; Liu, Chang; He, Yuqing; Wang, Gongwei

2017-01-01

The photoprotective processes conferred by nonphotochemical quenching (NPQ) serve fundamental roles in maintaining plant fitness and sustainable yield. So far, few loci have been reported to be involved in natural variation of NPQ capacity in rice ( Oryza sativa ), and the extents of variation explored are very limited. Here we conducted a genome-wide association study (GWAS) for NPQ capacity using a diverse worldwide collection of 529 O. sativa accessions. A total of 33 significant association loci were identified. To check the validity of the GWAS signals, three F2 mapping populations with parents selected from the association panel were constructed and assayed. All QTLs detected in mapping populations could correspond to at least one GWAS signal, indicating the GWAS results were quite reliable. OsPsbS1 was repeatedly detected and explained more than 40% of the variation in the whole association population in two years, and demonstrated to be a common major QTL in all three mapping populations derived from inter-group crosses. We revealed 43 single nucleotide polymorphisms (SNPs) and 7 insertions and deletions (InDels) within a 6,997-bp DNA fragment of OsPsbS1 , but found no non-synonymous SNPs or InDels in the coding region, indicating the PsbS1 protein sequence is highly conserved. Haplotypes with the 2,674-bp insertion in the promoter region exhibited significantly higher NPQ values and higher expression levels of OsPsbS1 . The OsPsbS1 RNAi plants and CRISPR/Cas9 mutants exhibited drastically decreased NPQ values. OsPsbS1 had specific and high-level expression in green tissues of rice. However, we didn't find significant function for OsPsbS2 , the other rice PsbS homologue. Manipulation of the significant loci or candidate genes identified may enhance photoprotection and improve photosynthesis and yield in rice.

Dissecting Pistil Responses to Incompatible and Compatible Pollen in Self-Incompatibility Brassica oleracea Using Comparative Proteomics.

PubMed

Zeng, Jing; Gao, Qiguo; Shi, Songmei; Lian, Xiaoping; Converse, Richard; Zhang, Hecui; Yang, Xiaohong; Ren, Xuesong; Chen, Song; Zhu, Liquan

2017-04-01

Angiosperms have developed self-incompatibility (SI) systems to reject self-pollen, thereby promoting outcrossing. The Brassicaceae belongs to typical sporophytic system, having a single S-locus controlled SI response, and was chosen as a model system to study SI-related intercellular signal transduction. In this regard, the downstream factor of EXO70A1 was unknown. Here, protein two-dimensional electrophoresis (2-DE) method and coupled with matrix-assisted laser desorption ionization/time of flight of flight mass spectrometry (MALDI-TOF -MS) and peptide mass fingerprinting (PMF) was used to further explore the mechanism of SI responses in Brassica oleracea L. var. capitata L. at protein level. To further confirm the time point of protein profile change, total proteins were collected from B. oleracea pistils at 0 min, 1 h, and 2 h after self-pollination. In total 902, 1088 and 1023 protein spots were separated in 0 min, 1 h and 2 h 2-DE maps, respectively. Our analyses of self-pollination profiles indicated that proteins mainly changed at 1 h post-pollination in B. oleracea. Moreover, 1077 protein spots were separated in cross-pollinated 1 h (CP) pistil 2-DE map. MALDI-TOF-MS and PMF successfully identified 34 differentially-expressed proteins (DEPs) in SP and CP 1 h 2-DE maps. Gene ontology and KEGG analysis revealed an array of proteins grouped in the following categories: stress and defense response (35%), protein metabolism (18%), carbohydrate and energy metabolism (12%), regulation of translation (9%), pollen tube development (12%), transport (9%) and cytoskeletal (6%). Sets of DEPs identified specifically in SP or only up-regulated expressed in CP pistils were chosen for funther investigating in floral organs and during the process of self- and cross-pollination. The function of these DEPs in terms of their potential involvement in SI in B. oleracea is discussed.

Some issues in data model mapping

NASA Technical Reports Server (NTRS)

Dominick, Wayne D. (Editor); Alsabbagh, Jamal R.

1985-01-01

Numerous data models have been reported in the literature since the early 1970's. They have been used as database interfaces and as conceptual design tools. The mapping between schemas expressed according to the same data model or according to different models is interesting for theoretical and practical purposes. This paper addresses some of the issues involved in such a mapping. Of special interest are the identification of the mapping parameters and some current approaches for handling the various situations that require a mapping.

Transgenic expression of Map3k4 rescues T-associated sex reversal (Tas) in mice

PubMed Central

Warr, Nick; Siggers, Pam; Carré, Gwenn-Aël; Bogani, Debora; Brixey, Rachel; Akiyoshi, Mika; Tachibana, Makoto; Teboul, Lydia; Wells, Sara; Sanderson, Jeremy; Greenfield, Andy

2014-01-01

Disorders of sex development in the human population range in severity from mild genital defects to gonadal sex reversal. XY female development has been associated with heterozygous mutations in several genes, including SOX9, WT1 and MAP3K1. In contrast, XY sex reversal in mice usually requires complete absence of testis-determining gene products. One exception to this involves T-associated sex reversal (Tas), a phenomenon characterized by the formation of ovotestes or ovaries in XY mice hemizygous for the hairpin-tail (Thp) or T-Orleans (TOrl) deletions on proximal mouse chromosome 17. We recently reported that mice heterozygous for a null allele of Map3k4, which resides in the Thp deletion, exhibit XY ovotestis development and occasional gonadal sex reversal on the sensitized C57BL/6J-YAKR (B6-YAKR) genetic background, reminiscent of the Tas phenotype. However, these experiments did not exclude the possibility that loss of other loci in the Thp deletion, or other effects of the deletion itself, might contribute to Tas. Here, we show that disruption to Sry expression underlies XY gonadal defects in B6-YAKR embryos harbouring the Thp deletion and that a functional Map3k4 bacterial artificial chromosome rescues these abnormalities by re-establishing a normal Sry expression profile. These data demonstrate that Map3k4 haploinsufficiency is the cause of T-associated sex reversal and that levels of this signalling molecule are a major determinant of the expression profile of Sry. PMID:24452333

Mapping the dynamics of cortical neuroplasticity of skilled motor learning using micro X-ray fluorescence and histofluorescence imaging of zinc in the rat

PubMed Central

Alaverdashvili, Mariam; Paterson, Phyllis G.

2017-01-01

Synchrotron-based X-ray fluorescence imaging (XFI) of zinc (Zn) has been recently implemented to understand the efficiency of various therapeutic interventions targeting post-stroke neuroprotection and neuroplasticity. However, it is uncertain if micro XFI can resolve neuroplasticity-induced changes. Thus, we explored if learning-associated behavioral changes would be accompanied by changes in cortical Zn concentration measured by XFI in healthy adult rats. Proficiency in a skilled reach-to-eat task during early and late stages of motor learning served as a functional measure of neuroplasticity. c-Fos protein and vesicular Zn expression were employed as indirect neuronal measures of brain plasticity. A total Zn map (20 × 20 × 30 μm3 resolution) generated by micro XFI failed to reflect increases in either c-Fos or vesicular Zn in the motor cortex contralateral to the trained forelimb or improved proficiency in the skilled reaching task. Remarkably, vesicular Zn increased in the late stage of motor learning along with a concurrent decrease in the number of c-fos-ip neurons relative to the early stage of motor learning. This inverse dynamics of c-fos and vesicular Zn level as the motor skill advances suggest that a qualitatively different neural population, comprised of fewer active but more efficiently connected neurons, supports a skilled action in the late versus early stage of motor learning. The lack of sensitivity of the XFI-generated Zn map to visualize the plasticity-associated changes in vesicular Zn suggests that the Zn level measured by micro XFI should not be used as a surrogate marker of neuroplasticity in response to the acquisition of skilled motor actions. Nanoscopic XFI could be explored in future as a means of imaging these subtle physiological changes. PMID:27840249

Exploring how students think: a new method combining think-aloud and concept mapping protocols.

PubMed

Pottier, Pierre; Hardouin, Jean-Benoit; Hodges, Brian D; Pistorius, Marc-Antoine; Connault, Jérome; Durant, Cécile; Clairand, Renaud; Sebille, Véronique; Barrier, Jacques-Henri; Planchon, Bernard

2010-09-01

A key element of medical competence is problem solving. Previous work has shown that doctors use inductive reasoning to progress from facts to hypotheses and deductive reasoning to move from hypotheses to the gathering of confirmatory information. No individual assessment method has been designed to quantify the use of inductive and deductive procedures within clinical reasoning. The aim of this study was to explore the feasibility and reliability of a new method which allows for the rapid identification of the style (inductive or deductive) of clinical reasoning in medical students and experts. The study included four groups of four participants. These comprised groups of medical students in Years 3, 4 and 5 and a group of specialists in internal medicine, all at a medical school with a 6-year curriculum in France. Participants were asked to solve four clinical problems by thinking aloud. The thinking expressed aloud was immediately transcribed into concept maps by one or two 'writers' trained to distinguish inductive and deductive links. Reliability was assessed by estimating the inter-writer correlation. The calculated rate of inductive reasoning, the richness score and the rate of exhaustiveness of reasoning were compared according to the level of expertise of the individual and the type of clinical problem. The total number of maps drawn amounted to 32 for students in Year 4, 32 for students in Year 5, 16 for students in Year 3 and 16 for experts. A positive correlation was found between writers (R = 0.66-0.93). Richness scores and rates of exhaustiveness of reasoning did not differ according to expertise level. The rate of inductive reasoning varied as expected according to the nature of the clinical problem and was lower in experts (41% versus 67%). This new method showed good reliability and may be a promising tool for the assessment of medical problem-solving skills, giving teachers a means of diagnosing how their students think when they are confronted with clinical problems.

Publishing Data on Physical Samples Using the GeoLink Ontology and Linked Data Platforms

NASA Astrophysics Data System (ADS)

Ji, P.; Arko, R. A.; Lehnert, K. A.; Song, L.; Carter, M. R.; Hsu, L.

2015-12-01

Interdisciplinary Earth Data Alliance (IEDA), one of partners in EarthCube GeoLink project, seeks to explore the extent to which the use of GeoLink reusable Ontology Design Patterns (ODPs) and linked data platforms in IEDA data infrastructure can make research data more easily accessible and valuable. Linked data for the System for Earth Sample Registration (SESAR) is the first effort of IEDA to show how linked data enhance the presentation of IEDA data system architecture. SESAR Linked Data maps each table and column in SESAR database to RDF class and property based on GeoLink view, which build on the top of GeoLink ODPs. Then, uses D2RQ dumping the contents of SESAR database into RDF triples on the basis of mapping results. And, the dumped RDF triples is loaded into GRAPHDB, an RDF graph database, as permanent data in the form of atomic facts expressed as subjects, predicates and objects which provide support for semantic interoperability between IEDA and other GeoLink partners. Finally, an integrated browsing and searching interface build on Callimachus, a highly scalable platform for publishing linked data, is introduced to make sense of data stored in triplestore. Drill down and through features are built in the interface to help users locating content efficiently. The drill down feature enables users to explore beyond the summary information in the instance list of a specific class and into the detail from the specific instance page. The drill through feature enables users to jump from one instance to another one by simply clicking the link of the latter nested in the former region. Additionally, OpenLayers map is embedded into the interface to enhance the attractiveness of the presentation of instance which has geospatial information. Furthermore, by linking instances in the SESAR datasets to matching or corresponding instances in external sets, the presentation has been enriched with additional information about related classes like person, cruise, etc.

Eye Tracking to Explore the Impacts of Photorealistic 3d Representations in Pedstrian Navigation Performance

NASA Astrophysics Data System (ADS)

Dong, Weihua; Liao, Hua

2016-06-01

Despite the now-ubiquitous two-dimensional (2D) maps, photorealistic three-dimensional (3D) representations of cities (e.g., Google Earth) have gained much attention by scientists and public users as another option. However, there is no consistent evidence on the influences of 3D photorealism on pedestrian navigation. Whether 3D photorealism can communicate cartographic information for navigation with higher effectiveness and efficiency and lower cognitive workload compared to the traditional symbolic 2D maps remains unknown. This study aims to explore whether the photorealistic 3D representation can facilitate processes of map reading and navigation in digital environments using a lab-based eye tracking approach. Here we show the differences of symbolic 2D maps versus photorealistic 3D representations depending on users' eye-movement and navigation behaviour data. We found that the participants using the 3D representation were less effective, less efficient and were required higher cognitive workload than using the 2D map for map reading. However, participants using the 3D representation performed more efficiently in self-localization and orientation at the complex decision points. The empirical results can be helpful to improve the usability of pedestrian navigation maps in future designs.

Hemichordates and the origin of chordates

NASA Technical Reports Server (NTRS)

Gerhart, John; Lowe, Christopher; Kirschner, Marc

2005-01-01

Hemichordates, the phylum of bilateral animals most closely related to chordates, could reveal the evolutionary origins of chordate traits such as the nerve cord, notochord, gill slits and tail. The anteroposterior maps of gene expression domains for 38 genes of chordate neural patterning are highly similar for hemichordates and chordates, even though hemichordates have a diffuse nerve-net. About 40% of the domains are not present in protostome maps. We propose that this map, the gill slits and the tail date to the deuterostome ancestor. The map of dorsoventral expression domains, centered on a Bmp-Chordin axis, differs between the two groups; hemichordates resemble protostomes more than they do chordates. The dorsoventral axis might have undergone extensive modification in the chordate line, including centralization of the nervous system, segregation of epidermis, derivation of the notochord, and an inversion of organization.

Charting Our Path with a Web Literacy Map

ERIC Educational Resources Information Center

Dalton, Bridget

2015-01-01

Being a literacy teacher today means being a teacher of Web literacies. This article features the "Web Literacy Map", an open source tool from Mozilla's Webmaker project. The map focuses on Exploring (Navigating the Web); Building (creating for the Web), and Connecting (Participating on the Web). Readers are invited to use resources,…

Regionalization: A Story Map Lesson on Regions

ERIC Educational Resources Information Center

Edmondson, Deborah

2018-01-01

This lesson introduces the concept of regionalization and types of regions. After a brief introductory activity, students explore a story map to learn the material. The teacher can project the story map on a screen for all students to follow or students may work individually on computers. Working individually will allow students to set their own…

Testing Beyond Words: Using Tests to Enhance Visuospatial Map Learning

ERIC Educational Resources Information Center

Carpenter, Shana K.; Pashler, Harold

2007-01-01

Psychological research shows that learning can be powerfully enhanced through testing, but this finding has so far been confined to memory tasks requiring verbal responses. We explored whether testing can enhance learning of visuospatial information in maps. Fifty subjects each studied 2 maps, one through conventional study, and the other through…

NOAA Office of Exploration and Research > About OER > Strategic Plan

Science.gov Websites

Organization Guiding Documents Organizational Structure Map of Staff and Affiliate Locations Strategic Plan Media News Room OER Symposium Overview Organization Guiding Documents Organizational Structure Map of Strategic Plan Home About OER Overview Organization Guiding Documents Organizational Structure Map of Staff

NOAA Office of Exploration and Research > About OER > Overview

Science.gov Websites

Organization Guiding Documents Organizational Structure Map of Staff and Affiliate Locations Strategic Plan Media News Room OER Symposium Overview Organization Guiding Documents Organizational Structure Map of Overview Home About OER Overview Organization Guiding Documents Organizational Structure Map of Staff and

NOAA Office of Exploration and Research > About OER > Contact Us

Science.gov Websites

Organization Guiding Documents Organizational Structure Map of Staff and Affiliate Locations Strategic Plan Media News Room OER Symposium Overview Organization Guiding Documents Organizational Structure Map of Contact Us Home About OER Overview Organization Guiding Documents Organizational Structure Map of Staff

NOAA Office of Exploration and Research > About OER > Program Review

Science.gov Websites

Organization Guiding Documents Organizational Structure Map of Staff and Affiliate Locations Strategic Plan Media News Room OER Symposium Overview Organization Guiding Documents Organizational Structure Map of Program Review Home About OER Overview Organization Guiding Documents Organizational Structure Map of

Drawing the Line with Google Earth: The Place of Digital Mapping outside of Geography

ERIC Educational Resources Information Center

Mercier, O. Ripeka; Rata, Arama

2017-01-01

The "Te Kawa a Maui Atlas" project explores how mapping activities support undergraduate student engagement and learning in Maori studies. This article describes two specific assignments, which used online mapping allowing students to engage with the work of their peers. By analysing student evaluations of these activities, we identify…

The Effect of College Students' Self-Generated Computerized Mind Mapping on Their Reading Achievement

ERIC Educational Resources Information Center

Sabbah, Sabah Salman

2015-01-01

This study explored the potential effect of college students' self-generated computerized mind maps on their reading comprehension. It also investigated the subjects' attitudes toward generating computerized mind maps for reading comprehension. The study was conducted in response to the inability of the foundation-level students, who were learning…

Gene expression pattern recognition algorithm inferences to classify samples exposed to chemical agents

NASA Astrophysics Data System (ADS)

Bushel, Pierre R.; Bennett, Lee; Hamadeh, Hisham; Green, James; Ableson, Alan; Misener, Steve; Paules, Richard; Afshari, Cynthia

2002-06-01

We present an analysis of pattern recognition procedures used to predict the classes of samples exposed to pharmacologic agents by comparing gene expression patterns from samples treated with two classes of compounds. Rat liver mRNA samples following exposure for 24 hours with phenobarbital or peroxisome proliferators were analyzed using a 1700 rat cDNA microarray platform. Sets of genes that were consistently differentially expressed in the rat liver samples following treatment were stored in the MicroArray Project System (MAPS) database. MAPS identified 238 genes in common that possessed a low probability (P < 0.01) of being randomly detected as differentially expressed at the 95% confidence level. Hierarchical cluster analysis on the 238 genes clustered specific gene expression profiles that separated samples based on exposure to a particular class of compound.

The MAP Autonomous Mission Control System

NASA Technical Reports Server (NTRS)

Breed, Juile; Coyle, Steven; Blahut, Kevin; Dent, Carolyn; Shendock, Robert; Rowe, Roger

2000-01-01

The Microwave Anisotropy Probe (MAP) mission is the second mission in NASA's Office of Space Science low-cost, Medium-class Explorers (MIDEX) program. The Explorers Program is designed to accomplish frequent, low cost, high quality space science investigations utilizing innovative, streamlined, efficient management, design and operations approaches. The MAP spacecraft will produce an accurate full-sky map of the cosmic microwave background temperature fluctuations with high sensitivity and angular resolution. The MAP spacecraft is planned for launch in early 2001, and will be staffed by only single-shift operations. During the rest of the time the spacecraft must be operated autonomously, with personnel available only on an on-call basis. Four (4) innovations will work cooperatively to enable a significant reduction in operations costs for the MAP spacecraft. First, the use of a common ground system for Spacecraft Integration and Test (I&T) as well as Operations. Second, the use of Finite State Modeling for intelligent autonomy. Third, the integration of a graphical planning engine to drive the autonomous systems without an intermediate manual step. And fourth, the ability for distributed operations via Web and pager access.

A Tangible Approach to Concept Mapping

NASA Astrophysics Data System (ADS)

Tanenbaum, Karen; Antle, Alissa N.

2009-05-01

The Tangible Concept Mapping project investigates using a tangible user interface to engage learners in concept map creation. This paper describes a prototype implementation of the system, presents some preliminary analysis of its ease of use and effectiveness, and discusses how elements of tangible interaction support concept mapping by helping users organize and structure their knowledge about a domain. The role of physical engagement and embodiment in supporting the mental activity of creating the concept map is explored as one of the benefits of a tangible approach to learning.

Topographic Maps from a Kiosk

USGS Publications Warehouse

,

2001-01-01

In April 2000, the U.S. Geological Survey (USGS) and National Geographic (NG) TOPO entered into a cooperative research and development agreement (CRADA) to explore a new technology that would allow a person to walk into a map retail store and print a personalized topographic map, vending machine style, from a self-service kiosk. Work began to develop systems that offer seamless, digitally stored USGS topographic maps using map-on-demand software from NG TOPO. The vending machine approach ensures that maps are never out of stock, allows customers to define their own map boundaries, and gives customers choices regarding shaded relief and the grids to be printed on the maps to get the exact maps they need.

A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages

PubMed Central

Yu, Ying; Fuscoe, James C.; Zhao, Chen; Guo, Chao; Jia, Meiwen; Qing, Tao; Bannon, Desmond I.; Lancashire, Lee; Bao, Wenjun; Du, Tingting; Luo, Heng; Su, Zhenqiang; Jones, Wendell D.; Moland, Carrie L.; Branham, William S.; Qian, Feng; Ning, Baitang; Li, Yan; Hong, Huixiao; Guo, Lei; Mei, Nan; Shi, Tieliu; Wang, Kevin Y.; Wolfinger, Russell D.; Nikolsky, Yuri; Walker, Stephen J.; Duerksen-Hughes, Penelope; Mason, Christopher E.; Tong, Weida; Thierry-Mieg, Jean; Thierry-Mieg, Danielle; Shi, Leming; Wang, Charles

2014-01-01

The rat has been used extensively as a model for evaluating chemical toxicities and for understanding drug mechanisms. However, its transcriptome across multiple organs, or developmental stages, has not yet been reported. Here we show, as part of the SEQC consortium efforts, a comprehensive rat transcriptomic BodyMap created by performing RNA-Seq on 320 samples from 11 organs of both sexes of juvenile, adolescent, adult and aged Fischer 344 rats. We catalogue the expression profiles of 40,064 genes, 65,167 transcripts, 31,909 alternatively spliced transcript variants and 2,367 non-coding genes/non-coding RNAs (ncRNAs) annotated in AceView. We find that organ-enriched, differentially expressed genes reflect the known organ-specific biological activities. A large number of transcripts show organ-specific, age-dependent or sex-specific differential expression patterns. We create a web-based, open-access rat BodyMap database of expression profiles with crosslinks to other widely used databases, anticipating that it will serve as a primary resource for biomedical research using the rat model. PMID:24510058

Passive mapping and intermittent exploration for mobile robots

NASA Technical Reports Server (NTRS)

Engleson, Sean P.

1994-01-01

An adaptive state space architecture is combined with diktiometric representation to provide the framework for designing a robot mapping system with flexible navigation planning tasks. This involves indexing waypoints described as expectations, geometric indexing, and perceptual indexing. Matching and updating the robot's projected position and sensory inputs with indexing waypoints involves matchers, dynamic priorities, transients, and waypoint restructuring. The robot's map learning can be opganized around the principles of passive mapping.

Making clinical case-based learning in veterinary medicine visible: analysis of collaborative concept-mapping processes and reflections.

PubMed

Khosa, Deep K; Volet, Simone E; Bolton, John R

2014-01-01

The value of collaborative concept mapping in assisting students to develop an understanding of complex concepts across a broad range of basic and applied science subjects is well documented. Less is known about students' learning processes that occur during the construction of a concept map, especially in the context of clinical cases in veterinary medicine. This study investigated the unfolding collaborative learning processes that took place in real-time concept mapping of a clinical case by veterinary medical students and explored students' and their teacher's reflections on the value of this activity. This study had two parts. The first part investigated the cognitive and metacognitive learning processes of two groups of students who displayed divergent learning outcomes in a concept mapping task. Meaningful group differences were found in their level of learning engagement in terms of the extent to which they spent time understanding and co-constructing knowledge along with completing the task at hand. The second part explored students' and their teacher's views on the value of concept mapping as a learning and teaching tool. The students' and their teacher's perceptions revealed congruent and contrasting notions about the usefulness of concept mapping. The relevance of concept mapping to clinical case-based learning in veterinary medicine is discussed, along with directions for future research.

Genetic validation of whole-transcriptome sequencing for mapping expression affected by cis-regulatory variation

PubMed Central

2010-01-01

Background Identifying associations between genotypes and gene expression levels using microarrays has enabled systematic interrogation of regulatory variation underlying complex phenotypes. This approach has vast potential for functional characterization of disease states, but its prohibitive cost, given hundreds to thousands of individual samples from populations have to be genotyped and expression profiled, has limited its widespread application. Results Here we demonstrate that genomic regions with allele-specific expression (ASE) detected by sequencing cDNA are highly enriched for cis-acting expression quantitative trait loci (cis-eQTL) identified by profiling of 500 animals in parallel, with up to 90% agreement on the allele that is preferentially expressed. We also observed widespread noncoding and antisense ASE and identified several allele-specific alternative splicing variants. Conclusion Monitoring ASE by sequencing cDNA from as little as one sample is a practical alternative to expression genetics for mapping cis-acting variation that regulates RNA transcription and processing. PMID:20707912

Exploring physics concepts among novice teachers through CMAP tools

NASA Astrophysics Data System (ADS)

Suprapto, N.; Suliyanah; Prahani, B. K.; Jauhariyah, M. N. R.; Admoko, S.

2018-03-01

Concept maps are graphical tools for organising, elaborating and representing knowledge. Through Cmap tools software, it can be explored the understanding and the hierarchical structuring of physics concepts among novice teachers. The software helps physics teachers indicated a physics context, focus questions, parking lots, cross-links, branching, hierarchy, and propositions. By using an exploratory quantitative study, a total 13-concept maps with different physics topics created by novice physics teachers were analysed. The main differences of scoring between lecturer and peer-teachers’ scoring were also illustrated. The study offered some implications, especially for physics educators to determine the hierarchical structure of the physics concepts, to construct a physics focus question, and to see how a concept in one domain of knowledge represented on the map is related to a concept in another domain shown on the map.

Leveling data in geochemical mapping: scope of application, pros and cons of existing methods

NASA Astrophysics Data System (ADS)

Pereira, Benoît; Vandeuren, Aubry; Sonnet, Philippe

2017-04-01

Geochemical mapping successfully met a range of needs from mineral exploration to environmental management. In Europe and around the world numerous geochemical datasets already exist. These datasets may originate from geochemical mapping projects or from the collection of sample analyses requested by environmental protection regulatory bodies. Combining datasets can be highly beneficial for establishing geochemical maps with increased resolution and/or coverage area. However this practice requires assessing the equivalence between datasets and, if needed, applying data leveling to remove possible biases between datasets. In the literature, several procedures for assessing dataset equivalence and leveling data are proposed. Daneshfar & Cameron (1998) proposed a method for the leveling of two adjacent datasets while Pereira et al. (2016) proposed two methods for the leveling of datasets that contain records located within the same geographical area. Each discussed method requires its own set of assumptions (underlying populations of data, spatial distribution of data, etc.). Here we propose to discuss the scope of application, pros, cons and practical recommendations for each method. This work is illustrated with several case studies in Wallonia (Southern Belgium) and in Europe involving trace element geochemical datasets. References: Daneshfar, B. & Cameron, E. (1998), Leveling geochemical data between map sheets, Journal of Geochemical Exploration 63(3), 189-201. Pereira, B.; Vandeuren, A.; Govaerts, B. B. & Sonnet, P. (2016), Assessing dataset equivalence and leveling data in geochemical mapping, Journal of Geochemical Exploration 168, 36-48.

Visualization of retinal vascular structure and perfusion with a nonconfocal adaptive optics scanning light ophthalmoscope

PubMed Central

Sulai, Yusufu N.; Scoles, Drew; Harvey, Zachary; Dubra, Alfredo

2015-01-01

Imaging of the retinal vascular structure and perfusion was explored by confocal illumination and nonconfocal detection in an adaptive optics scanning light ophthalmoscope (AOSLO), as an extension of the work by Chui et al. [Biomed. Opt. Express 3, 2537 (2012)]. Five different detection schemes were evaluated at multiple retinal locations: circular mask, annular mask, circular mask with filament, knife-edge, and split-detector. Given the superior image contrast in the reflectance and perfusion maps, the split-detection method was further tested using pupil apodization, polarized detection, and four different wavelengths. None of these variations provided noticeable contrast improvement. The noninvasive visualization of capillary flow and structure provided by AOSLO split-detection shows great promise for studying ocular and systemic conditions that affect the retinal vasculature. PMID:24690655

Facies and log signatures of sequence boundaries in Sembakung area, Tarakan Basin, East Kalimantan, Indonesia

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

Bambang, P.; Hardjono, M.; Silalahi, L.

1996-08-01

Tarakan basin is one of the basins in East Kalimantan having a complicated geological condition. Tectonic repetition developed in this area constructed various stratigraphic traps. Sedimentary development in log data shows continuous regression in Meliat and Tabul Formations (Middle Meocene), Santul Formation (Late Miocene), Tarakan Formation (Pliocene) and Bunyu Formation (Pleistocene), Supported by seismic data, stratigraphic sequence in the basin is obvious, especially in Sembakung-Bangkudulis area. The sequence boundaries, mainly {open_quotes}lowstand{close_quotes} distribution as good prospective trap, can be mapped by applying tract systems and studying wavelet extract as seismic expression character of a reservoir. Subtle changes in pattern of stratigraphicmore » sequences can become a hint of sedimentary environment and its lithology content, supporting both exploration and exploitation planning.« less

GhMAP3K65, a Cotton Raf-Like MAP3K Gene, Enhances Susceptibility to Pathogen Infection and Heat Stress by Negatively Modulating Growth and Development in Transgenic Nicotiana benthamiana.

PubMed

Zhai, Na; Jia, Haihong; Liu, Dongdong; Liu, Shuchang; Ma, Manli; Guo, Xingqi; Li, Han

2017-11-21

Mitogen-activated protein kinase kinase kinases (MAP3Ks), the top components of MAPK cascades, modulate many biological processes, such as growth, development and various environmental stresses. Nevertheless, the roles of MAP3Ks remain poorly understood in cotton. In this study, GhMAP3K65 was identified in cotton, and its transcription was inducible by pathogen infection, heat stress, and multiple signalling molecules. Silencing of GhMAP3K65 enhanced resistance to pathogen infection and heat stress in cotton. In contrast, overexpression of GhMAP3K65 enhanced susceptibility to pathogen infection and heat stress in transgenic Nicotiana benthamiana . The expression of defence-associated genes was activated in transgenic N. benthamiana plants after pathogen infection and heat stress, indicating that GhMAP3K65 positively regulates plant defence responses. Nevertheless, transgenic N. benthamiana plants impaired lignin biosynthesis and stomatal immunity in their leaves and repressed vitality of their root systems. In addition, the expression of lignin biosynthesis genes and lignin content were inhibited after pathogen infection and heat stress. Collectively, these results demonstrate that GhMAP3K65 enhances susceptibility to pathogen infection and heat stress by negatively modulating growth and development in transgenic N. benthamiana plants.

Transcriptome sequencing of Eucalyptus camaldulensis seedlings subjected to water stress reveals functional single nucleotide polymorphisms and genes under selection

PubMed Central

2012-01-01

Background Water stress limits plant survival and production in many parts of the world. Identification of genes and alleles responding to water stress conditions is important in breeding plants better adapted to drought. Currently there are no studies examining the transcriptome wide gene and allelic expression patterns under water stress conditions. We used RNA sequencing (RNA-seq) to identify the candidate genes and alleles and to explore the evolutionary signatures of selection. Results We studied the effect of water stress on gene expression in Eucalyptus camaldulensis seedlings derived from three natural populations. We used reference-guided transcriptome mapping to study gene expression. Several genes showed differential expression between control and stress conditions. Gene ontology (GO) enrichment tests revealed up-regulation of 140 stress-related gene categories and down-regulation of 35 metabolic and cell wall organisation gene categories. More than 190,000 single nucleotide polymorphisms (SNPs) were detected and 2737 of these showed differential allelic expression. Allelic expression of 52% of these variants was correlated with differential gene expression. Signatures of selection patterns were studied by estimating the proportion of nonsynonymous to synonymous substitution rates (Ka/Ks). The average Ka/Ks ratio among the 13,719 genes was 0.39 indicating that most of the genes are under purifying selection. Among the positively selected genes (Ka/Ks > 1.5) apoptosis and cell death categories were enriched. Of the 287 positively selected genes, ninety genes showed differential expression and 27 SNPs from 17 positively selected genes showed differential allelic expression between treatments. Conclusions Correlation of allelic expression of several SNPs with total gene expression indicates that these variants may be the cis-acting variants or in linkage disequilibrium with such variants. Enrichment of apoptosis and cell death gene categories among the positively selected genes reveals the past selection pressures experienced by the populations used in this study. PMID:22853646

Motor transfer from map ocular exploration to locomotion during spatial navigation from memory.

PubMed

Demichelis, Alixia; Olivier, Gérard; Berthoz, Alain

2013-02-01

Spatial navigation from memory can rely on two different strategies: a mental simulation of a kinesthetic spatial navigation (egocentric route strategy) or visual-spatial memory using a mental map (allocentric survey strategy). We hypothesized that a previously performed "oculomotor navigation" on a map could be used by the brain to perform a locomotor memory task. Participants were instructed to (1) learn a path on a map through a sequence of vertical and horizontal eyes movements and (2) walk on the slabs of a "magic carpet" to recall this path. The main results showed that the anisotropy of ocular movements (horizontal ones being more efficient than vertical ones) influenced performances of participants when they change direction on the central slab of the magic carpet. These data suggest that, to find their way through locomotor space, subjects mentally repeated their past ocular exploration of the map, and this visuo-motor memory was used as a template for the locomotor performance.

Function Clustering Self-Organization Maps (FCSOMs) for mining differentially expressed genes in Drosophila and its correlation with the growth medium.

PubMed

Liu, L L; Liu, M J; Ma, M

2015-09-28

The central task of this study was to mine the gene-to-medium relationship. Adequate knowledge of this relationship could potentially improve the accuracy of differentially expressed gene mining. One of the approaches to differentially expressed gene mining uses conventional clustering algorithms to identify the gene-to-medium relationship. Compared to conventional clustering algorithms, self-organization maps (SOMs) identify the nonlinear aspects of the gene-to-medium relationships by mapping the input space into another higher dimensional feature space. However, SOMs are not suitable for huge datasets consisting of millions of samples. Therefore, a new computational model, the Function Clustering Self-Organization Maps (FCSOMs), was developed. FCSOMs take advantage of the theory of granular computing as well as advanced statistical learning methodologies, and are built specifically for each information granule (a function cluster of genes), which are intelligently partitioned by the clustering algorithm provided by the DAVID_6.7 software platform. However, only the gene functions, and not their expression values, are considered in the fuzzy clustering algorithm of DAVID. Compared to the clustering algorithm of DAVID, these experimental results show a marked improvement in the accuracy of classification with the application of FCSOMs. FCSOMs can handle huge datasets and their complex classification problems, as each FCSOM (modeled for each function cluster) can be easily parallelized.

Tissue-Specific Chromatin Modifications at a Multigene Locus Generate Asymmetric Transcriptional Interactions

PubMed Central

Yoo, Eung Jae; Cajiao, Isabela; Kim, Jeong-Seon; Kimura, Atsushi P.; Zhang, Aiwen; Cooke, Nancy E.; Liebhaber, Stephen A.

2006-01-01

Random assortment within mammalian genomes juxtaposes genes with distinct expression profiles. This organization, along with the prevalence of long-range regulatory controls, generates a potential for aberrant transcriptional interactions. The human CD79b/GH locus contains six tightly linked genes with three mutually exclusive tissue specificities and interdigitated control elements. One consequence of this compact organization is that the pituitarycell-specific transcriptional events that activate hGH-N also trigger ectopic activation of CD79b. However, the B-cell-specific events that activate CD79b do not trigger reciprocal activation of hGH-N. Here we utilized DNase I hypersensitive site mapping, chromatin immunoprecipitation, and transgenic models to explore the basis for this asymmetric relationship. The results reveal tissue-specific patterns of chromatin structures and transcriptional controls at the CD79b/GH locus in B cells distinct from those in the pituitary gland and placenta. These three unique transcriptional environments suggest a set of corresponding gene expression pathways and transcriptional interactions that are likely to be found juxtaposed at multiple sites within the eukaryotic genome. PMID:16847312

Expression of Genes Involved in Drosophila Wing Morphogenesis and Vein Patterning Are Altered by Spaceflight

NASA Technical Reports Server (NTRS)

Parsons-Wingerter, Patricia A.; Hosamani, Ravikumar; Bhattacharya, Sharmila

2015-01-01

Imaginal wing discs of Drosophila melanogaster (fruit fly) defined during embryogenesis ultimately result in mature wings of stereotyped (specific) venation patterning. Major regulators of wing disc development are the epidermal growth factor receptor (EGF), Notch, Hedgehog (Hh), Wingless (Wg), and Dpp signaling pathways. Highly stereotyped vascular patterning is also characteristic of tissues in other organisms flown in space such as the mouse retina and leaves of Arabidopsis thaliana. Genetic and other adaptations of vascular patterning to space environmental factors have not yet been systematically quantified, despite widespread recognition of their critical importance for terrestrial and microgravity applications. Here we report changes in gene expression with space flight related to Drosophila wing morphogenesis and vein patterning. In addition, genetically modified phenotypes of increasingly abnormal ectopic wing venation in the Drosophila wing1 were analyzed by NASA's VESsel GENeration Analysis (VESGEN) software2. Our goal is to further develop insightful vascular mappings associated with bioinformatic dimensions of genetic or other molecular phenotypes for correlation with genetic and other molecular profiling relevant to NASA's GeneLab and other Space Biology exploration initiatives.

Identification of Odorant-Receptor Interactions by Global Mapping of the Human Odorome

PubMed Central

Audouze, Karine; Tromelin, Anne; Le Bon, Anne Marie; Belloir, Christine; Petersen, Rasmus Koefoed; Kristiansen, Karsten; Brunak, Søren; Taboureau, Olivier

2014-01-01

The human olfactory system recognizes a broad spectrum of odorants using approximately 400 different olfactory receptors (hORs). Although significant improvements of heterologous expression systems used to study interactions between ORs and odorant molecules have been made, screening the olfactory repertoire of hORs remains a tremendous challenge. We therefore developed a chemical systems level approach based on protein-protein association network to investigate novel hOR-odorant relationships. Using this new approach, we proposed and validated new bioactivities for odorant molecules and OR2W1, OR51E1 and OR5P3. As it remains largely unknown how human perception of odorants influence or prevent diseases, we also developed an odorant-protein matrix to explore global relationships between chemicals, biological targets and disease susceptibilities. We successfully experimentally demonstrated interactions between odorants and the cannabinoid receptor 1 (CB1) and the peroxisome proliferator-activated receptor gamma (PPARγ). Overall, these results illustrate the potential of integrative systems chemical biology to explore the impact of odorant molecules on human health, i.e. human odorome. PMID:24695519

Precambrian Field Camp at the University of Minnesota Duluth - Teaching Skills Applicable to Mapping Glaciated Terranes of the Canadian Shield

NASA Astrophysics Data System (ADS)

Miller, J. D.; Hudak, G. J.; Peterson, D.

2011-12-01

Since 2007, the central program of the Precambrian Research Center (PRC) at the University of Minnesota Duluth has been a six-week geology field camp focused on the Precambrian geology of the Canadian Shield. This field camp has two main purposes. First and foremost is to teach students specialized field skills and field mapping techniques that can be utilized to map and interpret Precambrian shield terranes characterized by sparse outcrop and abundant glacial cover. In addition to teaching basic outcrop mapping technique , students are introduced to geophysical surveying (gravity, magnetics), glacial drift prospecting, and drill core logging techniques in several of our geological mapping exercises. These mapping methodologies are particularly applicable to minerals exploration in shield terranes. The second and equally important goal of the PRC field camp is to teach students modern map-making and map production skills. During the fifth and sixth weeks of field camp, students conduct "capstone" mapping projects. These projects encompass one week of detailed bedrock mapping in remote regions of northern Minnesota that have not been mapped in detail (e.g. scales greater than 1:24,000) and a second week of map-making and map generation utilizing geographic information systems (currently ArcGIS10), graphics software packages (Adobe Illustrator CS4), and various imaging software for geophysical and topographic data. Over the past five years, PRC students and faculty have collaboratively published 21 geologic maps through the Precambrian Research Center Map Series. These maps are currently being utilized in a variety of ways by industry, academia, and government for mineral exploration programs, development of undergraduate, graduate, and faculty research projects, and for planning, archeological studies, and public education programs in Minnesota's state parks. Acquisition of specialized Precambrian geological mapping skills and geologic map-making proficiencies has enabled our students to be highly sought after for employment and/or subsequent graduate studies.

Poorly expressed endogenous ecotropic provirus of DBA/2 mice encodes a mutant Pr65gag protein that is not myristylated.

PubMed Central

Copeland, N G; Jenkins, N A; Nexø, B; Schultz, A M; Rein, A; Mikkelsen, T; Jørgensen, P

1988-01-01

DBA/2 mice carry a single endogenous ecotropic murine leukemia provirus designated Emv-3. Although this provirus appears to be nondefective by genomic restriction enzyme mapping, weanling mice do not produce virus and only about one-third of adult mice ever express virus. 5-Iododeoxyuridine and 5-azacytidine, two potent inducers of ecotropic virus expression, are relatively ineffective at inducing Emv-3 expression. However, the chemical carcinogen 7,12-dimethylbenz(a)anthracene can induce ecotropic virus expression in approximately 95% of treated DBA/2 mice. Previous experiments involving DNA transfection and marker rescue analysis of molecularly cloned Emv-3 DNA suggested that Emv-3 carries a small defect(s) in the gag gene, not detectable by restriction enzyme mapping, that inhibits virus expression in vivo and in vitro. Using a combination of approaches, including DNA sequencing, peptide mapping, and metabolic labeling of cells with [3H]myristate, we have demonstrated that the defect in Emv-3 most likely results from a single nucleotide substitution within the gene for p15gag that inhibits myristylation of the Pr65gag N terminus. Myristylation of Pr65gag is thought to be required for this protein to associate with the plasma membrane and is essential for virus particle formation. These results provide a conceptual framework for understanding how Emv-3 expression is regulated during development and after chemical induction. Images PMID:2826810

Visualizing Mobility of Public Transportation System.

PubMed

Zeng, Wei; Fu, Chi-Wing; Arisona, Stefan Müller; Erath, Alexander; Qu, Huamin

2014-12-01

Public transportation systems (PTSs) play an important role in modern cities, providing shared/massive transportation services that are essential for the general public. However, due to their increasing complexity, designing effective methods to visualize and explore PTS is highly challenging. Most existing techniques employ network visualization methods and focus on showing the network topology across stops while ignoring various mobility-related factors such as riding time, transfer time, waiting time, and round-the-clock patterns. This work aims to visualize and explore passenger mobility in a PTS with a family of analytical tasks based on inputs from transportation researchers. After exploring different design alternatives, we come up with an integrated solution with three visualization modules: isochrone map view for geographical information, isotime flow map view for effective temporal information comparison and manipulation, and OD-pair journey view for detailed visual analysis of mobility factors along routes between specific origin-destination pairs. The isotime flow map linearizes a flow map into a parallel isoline representation, maximizing the visualization of mobility information along the horizontal time axis while presenting clear and smooth pathways from origin to destinations. Moreover, we devise several interactive visual query methods for users to easily explore the dynamics of PTS mobility over space and time. Lastly, we also construct a PTS mobility model from millions of real passenger trajectories, and evaluate our visualization techniques with assorted case studies with the transportation researchers.

Planetary Exploration Rebooted! New Ways of Exploring the Moon, Mars and Beyond

NASA Technical Reports Server (NTRS)

Fong, Terrence W.

2010-01-01

In this talk, I will summarize how the NASA Ames Intelligent Robotics Group has been developing and field testing planetary robots for human exploration, creating automated planetary mapping systems, and engaging the public as citizen scientists.

NOAA Office of Exploration and Research > About OER > Program Review >

Science.gov Websites

OER Overview Organization Guiding Documents Organizational Structure Map of Staff and Affiliate Overview Organization Guiding Documents Organizational Structure Map of Staff and Affiliate Locations

Genetic architecture of wood properties based on association analysis and co-expression networks in white spruce.

PubMed

Lamara, Mebarek; Raherison, Elie; Lenz, Patrick; Beaulieu, Jean; Bousquet, Jean; MacKay, John

2016-04-01

Association studies are widely utilized to analyze complex traits but their ability to disclose genetic architectures is often limited by statistical constraints, and functional insights are usually minimal in nonmodel organisms like forest trees. We developed an approach to integrate association mapping results with co-expression networks. We tested single nucleotide polymorphisms (SNPs) in 2652 candidate genes for statistical associations with wood density, stiffness, microfibril angle and ring width in a population of 1694 white spruce trees (Picea glauca). Associations mapping identified 229-292 genes per wood trait using a statistical significance level of P < 0.05 to maximize discovery. Over-representation of genes associated for nearly all traits was found in a xylem preferential co-expression group developed in independent experiments. A xylem co-expression network was reconstructed with 180 wood associated genes and several known MYB and NAC regulators were identified as network hubs. The network revealed a link between the gene PgNAC8, wood stiffness and microfibril angle, as well as considerable within-season variation for both genetic control of wood traits and gene expression. Trait associations were distributed throughout the network suggesting complex interactions and pleiotropic effects. Our findings indicate that integration of association mapping and co-expression networks enhances our understanding of complex wood traits. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Analysis of the Bovine Monocyte-Derived Macrophage Response to Mycobacterium avium Subspecies Paratuberculosis Infection Using RNA-seq.

PubMed

Casey, Maura E; Meade, Kieran G; Nalpas, Nicolas C; Taraktsoglou, Maria; Browne, John A; Killick, Kate E; Park, Stephen D E; Gormley, Eamonn; Hokamp, Karsten; Magee, David A; MacHugh, David E

2015-01-01

Johne's disease, caused by infection with Mycobacterium avium subsp. paratuberculosis, (MAP), is a chronic intestinal disease of ruminants with serious economic consequences for cattle production in the United States and elsewhere. During infection, MAP bacilli are phagocytosed and subvert host macrophage processes, resulting in subclinical infections that can lead to immunopathology and dissemination of disease. Analysis of the host macrophage transcriptome during infection can therefore shed light on the molecular mechanisms and host-pathogen interplay associated with Johne's disease. Here, we describe results of an in vitro study of the bovine monocyte-derived macrophage (MDM) transcriptome response during MAP infection using RNA-seq. MDM were obtained from seven age- and sex-matched Holstein-Friesian cattle and were infected with MAP across a 6-h infection time course with non-infected controls. We observed 245 and 574 differentially expressed (DE) genes in MAP-infected versus non-infected control samples (adjusted P value ≤0.05) at 2 and 6 h post-infection, respectively. Functional analyses of these DE genes, including biological pathway enrichment, highlighted potential functional roles for genes that have not been previously described in the host response to infection with MAP bacilli. In addition, differential expression of pro- and anti-inflammatory cytokine genes, such as those associated with the IL-10 signaling pathway, and other immune-related genes that encode proteins involved in the bovine macrophage response to MAP infection emphasize the balance between protective host immunity and bacilli survival and proliferation. Systematic comparisons of RNA-seq gene expression results with Affymetrix(®) microarray data generated from the same experimental samples also demonstrated that RNA-seq represents a superior technology for studying host transcriptional responses to intracellular infection.

Analysis of the Bovine Monocyte-Derived Macrophage Response to Mycobacterium avium Subspecies Paratuberculosis Infection Using RNA-seq

PubMed Central

Casey, Maura E.; Meade, Kieran G.; Nalpas, Nicolas C.; Taraktsoglou, Maria; Browne, John A.; Killick, Kate E.; Park, Stephen D. E.; Gormley, Eamonn; Hokamp, Karsten; Magee, David A.; MacHugh, David E.

2015-01-01

Johne’s disease, caused by infection with Mycobacterium avium subsp. paratuberculosis, (MAP), is a chronic intestinal disease of ruminants with serious economic consequences for cattle production in the United States and elsewhere. During infection, MAP bacilli are phagocytosed and subvert host macrophage processes, resulting in subclinical infections that can lead to immunopathology and dissemination of disease. Analysis of the host macrophage transcriptome during infection can therefore shed light on the molecular mechanisms and host-pathogen interplay associated with Johne’s disease. Here, we describe results of an in vitro study of the bovine monocyte-derived macrophage (MDM) transcriptome response during MAP infection using RNA-seq. MDM were obtained from seven age- and sex-matched Holstein-Friesian cattle and were infected with MAP across a 6-h infection time course with non-infected controls. We observed 245 and 574 differentially expressed (DE) genes in MAP-infected versus non-infected control samples (adjusted P value ≤0.05) at 2 and 6 h post-infection, respectively. Functional analyses of these DE genes, including biological pathway enrichment, highlighted potential functional roles for genes that have not been previously described in the host response to infection with MAP bacilli. In addition, differential expression of pro- and anti-inflammatory cytokine genes, such as those associated with the IL-10 signaling pathway, and other immune-related genes that encode proteins involved in the bovine macrophage response to MAP infection emphasize the balance between protective host immunity and bacilli survival and proliferation. Systematic comparisons of RNA-seq gene expression results with Affymetrix® microarray data generated from the same experimental samples also demonstrated that RNA-seq represents a superior technology for studying host transcriptional responses to intracellular infection. PMID:25699042

Metalloproteinase-dependent transforming growth factor-alpha release mediates neurotensin-stimulated MAP kinase activation in human colonic epithelial cells.

PubMed

Zhao, Dezheng; Zhan, Yanai; Koon, Hon Wai; Zeng, Huiyan; Keates, Sarah; Moyer, Mary P; Pothoulakis, Charalabos

2004-10-15

Expression of the neuropeptide neurotensin (NT) and its high affinity receptor (NTR1) is increased during the course of Clostridium difficile toxin A-induced acute colitis, and NTR1 antagonism attenuates the severity of toxin A-induced inflammation. We recently demonstrated in non-transformed human colonic epithelial NCM460 cells that NT treatment caused activation of a Ras-mediated MAP kinase pathway that significantly contributes to NT-induced interleukin-8 (IL-8) secretion. Here we used NCM460 cells, which normally express low levels of NTR1, and NCM460 cells stably transfected with NTR1 to identify the upstream signaling molecules involved in NT-NTR1-mediated MAP kinase activation. We found that inhibition of the epidermal growth factor receptor (EGFR) by either an EGFR neutralizing antibody or by its specific inhibitor AG1478 (0.2 microm) blocked NT-induced MAP kinase activation. Moreover, NT stimulated tyrosine phosphorylation of the EGFR, and pretreatment with a broad spectrum metalloproteinase inhibitor batimastat reduced NT-induced MAP kinase activation. Using neutralizing antibodies against the EGFR ligands EGF, heparin-binding-EGF, transforming growth factor-alpha (TGFalpha), or amphiregulin we have shown that only the anti-TGFalpha antibody significantly decreases NT-induced phosphorylation of EGFR and MAP kinases. Furthermore, inhibition of the EGF receptor by AG1478 significantly reduced NT-induced IL-8 promoter activity and IL-8 secretion. This is the first report demonstrating that NT binding to NTR1 transactivates the EGFR and that this response is linked to NT-mediated proinflammatory signaling. Our findings indicate that matrix metalloproteinase-mediated release of TGFalpha and subsequent EGFR transactivation triggers a NT-mediated MAP kinase pathway that leads to IL-8 gene expression in human colonic epithelial cells.

Distributed subterranean exploration and mapping with teams of UAVs

NASA Astrophysics Data System (ADS)

Rogers, John G.; Sherrill, Ryan E.; Schang, Arthur; Meadows, Shava L.; Cox, Eric P.; Byrne, Brendan; Baran, David G.; Curtis, J. Willard; Brink, Kevin M.

2017-05-01

Teams of small autonomous UAVs can be used to map and explore unknown environments which are inaccessible to teams of human operators in humanitarian assistance and disaster relief efforts (HA/DR). In addition to HA/DR applications, teams of small autonomous UAVs can enhance Warfighter capabilities and provide operational stand-off for military operations such as cordon and search, counter-WMD, and other intelligence, surveillance, and reconnaissance (ISR) operations. This paper will present a hardware platform and software architecture to enable distributed teams of heterogeneous UAVs to navigate, explore, and coordinate their activities to accomplish a search task in a previously unknown environment.

Robustly detecting differential expression in RNA sequencing data using observation weights

PubMed Central

Zhou, Xiaobei; Lindsay, Helen; Robinson, Mark D.

2014-01-01

A popular approach for comparing gene expression levels between (replicated) conditions of RNA sequencing data relies on counting reads that map to features of interest. Within such count-based methods, many flexible and advanced statistical approaches now exist and offer the ability to adjust for covariates (e.g. batch effects). Often, these methods include some sort of ‘sharing of information’ across features to improve inferences in small samples. It is important to achieve an appropriate tradeoff between statistical power and protection against outliers. Here, we study the robustness of existing approaches for count-based differential expression analysis and propose a new strategy based on observation weights that can be used within existing frameworks. The results suggest that outliers can have a global effect on differential analyses. We demonstrate the effectiveness of our new approach with real data and simulated data that reflects properties of real datasets (e.g. dispersion-mean trend) and develop an extensible framework for comprehensive testing of current and future methods. In addition, we explore the origin of such outliers, in some cases highlighting additional biological or technical factors within the experiment. Further details can be downloaded from the project website: http://imlspenticton.uzh.ch/robinson_lab/edgeR_robust/. PMID:24753412

Rotation number of integrable symplectic mappings of the plane

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

Zolkin, Timofey; Nagaitsev, Sergei; Danilov, Viatcheslav

2017-04-11

Symplectic mappings are discrete-time analogs of Hamiltonian systems. They appear in many areas of physics, including, for example, accelerators, plasma, and fluids. Integrable mappings, a subclass of symplectic mappings, are equivalent to a Twist map, with a rotation number, constant along the phase trajectory. In this letter, we propose a succinct expression to determine the rotation number and present two examples. Similar to the period of the bounded motion in Hamiltonian systems, the rotation number is the most fundamental property of integrable maps and it provides a way to analyze the phase-space dynamics.

Structural exploration for the refinement of anticancer matrix metalloproteinase-2 inhibitor designing approaches through robust validated multi-QSARs

NASA Astrophysics Data System (ADS)

Adhikari, Nilanjan; Amin, Sk. Abdul; Saha, Achintya; Jha, Tarun

2018-03-01

Matrix metalloproteinase-2 (MMP-2) is a promising pharmacological target for designing potential anticancer drugs. MMP-2 plays critical functions in apoptosis by cleaving the DNA repair enzyme namely poly (ADP-ribose) polymerase (PARP). Moreover, MMP-2 expression triggers the vascular endothelial growth factor (VEGF) having a positive influence on tumor size, invasion, and angiogenesis. Therefore, it is an urgent need to develop potential MMP-2 inhibitors without any toxicity but better pharmacokinetic property. In this article, robust validated multi-quantitative structure-activity relationship (QSAR) modeling approaches were attempted on a dataset of 222 MMP-2 inhibitors to explore the important structural and pharmacophoric requirements for higher MMP-2 inhibition. Different validated regression and classification-based QSARs, pharmacophore mapping and 3D-QSAR techniques were performed. These results were challenged and subjected to further validation to explain 24 in house MMP-2 inhibitors to judge the reliability of these models further. All these models were individually validated internally as well as externally and were supported and validated by each other. These results were further justified by molecular docking analysis. Modeling techniques adopted here not only helps to explore the necessary structural and pharmacophoric requirements but also for the overall validation and refinement techniques for designing potential MMP-2 inhibitors.

Meaning of death: an exploration of perception of elderly in a Bangladeshi village.

PubMed

Joarder, Taufique; Cooper, Alicia; Zaman, Shahaduz

2014-09-01

The aim of this qualitative study was to explore the perceptions of meaning of death among the elderly in a Bangladeshi community, and to understand how the meaning of death affects one's overall well-being. Understandings of death were explored through the explanations respondents provided on the journey of the soul during lifetime and the afterlife, concepts of body-soul duality, and perceived "good" and "bad" deaths. The relationship to well-being was expressed in terms of longevity, anxiety/acceptance of death, and preferred circumstances for death. Seven in-depth interviews and one informal discussion session provided the bulk of the data, while Participatory Rapid Appraisal (PRA) tools, including daily routines and body mapping, supplemented our findings. Elderly members of the community had very specific ideas about the meaning of death, and provided clear explanations regarding the journey of the soul, drawing on ideas of body-soul duality to substantiate claims. Due to long coexistence fusion of Hindu and Muslim ideas around death was found. Anxiety/fear of death was associated with some secular issues, on the contrary the perception of longevity was found linked with spirituality. Insights revealed from this study of subtle differences in the perceptions regarding issues around death may aid the policy makers develop effective end-of-life interventions.

Sequential Pattern Analysis: Method and Application in Exploring How Students Develop Concept Maps

ERIC Educational Resources Information Center

Chiu, Chiung-Hui; Lin, Chien-Liang

2012-01-01

Concept mapping is a technique that represents knowledge in graphs. It has been widely adopted in science education and cognitive psychology to aid learning and assessment. To realize the sequential manner in which students develop concept maps, most research relies upon human-dependent, qualitative approaches. This article proposes a method for…

Visualizing the Logistic Map with a Microcontroller

ERIC Educational Resources Information Center

Serna, Juan D.; Joshi, Amitabh

2012-01-01

The logistic map is one of the simplest nonlinear dynamical systems that clearly exhibits the route to chaos. In this paper, we explore the evolution of the logistic map using an open-source microcontroller connected to an array of light-emitting diodes (LEDs). We divide the one-dimensional domain interval [0,1] into ten equal parts, an associate…

Using GIS Mapping to Assess Foster Care: A Picture Is Worth a Thousand Words

ERIC Educational Resources Information Center

Rine, Christine M.; Morales, Jocelyn; Vanyukevych, Anastasiya B.; Durand, Emily G.; Schroeder, Kurt A.

2012-01-01

Geographic Information Systems (GIS) have become widely used outside of traditional mapping applications, expanding their reach to social service organizations. The purpose of this article is to describe and explore the benefits of GIS mapping in identifying strengths and needs of foster care systems in rural settings through graphically assessing…

An Adult Education Study of Participatory Community Mapping for Indigenous Knowledge Production

ERIC Educational Resources Information Center

Campbell, Craig A., Jr.

2010-01-01

This dissertation explores the notion of participatory community mapping (PCM) for Indigenous knowledge production. Three major questions were posed in the study. First, how can PCM foster Indigenous knowledge production and documentation? Second, how can PCM be used to include local voice and input in mapping projects, and third, how can adult…

Using Concept Mapping as as Tool for Program Theory Development

ERIC Educational Resources Information Center

Orsi, Rebecca

2011-01-01

The purpose of this methodological study is to explore how well a process called "concept mapping" (Trochim, 1989) can articulate the theory which underlies a social program. Articulation of a program's theory is a key step in completing a sound theory based evaluation (Weiss, 1997a). In this study, concept mapping is used to…

PowerPoint and Concept Maps: A Great Double Act

ERIC Educational Resources Information Center

Simon, Jon

2015-01-01

This article explores how concept maps can provide a useful addition to PowerPoint slides to convey interconnections of knowledge and help students see how knowledge is often non-linear. While most accounting educators are familiar with PowerPoint, they are likely to be less familiar with concept maps and this article shows how the tool can be…

Beyond Event Segmentation: Spatial- and Social-Cognitive Processes in Verb-to-Action Mapping

ERIC Educational Resources Information Center

Friend, Margaret; Pace, Amy

2011-01-01

The present article investigates spatial- and social-cognitive processes in toddlers' mapping of concepts to real-world events. In 2 studies we explore how event segmentation might lay the groundwork for extracting actions from the event stream and conceptually mapping novel verbs to these actions. In Study 1, toddlers demonstrated the ability to…

An Analysis, Using Concept Mapping, of Diabetic Patients' Knowledge, before and after Patient Education.

ERIC Educational Resources Information Center

Marchand, C.; d'Ivernois, J. F.; Assal, J. P.; Slama, G.; Hivon, R.

2002-01-01

Assesses whether concept maps used with diabetic patients could describe their cognitive structure, before and after having followed an educational program. Involves 10 diabetic patients and shows that concept maps can be a suitable technique to explore the type and organization of the patients' prior knowledge and to visualize what they have…

Validation of yield component traits identified by GWA mapping in a rice tropical japonica x tropical japonica RIL mapping population

USDA-ARS?s Scientific Manuscript database

The Rice Diversity Panel 1 (RDP1) was developed for genome-wide association (GWA) mapping to explore the five diverse rice (Oryza sativa) subpopulations (indica, aus, aromatic, temperate japonica and tropical japonica). RDP1 was evaluated for over 30 agronomic and morphological traits, most of whic...

Integrating polarimetric synthetic aperture radar and imaging spectrometry for wildland fuel mapping in southern California

Treesearch

P.E. Dennison; D.A. Roberts; J. Regelbrugge; S.L. Ustin

2000-01-01

Polarimetric synthetic aperture radar (SAR) and imaging spectrometry exemplify advanced technologies for mapping wildland fuels in chaparral ecosystems. In this study, we explore the potential of integrating polarimetric SAR and imaging spectrometry for mapping wildland fuels. P-band SAR and ratios containing P-band polarizations are sensitive to variations in stand...

Mapping Their Place: Preschoolers Explore Space, Place, and Literacy

ERIC Educational Resources Information Center

Fantozzi, Victoria B.; Cottino, Elizabeth; Gennarelli, Cindy

2013-01-01

While maps and globes continue to be an important part of the geography and social studies curricula, there has been some debate about the ability of young children to engage in maps in a meaningful way. Some researchers have argued that children younger than seven do not have the spatial-cognitive abilities to truly understand the perspective and…

Male Learners' Vocabulary Achievement through Concept Mapping and Mind Mapping: Differences and Similarities

ERIC Educational Resources Information Center

Tarkashvand, Zahra

2015-01-01

While learning English plays an essential role in today's life, vocabulary achievement is helpful to overcome the difficulties of commanding the language. Drawing on data from three months experimental work, this article explores how two mapping strategies affect the learning vocabularies in EFL male learners. While females were studied before,…

The citrus postharvest pathogen Penicillium digitatum depends on the PdMpkB kinase for developmental and virulence functions.

PubMed

Ma, Haijie; Sun, Xuepeng; Wang, Mingshuang; Gai, Yunpeng; Chung, Kuang-Ren; Li, Hongye

2016-11-07

The postharvest pathogen Penicillium digitatum causes green mold decay on citrus fruit, resulting in severe economic losses. To explore possible factors involved in fungal pathogenesis, phenotypic characterization of the budding yeast Fus3/Kiss1 mitogen-activated protein (MAP) kinase homolog was carried out. The P. digitatum MAP kinase B coding gene, designated PdMpkB, was functionally inactivated via homologous recombination. The fungal strain (∆PdMpkB) carrying a PdMpkBdeletion demonstrated altered gene expression profiles, reduced growth and conidiogenesis, elevated resistance to osmotic stress, and failed to induce green mold decay on citrus fruit. ∆PdMpkB was more resistant to CaCl2, NaCl and sorbitol than its progenitor strain, indicating a negative regulatory function of PdMpkB in osmotic stress adaptation. Fungal infection assays on citrus fruit revealed that ∆PdMpkB proliferated poorly within host tissues, induced water-soaking lesions, failed to break through host cuticle layers and thus, failed to produce aerial hyphae and conidia. Introduction of a functional copy of PdMpkB into a null mutant restored all defective phenotypes. Transcriptome analysis revealed that inactivation of PdMpkB impacted expression of the genes associated with cell wall-degrading enzyme activities, carbohydrate and amino acid metabolisms, conidial formation, and numerous metabolic processes. Our results define pivotal roles of the PdMpkB-mediated signaling pathway in developmental and pathological functions in the citrus postharvest pathogen P. digitatum. Copyright © 2016 Elsevier B.V. All rights reserved.

High humidity suppresses ssi4-mediated cell death and disease resistance upstream of MAP kinase activation, H2O2 production and defense gene expression.

PubMed

Zhou, Fasong; Menke, Frank L H; Yoshioka, Keiko; Moder, Wolfgang; Shirano, Yumiko; Klessig, Daniel F

2004-09-01

The Arabidopsis ssi4 mutant, which exhibits spontaneous lesion formation, constitutive expression of pathogenesis-related (PR) genes and enhanced resistance to virulent bacterial and oomycete pathogens, contains a gain-of-function mutation in a TIR-NBS-LRR type R gene. Epistatic analyses revealed that both PR gene expression and disease resistance are activated via a salicylic acid (SA)- and EDS1-dependent, but NPR1- and NDR1-independent signaling pathway. In this study, we demonstrate that in moderate relative humidity (RH; 60%), the ssi4 mutant accumulates H(2)O(2) and SA prior to lesion formation and displays constitutive activation of the MAP kinases AtMPK6 and AtMPK3. It also constitutively expresses a variety of defense-associated genes, including those encoding the WRKY transcription factors AtWRKY29 and AtWRKY6, the MAP kinases AtMPK6 and AtMPK3, the powdery mildew R proteins RPW8.1 and RPW8.2, EDS1 and PR proteins. All of these ssi4-induced responses, as well as the chlorotic, stunted morphology and enhanced disease resistance phenotype, are suppressed by high RH (95%) growth conditions. Thus, a humidity sensitive factor (HSF) appears to function at an early point in the ssi4 signaling pathway. All ssi4 phenotypes, except for MAP kinase activation, also were suppressed by the eds1-1 mutation. Thus, ssi4-induced MAP kinase activation occurs downstream of the HSF but either upstream of EDS1 or on a separate branch of the ssi4 signaling pathway. SA is a critical signaling component in ssi4-mediated defense responses. However, exogenously supplied SA failed to restore lesion formation in high RH-grown ssi4 plants, although it induced defense gene expression. Thus, additional signals also are involved.

Fine mapping and identification of candidate genes for the sy-2 locus in a temperature-sensitive chili pepper (Capsicum chinense).

PubMed

Liu, Li; Venkatesh, Jelli; Jo, Yeong Deuk; Koeda, Sota; Hosokawa, Munetaka; Kang, Jin-Ho; Goritschnig, Sandra; Kang, Byoung-Cheorl

2016-08-01

The sy - 2 temperature-sensitive gene from Capsicum chinense was fine mapped to a 138.8-kb region at the distal portion of pepper chromosome 1. Based on expression analyses, two putative F-box genes were identified as sy - 2 candidate genes. Seychelles-2 ('sy-2') is a temperature-sensitive natural mutant of Capsicum chinense, which exhibits an abnormal leaf phenotype when grown at temperatures below 24 °C. We previously showed that the sy-2 phenotype is controlled by a single recessive gene, sy-2, located on pepper chromosome 1. In this study, a high-resolution genetic and physical map for the sy-2 locus was constructed using two individual F2 mapping populations derived from a cross between C. chinense mutant 'sy-2' and wild-type 'No. 3341'. The sy-2 gene was fine mapped to a 138.8-kb region between markers SNP 5-5 and SNP 3-8 at the distal portion of chromosome 1, based on comparative genomic analysis and genomic information from pepper. The sy-2 target region was predicted to contain 27 genes. Expression analysis of these predicted genes showed a differential expression pattern for ORF10 and ORF20 between mutant and wild-type plants; with both having significantly lower expression in 'sy-2' than in wild-type plants. In addition, the coding sequences of both ORF10 and ORF20 contained single nucleotide polymorphisms (SNPs) causing amino acid changes, which may have important functional consequences. ORF10 and ORF20 are predicted to encode F-box proteins, which are components of the SCF complex. Based on the differential expression pattern and the presence of nonsynonymous SNPs, we suggest that these two putative F-box genes are most likely responsible for the temperature-sensitive phenotypes in pepper. Further investigation of these genes may enable a better understanding of the molecular mechanisms of low temperature sensitivity in plants.

Identification of Regulatory DNA Elements Using Genome-wide Mapping of DNase I Hypersensitive Sites during Tomato Fruit Development.

PubMed

Qiu, Zhengkun; Li, Ren; Zhang, Shuaibin; Wang, Ketao; Xu, Meng; Li, Jiayang; Du, Yongchen; Yu, Hong; Cui, Xia

2016-08-01

Development and ripening of tomato fruit are precisely controlled by transcriptional regulation, which depends on the orchestrated accessibility of regulatory proteins to promoters and other cis-regulatory DNA elements. This accessibility and its effect on gene expression play a major role in defining the developmental process. To understand the regulatory mechanism and functional elements modulating morphological and anatomical changes during fruit development, we generated genome-wide high-resolution maps of DNase I hypersensitive sites (DHSs) from the fruit tissues of the tomato cultivar "Moneymaker" at 20 days post anthesis as well as break stage. By exploring variation of DHSs across fruit development stages, we pinpointed the most likely hypersensitive sites related to development-specific genes. By detecting binding motifs on DHSs of these development-specific genes or genes in the ascorbic acid biosynthetic pathway, we revealed the common regulatory elements contributing to coordinating gene transcription of plant ripening and specialized metabolic pathways. Our results contribute to a better understanding of the regulatory dynamics of genes involved in tomato fruit development and ripening. Copyright © 2016 The Author. Published by Elsevier Inc. All rights reserved.

Omics Data Complementarity Underlines Functional Cross-Communication in Yeast.

PubMed

Malod-Dognin, Noël; Pržulj, Nataša

2017-06-10

Mapping the complete functional layout of a cell and understanding the cross-talk between different processes are fundamental challenges. They elude us because of the incompleteness and noisiness of molecular data and because of the computational intractability of finding the exact answer. We perform a simple integration of three types of baker's yeast omics data to elucidate the functional organization and lines of cross-functional communication. We examine protein-protein interaction (PPI), co-expression (COEX) and genetic interaction (GI) data, and explore their relationship with the gold standard of functional organization, the Gene Ontology (GO). We utilize a simple framework that identifies functional cross-communication lines in each of the three data types, in GO, and collectively in the integrated model of the three omics data types; we present each of them in our new Functional Organization Map (FOM) model. We compare the FOMs of the three omics datasets with the FOM of GO and find that GI is in best agreement with GO, followed COEX and PPI. We integrate the three FOMs into a unified FOM and find that it is in better agreement with the FOM of GO than those of any omics dataset alone, demonstrating functional complementarity of different omics data.

A monolingual mind can have two time lines: Exploring space-time mappings in Mandarin monolinguals.

PubMed

Yang, Wenxing; Sun, Ying

2016-06-01

Can a mind accommodate two time lines? Miles, Tan, Noble, Lumsden and Macrae (Psychonomic Bulletin & Review 18, 598-604, 2011) shows that Mandarin-English bilinguals have both a horizontal space-time mapping consistent with linguistic conventions within English and a vertical representation of time commensurate with Mandarin. However, the present study, via two experiments, demonstrates that Mandarin monolinguals possess two mental time lines, i.e., one horizontal and one vertical line. This study concludes that a Mandarin speaker has two mental time lines not because he/she has acquired L2 English, but because there are both horizontal and vertical expressions in Mandarin spatiotemporal metaphors. Specifically, this study highlights the fact that a horizontal time line does exist in a Mandarin speaker's cognition, even if he/she is a Mandarin monolingual instead of a ME bilingual. Taken together, the evidence in hand is far from sufficient to support Miles et al.'s (2011) conclusion that ME bilinguals' horizontal concept of time is manipulated by English. Implications for theoretical issues concerning the language-thought relationship in general and the effect of bilingualism on cognition in particular are discussed.

Anterograde or Retrograde Transsynaptic Circuit Tracing in Vertebrates with Vesicular Stomatitis Virus Vectors

PubMed Central

Beier, Kevin T.; Mundell, Nathan A.; Pan, Y. Albert; Cepko, Constance L.

2016-01-01

Viruses have been used as transsynaptic tracers, allowing one to map the inputs and outputs of neuronal populations, due to their ability to replicate in neurons and transmit in vivo only across synaptically connected cells. To date, their use has been largely restricted to mammals. In order to explore the use of such viruses in an expanded host range, we tested the transsynaptic tracing ability of recombinant vesicular stomatitis virus (rVSV) vectors in a variety of organisms. Successful infection and gene expression were achieved in a wide range of organisms, including vertebrate and invertebrate model organisms. Moreover, rVSV enabled transsynaptic tracing of neural circuitry in predictable directions dictated by the viral envelope glycoprotein (G), derived from either VSV or rabies virus (RABV). Anterograde and retrograde labeling, from initial infection and/or viral replication and transmission, was observed in Old and New World monkeys, seahorses, jellyfish, zebrafish, chickens, and mice. These vectors are widely applicable for gene delivery, afferent tract tracing, and/or directional connectivity mapping. Here, we detail the use of these vectors and provide protocols for propagating virus, changing the surface glycoprotein, and infecting multiple organisms using several injection strategies. PMID:26729030

Anterograde or Retrograde Transsynaptic Circuit Tracing in Vertebrates with Vesicular Stomatitis Virus Vectors.

PubMed

Beier, Kevin T; Mundell, Nathan A; Pan, Y Albert; Cepko, Constance L

2016-01-04

Viruses have been used as transsynaptic tracers, allowing one to map the inputs and outputs of neuronal populations, due to their ability to replicate in neurons and transmit in vivo only across synaptically connected cells. To date, their use has been largely restricted to mammals. In order to explore the use of such viruses in an expanded host range, we tested the transsynaptic tracing ability of recombinant vesicular stomatitis virus (rVSV) vectors in a variety of organisms. Successful infection and gene expression were achieved in a wide range of organisms, including vertebrate and invertebrate model organisms. Moreover, rVSV enabled transsynaptic tracing of neural circuitry in predictable directions dictated by the viral envelope glycoprotein (G), derived from either VSV or rabies virus (RABV). Anterograde and retrograde labeling, from initial infection and/or viral replication and transmission, was observed in Old and New World monkeys, seahorses, jellyfish, zebrafish, chickens, and mice. These vectors are widely applicable for gene delivery, afferent tract tracing, and/or directional connectivity mapping. Here, we detail the use of these vectors and provide protocols for propagating virus, changing the surface glycoprotein, and infecting multiple organisms using several injection strategies. Copyright © 2016 John Wiley & Sons, Inc.

Tactile exploration of virtual objects for blind and sighted people: the role of beta 1 EEG band in sensory substitution and supramodal mental mapping

PubMed Central

Brayda, L.; De Carli, F.; Chellali, R.; Famà, F.; Bruzzo, C.; Lucagrossi, L.; Rodriguez, G.

2012-01-01

The neural correlates of exploration and cognitive mapping in blindness remain elusive. The role of visuo-spatial pathways in blind vs. sighted subjects is still under debate. In this preliminary study, we investigate, as a possible estimation of the activity in the visuo-spatial pathways, the EEG patterns of blind and blindfolded-sighted subjects during the active tactile construction of cognitive maps from virtual objects compared with rest and passive tactile stimulation. Ten blind and ten matched, blindfolded-sighted subjects participated in the study. Events were defined as moments when the finger was only stimulated (passive stimulation) or the contour of a virtual object was touched (during active exploration). Event-related spectral power and coherence perturbations were evaluated within the beta 1 band (14–18 Hz). They were then related to a subjective cognitive-load estimation required by the explorations [namely, perceived levels of difficulty (PLD)]. We found complementary cues for sensory substitution and spatial processing in both groups: both blind and sighted subjects showed, while exploring, late power decreases and early power increases, potentially associated with motor programming and touch, respectively. The latter involved occipital areas only for blind subjects (long-term plasticity) and only during active exploration, thus supporting tactile-to-visual sensory substitution. In both groups, coherences emerged among the fronto-central, centro-parietal, and occipito-temporal derivations associated with visuo-spatial processing. This seems in accordance with mental map construction involving spatial processing, sensory-motor processing, and working memory. The observed involvement of the occipital regions suggests that a substitution process also occurs in sighted subjects. Only during explorations did coherence correlate positively with PLD for both groups and in derivations, which can be related to visuo-spatial processing, supporting the existence of supramodal spatial processing independently of vision capabilities. PMID:22338024

Role of DAF-21protein in Caenorhabditis elegans immunity against Proteus mirabilis infection.

PubMed

JebaMercy, Gnanasekaran; Durai, Sellegounder; Prithika, Udayakumar; Marudhupandiyan, Shanmugam; Dasauni, Pushpanjali; Kundu, Suman; Balamurugan, Krishnaswamy

2016-08-11

Caenorhabditis elegans is emerging as one of the handy model for proteome related studies due to its simplest system biology. The present study, deals with changes in protein expression in C. elegans infected with Proteus mirabilis. Proteins were separated using two-dimensional differential gel electrophoresis (2D-DIGE) and identified using MALDI-TOF. Twelve distinctly regulated proteins identified in the infected worms, included heat shock proteins involved stress pathway (HSP-1 and HSP-6), proteins involved in immune response pathway (DAF-21), enzymes involved in normal cellular process (Eukaryotic translation Elongation Factor, actin family member, S-adenosyl homocysteine hydrolase ortholog, glutamate dehydrogenase and Vacuolar H ATPase family member) and few least characterized proteins (H28O16.1 and H08J11.2). The regulation of selected players at the transcriptional level during Proteus mirabilis infection was analyzed using qPCR. Physiological experiments revealed the ability of P. mirabilis to kill daf-21 mutant C. elegans significantly compared with the wild type. This is the first report studying proteome changes in C. elegans and exploring the involvement of MAP Kinase pathway during P. mirabilis infection. This is the first report studying proteome changes in C. elegans during P. mirabilis infection. The present study explores the role and contribution of MAP Kinase pathway and its regulator protein DAF-21 involvement in the immunity against opportunistic pathogen P. mirabilis infection. Manipulation of this DAF-21 protein in host, may pave the way for new drug development or disease control strategy during opportunistic pathogen infections. Copyright © 2016 Elsevier B.V. All rights reserved.

Systems genetics: a paradigm to improve discovery of candidate genes and mechanisms underlying complex traits.

PubMed

Feltus, F Alex

2014-06-01

Understanding the control of any trait optimally requires the detection of causal genes, gene interaction, and mechanism of action to discover and model the biochemical pathways underlying the expressed phenotype. Functional genomics techniques, including RNA expression profiling via microarray and high-throughput DNA sequencing, allow for the precise genome localization of biological information. Powerful genetic approaches, including quantitative trait locus (QTL) and genome-wide association study mapping, link phenotype with genome positions, yet genetics is less precise in localizing the relevant mechanistic information encoded in DNA. The coupling of salient functional genomic signals with genetically mapped positions is an appealing approach to discover meaningful gene-phenotype relationships. Techniques used to define this genetic-genomic convergence comprise the field of systems genetics. This short review will address an application of systems genetics where RNA profiles are associated with genetically mapped genome positions of individual genes (eQTL mapping) or as gene sets (co-expression network modules). Both approaches can be applied for knowledge independent selection of candidate genes (and possible control mechanisms) underlying complex traits where multiple, likely unlinked, genomic regions might control specific complex traits. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Allelic expression mapping across cellular lineages to establish impact of non-coding SNPs

PubMed Central

Adoue, Veronique; Schiavi, Alicia; Light, Nicholas; Almlöf, Jonas Carlsson; Lundmark, Per; Ge, Bing; Kwan, Tony; Caron, Maxime; Rönnblom, Lars; Wang, Chuan; Chen, Shu-Huang; Goodall, Alison H; Cambien, Francois; Deloukas, Panos; Ouwehand, Willem H; Syvänen, Ann-Christine; Pastinen, Tomi

2014-01-01

Most complex disease-associated genetic variants are located in non-coding regions and are therefore thought to be regulatory in nature. Association mapping of differential allelic expression (AE) is a powerful method to identify SNPs with direct cis-regulatory impact (cis-rSNPs). We used AE mapping to identify cis-rSNPs regulating gene expression in 55 and 63 HapMap lymphoblastoid cell lines from a Caucasian and an African population, respectively, 70 fibroblast cell lines, and 188 purified monocyte samples and found 40–60% of these cis-rSNPs to be shared across cell types. We uncover a new class of cis-rSNPs, which disrupt footprint-derived de novo motifs that are predominantly bound by repressive factors and are implicated in disease susceptibility through overlaps with GWAS SNPs. Finally, we provide the proof-of-principle for a new approach for genome-wide functional validation of transcription factor–SNP interactions. By perturbing NFκB action in lymphoblasts, we identified 489 cis-regulated transcripts with altered AE after NFκB perturbation. Altogether, we perform a comprehensive analysis of cis-variation in four cell populations and provide new tools for the identification of functional variants associated to complex diseases. PMID:25326100

The relationship between phonological short-term memory, receptive vocabulary, and fast mapping in children with specific language impairment.

PubMed

Jackson, Emily; Leitao, Suze; Claessen, Mary

2016-01-01

Children with specific language impairment (SLI) often experience word-learning difficulties, which are suggested to originate in the early stage of word learning: fast mapping. Some previous research indicates significantly poorer fast mapping capabilities in children with SLI compared with typically developing (TD) counterparts, with a range of methodological factors impacting on the consistency of this finding. Research has explored key issues that might underlie fast mapping difficulties in children with SLI, with strong theoretical support but little empirical evidence for the role of phonological short-term memory (STM). Additionally, further research is required to explore the influence of receptive vocabulary on fast mapping capabilities. Understanding the factors associated with fast mapping difficulties that are experienced by children with SLI may lead to greater theoretically driven word-learning intervention. To investigate whether children with SLI demonstrate significant difficulties with fast mapping, and to explore the related factors. It was hypothesized that children with SLI would score significantly lower on a fast mapping production task compared with TD children, and that phonological STM and receptive vocabulary would significantly predict fast mapping production scores in both groups of children. Twenty-three children with SLI (mean = 64.39 months, SD = 4.10 months) and 26 TD children (mean = 65.92 months, SD = 2.98) were recruited from specialist language and mainstream schools. All participants took part in a unique, interactive fast-mapping task whereby nine novel objects with non-word labels were presented and production accuracy was assessed. A non-word repetition test and the Peabody Picture Vocabulary Test-Fourth Edition (PPVT-IV) were also administered as measures of phonological STM capacity and receptive vocabulary, respectively. Results of the fast-mapping task indicated that children with SLI had significantly poorer fast mapping production scores than TD children. Scores from the non-word repetition task were also significantly lower for the SLI group, revealing reduced phonological STM capacity. Phonological STM capacity and receptive vocabulary emerged as significant predictors of fast mapping performance when the group data were combined in a multiple regression analysis. These results suggest that the word-learning difficulties experienced by children with SLI may originate at the fast mapping stage, and that phonological STM and receptive vocabulary significantly predict fast mapping ability. These findings contribute to the theoretical understanding of word-learning difficulties in children with SLI and may inform lexical learning intervention. © 2015 Royal College of Speech and Language Therapists.

Characterization of Smoc-1 uncovers two transcript variants showing differential tissue and age specific expression in Bubalus bubalis

PubMed Central

Srivastava, Jyoti; Premi, Sanjay; Kumar, Sudhir; Parwez, Iqbal; Ali, Sher

2007-01-01

Background Secreted modular calcium binding protein-1 (Smoc-1) belongs to the BM-40 family which has been implicated with tissue remodeling, angiogenesis and bone mineralization. Besides its anticipated role in embryogenesis, Smoc-1 has been characterized only in a few mammalian species. We made use of the consensus sequence (5' CACCTCTCCACCTGCC 3') of 33.15 repeat loci to explore the buffalo transcriptome and uncovered the Smoc-1 transcript tagged with this repeat. The main objective of this study was to gain an insight into its structural and functional organization, and expressional status of Smoc-1 in water buffalo, Bubalus bubalis. Results We cloned and characterized the buffalo Smoc-1, including its copy number status, in-vitro protein expression, tissue & age specific transcription/translation, chromosomal mapping and localization to the basement membrane zone. Buffalo Smoc-1 was found to encode a secreted matricellular glycoprotein containing two EF-hand calcium binding motifs homologous to that of BM-40/SPARC family. In buffalo, this single copy gene consisted of 12 exons and was mapped onto the acrocentric chromosome 11. Though this gene was found to be evolutionarily conserved, the buffalo Smoc-1 showed conspicuous nucleotide/amino acid changes altering its secondary structure compared to that in other mammals. In silico analysis of the Smoc-1 proposed its glycoprotein nature with a calcium dependent conformation. Further, we unveiled two transcript variants of this gene, varying in their 3'UTR lengths but both coding for identical protein(s). Smoc-1 evinced highest expression of both the variants in liver and modest to negligible in other tissues. The relative expression of variant-02 was markedly higher compared to that of variant-01 in all the tissues examined. Moreover, expression of Smoc-1, though modest during the early ages, was conspicuously enhanced after 1 year and remained consistently higher during the entire life span of buffalo with gradual increment in expression of variant-02. Immunohistochemically, Smoc-1 was localized in the basement membrane zones and extracellular matrices of various tissues. Conclusion These data added to our understandings about the tissue, age and species specific functions of the Smoc-1. It also enabled us to demonstrate varying expression of the two transcript variants of Smoc-1 amongst different somatic tissues/gonads and ages, in spite of their identical coding frames. Pursuance of these variants for their roles in various disease phenotypes such as hepatocellular carcinoma and angiogenesis is envisaged to establish broader biological significance of this gene. PMID:18042303

Map and data for Quaternary faults and folds in Washington state

USGS Publications Warehouse

Lidke, David J.; Johnson, Samuel Y.; McCrory, Patricia A.; Personius, Stephen F.; Nelson, Alan R.; Dart, Richard L.; Bradley, Lee-Ann; Haller, Kathleen M.; Machette, Michael N.

2004-01-01

The map shows faults and folds in Washington State that exhibit evidence of Quaternary deformation and includes data on timing of most recent movement, sense of movement, slip rate, and continuity of surface expression.

Planetary Geologic Mapping Handbook - 2009

NASA Technical Reports Server (NTRS)

Tanaka, K. L.; Skinner, J. A.; Hare, T. M.

2009-01-01

Geologic maps present, in an historical context, fundamental syntheses of interpretations of the materials, landforms, structures, and processes that characterize planetary surfaces and shallow subsurfaces (e.g., Varnes, 1974). Such maps also provide a contextual framework for summarizing and evaluating thematic research for a given region or body. In planetary exploration, for example, geologic maps are used for specialized investigations such as targeting regions of interest for data collection and for characterizing sites for landed missions. Whereas most modern terrestrial geologic maps are constructed from regional views provided by remote sensing data and supplemented in detail by field-based observations and measurements, planetary maps have been largely based on analyses of orbital photography. For planetary bodies in particular, geologic maps commonly represent a snapshot of a surface, because they are based on available information at a time when new data are still being acquired. Thus the field of planetary geologic mapping has been evolving rapidly to embrace the use of new data and modern technology and to accommodate the growing needs of planetary exploration. Planetary geologic maps have been published by the U.S. Geological Survey (USGS) since 1962 (Hackman, 1962). Over this time, numerous maps of several planetary bodies have been prepared at a variety of scales and projections using the best available image and topographic bases. Early geologic map bases commonly consisted of hand-mosaicked photographs or airbrushed shaded-relief views and geologic linework was manually drafted using mylar bases and ink drafting pens. Map publishing required a tedious process of scribing, color peel-coat preparation, typesetting, and photo-laboratory work. Beginning in the 1990s, inexpensive computing, display capability and user-friendly illustration software allowed maps to be drawn using digital tools rather than pen and ink, and mylar bases became obsolete. Terrestrial geologic maps published by the USGS now are primarily digital products using geographic information system (GIS) software and file formats. GIS mapping tools permit easy spatial comparison, generation, importation, manipulation, and analysis of multiple raster image, gridded, and vector data sets. GIS software has also permitted the development of project-specific tools and the sharing of geospatial products among researchers. GIS approaches are now being used in planetary geologic mapping as well (e.g., Hare and others, 2009). Guidelines or handbooks on techniques in planetary geologic mapping have been developed periodically (e.g., Wilhelms, 1972, 1990; Tanaka and others, 1994). As records of the heritage of mapping methods and data, these remain extremely useful guides. However, many of the fundamental aspects of earlier mapping handbooks have evolved significantly, and a comprehensive review of currently accepted mapping methodologies is now warranted. As documented in this handbook, such a review incorporates additional guidelines developed in recent years for planetary geologic mapping by the NASA Planetary Geology and Geophysics (PGG) Program s Planetary Cartography and Geologic Mapping Working Group s (PCGMWG) Geologic Mapping Subcommittee (GEMS) on the selection and use of map bases as well as map preparation, review, publication, and distribution. In light of the current boom in planetary exploration and the ongoing rapid evolution of available data for planetary mapping, this handbook is especially timely.

Joint sparse learning for 3-D facial expression generation.

PubMed

Song, Mingli; Tao, Dacheng; Sun, Shengpeng; Chen, Chun; Bu, Jiajun

2013-08-01

3-D facial expression generation, including synthesis and retargeting, has received intensive attentions in recent years, because it is important to produce realistic 3-D faces with specific expressions in modern film production and computer games. In this paper, we present joint sparse learning (JSL) to learn mapping functions and their respective inverses to model the relationship between the high-dimensional 3-D faces (of different expressions and identities) and their corresponding low-dimensional representations. Based on JSL, we can effectively and efficiently generate various expressions of a 3-D face by either synthesizing or retargeting. Furthermore, JSL is able to restore 3-D faces with holes by learning a mapping function between incomplete and intact data. Experimental results on a wide range of 3-D faces demonstrate the effectiveness of the proposed approach by comparing with representative ones in terms of quality, time cost, and robustness.

Mapping of wildlife habitat in Farmington Bay, Utah

NASA Technical Reports Server (NTRS)

Jaynes, R. A.; Willie, R. D. (Principal Investigator)

1982-01-01

Mapping was accomplished through the interpretation of high-altitude color infrared photography. The feasibility of utilizing LANDSAT digital data to augment the analysis was explored; complex patterns of wildlife habitat and confusion of spectral classes resulted in the decision to make limited use of LANDSAT data in the analysis. The final product is a map which delineates wildlife habitat at a scale of 1:24,000. The map is registered to and printed on a screened U.S.G.S. quadrangle base map. Screened delineations of shoreline contours, mapped from a previous study, are also shown on the map. Intensive field checking of the map was accomplished for the Farmington Bay Waterfowl Management Area in August 1981; other areas on the map received only spot field checking.

Functional characterization of a novel Brassica LEAFY homolog from Indian mustard: Expression pattern and gain-of-function studies.

PubMed

Dhakate, Priyanka; Tyagi, Shikha; Singh, Anupama; Singh, Anandita

2017-05-01

LEAFY plays a central role in regulation of flowering time and floral meristem identity in plants. Unfortunately, LFY function remains uncharacterized in agronomicaly important Brassicas. Herein, we illustrate fine-mapping of expression domains of LFY in 15 cultivars of 6 Brassica species and describe gain-of-function phenotypes in Arabidopsis and Brassica. We depict early flowering and altered fatty-acid composition in transgenic seed. The cDNA encoding BjuLFY (417aa) shared only 85% identity with reported homolog of B.juncea implying distinctness. Quantitative RT-PCR based coarse expression mapping of BjuLFY in tissue samples representing 3 time points at specific days after sowing (DAS), pre-flowering (30 DAS), flowering (75 DAS) and post-flowering (110 DAS), depicted an intense pulse of BjuLFY expression restricted to primary floral buds (75 DAS) which subsided in secondary floral buds (110 DAS); expression in root samples was also recorded implying neo-functionalization. Fine-mapping of expression during flowering confirmed tightly regulated LFY expression during early stages of bud development in 15 cultivars of 6 Brassica species implying functional conservation. Ectopic expression of BjuLFY in A. thaliana and B. juncea caused floral meristem defects and precocious flowering. B. juncea transgenics (T 1 ) over-expressing BjuLFY flowered 20days earlier produced normal flowers. GC-MS analysis of mature seed from Brassica transgenics showed an altered fatty-acid profile suggestive of seed maturation occurring at lower temperatures vis-à-vis control. Our findings implicate BjuLFY as a regulator of flowering in B. juncea and suggest its application in developing climate resilient crops. Copyright © 2017 Elsevier B.V. All rights reserved.

Connectivity Mapping for Candidate Therapeutics Identification Using Next Generation Sequencing RNA-Seq Data

PubMed Central

McArt, Darragh G.; Dunne, Philip D.; Blayney, Jaine K.; Salto-Tellez, Manuel; Van Schaeybroeck, Sandra; Hamilton, Peter W.; Zhang, Shu-Dong

2013-01-01

The advent of next generation sequencing technologies (NGS) has expanded the area of genomic research, offering high coverage and increased sensitivity over older microarray platforms. Although the current cost of next generation sequencing is still exceeding that of microarray approaches, the rapid advances in NGS will likely make it the platform of choice for future research in differential gene expression. Connectivity mapping is a procedure for examining the connections among diseases, genes and drugs by differential gene expression initially based on microarray technology, with which a large collection of compound-induced reference gene expression profiles have been accumulated. In this work, we aim to test the feasibility of incorporating NGS RNA-Seq data into the current connectivity mapping framework by utilizing the microarray based reference profiles and the construction of a differentially expressed gene signature from a NGS dataset. This would allow for the establishment of connections between the NGS gene signature and those microarray reference profiles, alleviating the associated incurring cost of re-creating drug profiles with NGS technology. We examined the connectivity mapping approach on a publicly available NGS dataset with androgen stimulation of LNCaP cells in order to extract candidate compounds that could inhibit the proliferative phenotype of LNCaP cells and to elucidate their potential in a laboratory setting. In addition, we also analyzed an independent microarray dataset of similar experimental settings. We found a high level of concordance between the top compounds identified using the gene signatures from the two datasets. The nicotine derivative cotinine was returned as the top candidate among the overlapping compounds with potential to suppress this proliferative phenotype. Subsequent lab experiments validated this connectivity mapping hit, showing that cotinine inhibits cell proliferation in an androgen dependent manner. Thus the results in this study suggest a promising prospect of integrating NGS data with connectivity mapping. PMID:23840550

An embodied perspective on expertise in solving the problem of making a geologic map

NASA Astrophysics Data System (ADS)

Callahan, Caitlin Norah

The task of constructing a geologic map is a cognitively and physically demanding field-based problem. The map produced is understood to be an individual's two-dimensional interpretation or mental model of the three-dimensional underlying geology. A popular view within the geoscience community is that teaching students how to make a geologic map is valuable for preparing them to deal with disparate and incomplete data sets, for helping them develop problem-solving skills, and for acquiring expertise in geology. Few previous studies have focused specifically on expertise in geologic mapping. Drawing from literature related to expertise, to problem solving, and to mental models, two overarching research questions were identified: How do geologists of different levels of expertise constrain and solve an ill-structured problem such as making a geologic map? How do geologists address the uncertainties inherent to the processes and interpretations involved in solving a geologic mapping problem? These questions were answered using a methodology that captured the physical actions, expressed thoughts, and navigation paths of geologists as they made a geologic map. Eight geologists, from novice to expert, wore a head-mounted video camera with an attached microphone to record those actions and thoughts, creating "video logs" while in the field. The video logs were also time-stamped, which allowed the visual and audio data to be synchronized with the GPS data that tracked participants' movements in the field. Analysis of the video logs yielded evidence that all eight participants expressed thoughts that reflected the process of becoming mentally situated in the mapping task (e.g. relating between distance on a map and distance in three-dimensional space); the prominence of several of these early thoughts waned in the expressed thoughts later in the day. All participants collected several types of data while in the field; novices, however, did so more continuously throughout the day whereas the experts collected more of their data earlier in the day. Experts and novices also differed in that experts focused more on evaluating certainty in their interpretations; the novices focused more on evaluating the certainty of their observations and sense of location.

Exploration for fossil and nuclear fuels from orbital altitudes

NASA Technical Reports Server (NTRS)

Short, N. M.

1977-01-01

The paper discusses the application of remotely sensed data from orbital satellites to the exploration for fossil and nuclear fuels. Geological applications of Landsat data are described including map editing, lithologic identification, structural geology, and mineral exploration. Specific results in fuel exploration are reviewed and a series of related Landsat images is included.

The quality of radiation care: the results of focus group interviews and concept mapping to explore the patient's perspective.

PubMed

Nijman, Jessica L; Sixma, Herman; van Triest, Baukelien; Keus, Ronald B; Hendriks, Michelle

2012-01-01

In this study, we explore the quality aspects of radiation care from the patient's perspective in order to develop a draft Consumer Quality Index (CQI) Radiation Care instrument. Four focus group discussions with (former) cancer patients were held to explore the aspects determining the quality of radiation care. The list of aspects generated was categorised based on similarity and importance in a concept mapping procedure. Four focus group discussions revealed seven main themes related to the quality of radiation care: information provision, a patient-centred approach, professional competence, planning and waiting times, accessibility, cooperation and communication, and follow-up care. Results of concept mapping procedures revealed which items the patients considered to be most important. A radiation oncologist who is up to date about the patient's file is of paramount importance for cancer patients receiving radiotherapy. The quality aspects found through focus group discussions provided useful insight into how patients experience radiation care. Furthermore, concept mapping made these results more solid. To evaluate the quality of radiation care from the patient's perspective, these quality aspects will be guiding in the development of a CQI Radiation Care. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Petroleum system of Northwest Java basin based on gravity data analysis

NASA Astrophysics Data System (ADS)

Widianto, E.

2018-01-01

Energy management in the upstream oil and gas sector becomes very important for the country’s energy security. The renewal of energy resources and reserves becomes necessary and is a must. In the oil and gas industry, gravity data is usually used only for regional surveys, but with the development of instrumentation technology and gravity software development, this method can be used for assessing oil and gas survey stages from exploration to production. This study was conducted to evaluate aspects of petroleum system and exploration play concept in the part of Northwest Java Basin, covering source rock deposition regions (source kitchen area, migration direction), development of reservoirs, structural and stratigraphic trap, based on gravity data. This study uses data from Bouguer gravity anomaly map by filtering process to produce a residual map depicting sedimentation basin configuration. The mapping generated 20 sedimentary basins in Java Island with the total hydrocarbon resources of 113 BBOE (Billion Barrel of Oil Equivalent). The petroleum system analysis was conducted in the Northwest Basin section. The final map produced illustrates the condition of petroleum system and play concept that can be used as exploration direction, expectedly reducing the risk of drilling failure.

NOAA Office of Exploration and Research > About OER > Program Review >

Science.gov Websites

About OER Overview Organization Guiding Documents Organizational Structure Map of Staff and Affiliate About OER Overview Organization Guiding Documents Organizational Structure Map of Staff and Affiliate

Universal map for cellular automata

NASA Astrophysics Data System (ADS)

García-Morales, V.

2012-08-01

A universal map is derived for all deterministic 1D cellular automata (CAs) containing no freely adjustable parameters and valid for any alphabet size and any neighborhood range (including non-symmetrical neighborhoods). The map can be extended to an arbitrary number of dimensions and topologies and to arbitrary order in time. Specific CA maps for the famous Conway's Game of Life and Wolfram's 256 elementary CAs are given. An induction method for CAs, based in the universal map, allows mathematical expressions for the orbits of a wide variety of elementary CAs to be systematically derived.