Database resources of the National Center for Biotechnology Information.

PubMed

2015-01-01

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

Evaluation of Targeted Sequencing for Transcriptional Analysis of Archival Formalin-Fixed Paraffin-Embedded (FFPE) Samples

EPA Science Inventory

Next-generation sequencing provides unprecedented access to genomic information in archival FFPE tissue samples. However, costs and technical challenges related to RNA isolation and enrichment limit use of whole-genome RNA-sequencing for large-scale studies of FFPE specimens. Rec...

Trace metal depositional patterns from an open pit mining activity as revealed by archived avian gizzard contents.

PubMed

Bendell, L I

2011-02-15

Archived samples of blue grouse (Dendragapus obscurus) gizzard contents, inclusive of grit, collected yearly between 1959 and 1970 were analyzed for cadmium, lead, zinc, and copper content. Approximately halfway through the 12-year sampling period, an open-pit copper mine began activities, then ceased operations 2 years later. Thus the archived samples provided a unique opportunity to determine if avian gizzard contents, inclusive of grit, could reveal patterns in the anthropogenic deposition of trace metals associated with mining activities. Gizzard concentrations of cadmium and copper strongly coincided with the onset of opening and the closing of the pit mining activity. Gizzard zinc and lead demonstrated significant among year variation; however, maximum concentrations did not correlate to mining activity. The archived gizzard contents did provide a useful tool for documenting trends in metal depositional patterns related to an anthropogenic activity. Further, blue grouse ingesting grit particles during the time of active mining activity would have been exposed to toxicologically significant levels of cadmium. Gizzard lead concentrations were also of toxicological significance but not related to mining activity. This type of "pulse" toxic metal exposure as a consequence of open-pit mining activity would not necessarily have been revealed through a "snap-shot" of soil, plant or avian tissue trace metal analysis post-mining activity. Copyright © 2010 Elsevier B.V. All rights reserved.

Calculating the quality of public high-throughput sequencing data to obtain a suitable subset for reanalysis from the Sequence Read Archive.

PubMed

Ohta, Tazro; Nakazato, Takeru; Bono, Hidemasa

2017-06-01

It is important for public data repositories to promote the reuse of archived data. In the growing field of omics science, however, the increasing number of submissions of high-throughput sequencing (HTSeq) data to public repositories prevents users from choosing a suitable data set from among the large number of search results. Repository users need to be able to set a threshold to reduce the number of results to obtain a suitable subset of high-quality data for reanalysis. We calculated the quality of sequencing data archived in a public data repository, the Sequence Read Archive (SRA), by using the quality control software FastQC. We obtained quality values for 1 171 313 experiments, which can be used to evaluate the suitability of data for reuse. We also visualized the data distribution in SRA by integrating the quality information and metadata of experiments and samples. We provide quality information of all of the archived sequencing data, which enable users to obtain sufficient quality sequencing data for reanalyses. The calculated quality data are available to the public in various formats. Our data also provide an example of enhancing the reuse of public data by adding metadata to published research data by a third party. © The Authors 2017. Published by Oxford University Press.

Dose-Response Analysis of RNA-Seq Profiles in Archival ...

EPA Pesticide Factsheets

Use of archival resources has been limited to date by inconsistent methods for genomic profiling of degraded RNA from formalin-fixed paraffin-embedded (FFPE) samples. RNA-sequencing offers a promising way to address this problem. Here we evaluated transcriptomic dose responses using RNA-sequencing in paired FFPE and frozen (FROZ) samples from two archival studies in mice, one 20 years old. Experimental treatments included 3 different doses of di(2-ethylhexyl)phthalate or dichloroacetic acid for the recently archived and older studies, respectively. Total RNA was ribo-depleted and sequenced using the Illumina HiSeq platform. In the recently archived study, FFPE samples had 35% lower total counts compared to FROZ samples but high concordance in fold-change values of differentially expressed genes (DEGs) (r2 = 0.99), highly enriched pathways (90% overlap with FROZ), and benchmark dose estimates for preselected target genes (2% difference vs FROZ). In contrast, older FFPE samples had markedly lower total counts (3% of FROZ) and poor concordance in global DEGs and pathways. However, counts from FFPE and FROZ samples still positively correlated (r2 = 0.84 across all transcripts) and showed comparable dose responses for more highly expressed target genes. These findings highlight potential applications and issues in using RNA-sequencing data from FFPE samples. Recently archived FFPE samples were highly similar to FROZ samples in sequencing q

NHEXAS PHASE I ARIZONA STUDY--STANDARD OPERATING PROCEDURE FOR ARCHIVE PROCEDURE FOR STUDY SAMPLES (UA-G-4.0)

EPA Science Inventory

The purpose of this SOP is to outline the archive/custody guidelines used by the NHEXAS Arizona research project. This procedure was followed to maintain and locate samples, extracts, tracings and hard copy results after laboratory analysis during the Arizona NHEXAS project and ...

Evolution of Archival Storage (from Tape to Memory)

NASA Technical Reports Server (NTRS)

Ramapriyan, Hampapuram K.

2015-01-01

Over the last three decades, there has been a significant evolution in storage technologies supporting archival of remote sensing data. This section provides a brief survey of how these technologies have evolved. Three main technologies are considered - tape, hard disk and solid state disk. Their historical evolution is traced, summarizing how reductions in cost have helped being able to store larger volumes of data on faster media. The cost per GB of media is only one of the considerations in determining the best approach to archival storage. Active archives generally require faster response to user requests for data than permanent archives. The archive costs have to consider facilities and other capital costs, operations costs, software licenses, utilities costs, etc. For meeting requirements in any organization, typically a mix of technologies is needed.

U.S.-MEXICO BORDER PROGRAM ARIZONA BORDER STUDY--STANDARD OPERATING PROCEDURE FOR ARCHIVE PROCEDURE FOR STUDY SAMPLES (UA-G-4.0)

EPA Science Inventory

The purpose of this SOP is to outline the archive/custody guidelines used by the Arizona Border Study. This procedure was followed to maintain and locate samples, extracts, tracings and hard copy results after laboratory analysis during the Arizona NHEXAS project and the Border ...

DNA sequence chromatogram browsing using JAVA and CORBA.

PubMed

Parsons, J D; Buehler, E; Hillier, L

1999-03-01

DNA sequence chromatograms (traces) are the primary data source for all large-scale genomic and expressed sequence tags (ESTs) sequencing projects. Access to the sequencing trace assists many later analyses, for example contig assembly and polymorphism detection, but obtaining and using traces is problematic. Traces are not collected and published centrally, they are much larger than the base calls derived from them, and viewing them requires the interactivity of a local graphical client with local data. To provide efficient global access to DNA traces, we developed a client/server system based on flexible Java components integrated into other applications including an applet for use in a WWW browser and a stand-alone trace viewer. Client/server interaction is facilitated by CORBA middleware which provides a well-defined interface, a naming service, and location independence. [The software is packaged as a Jar file available from the following URL: http://www.ebi.ac.uk/jparsons. Links to working examples of the trace viewers can be found at http://corba.ebi.ac.uk/EST. All the Washington University mouse EST traces are available for browsing at the same URL.

Evaluating Quality of Aged Archival Formalin-Fixed Paraffin-Embedded Samples for RNA-Sequencing

EPA Science Inventory

Archival formalin-fixed paraffin-embedded (FFPE) samples offer a vast, untapped source of genomic data for biomarker discovery. However, the quality of FFPE samples is often highly variable, and conventional methods to assess RNA quality for RNA-sequencing (RNA-seq) are not infor...

The ExoMars Rover Science Archive: Status and Plans

NASA Astrophysics Data System (ADS)

Heather, D.; Lim, T.; Metcalfe, L.

2017-09-01

The ExoMars program is a co-operation between ESA and Roscosmos comprising two missions: the first, launched on 14 March 2016, included the Trace Gas Orbiter and Schiaparelli lander; the second, due for launch in 2020, will be a Rover and Surface Platform (RSP). The ExoMars Rover and Surface Platform deliveries will be among the first data in the PSA to be formatted according to the new PDS4 Standards, and will be the first rover data to be hosted within the archive at all. The archiving and management of the science data to be returned from ExoMars will require a significant development effort for the new Planetary Science Archive (PSA). This presentation will outline the current plans for archiving of the ExoMars Rover and Surface Platform science data.

Peat Bog Archives: from human history, vegetation change and Holocene climate, to atmospheric dusts and trace elements of natural and anthropogenic origin

NASA Astrophysics Data System (ADS)

Shotyk, William

2010-05-01

For at least two centuries, peat has been recognized as an excellent archive of environmental change. William Rennie (1807), for example, interpreted stratigraphic changes in Scottish bogs not only in terms of natural changes in paleoclimate, but was also able to identify environmental changes induced by humans, namely deforestation and the hydrological impacts which result from such activities. The use of bogs as archives of climate change in the early 20th century was accelerated by studies of fossil plant remains such as those by Lewis in Scotland, and by systematic investigations of pollen grains pioneered by von Post in Sweden. In Denmark, Glob outlined the remarkably well-preserved remains of bog bodies and associated artefacts (of cloth, wood, ceramic and metal) in Danish bogs. In Britain, Godwin provided an introduction to the use of bogs as archives of human history, vegetation change, and Holocene climate, with a more recent survey provided by Charman. Recent decades have provided many mineralogical studies of peat and there is growing evidence that many silicate minerals, whether derived from the surrounding watershed or the atmosphere (soil-derived dusts and particles emitted from volcanoes), also are well preserved in anoxic peatland waters. Similarly, geochemical studies have shown that a long list of trace metals, of both natural and anthropogenic origin, also are remarkably well preserved in peat bogs. Thus, there is growing evidence that ombrotrophic (ie 'rain-fed') peat bogs are reliable archives of atmospheric deposition of a wide range of trace elements, including conservative, lithogenic metals such as Al, Sc, Ti, Y, Zr, Hf and the REE, but also the potentially toxic Class B, or 'heavy metals' such as Cu, Ag, Hg, Pb, Sb and Tl. When high quality measurements of these elements is combined with accurate radiometric age dating, it becomes possible to create high resolution reconstructions of atmospheric soil dust fluxes, ancient and modern metal pollution, and Holocene climate change.

Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past.

PubMed

Der Sarkissian, Clio; Pichereau, Vianney; Dupont, Catherine; Ilsøe, Peter C; Perrigault, Mickael; Butler, Paul; Chauvaud, Laurent; Eiríksson, Jón; Scourse, James; Paillard, Christine; Orlando, Ludovic

2017-09-01

Marine mollusc shells enclose a wealth of information on coastal organisms and their environment. Their life history traits as well as (palaeo-) environmental conditions, including temperature, food availability, salinity and pollution, can be traced through the analysis of their shell (micro-) structure and biogeochemical composition. Adding to this list, the DNA entrapped in shell carbonate biominerals potentially offers a novel and complementary proxy both for reconstructing palaeoenvironments and tracking mollusc evolutionary trajectories. Here, we assess this potential by applying DNA extraction, high-throughput shotgun DNA sequencing and metagenomic analyses to marine mollusc shells spanning the last ~7,000 years. We report successful DNA extraction from shells, including a variety of ancient specimens, and find that DNA recovery is highly dependent on their biomineral structure, carbonate layer preservation and disease state. We demonstrate positive taxonomic identification of mollusc species using a combination of mitochondrial DNA genomes, barcodes, genome-scale data and metagenomic approaches. We also find shell biominerals to contain a diversity of microbial DNA from the marine environment. Finally, we reconstruct genomic sequences of organisms closely related to the Vibrio tapetis bacteria from Manila clam shells previously diagnosed with Brown Ring Disease. Our results reveal marine mollusc shells as novel genetic archives of the past, which opens new perspectives in ancient DNA research, with the potential to reconstruct the evolutionary history of molluscs, microbial communities and pathogens in the face of environmental changes. Other future applications include conservation of endangered mollusc species and aquaculture management. © 2017 John Wiley & Sons Ltd.

RefSeq microbial genomes database: new representation and annotation strategy.

PubMed

Tatusova, Tatiana; Ciufo, Stacy; Fedorov, Boris; O'Neill, Kathleen; Tolstoy, Igor

2014-01-01

The source of the microbial genomic sequences in the RefSeq collection is the set of primary sequence records submitted to the International Nucleotide Sequence Database public archives. These can be accessed through the Entrez search and retrieval system at http://www.ncbi.nlm.nih.gov/genome. Next-generation sequencing has enabled researchers to perform genomic sequencing at rates that were unimaginable in the past. Microbial genomes can now be sequenced in a matter of hours, which has led to a significant increase in the number of assembled genomes deposited in the public archives. This huge increase in DNA sequence data presents new challenges for the annotation, analysis and visualization bioinformatics tools. New strategies have been developed for the annotation and representation of reference genomes and sequence variations derived from population studies and clinical outbreaks.

A Systematic Analysis of the Structures of Heterologously Expressed Proteins and Those from Their Native Hosts in the RCSB PDB Archive.

PubMed

Zhou, Ren-Bin; Lu, Hui-Meng; Liu, Jie; Shi, Jian-Yu; Zhu, Jing; Lu, Qin-Qin; Yin, Da-Chuan

2016-01-01

Recombinant expression of proteins has become an indispensable tool in modern day research. The large yields of recombinantly expressed proteins accelerate the structural and functional characterization of proteins. Nevertheless, there are literature reported that the recombinant proteins show some differences in structure and function as compared with the native ones. Now there have been more than 100,000 structures (from both recombinant and native sources) publicly available in the Protein Data Bank (PDB) archive, which makes it possible to investigate if there exist any proteins in the RCSB PDB archive that have identical sequence but have some difference in structures. In this paper, we present the results of a systematic comparative study of the 3D structures of identical naturally purified versus recombinantly expressed proteins. The structural data and sequence information of the proteins were mined from the RCSB PDB archive. The combinatorial extension (CE), FATCAT-flexible and TM-Align methods were employed to align the protein structures. The root-mean-square distance (RMSD), TM-score, P-value, Z-score, secondary structural elements and hydrogen bonds were used to assess the structure similarity. A thorough analysis of the PDB archive generated five-hundred-seventeen pairs of native and recombinant proteins that have identical sequence. There were no pairs of proteins that had the same sequence and significantly different structural fold, which support the hypothesis that expression in a heterologous host usually could fold correctly into their native forms.

A Systematic Analysis of the Structures of Heterologously Expressed Proteins and Those from Their Native Hosts in the RCSB PDB Archive

PubMed Central

Zhou, Ren-Bin; Lu, Hui-Meng; Liu, Jie; Shi, Jian-Yu; Zhu, Jing; Lu, Qin-Qin; Yin, Da-Chuan

2016-01-01

Recombinant expression of proteins has become an indispensable tool in modern day research. The large yields of recombinantly expressed proteins accelerate the structural and functional characterization of proteins. Nevertheless, there are literature reported that the recombinant proteins show some differences in structure and function as compared with the native ones. Now there have been more than 100,000 structures (from both recombinant and native sources) publicly available in the Protein Data Bank (PDB) archive, which makes it possible to investigate if there exist any proteins in the RCSB PDB archive that have identical sequence but have some difference in structures. In this paper, we present the results of a systematic comparative study of the 3D structures of identical naturally purified versus recombinantly expressed proteins. The structural data and sequence information of the proteins were mined from the RCSB PDB archive. The combinatorial extension (CE), FATCAT-flexible and TM-Align methods were employed to align the protein structures. The root-mean-square distance (RMSD), TM-score, P-value, Z-score, secondary structural elements and hydrogen bonds were used to assess the structure similarity. A thorough analysis of the PDB archive generated five-hundred-seventeen pairs of native and recombinant proteins that have identical sequence. There were no pairs of proteins that had the same sequence and significantly different structural fold, which support the hypothesis that expression in a heterologous host usually could fold correctly into their native forms. PMID:27517583

Detection of viral sequences in archival spinal cords from fatal cases of poliomyelitis in 1951-1952.

PubMed

Rekand, Tiina; Male, Rune; Myking, Andreas O; Nygaard, Svein J T; Aarli, Johan A; Haarr, Lars; Langeland, Nina

2003-12-01

Poliovirus (PV) subjected to genetic characterization is often isolated from faecal carriage. Such virus is not necessarily identical to the virus causing paralytic disease since genetic modifications may occur during replication outside the nervous system. We have searched for poliovirus genomes in the 14 fatal cases occurring during the last epidemics in Norway in 1951-1952. A method was developed for isolation and analysis of poliovirus RNA from formalin-fixed and paraffin-embedded archival tissue. RNA was purified by incubation with Chelex-100 and heating followed by treatment with the proteinase K and chloroform extraction. Viral sequences were amplified by a reverse transcriptase-polymerase chain reaction (RT-PCR), the products subjected to TA cloning and sequenced. RNA from the beta-actin gene, as a control, was identified in 13 cases, while sequences specific for poliovirus were achieved in 11 cases. The sequences from the 2C region of poliovirus were rather conserved while those in the 5'-untranslated region were variable. The developed method should be suitable also for other genetic studies of old archival material.

High resolution trace element records from the deep sea hydrocoral Stylaster venustus: Implications for stylasterids as a paleoceanographic archive

NASA Astrophysics Data System (ADS)

Aranha, R. S.; Layne, G. D.; Edinger, E.; Piercey, G.

2009-12-01

Stylasterids are one of the lesser known groups of deep sea corals, but appear to have potential to serve as viable geochemical archives for reconstructing temperature, salinity and nutrient regimes in the deep ocean. This group of hydrocorals are present in most, if not all of the world’s major oceans. Stylasterid species dominantly have aragonitic skeletons, with a small percentage of species having calcitic skeletons (1). A recent study on the biomineralization of a deep sea stylasterid (Errina dabneyi) has revealed that during the organism’s growth, a steady dissolution and reprecipitation of skeletal material occurs in the central canals of the skeleton. This skeletal modification likely alters the stable isotope and/or trace element profiles of these corals, making them potentially less reliable as geochemical archives, depending on the scale of sampling (2). Recent specimens of Stylaster venustus were collected in July, 2008 from the Olympic Coast National Marine sanctuary off the coast of Washington at depths of 200 - 350 m. We used a Cameca IMS 4f Secondary Ion Mass Spectrometer (SIMS) to perform high spatial resolution (<25 µm) spot analyses of Sr/Ca, Mg/Ca and Na/Ca in detailed traverses across the basal cross-sections from three of these specimens. We identified the remineralized material by remnant porous texture and/or a substantially different trace element composition. Spot analyses corresponding to the remineralized material were eliminated from the dataset. In all three specimens we observed a pronounced inverse correlation (r = -0.36) of Mg/Ca and Sr/Ca profiles throughout the length of the transects . A positive correlation (r =0.46) between Na/Ca and Mg/Ca profiles was also noted in two of the specimens analyzed. These correlations strongly imply that the coral skeleton is recording either cyclical or episodic variations in temperature, with possible overprinting from other environmental variation. The exact relationship between the visible banding in the skeletal cross-section and any cyclicity of trace element profiles is currently ambiguous. However, our analyses demonstrate that microanalytical techniques are a viable means of extracting trace element records from these corals. Further statistical analysis of the trace element transects, in combination with a variety of imaging analyses of the same samples, should help us elucidate what portion of the geochemical signal is temperature dependent and what magnitude of temperature change is actually being recorded. Correlating these trace element profiles with instrumental temperature records will help confirm that useful geochemical archives are preserved by stylasterid skeletons. References: (1) Cairns SD and Macintyre IG. 1992. Phylogenetic implications of calcium carbonate mineralogy in the Stylasteridae (Cnidaria:Hydrozoa).Palaios 7: 96-107. (2) Wisshak M, López Correa M, Zibrowius H, Jakobsen J & Freiwald. (in press). Skeletal reorganisation affects geochemical signals, exemplified in the stylasterid hydrocoral Errina dabneyi (Azores Archipelago). Marine Ecology Progress Series.

Noncharacteristic Slip on the Northern San Andreas Fault at the Vedanta Marsh, Marin County, CA

NASA Astrophysics Data System (ADS)

Zhang, H.; Niemi, T. M.; Allison, A.; Fumal, T. E.

2004-12-01

Three-dimensional excavations along the 1906 trace of the northern San Andreas fault at the Vedanta marsh paleoseismic site near Olema, CA have yielded new data on the timing and amount of slip during the penultimate earthquake on this fault section. The excavations exposed a 3-m-wide paleochannel that has been offset right-laterally 7.8-8.3 m by coseismic slip during the past two large earthquakes: 1906 and the penultimate earthquake. The paleochannel was eroded into a silty clay marsh deposit and was filled after AD 1400. Both the silty clay layer and the paleochannel deposit are directly overlain by an in situ burn/peat sequence. The penultimate earthquake occurred while the peat was at the ground surface whereas faulting from the 1906 earthquake terminates within an overlying gravel/fill sequence. Preliminary OxCal analyses of radiocarbon dates indicate that the penultimate earthquake occurred in the late 17th to early 18th century. In plan view, two main fault traces were mapped in the excavation. The northwestern portion of the paleochannel is offset across a single fault trace. Just southeast of this portion of the channel the fault splits into two traces. We believe that one of these traces likely slipped only during 1906 and the other trace slipped on during the penultimate earthquake. Unfortunately, the overlying stratigraphic section that could resolve the exact reconstruction of movement on these faults is missing due to the excavation of an artificial drainage ditch at this location in the 1940's. Matching the north margin of the paleochannel to the first exposure of gravel in the zone between the two fault traces gives an offset of 5 m. We have historic records that show the 1906 coseismic slip near the study site was about 5m from field notes of David Starr Jordan (Stanford University Archives) who describes two 16 ft (5m) offsets: one of a tree located about 150m SE of the offset channel and the other of a path to the Shafter barn located about 300m NW. As the locations of these two historical records are so close to the study site, it is reasonable to assume that our excavation site has the same amount of coseismic slip in 1906. Our data indicate that the paleochannel was offset about 2.8 to 3.3 m during the penultimate earthquake which occurred in the late 17th to early 18th century, and that the San Andreas fault at this section is capable of slip in earthquakes smaller than 1906.

Real-time detection of BRAF V600E mutation from archival hairy cell leukemia FFPE tissue by nanopore sequencing.

PubMed

Vacca, Davide; Cancila, Valeria; Gulino, Alessandro; Lo Bosco, Giosuè; Belmonte, Beatrice; Di Napoli, Arianna; Florena, Ada Maria; Tripodo, Claudio; Arancio, Walter

2018-02-01

The MinION is a miniaturized high-throughput next generation sequencing platform of novel conception. The use of nucleic acids derived from formalin-fixed paraffin-embedded samples is highly desirable, but their adoption for molecular assays is hurdled by the high degree of fragmentation and by the chemical-induced mutations stemming from the fixation protocols. In order to investigate the suitability of MinION sequencing on formalin-fixed paraffin-embedded samples, the presence and frequency of BRAF c.1799T > A mutation was investigated in two archival tissue specimens of Hairy cell leukemia and Hairy cell leukemia Variant. Despite the poor quality of the starting DNA, BRAF mutation was successfully detected in the Hairy cell leukemia sample with around 50% of the reads obtained within 2 h of the sequencing start. Notably, the mutational burden of the Hairy cell leukemia sample as derived from nanopore sequencing proved to be comparable to a sensitive method for the detection of point mutations, namely the Digital PCR, using a validated assay. Nanopore sequencing can be adopted for targeted sequencing of genetic lesions on critical DNA samples such as those extracted from archival routine formalin-fixed paraffin-embedded samples. This result let speculating about the possibility that the nanopore sequencing could be trustably adopted for the real-time targeted sequencing of genetic lesions. Our report opens the window for the adoption of nanopore sequencing in molecular pathology for research and diagnostics.

Evaluation and Adaptation of a Laboratory-Based cDNA Library Preparation Protocol for Retrospective Sequencing of Archived MicroRNAs from up to 35-Year-Old Clinical FFPE Specimens

PubMed Central

Loudig, Olivier; Wang, Tao; Ye, Kenny; Lin, Juan; Wang, Yihong; Ramnauth, Andrew; Liu, Christina; Stark, Azadeh; Chitale, Dhananjay; Greenlee, Robert; Multerer, Deborah; Honda, Stacey; Daida, Yihe; Spencer Feigelson, Heather; Glass, Andrew; Couch, Fergus J.; Rohan, Thomas; Ben-Dov, Iddo Z.

2017-01-01

Formalin-fixed paraffin-embedded (FFPE) specimens, when used in conjunction with patient clinical data history, represent an invaluable resource for molecular studies of cancer. Even though nucleic acids extracted from archived FFPE tissues are degraded, their molecular analysis has become possible. In this study, we optimized a laboratory-based next-generation sequencing barcoded cDNA library preparation protocol for analysis of small RNAs recovered from archived FFPE tissues. Using matched fresh and FFPE specimens, we evaluated the robustness and reproducibility of our optimized approach, as well as its applicability to archived clinical specimens stored for up to 35 years. We then evaluated this cDNA library preparation protocol by performing a miRNA expression analysis of archived breast ductal carcinoma in situ (DCIS) specimens, selected for their relation to the risk of subsequent breast cancer development and obtained from six different institutions. Our analyses identified six miRNAs (miR-29a, miR-221, miR-375, miR-184, miR-363, miR-455-5p) differentially expressed between DCIS lesions from women who subsequently developed an invasive breast cancer (cases) and women who did not develop invasive breast cancer within the same time interval (control). Our thorough evaluation and application of this laboratory-based miRNA sequencing analysis indicates that the preparation of small RNA cDNA libraries can reliably be performed on older, archived, clinically-classified specimens. PMID:28335433

Sequence History Update Tool

NASA Technical Reports Server (NTRS)

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

2008-01-01

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

Whole Genome Amplification and Reduced-Representation Genome Sequencing of Schistosoma japonicum Miracidia.

PubMed

Shortt, Jonathan A; Card, Daren C; Schield, Drew R; Liu, Yang; Zhong, Bo; Castoe, Todd A; Carlton, Elizabeth J; Pollock, David D

2017-01-01

In areas where schistosomiasis control programs have been implemented, morbidity and prevalence have been greatly reduced. However, to sustain these reductions and move towards interruption of transmission, new tools for disease surveillance are needed. Genomic methods have the potential to help trace the sources of new infections, and allow us to monitor drug resistance. Large-scale genotyping efforts for schistosome species have been hindered by cost, limited numbers of established target loci, and the small amount of DNA obtained from miracidia, the life stage most readily acquired from humans. Here, we present a method using next generation sequencing to provide high-resolution genomic data from S. japonicum for population-based studies. We applied whole genome amplification followed by double digest restriction site associated DNA sequencing (ddRADseq) to individual S. japonicum miracidia preserved on Whatman FTA cards. We found that we could effectively and consistently survey hundreds of thousands of variants from 10,000 to 30,000 loci from archived miracidia as old as six years. An analysis of variation from eight miracidia obtained from three hosts in two villages in Sichuan showed clear population structuring by village and host even within this limited sample. This high-resolution sequencing approach yields three orders of magnitude more information than microsatellite genotyping methods that have been employed over the last decade, creating the potential to answer detailed questions about the sources of human infections and to monitor drug resistance. Costs per sample range from $50-$200, depending on the amount of sequence information desired, and we expect these costs can be reduced further given continued reductions in sequencing costs, improvement of protocols, and parallelization. This approach provides new promise for using modern genome-scale sampling to S. japonicum surveillance, and could be applied to other schistosome species and other parasitic helminthes.

Widespread pollution of the South American atmosphere predates the industrial revolution by 240 years

NASA Astrophysics Data System (ADS)

Uglietti, Chiara; Gabrielli, Paolo; Cooke, Colin; Vallelonga, Paul; Thompson, Lonnie

2015-04-01

In the Southern Hemisphere, evidence for preindustrial atmospheric pollution is restricted to a few geological archives of low temporal resolution that record trace element deposition originating from past mining and metallurgical operations in South America. Therefore the timing and the spatial impact of these activities on the past atmosphere remain poorly constrained. Here we present an annually resolved ice-core record (793-1989 AD) from the high altitude drilling site of Quelccaya (Peru) that archives preindustrial and industrial variations in trace elements. During the pre-colonial period (i.e., pre-1532 AD), the deposition of trace elements was mainly dominated by the fallout of aeolian dust and of ash from occasional volcanic eruptions indicating that metallurgic production during the Inca Empire (1438-1532 AD) had a negligible impact on the South American atmosphere. In contrast, a widespread anthropogenic signal is evident after 1540 AD, which corresponds with the beginning of colonial mining and metallurgy in Peru and Bolivia, 240 years prior to the Industrial Revolution. This shift was due to a major technological transition for silver extraction in South America (1572 AD), from lead-based smelting to mercury amalgamation, which precipitated a massive increase in mining activities. However, deposition of toxic trace metals during the Colonial era was still several factors lower than 20th century pollution that was unprecedented over the entirety of human history.

Widespread pollution of the South American atmosphere predates the industrial revolution by 240 y.

PubMed

Uglietti, Chiara; Gabrielli, Paolo; Cooke, Colin A; Vallelonga, Paul; Thompson, Lonnie G

2015-02-24

In the Southern Hemisphere, evidence for preindustrial atmospheric pollution is restricted to a few geological archives of low temporal resolution that record trace element deposition originating from past mining and metallurgical operations in South America. Therefore, the timing and the spatial impact of these activities on the past atmosphere remain poorly constrained. Here we present an annually resolved ice core record (A.D. 793-1989) from the high-altitude drilling site of Quelccaya (Peru) that archives preindustrial and industrial variations in trace elements. During the precolonial period (i.e., pre-A.D. 1532), the deposition of trace elements was mainly dominated by the fallout of aeolian dust and of ash from occasional volcanic eruptions, indicating that metallurgic production during the Inca Empire (A.D. 1438-1532) had a negligible impact on the South American atmosphere. In contrast, a widespread anthropogenic signal is evident after around A.D. 1540, which corresponds with the beginning of colonial mining and metallurgy in Peru and Bolivia, ∼240 y before the Industrial Revolution. This shift was due to a major technological transition for silver extraction in South America (A.D. 1572), from lead-based smelting to mercury amalgamation, which precipitated a massive increase in mining activities. However, deposition of toxic trace metals during the Colonial era was still several factors lower than 20th century pollution that was unprecedented over the entirety of human history.

Archive of Digital Chirp Subbottom Profile Data Collected During USGS Cruise 14BIM05 Offshore of Breton Island, Louisiana, August 2014

USGS Publications Warehouse

Forde, Arnell S.; Flocks, James G.; Wiese, Dana S.; Fredericks, Jake J.

2016-03-29

The archived trace data are in standard SEG Y rev. 0 format (Barry and others, 1975); the first 3,200 bytes of the card image header are in American Standard Code for Information Interchange (ASCII) format instead of Extended Binary Coded Decimal Interchange Code (EBCDIC) format. The SEG Y files are available on the DVD version of this report or online, downloadable via the USGS Coastal and Marine Geoscience Data System (http://cmgds.marine.usgs.gov). The data are also available for viewing using GeoMapApp (http://www.geomapapp.org) and Virtual Ocean (http://www.virtualocean.org) multi-platform open source software. The Web version of this archive does not contain the SEG Y trace files. To obtain the complete DVD archive, contact USGS Information Services at 1-888-ASK-USGS or infoservices@usgs.gov. The SEG Y files may be downloaded and processed with commercial or public domain software such as Seismic Unix (SU) (Cohen and Stockwell, 2010). See the How To Download SEG Y Data page for download instructions. The printable profiles are provided as Graphics Interchange Format (GIF) images processed and gained using SU software and can be viewed from theProfiles page or by using the links located on the trackline maps; refer to the Software page for links to example SU processing scripts.

Hierarchical Traces for Reduced NSM Memory Requirements

NASA Astrophysics Data System (ADS)

Dahl, Torbjørn S.

This paper presents work on using hierarchical long term memory to reduce the memory requirements of nearest sequence memory (NSM) learning, a previously published, instance-based reinforcement learning algorithm. A hierarchical memory representation reduces the memory requirements by allowing traces to share common sub-sequences. We present moderated mechanisms for estimating discounted future rewards and for dealing with hidden state using hierarchical memory. We also present an experimental analysis of how the sub-sequence length affects the memory compression achieved and show that the reduced memory requirements do not effect the speed of learning. Finally, we analyse and discuss the persistence of the sub-sequences independent of specific trace instances.

Extreme variability among mammalian V1R gene families.

PubMed

Young, Janet M; Massa, Hillary F; Hsu, Li; Trask, Barbara J

2010-01-01

We report an evolutionary analysis of the V1R gene family across 37 mammalian genomes. V1Rs comprise one of three chemosensory receptor families expressed in the vomeronasal organ, and contribute to pheromone detection. We first demonstrate that Trace Archive data can be used effectively to determine V1R family sizes and to obtain sequences of most V1R family members. Analyses of V1R sequences from trace data and genome assemblies show that species-specific expansions previously observed in only eight species were prevalent throughout mammalian evolution, resulting in "semi-private" V1R repertoires for most mammals. The largest families are found in mouse and platypus, whose V1R repertoires have been published previously, followed by mouse lemur and rabbit (approximately 215 and approximately 160 intact V1Rs, respectively). In contrast, two bat species and dolphin possess no functional V1Rs, only pseudogenes, and suffered inactivating mutations in the vomeronasal signal transduction gene Trpc2. We show that primate V1R decline happened prior to acquisition of trichromatic vision, earlier during evolution than was previously thought. We also show that it is extremely unlikely that decline of the dog V1R repertoire occurred in response to selective pressures imposed by humans during domestication. Functional repertoire sizes in each species correlate roughly with anatomical observations of vomeronasal organ size and quality; however, no single ecological correlate explains the very diverse fates of this gene family in different mammalian genomes. V1Rs provide one of the most extreme examples observed to date of massive gene duplication in some genomes, with loss of all functional genes in other species.

preAssemble: a tool for automatic sequencer trace data processing.

PubMed

Adzhubei, Alexei A; Laerdahl, Jon K; Vlasova, Anna V

2006-01-17

Trace or chromatogram files (raw data) are produced by automatic nucleic acid sequencing equipment or sequencers. Each file contains information which can be interpreted by specialised software to reveal the sequence (base calling). This is done by the sequencer proprietary software or publicly available programs. Depending on the size of a sequencing project the number of trace files can vary from just a few to thousands of files. Sequencing quality assessment on various criteria is important at the stage preceding clustering and contig assembly. Two major publicly available packages--Phred and Staden are used by preAssemble to perform sequence quality processing. The preAssemble pre-assembly sequence processing pipeline has been developed for small to large scale automatic processing of DNA sequencer chromatogram (trace) data. The Staden Package Pregap4 module and base-calling program Phred are utilized in the pipeline, which produces detailed and self-explanatory output that can be displayed with a web browser. preAssemble can be used successfully with very little previous experience, however options for parameter tuning are provided for advanced users. preAssemble runs under UNIX and LINUX operating systems. It is available for downloading and will run as stand-alone software. It can also be accessed on the Norwegian Salmon Genome Project web site where preAssemble jobs can be run on the project server. preAssemble is a tool allowing to perform quality assessment of sequences generated by automatic sequencing equipment. preAssemble is flexible since both interactive jobs on the preAssemble server and the stand alone downloadable version are available. Virtually no previous experience is necessary to run a default preAssemble job, on the other hand options for parameter tuning are provided. Consequently preAssemble can be used as efficiently for just several trace files as for large scale sequence processing.

Particular geoscientific perspectives on stable isotope analysis in the arboreal system

NASA Astrophysics Data System (ADS)

Helle, Gerhard; Balting, Daniel; Pauly, Maren; Slotta, Franziska

2017-04-01

In geosciences stable isotopes of carbon, oxygen and hydrogen from the tree ring archive have been used for several decades to trace the course of past environmental and climatological fluctuations. In contrast to ice cores, the tree ring archive is of biological nature (like many other terrestrial archives), but provides the opportunity to establish site networks with very high resolution in space and time. Many of the basic physical mechanisms of isotope shifts are known, but biologically mediated processes may lead to isotope effects that are poorly understood. This implies that the many processes within the arboreal system leading to archived isotope ratios in wood material are governed by a multitude of environmental variables that are not only tied to the isotopic composition of atmospheric source values (precipitation, CO2), but also to seasonally changing metabolic flux rates and pool sizes of photosynthates within the trees. Consequently, the extraction of climate and environmental information is particularly challenging and reconstructions are still of rather qualitative nature. Over the last 10 years or so, monitoring studies have been implemented to investigate stable isotope, climate and environmental signal transfer within the arboreal system to develop transfer or response functions that can translate the relevant isotope values extracted from tree rings into climate or other environmental variables. To what extent have these efforts lead to a better understanding that helps improving the meaningfulness of tree ring isotope signals? For example, do monitoring studies help deciphering the causes for age-related trends in tree ring stable isotope sequences that are published in a growing number of papers. Are existing monitoring studies going into detail enough or is it already too much effort for the outcome? Based on what we know already particularly in mesic habitats, tree ring stable isotopes are much better climate proxies than other tree ring parameters. However, millennial or multi-millennial high quality reconstructions from tree ring isotopes are still rare. This is because of i) methodological constraints related to mass spectrometric analyses and ii) the nature of tree-ring chronologies that are put together by many trees of various individual ages. In view of this: What is the state-of-the-art in high throughput tree ring stable isotope analyses? Is it necessary to advance existing methodologies further to conserve the annual time resolution provided by the tree-ring archive? Other terrestrial archives, like lake sediments and speleothems rarely provide annually resolved stable isotope data. Furthermore, certain tree species from tropical or sub-tropical regions cannot be dated properly by dendrochronology and hence demand specific stable isotope measuring strategies, etc.. Although the points raised here do specifically apply for the tree ring archive, some of them are important for all proxy archives of organic origin.

Archive of digital CHIRP seismic reflection data collected during USGS cruise 06FSH01 offshore of Siesta Key, Florida, May 2006

USGS Publications Warehouse

Harrison, Arnell S.; Dadisman, Shawn V.; Flocks, James G.; Wiese, Dana S.; Robbins, Lisa L.

2007-01-01

In May of 2006, the U.S. Geological Survey conducted geophysical surveys offshore of Siesta Key, Florida. This report serves as an archive of unprocessed digital chirp seismic reflection data, trackline maps, navigation files, GIS information, Field Activity Collection System (FACS) logs, observer's logbook, and formal FGDC metadata. Gained digital images of the seismic profiles are also provided. The archived trace data are in standard Society of Exploration Geophysicists (SEG) SEG-Y format (Barry and others, 1975) and may be downloaded and processed with commercial or public domain software such as Seismic Unix (SU). Example SU processing scripts and USGS software for viewing the SEG-Y files (Zihlman, 1992) are also provided.

Archive of digital CHIRP seismic reflection data collected during USGS cruise 06SCC01 offshore of Isles Dernieres, Louisiana, June 2006

USGS Publications Warehouse

Harrison, Arnell S.; Dadisman, Shawn V.; Ferina, Nick F.; Wiese, Dana S.; Flocks, James G.

2007-01-01

In June of 2006, the U.S. Geological Survey conducted a geophysical survey offshore of Isles Dernieres, Louisiana. This report serves as an archive of unprocessed digital CHIRP seismic reflection data, trackline maps, navigation files, GIS information, Field Activity Collection System (FACS) logs, observer's logbook, and formal FGDC metadata. Gained digital images of the seismic profiles are also provided. The archived trace data are in standard Society of Exploration Geophysicists (SEG) SEG-Y format (Barry and others, 1975) and may be downloaded and processed with commercial or public domain software such as Seismic UNIX (SU). Example SU processing scripts and USGS software for viewing the SEG-Y files (Zihlman, 1992) are also provided.

Improvements to a Major Digital Archive of Seismic Waveforms from Nuclear Explosions

DTIC Science & Technology

2010-03-23

Semipalatinsk Test site ; Novaya Zemlya (461 traces) in Russia; and Lop Nor (120 traces) in China; and also from many Peaceful Nuclear Explosions (552... Semipalatinsk Test Site (circles) recorded at Borovoye (BRV) during 1966- 1989.The Balapan, Degelen, and Murzhik regions are indicated. 5 3. Locations of... Semipalatinsk Test Site , Kazakhstan; test of 1968 June 19 70 35. Last of seven sets of BRV seismograms on the KOD system for a UNE at the Balapan area

Seasonality Records From Stable Isotopes and Trace Elements in Mussel and Limpet Shells From Archaeological Sites on Gibraltar

NASA Astrophysics Data System (ADS)

Fa, D.; Ferguson, J. E.; Atkinson, T. C.; Barton, R. N.; Ditchfield, P.; Finlayson, G.; Finlayson, J. C.; Henderson, G. M.

2007-12-01

Seasonal resolution climate records from mid and high latitudes would allow investigation of the role of seasonality in controlling mean climate on diverse timescales, and of the evolution of climate systems such as the North Atlantic Oscillation (NAO). But achieving such seasonal resolution is difficult for regions outside the growth range of surface corals. Marine mollusc shells provide a possible archive and contain growth increments varying in scale from tidal to annual. However, finding and dating sequences of marine mollusc shells spanning long periods of time is difficult due to sea-level change and the destructional nature of most coastal environments. In this study, we have made use of the habit of hominins on Gibraltar to collect molluscs for food over at least the last 120 kyr. In archaeological excavations of two caves (Gorham's and Vanguard Caves), mollusc shells were found, in habitation levels and in sediment blown into the caves. Existing 14C, OSL, and U-series chronologies provide a chronological framework for this suite of samples. The species found are predominantly Mytilus (mussels) or Patella (limpets). Gibraltar is an interesting location for paleoclimate reconstruction due to its proximity to the boundary of modern day climate belts but also due to its anthropological and archaeological importance. To gain a quantitative understanding of the local controls on stable isotopes and trace elements within Gibraltarian shells, we have initiated a water-sampling programme; emplaced a temperature and salinity logger near the sampling site; and marked live Patella and Mytilus with fluorescent dye to firmly establish growth rates and controls on chemical composition. We have also conducted stable-isotope and trace-element analysis of modern and fossil Patella and Mytilus shells by micromilling. Recent Patella and Mytilus shells show that the oxygen isotope composition of modern shells allow the accurate reconstruction of the full seasonal range in sea-surface temperature. Analysis of three fossil Mytilus samples contained within a Neanderthal occupation level from approximately 115 kyr show clear annual cycles in δ 18O but with different absolute values. Patella samples have also been analysed from the last glacial and from 800-300B.C. Results allow an assessment of past changes in seasonality and of the utility of this archeological shell material as an archive for past change.

The Genomic Observatories Metadatabase (GeOMe): A new repository for field and sampling event metadata associated with genetic samples.

PubMed

Deck, John; Gaither, Michelle R; Ewing, Rodney; Bird, Christopher E; Davies, Neil; Meyer, Christopher; Riginos, Cynthia; Toonen, Robert J; Crandall, Eric D

2017-08-01

The Genomic Observatories Metadatabase (GeOMe, http://www.geome-db.org/) is an open access repository for geographic and ecological metadata associated with biosamples and genetic data. Whereas public databases have served as vital repositories for nucleotide sequences, they do not accession all the metadata required for ecological or evolutionary analyses. GeOMe fills this need, providing a user-friendly, web-based interface for both data contributors and data recipients. The interface allows data contributors to create a customized yet standard-compliant spreadsheet that captures the temporal and geospatial context of each biosample. These metadata are then validated and permanently linked to archived genetic data stored in the National Center for Biotechnology Information's (NCBI's) Sequence Read Archive (SRA) via unique persistent identifiers. By linking ecologically and evolutionarily relevant metadata with publicly archived sequence data in a structured manner, GeOMe sets a gold standard for data management in biodiversity science.

The Genomic Observatories Metadatabase (GeOMe): A new repository for field and sampling event metadata associated with genetic samples

PubMed Central

Deck, John; Gaither, Michelle R.; Ewing, Rodney; Bird, Christopher E.; Davies, Neil; Meyer, Christopher; Riginos, Cynthia; Toonen, Robert J.; Crandall, Eric D.

2017-01-01

The Genomic Observatories Metadatabase (GeOMe, http://www.geome-db.org/) is an open access repository for geographic and ecological metadata associated with biosamples and genetic data. Whereas public databases have served as vital repositories for nucleotide sequences, they do not accession all the metadata required for ecological or evolutionary analyses. GeOMe fills this need, providing a user-friendly, web-based interface for both data contributors and data recipients. The interface allows data contributors to create a customized yet standard-compliant spreadsheet that captures the temporal and geospatial context of each biosample. These metadata are then validated and permanently linked to archived genetic data stored in the National Center for Biotechnology Information’s (NCBI’s) Sequence Read Archive (SRA) via unique persistent identifiers. By linking ecologically and evolutionarily relevant metadata with publicly archived sequence data in a structured manner, GeOMe sets a gold standard for data management in biodiversity science. PMID:28771471

Phoneme restoration and empirical coverage of interactive activation and adaptive resonance models of human speech processing

PubMed Central

Magnuson, James S.

2015-01-01

Grossberg and Kazerounian [(2011). J. Acoust. Soc. Am. 130, 440–460] present a model of sequence representation for spoken word recognition, the cARTWORD model, which simulates essential aspects of phoneme restoration. Grossberg and Kazerounian also include simulations with the TRACE model presented by McClelland and Elman [(1986). Cognit. Psychol. 18, 1–86] that seem to indicate that TRACE cannot simulate phoneme restoration. Grossberg and Kazerounian also claim cARTWORD should be preferred to TRACE because of TRACE's implausible approach to sequence representation (reduplication of time-specific units) and use of non-modulatory feedback (i.e., without position-specific bottom-up support). This paper responds to Grossberg and Kazerounian first with TRACE simulations that account for phoneme restoration when appropriately constructed noise is used (and with minor changes to TRACE phoneme definitions), then reviews the case for reduplicated units and feedback as implemented in TRACE, as well as TRACE's broad and deep coverage of empirical data. Finally, it is argued that cARTWORD is not comparable to TRACE because cARTWORD cannot represent sequences with repeated elements, has only been implemented with small phoneme and lexical inventories, and has been applied to only one phenomenon (phoneme restoration). Without evidence that cARTWORD captures a similar range and detail of human spoken language processing as alternative models, it is premature to prefer cARTWORD to TRACE. PMID:25786959

The Rickettsia Endosymbiont of Ixodes pacificus Contains All the Genes of De Novo Folate Biosynthesis

PubMed Central

Bodnar, James; Mortazavi, Bobak; Laurent, Timothy; Deason, Jeff; Thephavongsa, Khanhkeo; Zhong, Jianmin

2015-01-01

Ticks and other arthropods often are hosts to nutrient providing bacterial endosymbionts, which contribute to their host’s fitness by supplying nutrients such as vitamins and amino acids. It has been detected, in our lab, that Ixodes pacificus is host to Rickettsia species phylotype G021. This endosymbiont is predominantly present, and 100% maternally transmitted in I. pacificus. To study roles of phylotype G021 in I. pacificus, bioinformatic and molecular approaches were carried out. MUMmer genome alignments of whole genome sequence of I. scapularis, a close relative to I. pacificus, against completely sequenced genomes of R. bellii OSU85-389, R. conorii, and R. felis, identified 8,190 unique sequences that are homologous to Rickettsia sequences in the NCBI Trace Archive. MetaCyc metabolic reconstructions revealed that all folate gene orthologues (folA, folC, folE, folKP, ptpS) required for de novo folate biosynthesis are present in the genome of Rickettsia buchneri in I. scapularis. To examine the metabolic capability of phylotype G021 in I. pacificus, genes of the folate biosynthesis pathway of the bacterium were PCR amplified using degenerate primers. BLAST searches identified that nucleotide sequences of the folA, folC, folE, folKP, and ptpS genes possess 98.6%, 98.8%, 98.9%, 98.5% and 99.0% identity respectively to the corresponding genes of Rickettsia buchneri. Phylogenetic tree constructions show that the folate genes of phylotype G021 and homologous genes from various Rickettsia species are monophyletic. This study has shown that all folate genes exist in the genome of Rickettsia species phylotype G021 and that this bacterium has the genetic capability for de novo folate synthesis. PMID:26650541

Sex Genotyping of Archival Fixed and Immunolabeled Guinea Pig Cochleas.

PubMed

Depreux, Frédéric F; Czech, Lyubov; Whitlon, Donna S

2018-03-26

For decades, outbred guinea pigs (GP) have been used as research models. Various past research studies using guinea pigs used measures that, unknown at the time, may be sex-dependent, but from which today, archival tissues may be all that remain. We aimed to provide a protocol for sex-typing archival guinea pig tissue, whereby past experiments could be re-evaluated for sex effects. No PCR sex-genotyping protocols existed for GP. We found that published sequence of the GP Sry gene differed from that in two separate GP stocks. We used sequences from other species to deduce PCR primers for Sry. After developing a genomic DNA extraction for archival, fixed, decalcified, immunolabeled, guinea pig cochlear half-turns, we used a multiplex assay (Y-specific Sry; X-specific Dystrophin) to assign sex to tissue as old as 3 years. This procedure should allow reevaluation of prior guinea pig studies in various research areas for the effects of sex on experimental outcomes.

Cloud computing for genomic data analysis and collaboration.

PubMed

Langmead, Ben; Nellore, Abhinav

2018-04-01

Next-generation sequencing has made major strides in the past decade. Studies based on large sequencing data sets are growing in number, and public archives for raw sequencing data have been doubling in size every 18 months. Leveraging these data requires researchers to use large-scale computational resources. Cloud computing, a model whereby users rent computers and storage from large data centres, is a solution that is gaining traction in genomics research. Here, we describe how cloud computing is used in genomics for research and large-scale collaborations, and argue that its elasticity, reproducibility and privacy features make it ideally suited for the large-scale reanalysis of publicly available archived data, including privacy-protected data.

Widespread pollution of the South American atmosphere predates the industrial revolution by 240 y

PubMed Central

Uglietti, Chiara; Gabrielli, Paolo; Cooke, Colin A.; Vallelonga, Paul; Thompson, Lonnie G.

2015-01-01

In the Southern Hemisphere, evidence for preindustrial atmospheric pollution is restricted to a few geological archives of low temporal resolution that record trace element deposition originating from past mining and metallurgical operations in South America. Therefore, the timing and the spatial impact of these activities on the past atmosphere remain poorly constrained. Here we present an annually resolved ice core record (A.D. 793–1989) from the high-altitude drilling site of Quelccaya (Peru) that archives preindustrial and industrial variations in trace elements. During the precolonial period (i.e., pre-A.D. 1532), the deposition of trace elements was mainly dominated by the fallout of aeolian dust and of ash from occasional volcanic eruptions, indicating that metallurgic production during the Inca Empire (A.D. 1438−1532) had a negligible impact on the South American atmosphere. In contrast, a widespread anthropogenic signal is evident after around A.D. 1540, which corresponds with the beginning of colonial mining and metallurgy in Peru and Bolivia, ∼240 y before the Industrial Revolution. This shift was due to a major technological transition for silver extraction in South America (A.D. 1572), from lead-based smelting to mercury amalgamation, which precipitated a massive increase in mining activities. However, deposition of toxic trace metals during the Colonial era was still several factors lower than 20th century pollution that was unprecedented over the entirety of human history. PMID:25675506

From the archives of scientific diplomacy: science and the shared interests of Samuel Hartlib's London and Frederick Clodius's Gottorf.

PubMed

Keller, Vera; Penman, Leigh T I

2015-03-01

Many historians have traced the accumulation of scientific archives via communication networks. Engines for communication in early modernity have included trade, the extrapolitical Republic of Letters, religious enthusiasm, and the centralization of large emerging information states. The communication between Samuel Hartlib, John Dury, Duke Friedrich III of Gottorf-Holstein, and his key agent in England, Frederick Clodius, points to a less obvious but no less important impetus--the international negotiations of smaller states. Smaller states shaped communication networks in an international (albeit politically and religiously slanted) direction. Their networks of negotiation contributed to the internationalization of emerging science through a political and religious concept of shared interest. While interest has been central to social studies of science, interest itself has not often been historicized within the history of science. This case study demonstrates the co-production of science and society by tracing how period concepts of interest made science international.

Archive of digital boomer and CHIRP seismic reflection data collected during USGS cruise 06FSH03 offshore of Fort Lauderdale, Florida, September 2006

USGS Publications Warehouse

Harrison, Arnell S.; Dadisman, Shawn V.; Reich, Christopher D.; Wiese, Dana S.; Greenwood, Jason W.; Swarzenski, Peter W.

2007-01-01

In September of 2006, the U.S. Geological Survey conducted geophysical surveys offshore of Fort Lauderdale, FL. This report serves as an archive of unprocessed digital boomer and CHIRP seismic reflection data, trackline maps, navigation files, GIS information, Field Activity Collection System (FACS) logs, observer's logbook, and formal FGDC metadata. Filtered and gained digital images of the seismic profiles are also provided. The archived trace data are in standard Society of Exploration Geophysicists (SEG) SEG-Y format (Barry and others, 1975) and may be downloaded and processed with commercial or public domain software such as Seismic Unix (SU). Example SU processing scripts and USGS software for viewing the SEG-Y files (Zihlman, 1992) are also provided.

Accommodation space, relative sea level, and the archiving of paleo-earthquakes along subduction zones

USGS Publications Warehouse

Kelsey, Harvey M.; Engelhart, Simon E.; Pilarczyk, Jessica E.; Horton, Benjamin P.; Rubin, Charles; Daryono, Mudrik; Ismail, Nazli; Hawkes, Andrea D.; Bernhardt, Christopher E.; Cahill, Niamh

2015-01-01

The spatial variability of Holocene relative sea-level (RSL) change influences the capacities of coastal environments to accommodate a sedimentary record of paleoenvironmental change. In this study we couch a specific investigation in more general terms in order to demonstrate the applicability of the relative sea-level history approach to paleoseismic investigations. Using subsidence stratigraphy, we trace the different modes of coastal sedimentation over the course of time in the eastern Indian Ocean where RSL change evolved from rapidly rising to static from 8000 yr ago to present. Initially, the coastal sites from the Aceh, Sumatra, coastal plain, which are subject to repeated great earthquakes and tsunamis, built up a sedimentary sequence in response to a RSL rise of 1.4 mm/yr. The sequence found at 2 sites 8 km apart contained 3 soils of a mangrove origin (Rhizophora,Bruguiera/Ceriops, Avicennia pollen, and/or intertidal foraminifera) buried by sudden submergence related to coseismic subsidence and 6 tsunami sands that contain pristine subtidal and planktic foraminifera. After 3800 cal yr B.P. (years before A.D. 1950), sea level stabilized and remained such to the present. The stable relative sea level reduced accommodation space in the late Holocene, suggesting that the continued aggradation of the coastal plain was a consequence of periodic coastal inundation by tsunamis.

Characterization of the canine desmin (DES) gene and evaluation as a candidate gene for dilated cardiomyopathy in the Dobermann.

PubMed

Stabej, Polona; Imholz, Sandra; Versteeg, Serge A; Zijlstra, Carla; Stokhof, Arnold A; Domanjko-Petric, Aleksandra; Leegwater, Peter A J; van Oost, Bernard A

2004-10-13

Canine-dilated cardiomyopathy (DCM) in dogs is a disease of the myocardium associated with dilatation and impaired contraction of the ventricles and is suspected to have a genetic cause. A missense mutation in the desmin gene (DES) causes DCM in a human family. Human DCM closely resembles the canine disease. In the present study, we evaluated whether DES gene mutations are responsible for DCM in Dobermann dogs. We have isolated bacterial artificial chromosome clones (BACs) containing the canine DES gene and determined the chromosomal location by fluorescence in situ hybridization (FISH). Using data deposited in the NCBI trace archive and GenBank, the canine DES gene DNA sequence was assembled and seven single nucleotide polymorphisms (SNPs) were identified. From the canine DES gene BAC clones, a polymorphic microsatellite marker was isolated. The microsatellite marker and four informative desmin SNPs were typed in a Dobermann family with frequent DCM occurrence, but the disease phenotype did not associate with a desmin haplotype. We concluded that mutations in the DES gene do not play a role in Dobermann DCM. Availability of the microsatellite marker, SNPs and DNA sequence reported in this study enable fast evaluation of the DES gene as a DCM candidate gene in other dog breeds with DCM occurrence.

Tracing the influence of Mediterranean climate on Southeastern Europe during the past 350,000 years

PubMed Central

Obreht, Igor; Zeeden, Christian; Hambach, Ulrich; Veres, Daniel; Marković, Slobodan B.; Bösken, Janina; Svirčev, Zorica; Bačević, Nikola; Gavrilov, Milivoj B.; Lehmkuhl, Frank

2016-01-01

Loess-palaeosol sequences are valuable archives of past environmental changes. Although regional palaeoclimatic trends and conditions in Southeastern Europe have been inferred from loess sequences, large scale forcing mechanisms responsible for their formation have yet to be determined. Southeastern Europe is a climatically sensitive region, existing under the strong influence of both Mediterranean and continental climates. Establishment of the spatial and temporal evolution and interaction of these climatic areas is essential to understand the mechanisms of loess formation. Here we present high-resolution grain-size, environmental magnetic, spectrophotometric and geochemical data from the Stalać section in the Central Balkans (Serbia) for the past ~350,000 years. The goal of this study is to determine the influence of the Mediterranean climate during this period. Data show that the Central Balkans were under different atmospheric circulation regimes, especially during Marine Isotope Stages 9 and 7, while continental climate prevailed further north. We observe a general weakening of the Mediterranean climate influence with time. Our data suggest that Marine Isotope Stage 5 was the first interglacial in the Central Balkans that had continental climate characteristics. This prominent shift in climatic conditions resulted in unexpectedly warm and humid conditions during the last glacial. PMID:27824102

Chemically-dissected Rotation Curves of the Galactic Bulge from Hubble Space Telescope Proper Motions on the Main Sequence

NASA Astrophysics Data System (ADS)

Clarkson, William I.; Calamida, Annalisa; Sahu, Kailash C.; Gennaro, Mario; Brown, Thomas M.; Avila, Roberto J.; Rich, R. Michael; Debattista, Victor P.

2018-01-01

We report results from a pilot study using archival Hubble Space Telescope imaging observations in seven filters over a multi-year time-baseline to probe the co-dependence of chemical abundance and kinematics, using proper motion-based rotation curves selected on relative metallicity. With spectroscopic studies suggesting the metallicity distribution of the Bulge may be bimodal, we follow a data-driven approach to classify stars as belonging to metal-rich or metal-poor ends of the observed relative photometric metallicity distribution, with classification implemented using standard unsupervised learning techniques. We detect clear differences in both slope and amplitude of the proper motion-based rotation curve as traced by the more “metal-rich” and “metal-poor” samples. The sense of the discrepancy is qualitatively in agreement both with recent observational and theoretical indications; the “metal-poor” sample does indeed show a weaker rotation signature.This is the first study to dissect the proper motion rotation curve of the Bulge by chemical abundance using main-sequence targets, which are orders of magnitude more common on the sky than bright giants. These techniques thus offer a pencil-beam complement to wide-field studies that use more traditional tracer populations.

Experimental Design-Based Functional Mining and Characterization of High-Throughput Sequencing Data in the Sequence Read Archive

PubMed Central

Nakazato, Takeru; Ohta, Tazro; Bono, Hidemasa

2013-01-01

High-throughput sequencing technology, also called next-generation sequencing (NGS), has the potential to revolutionize the whole process of genome sequencing, transcriptomics, and epigenetics. Sequencing data is captured in a public primary data archive, the Sequence Read Archive (SRA). As of January 2013, data from more than 14,000 projects have been submitted to SRA, which is double that of the previous year. Researchers can download raw sequence data from SRA website to perform further analyses and to compare with their own data. However, it is extremely difficult to search entries and download raw sequences of interests with SRA because the data structure is complicated, and experimental conditions along with raw sequences are partly described in natural language. Additionally, some sequences are of inconsistent quality because anyone can submit sequencing data to SRA with no quality check. Therefore, as a criterion of data quality, we focused on SRA entries that were cited in journal articles. We extracted SRA IDs and PubMed IDs (PMIDs) from SRA and full-text versions of journal articles and retrieved 2748 SRA ID-PMID pairs. We constructed a publication list referring to SRA entries. Since, one of the main themes of -omics analyses is clarification of disease mechanisms, we also characterized SRA entries by disease keywords, according to the Medical Subject Headings (MeSH) extracted from articles assigned to each SRA entry. We obtained 989 SRA ID-MeSH disease term pairs, and constructed a disease list referring to SRA data. We previously developed feature profiles of diseases in a system called “Gendoo”. We generated hyperlinks between diseases extracted from SRA and the feature profiles of it. The developed project, publication and disease lists resulting from this study are available at our web service, called “DBCLS SRA” (http://sra.dbcls.jp/). This service will improve accessibility to high-quality data from SRA. PMID:24167589

Performance Data Gathering and Representation from Fixed-Size Statistical Data

NASA Technical Reports Server (NTRS)

Yan, Jerry C.; Jin, Haoqiang H.; Schmidt, Melisa A.; Kutler, Paul (Technical Monitor)

1997-01-01

The two commonly-used performance data types in the super-computing community, statistics and event traces, are discussed and compared. Statistical data are much more compact but lack the probative power event traces offer. Event traces, on the other hand, are unbounded and can easily fill up the entire file system during program execution. In this paper, we propose an innovative methodology for performance data gathering and representation that offers a middle ground. Two basic ideas are employed: the use of averages to replace recording data for each instance and 'formulae' to represent sequences associated with communication and control flow. The user can trade off tracing overhead, trace data size with data quality incrementally. In other words, the user will be able to limit the amount of trace data collected and, at the same time, carry out some of the analysis event traces offer using space-time views. With the help of a few simple examples, we illustrate the use of these techniques in performance tuning and compare the quality of the traces we collected with event traces. We found that the trace files thus obtained are, indeed, small, bounded and predictable before program execution, and that the quality of the space-time views generated from these statistical data are excellent. Furthermore, experimental results showed that the formulae proposed were able to capture all the sequences associated with 11 of the 15 applications tested. The performance of the formulae can be incrementally improved by allocating more memory at runtime to learn longer sequences.

Dose-Response Analysis of RNA-Seq Profiles in Archival Formalin-Fixed Paraffin-Embedded (FFPE) Samples.

EPA Science Inventory

Use of archival resources has been limited to date by inconsistent methods for genomic profiling of degraded RNA from formalin-fixed paraffin-embedded (FFPE) samples. RNA-sequencing offers a promising way to address this problem. Here we evaluated transcriptomic dose responses us...

TOTAL PRECIPITATION DATA - U.S HISTORICAL CLIMATOLOGY NETWORK (HCN)

EPA Science Inventory

The Carbon Dioxide Information Analysis Center, which includes the World Data Center-A for Atmospheric Trace Gases, is the primary global-change data and information analysis center of the U.S. Department of Energy (DOE). More than just an archive of data sets and publications, ...

Automated method for tracing leading and trailing processes of migrating neurons in confocal image sequences

NASA Astrophysics Data System (ADS)

Kerekes, Ryan A.; Gleason, Shaun S.; Trivedi, Niraj; Solecki, David J.

2010-03-01

Segmentation, tracking, and tracing of neurons in video imagery are important steps in many neuronal migration studies and can be inaccurate and time-consuming when performed manually. In this paper, we present an automated method for tracing the leading and trailing processes of migrating neurons in time-lapse image stacks acquired with a confocal fluorescence microscope. In our approach, we first locate and track the soma of the cell of interest by smoothing each frame and tracking the local maxima through the sequence. We then trace the leading process in each frame by starting at the center of the soma and stepping repeatedly in the most likely direction of the leading process. This direction is found at each step by examining second derivatives of fluorescent intensity along curves of constant radius around the current point. Tracing terminates after a fixed number of steps or when fluorescent intensity drops below a fixed threshold. We evolve the resulting trace to form an improved trace that more closely follows the approximate centerline of the leading process. We apply a similar algorithm to the trailing process of the cell by starting the trace in the opposite direction. We demonstrate our algorithm on two time-lapse confocal video sequences of migrating cerebellar granule neurons (CGNs). We show that the automated traces closely approximate ground truth traces to within 1 or 2 pixels on average. Additionally, we compute line intensity profiles of fluorescence along the automated traces and quantitatively demonstrate their similarity to manually generated profiles in terms of fluorescence peak locations.

Insights into transcriptomes of Big and Low sagebrush

Treesearch

Mark D. Huynh; Justin T. Page; Bryce A. Richardson; Joshua A. Udall

2015-01-01

We report the sequencing and assembly of three transcriptomes from Big (Artemisia tridentatassp. wyomingensis and A. tridentatassp. tridentata) and Low (A. arbuscula ssp. arbuscula) sagebrush. The sequence reads are available in the Sequence Read Archive of NCBI. We demonstrate the utilities of these transcriptomes for gene discovery and phylogenomic analysis. An...

Techno-Nationalism and the Construction of University Technology Transfer

ERIC Educational Resources Information Center

Sá, Creso; Kretz, Andrew; Sigurdson, Kristjan

2013-01-01

Our historical study of Canada's main research university illuminates the overlooked influence of national identities and interests as forces shaping the institutionalization of technology transfer. Through the use of archival sources we trace the rise and influence of Canadian technological nationalism--a response to Canada's perceived dependency…

History of School of Education

ERIC Educational Resources Information Center

Gill, Wanda Eileen; Kosub, Mariann

2006-01-01

The history of the Bowie State University School of Education is traced from very humble beginnings in 1865 with its formation to provide teachers for Freedmen following the Civil War to a School of Education in a comprehensive university. Maryland Archives, student publications, college catalogues, legislative and other records were searched to…

Beyond the Archive: Cultural Memory in Dance and Theater

ERIC Educational Resources Information Center

Bernstein, Carol L.

2007-01-01

This essay uses the concept of the constellation to characterize the relations among interdisciplinarity, cultural memory, and comparative literature. To do so entails: (a) reviewing the paradoxical interdisciplinarity of comparative literature, (b) tracing its establishment at a liberal arts college (Bryn Mawr College, USA), and (c) describing a…

Language Policy and Language Planning in Cyprus

ERIC Educational Resources Information Center

Hadjioannou, Xenia; Tsiplakou, Stavroula; Kappler, Matthias

2011-01-01

The aim of this monograph is to provide a detailed account of language policy and language planning in Cyprus. Using both historical and synchronic data and adopting a mixed-methods approach (archival research, ethnographic tools and insights from sociolinguistics and Critical Discourse Analysis), this study attempts to trace the origins and the…

Harmonization of Training in Librarianship, Information Science and Archives.

ERIC Educational Resources Information Center

United Nations Educational, Scientific and Cultural Organization, Paris (France). General Information Programme.

This pamphlet is designed to show why there are many advantages in a harmonized approach to the training of archivists, librarians, and specialists in information science and what these advantages are. Following introductory discussions of the concept of harmonization, a brief history traces Unesco's role in training information professionals in…

Cyber infrastructure for Fusarium: three integrated platforms supporting strain identification, phylogenetics, comparative genomics and knowledge sharing.

PubMed

Park, Bongsoo; Park, Jongsun; Cheong, Kyeong-Chae; Choi, Jaeyoung; Jung, Kyongyong; Kim, Donghan; Lee, Yong-Hwan; Ward, Todd J; O'Donnell, Kerry; Geiser, David M; Kang, Seogchan

2011-01-01

The fungal genus Fusarium includes many plant and/or animal pathogenic species and produces diverse toxins. Although accurate species identification is critical for managing such threats, it is difficult to identify Fusarium morphologically. Fortunately, extensive molecular phylogenetic studies, founded on well-preserved culture collections, have established a robust foundation for Fusarium classification. Genomes of four Fusarium species have been published with more being currently sequenced. The Cyber infrastructure for Fusarium (CiF; http://www.fusariumdb.org/) was built to support archiving and utilization of rapidly increasing data and knowledge and consists of Fusarium-ID, Fusarium Comparative Genomics Platform (FCGP) and Fusarium Community Platform (FCP). The Fusarium-ID archives phylogenetic marker sequences from most known species along with information associated with characterized isolates and supports strain identification and phylogenetic analyses. The FCGP currently archives five genomes from four species. Besides supporting genome browsing and analysis, the FCGP presents computed characteristics of multiple gene families and functional groups. The Cart/Favorite function allows users to collect sequences from Fusarium-ID and the FCGP and analyze them later using multiple tools without requiring repeated copying-and-pasting of sequences. The FCP is designed to serve as an online community forum for sharing and preserving accumulated experience and knowledge to support future research and education.

Cyber infrastructure for Fusarium: three integrated platforms supporting strain identification, phylogenetics, comparative genomics and knowledge sharing

PubMed Central

Park, Bongsoo; Park, Jongsun; Cheong, Kyeong-Chae; Choi, Jaeyoung; Jung, Kyongyong; Kim, Donghan; Lee, Yong-Hwan; Ward, Todd J.; O'Donnell, Kerry; Geiser, David M.; Kang, Seogchan

2011-01-01

The fungal genus Fusarium includes many plant and/or animal pathogenic species and produces diverse toxins. Although accurate species identification is critical for managing such threats, it is difficult to identify Fusarium morphologically. Fortunately, extensive molecular phylogenetic studies, founded on well-preserved culture collections, have established a robust foundation for Fusarium classification. Genomes of four Fusarium species have been published with more being currently sequenced. The Cyber infrastructure for Fusarium (CiF; http://www.fusariumdb.org/) was built to support archiving and utilization of rapidly increasing data and knowledge and consists of Fusarium-ID, Fusarium Comparative Genomics Platform (FCGP) and Fusarium Community Platform (FCP). The Fusarium-ID archives phylogenetic marker sequences from most known species along with information associated with characterized isolates and supports strain identification and phylogenetic analyses. The FCGP currently archives five genomes from four species. Besides supporting genome browsing and analysis, the FCGP presents computed characteristics of multiple gene families and functional groups. The Cart/Favorite function allows users to collect sequences from Fusarium-ID and the FCGP and analyze them later using multiple tools without requiring repeated copying-and-pasting of sequences. The FCP is designed to serve as an online community forum for sharing and preserving accumulated experience and knowledge to support future research and education. PMID:21087991

Archive of digital and digitized analog boomer seismic reflection data collected during USGS cruise 96CCT02 in Copano, Corpus Christi, and Nueces Bays and Corpus Christi Bayou, Texas, July 1996

USGS Publications Warehouse

Harrison, Arnell S.; Dadisman, Shawn V.; Kindinger, Jack G.; Morton, Robert A.; Blum, Mike D.; Wiese, Dana S.; Subiño, Janice A.

2007-01-01

In June of 1996, the U.S. Geological Survey conducted geophysical surveys from Nueces to Copano Bays, Texas. This report serves as an archive of unprocessed digital boomer seismic reflection data, trackline maps, navigation files, GIS information, cruise log, and formal FGDC metadata. Filtered and gained digital images of the seismic profiles and high resolution scanned TIFF images of the original paper printouts are also provided. The archived trace data are in standard Society of Exploration Geophysicists (SEG) SEG-Y format (Barry and others, 1975) and may be downloaded and processed with commercial or public domain software such as Seismic Unix (SU). Example SU processing scripts and USGS software for viewing the SEG-Y files (Zihlman, 1992) are also provided.

Archive of Digital Boomer Seismic Reflection Data Collected During USGS Field Activity 08LCA04 in Lakes Cherry, Helen, Hiawassee, Louisa, and Prevatt, Central Florida, September 2008

USGS Publications Warehouse

Harrison, Arnell S.; Dadisman, Shawn V.; Davis, Jeffrey B.; Flocks, James G.; Wiese, Dana S.

2009-01-01

From September 2 through 4, 2008, the U.S. Geological Survey and St. Johns River Water Management District (SJRWMD) conducted geophysical surveys in Lakes Cherry, Helen, Hiawassee, Louisa, and Prevatt, central Florida. This report serves as an archive of unprocessed digital boomer seismic reflection data, trackline maps, navigation files, GIS information, FACS logs, and formal FGDC metadata. Filtered and gained digital images of the seismic profiles are also provided. The archived trace data are in standard Society of Exploration Geophysicists (SEG) SEG-Y format (Barry and others, 1975) and may be downloaded and processed with commercial or public domain software such as Seismic Unix (SU). Example SU processing scripts and USGS software for viewing the SEG-Y files (Zihlman, 1992) are also provided.

A Method to Evaluate Genome-Wide Methylation in Archival Formalin-Fixed, Paraffin-Embedded Ovarian Epithelial Cells

PubMed Central

Li, Qiling; Li, Min; Ma, Li; Li, Wenzhi; Wu, Xuehong; Richards, Jendai; Fu, Guoxing; Xu, Wei; Bythwood, Tameka; Li, Xu; Wang, Jianxin; Song, Qing

2014-01-01

Background The use of DNA from archival formalin and paraffin embedded (FFPE) tissue for genetic and epigenetic analyses may be problematic, since the DNA is often degraded and only limited amounts may be available. Thus, it is currently not known whether genome-wide methylation can be reliably assessed in DNA from archival FFPE tissue. Methodology/Principal Findings Ovarian tissues, which were obtained and formalin-fixed and paraffin-embedded in either 1999 or 2011, were sectioned and stained with hematoxylin-eosin (H&E).Epithelial cells were captured by laser micro dissection, and their DNA subjected to whole genomic bisulfite conversion, whole genomic polymerase chain reaction (PCR) amplification, and purification. Sequencing and software analyses were performed to identify the extent of genomic methylation. We observed that 31.7% of sequence reads from the DNA in the 1999 archival FFPE tissue, and 70.6% of the reads from the 2011 sample, could be matched with the genome. Methylation rates of CpG on the Watson and Crick strands were 32.2% and 45.5%, respectively, in the 1999 sample, and 65.1% and 42.7% in the 2011 sample. Conclusions/Significance We have developed an efficient method that allows DNA methylation to be assessed in archival FFPE tissue samples. PMID:25133528

Whole Genome Amplification and Reduced-Representation Genome Sequencing of Schistosoma japonicum Miracidia

PubMed Central

Shortt, Jonathan A.; Card, Daren C.; Schield, Drew R.; Liu, Yang; Zhong, Bo; Castoe, Todd A.

2017-01-01

Background In areas where schistosomiasis control programs have been implemented, morbidity and prevalence have been greatly reduced. However, to sustain these reductions and move towards interruption of transmission, new tools for disease surveillance are needed. Genomic methods have the potential to help trace the sources of new infections, and allow us to monitor drug resistance. Large-scale genotyping efforts for schistosome species have been hindered by cost, limited numbers of established target loci, and the small amount of DNA obtained from miracidia, the life stage most readily acquired from humans. Here, we present a method using next generation sequencing to provide high-resolution genomic data from S. japonicum for population-based studies. Methodology/Principal Findings We applied whole genome amplification followed by double digest restriction site associated DNA sequencing (ddRADseq) to individual S. japonicum miracidia preserved on Whatman FTA cards. We found that we could effectively and consistently survey hundreds of thousands of variants from 10,000 to 30,000 loci from archived miracidia as old as six years. An analysis of variation from eight miracidia obtained from three hosts in two villages in Sichuan showed clear population structuring by village and host even within this limited sample. Conclusions/Significance This high-resolution sequencing approach yields three orders of magnitude more information than microsatellite genotyping methods that have been employed over the last decade, creating the potential to answer detailed questions about the sources of human infections and to monitor drug resistance. Costs per sample range from $50-$200, depending on the amount of sequence information desired, and we expect these costs can be reduced further given continued reductions in sequencing costs, improvement of protocols, and parallelization. This approach provides new promise for using modern genome-scale sampling to S. japonicum surveillance, and could be applied to other schistosome species and other parasitic helminthes. PMID:28107347

Single-Center Experience with a Targeted Next Generation Sequencing Assay for Assessment of Relevant Somatic Alterations in Solid Tumors.

PubMed

Paasinen-Sohns, Aino; Koelzer, Viktor H; Frank, Angela; Schafroth, Julian; Gisler, Aline; Sachs, Melanie; Graber, Anne; Rothschild, Sacha I; Wicki, Andreas; Cathomas, Gieri; Mertz, Kirsten D

2017-03-01

Companion diagnostics rely on genomic testing of molecular alterations to enable effective cancer treatment. Here we report the clinical application and validation of the Oncomine Focus Assay (OFA), an integrated, commercially available next-generation sequencing (NGS) assay for the rapid and simultaneous detection of single nucleotide variants, short insertions and deletions, copy number variations, and gene rearrangements in 52 cancer genes with therapeutic relevance. Two independent patient cohorts were investigated to define the workflow, turnaround times, feasibility, and reliability of OFA targeted sequencing in clinical application and using archival material. Cohort I consisted of 59 diagnostic clinical samples from the daily routine submitted for molecular testing over a 4-month time period. Cohort II consisted of 39 archival melanoma samples that were up to 15years old. Libraries were prepared from isolated nucleic acids and sequenced on the Ion Torrent PGM sequencer. Sequencing datasets were analyzed using the Ion Reporter software. Genomic alterations were identified and validated by orthogonal conventional assays including pyrosequencing and immunohistochemistry. Sequencing results of both cohorts, including archival formalin-fixed, paraffin-embedded material stored up to 15years, were consistent with published variant frequencies. A concordance of 100% between established assays and OFA targeted NGS was observed. The OFA workflow enabled a turnaround of 3½ days. Taken together, OFA was found to be a convenient tool for fast, reliable, broadly applicable and cost-effective targeted NGS of tumor samples in routine diagnostics. Thus, OFA has strong potential to become an important asset for precision oncology. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Studies of Global Solar Magnetic Field Patterns Using a Newly Digitized Archive

NASA Astrophysics Data System (ADS)

Hewins, I.; Webb, D. F.; Gibson, S. E.; McFadden, R.; Emery, B. A.; Malanushenko, A. V.

2017-12-01

The McIntosh Archive consists of a set of hand-drawn solar Carrington maps created by Patrick McIntosh from 1964 to 2009. McIntosh used mainly Ha, He 10830Å and photospheric magnetic measurements from both ground-based and NASA satellite observations. With these he traced polarity inversion lines (PILs), filaments, sunspots and plage and, later, coronal holes, yielding a unique 45-year record of features associated with the large-scale organization of the solar magnetic field. We discuss our efforts to preserve and digitize this archive; the original hand-drawn maps have been scanned, a method for processing these scans into digital, searchable format has been developed, and a website and an archival repository at NOAA's National Centers for Environmental Information (NCEI) has been created. The archive is complete for SC 23 and partially complete for SCs 21 and 22. In this paper we show examples of how the data base can be utilized for scientific applications. We compare the evolution of the areas and boundaries of CHs with other recent results, and we use the maps to track the global, SC-evolution of filaments, large-scale positive and negative polarity regions, PILs and sunspots.

HIV-TRACE (Transmission Cluster Engine): a tool for large scale molecular epidemiology of HIV-1 and other rapidly evolving pathogens.

PubMed

Kosakovsky Pond, Sergei L; Weaver, Steven; Leigh Brown, Andrew J; Wertheim, Joel O

2018-01-31

In modern applications of molecular epidemiology, genetic sequence data are routinely used to identify clusters of transmission in rapidly evolving pathogens, most notably HIV-1. Traditional 'shoeleather' epidemiology infers transmission clusters by tracing chains of partners sharing epidemiological connections (e.g., sexual contact). Here, we present a computational tool for identifying a molecular transmission analog of such clusters: HIV-TRACE (TRAnsmission Cluster Engine). HIV-TRACE implements an approach inspired by traditional epidemiology, by identifying chains of partners whose viral genetic relatedness imply direct or indirect epidemiological connections. Molecular transmission clusters are constructed using codon-aware pairwise alignment to a reference sequence followed by pairwise genetic distance estimation among all sequences. This approach is computationally tractable and is capable of identifying HIV-1 transmission clusters in large surveillance databases comprising tens or hundreds of thousands of sequences in near real time, i.e., on the order of minutes to hours. HIV-TRACE is available at www.hivtrace.org and from github.com/veg/hivtrace, along with the accompanying result visualization module from github.com/veg/hivtrace-viz. Importantly, the approach underlying HIV-TRACE is not limited to the study of HIV-1 and can be applied to study outbreaks and epidemics of other rapidly evolving pathogens. © The Author 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Listening to the Mind: Tracing the Auditory History of Mental Illness in Archives and Exhibitions.

PubMed

Birdsall, Carolyn; Parry, Manon; Tkaczyk, Viktoria

2015-11-01

With increasing interest in the representation of histories of mental health in museums, sound has played a key role as a tool to access a range of voices. This essay discusses how sound can be used to give voice to those previously silenced. The focus is on the use of sound recording in the history of mental health care, and the archival sources left behind for potential reuse. Exhibition strategies explored include the use of sound to interrogate established narratives, to interrupt associations visitors make when viewing the material culture of mental health, and to foster empathic listening among audiences.

The Miracle of Microfilm: The Foundation of the Largest Genealogical Record Collection in the World.

ERIC Educational Resources Information Center

Powell, Ted F.

1985-01-01

Traces origins of the Genealogical Department of The Church of Jesus Christ of Latter-Day Saints (Mormon), highlighting microfilm technology, equipment used, development of the 16mm camera, film processing, quality control, filming techniques, specialized microfilming, archival storage (The Granite Mountain Records Vault), the genealogical library…

Archaeological Feature Detection from Archive Aerial Photography with a Sfm-Mvs and Image Enhancement Pipeline

NASA Astrophysics Data System (ADS)

Peppa, M. V.; Mills, J. P.; Fieber, K. D.; Haynes, I.; Turner, S.; Turner, A.; Douglas, M.; Bryan, P. G.

2018-05-01

Understanding and protecting cultural heritage involves the detection and long-term documentation of archaeological remains alongside the spatio-temporal analysis of their landscape evolution. Archive aerial photography can illuminate traces of ancient features which typically appear with different brightness values from their surrounding environment, but are not always well defined. This research investigates the implementation of the Structure-from-Motion - Multi-View Stereo image matching approach with an image enhancement algorithm to derive three epochs of orthomosaics and digital surface models from visible and near infrared historic aerial photography. The enhancement algorithm uses decorrelation stretching to improve the contrast of the orthomosaics so as archaeological features are better detected. Results include 2D / 3D locations of detected archaeological traces stored into a geodatabase for further archaeological interpretation and correlation with benchmark observations. The study also discusses the merits and difficulties of the process involved. This research is based on a European-wide project, entitled "Cultural Heritage Through Time", and the case study research was carried out as a component of the project in the UK.

Constructing Space-Time Views from Fixed Size Statistical Data: Getting the Best of both Worlds

NASA Technical Reports Server (NTRS)

Schmidt, Melisa; Yan, Jerry C.

1997-01-01

Many performance monitoring tools are currently available to the super-computing community. The performance data gathered and analyzed by these tools fall under two categories: statistics and event traces. Statistical data is much more compact but lacks the probative power event traces offer. Event traces, on the other hand, can easily fill up the entire file system during execution such that the instrumented execution may have to be terminated half way through. In this paper, we propose an innovative methodology for performance data gathering and representation that offers a middle ground. The user can trade-off tracing overhead, trace data size vs. data quality incrementally. In other words, the user will be able to limit the amount of trace collected and, at the same time, carry out some of the analysis event traces offer using space-time views for the entire execution. Two basic ideas arc employed: the use of averages to replace recording data for each instance and formulae to represent sequences associated with communication and control flow. With the help of a few simple examples, we illustrate the use of these techniques in performance tuning and compare the quality of the traces we collected vs. event traces. We found that the trace files thus obtained are, in deed, small, bounded and predictable before program execution and that the quality of the space time views generated from these statistical data are excellent. Furthermore, experimental results showed that the formulae proposed were able to capture 100% of all the sequences associated with 11 of the 15 applications tested. The performance of the formulae can be incrementally improved by allocating more memory at run-time to learn longer sequences.

Constructing Space-Time Views from Fixed Size Statistical Data: Getting the Best of Both Worlds

NASA Technical Reports Server (NTRS)

Schmidt, Melisa; Yan, Jerry C.; Bailey, David (Technical Monitor)

1996-01-01

Many performance monitoring tools are currently available to the super-computing community. The performance data gathered and analyzed by these tools fall under two categories: statistics and event traces. Statistical data is much more compact but lacks the probative power event traces offer. Event traces, on the other hand, can easily fill up the entire file system during execution such that the instrumented execution may have to be terminated half way through. In this paper, we propose an innovative methodology for performance data gathering and representation that offers a middle ground. The user can trade-off tracing overhead, trace data size vs. data quality incrementally. In other words, the user will be able to limit the amount of trace collected and, at the same time, carry out some of the analysis event traces offer using spacetime views for the entire execution. Two basic ideas are employed: the use of averages to replace recording data for each instance and "formulae" to represent sequences associated with communication and control flow. With the help of a few simple examples, we illustrate the use of these techniques in performance tuning and compare the quality of the traces we collected vs. event traces. We found that the trace files thus obtained are, in deed, small, bounded and predictable before program execution and that the quality of the space time views generated from these statistical data are excellent. Furthermore, experimental results showed that the formulae proposed were able to capture 100% of all the sequences associated with 11 of the 15 applications tested. The performance of the formulae can be incrementally improved by allocating more memory at run-time to learn longer sequences.

A new sequence for single-shot diffusion-weighted NMR spectroscopy by the trace of the diffusion tensor.

PubMed

Valette, Julien; Giraudeau, Céline; Marchadour, Charlotte; Djemai, Boucif; Geffroy, Françoise; Ghaly, Mohamed Ahmed; Le Bihan, Denis; Hantraye, Philippe; Lebon, Vincent; Lethimonnier, Franck

2012-12-01

Diffusion-weighted spectroscopy is a unique tool for exploring the intracellular microenvironment in vivo. In living systems, diffusion may be anisotropic, when biological membranes exhibit particular orientation patterns. In this work, a volume selective diffusion-weighted sequence is proposed, allowing single-shot measurement of the trace of the diffusion tensor, which does not depend on tissue anisotropy. With this sequence, the minimal echo time is only three times the diffusion time. In addition, cross-terms between diffusion gradients and other gradients are cancelled out. An adiabatic version, similar to localization by adiabatic selective refocusing sequence, is then derived, providing partial immunity against cross-terms. Proof of concept is performed ex vivo on chicken skeletal muscle by varying tissue orientation and intra-voxel shim. In vivo performance of the sequence is finally illustrated in a U87 glioblastoma mouse model, allowing the measurement of the trace apparent diffusion coefficient for six metabolites, including J-modulated metabolites. Although measurement performed along three separate orthogonal directions would bring similar accuracy on trace apparent diffusion coefficient under ideal conditions, the method described here should be useful for probing intimate properties of the cells with minimal experimental bias. Copyright © 2012 Wiley Periodicals, Inc.

Basecalling with LifeTrace

PubMed Central

Walther, Dirk; Bartha, Gábor; Morris, Macdonald

2001-01-01

A pivotal step in electrophoresis sequencing is the conversion of the raw, continuous chromatogram data into the actual sequence of discrete nucleotides, a process referred to as basecalling. We describe a novel algorithm for basecalling implemented in the program LifeTrace. Like Phred, currently the most widely used basecalling software program, LifeTrace takes processed trace data as input. It was designed to be tolerant to variable peak spacing by means of an improved peak-detection algorithm that emphasizes local chromatogram information over global properties. LifeTrace is shown to generate high-quality basecalls and reliable quality scores. It proved particularly effective when applied to MegaBACE capillary sequencing machines. In a benchmark test of 8372 dye-primer MegaBACE chromatograms, LifeTrace generated 17% fewer substitution errors, 16% fewer insertion/deletion errors, and 2.4% more aligned bases to the finished sequence than did Phred. For two sets totaling 6624 dye-terminator chromatograms, the performance improvement was 15% fewer substitution errors, 10% fewer insertion/deletion errors, and 2.1% more aligned bases. The processing time required by LifeTrace is comparable to that of Phred. The predicted quality scores were in line with observed quality scores, permitting direct use for quality clipping and in silico single nucleotide polymorphism (SNP) detection. Furthermore, we introduce a new type of quality score associated with every basecall: the gap-quality. It estimates the probability of a deletion error between the current and the following basecall. This additional quality score improves detection of single basepair deletions when used for locating potential basecalling errors during the alignment. We also describe a new protocol for benchmarking that we believe better discerns basecaller performance differences than methods previously published. PMID:11337481

On missing Data Treatment for degraded video and film archives: a survey and a new Bayesian approach.

PubMed

Kokaram, Anil C

2004-03-01

Image sequence restoration has been steadily gaining in importance with the increasing prevalence of visual digital media. The demand for content increases the pressure on archives to automate their restoration activities for preservation of the cultural heritage that they hold. There are many defects that affect archived visual material and one central issue is that of Dirt and Sparkle, or "Blotches." Research in archive restoration has been conducted for more than a decade and this paper places that material in context to highlight the advances made during that time. The paper also presents a new and simpler Bayesian framework that achieves joint processing of noise, missing data, and occlusion.

The McIntosh Archive: A solar feature database spanning four solar cycles

NASA Astrophysics Data System (ADS)

Gibson, S. E.; Malanushenko, A. V.; Hewins, I.; McFadden, R.; Emery, B.; Webb, D. F.; Denig, W. F.

2016-12-01

The McIntosh Archive consists of a set of hand-drawn solar Carrington maps created by Patrick McIntosh from 1964 to 2009. McIntosh used mainly H-alpha, He-1 10830 and photospheric magnetic measurements from both ground-based and NASA satellite observations. With these he traced coronal holes, polarity inversion lines, filaments, sunspots and plage, yielding a unique 45-year record of the features associated with the large-scale solar magnetic field. We will present the results of recent efforts to preserve and digitize this archive. Most of the original hand-drawn maps have been scanned, a method for processing these scans into digital, searchable format has been developed and streamlined, and an archival repository at NOAA's National Centers for Environmental Information (NCEI) has been created. We will demonstrate how Solar Cycle 23 data may now be accessed and how it may be utilized for scientific applications. In addition, we will discuss how this database of human-recognized features, which overlaps with the onset of high-resolution, continuous modern solar data, may act as a training set for computer feature recognition algorithms.

Coral skeletal geochemistry as a monitor of inshore water quality.

PubMed

Saha, Narottam; Webb, Gregory E; Zhao, Jian-Xin

2016-10-01

Coral reefs maintain extraordinary biodiversity and provide protection from tsunamis and storm surge, but inshore coral reef health is degrading in many regions due to deteriorating water quality. Deconvolving natural and anthropogenic changes to water quality is hampered by the lack of long term, dated water quality data but such records are required for forward modelling of reef health to aid their management. Reef corals provide an excellent archive of high resolution geochemical (trace element) proxies that can span hundreds of years and potentially provide records used through the Holocene. Hence, geochemical proxies in corals hold great promise for understanding changes in ancient water quality that can inform broader oceanographic and climatic changes in a given region. This article reviews and highlights the use of coral-based trace metal archives, including metal transported from rivers to the ocean, incorporation of trace metals into coral skeletons and the current 'state of the art' in utilizing coral trace metal proxies as tools for monitoring various types of local and regional source-specific pollution (river discharge, land use changes, dredging and dumping, mining, oil spills, antifouling paints, atmospheric sources, sewage). The three most commonly used coral trace element proxies (i.e., Ba/Ca, Mn/Ca, and Y/Ca) are closely associated with river runoff in the Great Barrier Reef, but considerable uncertainty remains regarding their complex biogeochemical cycling and controlling mechanisms. However, coral-based water quality reconstructions have suffered from a lack of understanding of so-called vital effects and early marine diagenesis. The main challenge is to identify and eliminate the influence of extraneous local factors in order to allow accurate water quality reconstructions and to develop alternate proxies to monitor water pollution. Rare earth elements have great potential as they are self-referencing and reflect basic terrestrial input. Copyright © 2016 Elsevier B.V. All rights reserved.

Coding Complete Genome for the Mogiana Tick Virus, a Jingmenvirus Isolated from Ticks in Brazil

DTIC Science & Technology

2017-05-04

sequences for all four genome segments. We downloaded the raw Illumina sequence reads from the NCBI Short Read Archive (GenBank...MGTV genome segments through sequence similarity (BLASTN) to the published genome of Jingmen tick virus (JMTV) isolate SY84 (GenBank: KJ001579-KJ001582...2014. Standards for sequencing viral genomes in the era of high-throughput sequencing . MBio 5:e01360–14. 8. Bankevich A, Nurk S, Antipov

The use of museum specimens with high-throughput DNA sequencers

PubMed Central

Burrell, Andrew S.; Disotell, Todd R.; Bergey, Christina M.

2015-01-01

Natural history collections have long been used by morphologists, anatomists, and taxonomists to probe the evolutionary process and describe biological diversity. These biological archives also offer great opportunities for genetic research in taxonomy, conservation, systematics, and population biology. They allow assays of past populations, including those of extinct species, giving context to present patterns of genetic variation and direct measures of evolutionary processes. Despite this potential, museum specimens are difficult to work with because natural postmortem processes and preservation methods fragment and damage DNA. These problems have restricted geneticists’ ability to use natural history collections primarily by limiting how much of the genome can be surveyed. Recent advances in DNA sequencing technology, however, have radically changed this, making truly genomic studies from museum specimens possible. We review the opportunities and drawbacks of the use of museum specimens, and suggest how to best execute projects when incorporating such samples. Several high-throughput (HT) sequencing methodologies, including whole genome shotgun sequencing, sequence capture, and restriction digests (demonstrated here), can be used with archived biomaterials. PMID:25532801

The ExoMars science data archive: status and plans

NASA Astrophysics Data System (ADS)

Heather, David

2016-07-01

The ExoMars program, a cooperation between ESA and Roscosmos, comprises two missions: the Trace Gas Orbiter, to be launched in 2016, and a rover and surface platform, due for launch in 2018. This will be the first time ESA has operated a rover, and the archiving and management of the science data to be returned will require a significant effort in development of the new Planetary Science Archive (PSA). The ExoMars mission data will also be formatted according to the new PDS4 Standards, based in XML, and this will be the first data of that format to be archived in the PSA. There are significant differences in the way in which a scientist will want to query, retrieve, and use data from a suite of rover instruments as opposed to remote sensing instrumentation from an orbiter. The PSA data holdings and the accompanying services are currently driven more towards the management of remote sensing data, so some significant changes will be needed. Among them will be a much closer link to the operational information than is currently available for our missions. NASA have a strong user community interaction with their analysts notebook, which provides detailed operational information to explain why, where and when operations took place. A similar approach will be needed for the future PSA, which is currently being designed. In addition to the archiving interface itself, there are differences with the overall archiving process being followed for ExoMars compared to previous ESA planetary missions. The Trace Gas Orbiter data pipelines for the first level of processing from telemetry to raw data, will be hosted directly by ESA's ground segment at ESAC in Madrid, where the archive itself resides. Data will have a continuous flow direct to the PSA, where after the given proprietary period, it will be directly released to the community via the new user interface. For the rover mission, the data pipelines are being developed by European industry, in close collaboration with ESA PSA experts and with the instrument teams. The first level of data processing will be carried out for all instruments at ALTEC in Turin where the pipelines are developed, and from where the rover operations will also be run. The PDS4 data will be directly produced and used for planning purposes within the operations centre before being passed on the the PSA for long term archiving. While this has clear advantages in the long-term regarding the timely population of the archive with at least the first level of data, the outsourcing of the pipelines to industry introduces complications. Firstly, it is difficult to have the necessary expertise on hand to train the individuals designing the pipelines, and to define the archiving conventions needed to meet the scientific needs of the mission. It also introduces issues in terms of driving the schedule, as industry is committed to making deliveries within fixed budgets and time-frames that may not necessarily be in line with the needs of archiving, and may not be able to respond well to the ongoing evolution of the PDS4 standards. This presentation will focus on the challenges involved in archiving rover data for the PSA, and will outline the plans and current status of the system being developed to respond to the needs of the mission.

The Slogan of the Century: "Music for Every Child; Every Child for Music"

ERIC Educational Resources Information Center

Heidingsfelder, Lauren

2014-01-01

This article is a review of literature detailing the 1923 origin of the phrase "Music for Every Child; Every Child for Music" and tracing its use in music education periodicals through the next nine decades. By delving into the now century-old archives for "Music Educators Journal" to research the historic declaration of Karl…

Processes and Dynamics behind Whole-School Reform: Nine-Year Journeys of Four Primary Schools

ERIC Educational Resources Information Center

Li, Yuk Yung

2017-01-01

Despite decades of research, little is known about the dynamics of sustaining change in school reform and how the process of change unfolds. By tracing the nine-year reform journeys of four primary schools in Hong Kong (using multiyear interview, observational, and archival data), this study uncovers the micro-processes the schools experienced…

Whole Transcriptome Sequencing Enables Discovery and Analysis of Viruses in Archived Primary Central Nervous System Lymphomas

PubMed Central

DeBoever, Christopher; Reid, Erin G.; Smith, Erin N.; Wang, Xiaoyun; Dumaop, Wilmar; Harismendy, Olivier; Carson, Dennis; Richman, Douglas; Masliah, Eliezer; Frazer, Kelly A.

2013-01-01

Primary central nervous system lymphomas (PCNSL) have a dramatically increased prevalence among persons living with AIDS and are known to be associated with human Epstein Barr virus (EBV) infection. Previous work suggests that in some cases, co-infection with other viruses may be important for PCNSL pathogenesis. Viral transcription in tumor samples can be measured using next generation transcriptome sequencing. We demonstrate the ability of transcriptome sequencing to identify viruses, characterize viral expression, and identify viral variants by sequencing four archived AIDS-related PCNSL tissue samples and analyzing raw sequencing reads. EBV was detected in all four PCNSL samples and cytomegalovirus (CMV), JC polyomavirus (JCV), and HIV were also discovered, consistent with clinical diagnoses. CMV was found to express three long non-coding RNAs recently reported as expressed during active infection. Single nucleotide variants were observed in each of the viruses observed and three indels were found in CMV. No viruses were found in several control tumor types including 32 diffuse large B-cell lymphoma samples. This study demonstrates the ability of next generation transcriptome sequencing to accurately identify viruses, including DNA viruses, in solid human cancer tissue samples. PMID:24023918

From non-random molecular structure to life and mind

NASA Technical Reports Server (NTRS)

Fox, S. W.

1989-01-01

The evolutionary hierarchy molecular structure-->macromolecular structure-->protobiological structure-->biological structure-->biological functions has been traced by experiments. The sequence always moves through protein. Extension of the experiments traces the formation of nucleic acids instructed by proteins. The proteins themselves were, in this picture, instructed by the self-sequencing of precursor amino acids. While the sequence indicated explains the thread of the emergence of life, protein in cellular membrane also provides the only known material basis for the emergence of mind in the context of emergence of life.

Using the Tools and Resources of the RCSB Protein Data Bank.

PubMed

Costanzo, Luigi Di; Ghosh, Sutapa; Zardecki, Christine; Burley, Stephen K

2016-09-07

The Protein Data Bank (PDB) archive is the worldwide repository of experimentally determined three-dimensional structures of large biological molecules found in all three kingdoms of life. Atomic-level structures of these proteins, nucleic acids, and complex assemblies thereof are central to research and education in molecular, cellular, and organismal biology, biochemistry, biophysics, materials science, bioengineering, ecology, and medicine. Several types of information are associated with each PDB archival entry, including atomic coordinates, primary experimental data, polymer sequence(s), and summary metadata. The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) serves as the U.S. data center for the PDB, distributing archival data and supporting both simple and complex queries that return results. These data can be freely downloaded, analyzed, and visualized using RCSB PDB tools and resources to gain a deeper understanding of fundamental biological processes, molecular evolution, human health and disease, and drug discovery. © 2016 by John Wiley & Sons, Inc. Copyright © 2016 John Wiley & Sons, Inc.

A search for T Tauri stars and related objects: Archival photometry of candidate variables in V733 Cep field

NASA Astrophysics Data System (ADS)

Jurdana-Šepić, R.; Poljančić Beljan, I.

Searching for T Tauri stars or related early type variables we carried out a BVRI photometric measurements of five candidates with positions within the field of the pre-main sequence object V733 Cephei (Persson's star) located in the dark cloud L1216 near to Cepheus OB3 Association: VES 946, VES 950, NSV 14333, NSV 25966 and V385 Cep. Their magnitudes are determined on the plates from Asiago Observatory historical photographic archive exposed 1971 - 1978. We provide finding charts for program stars and comparison sequence stars, magnitude estimations, magnitude mean values and BVR_cI_c light curves of program stars.

Curated eutherian third party data gene data sets.

PubMed

Premzl, Marko

2016-03-01

The free available eutherian genomic sequence data sets advanced scientific field of genomics. Of note, future revisions of gene data sets were expected, due to incompleteness of public eutherian genomic sequence assemblies and potential genomic sequence errors. The eutherian comparative genomic analysis protocol was proposed as guidance in protection against potential genomic sequence errors in public eutherian genomic sequences. The protocol was applicable in updates of 7 major eutherian gene data sets, including 812 complete coding sequences deposited in European Nucleotide Archive as curated third party data gene data sets.

An Outbreak of Respiratory Tularemia Caused by Diverse Clones of Francisella tularensis

PubMed Central

Johansson, Anders; Lärkeryd, Adrian; Widerström, Micael; Mörtberg, Sara; Myrtännäs, Kerstin; Öhrman, Caroline; Birdsell, Dawn; Keim, Paul; Wagner, David M.; Forsman, Mats; Larsson, Pär

2014-01-01

Background. The bacterium Francisella tularensis is recognized for its virulence, infectivity, genetic homogeneity, and potential as a bioterrorism agent. Outbreaks of respiratory tularemia, caused by inhalation of this bacterium, are poorly understood. Such outbreaks are exceedingly rare, and F. tularensis is seldom recovered from clinical specimens. Methods. A localized outbreak of tularemia in Sweden was investigated. Sixty-seven humans contracted laboratory-verified respiratory tularemia. F. tularensis subspecies holarctica was isolated from the blood or pleural fluid of 10 individuals from July to September 2010. Using whole-genome sequencing and analysis of single-nucleotide polymorphisms (SNPs), outbreak isolates were compared with 110 archived global isolates. Results. There were 757 SNPs among the genomes of the 10 outbreak isolates and the 25 most closely related archival isolates (all from Sweden/Finland). Whole genomes of outbreak isolates were >99.9% similar at the nucleotide level and clustered into 3 distinct genetic clades. Unexpectedly, high-sequence similarity grouped some outbreak and archival isolates that originated from patients from different geographic regions and up to 10 years apart. Outbreak and archival genomes frequently differed by only 1–3 of 1 585 229 examined nucleotides. Conclusions. The outbreak was caused by diverse clones of F. tularensis that occurred concomitantly, were widespread, and apparently persisted in the environment. Multiple independent acquisitions of F. tularensis from the environment over a short time period suggest that natural outbreaks of respiratory tularemia are triggered by environmental cues. The findings additionally caution against interpreting genome sequence identity for this pathogen as proof of a direct epidemiological link. PMID:25097081

ArrayExpress update--trends in database growth and links to data analysis tools.

PubMed

Rustici, Gabriella; Kolesnikov, Nikolay; Brandizi, Marco; Burdett, Tony; Dylag, Miroslaw; Emam, Ibrahim; Farne, Anna; Hastings, Emma; Ison, Jon; Keays, Maria; Kurbatova, Natalja; Malone, James; Mani, Roby; Mupo, Annalisa; Pedro Pereira, Rui; Pilicheva, Ekaterina; Rung, Johan; Sharma, Anjan; Tang, Y Amy; Ternent, Tobias; Tikhonov, Andrew; Welter, Danielle; Williams, Eleanor; Brazma, Alvis; Parkinson, Helen; Sarkans, Ugis

2013-01-01

The ArrayExpress Archive of Functional Genomics Data (http://www.ebi.ac.uk/arrayexpress) is one of three international functional genomics public data repositories, alongside the Gene Expression Omnibus at NCBI and the DDBJ Omics Archive, supporting peer-reviewed publications. It accepts data generated by sequencing or array-based technologies and currently contains data from almost a million assays, from over 30 000 experiments. The proportion of sequencing-based submissions has grown significantly over the last 2 years and has reached, in 2012, 15% of all new data. All data are available from ArrayExpress in MAGE-TAB format, which allows robust linking to data analysis and visualization tools, including Bioconductor and GenomeSpace. Additionally, R objects, for microarray data, and binary alignment format files, for sequencing data, have been generated for a significant proportion of ArrayExpress data.

The Montessori Experiment in Rhode Island (1913-1940): Tracing Theory to Implementation over 25 Years

ERIC Educational Resources Information Center

Zoll, Susan

2017-01-01

This article highlights archived documents pertaining to a 25-year experimental classroom implemented by Clara Craig, then supervisor of training at the Rhode Island Normal School. Craig is notable as she was the only participant in the first International Montessori Training Course in Rome, Italy, in 1913, to gain approval from the Rhode Island…

Early Childhood Education and Care for Native Hawaiian Children in Hawai'i: A Brief History

ERIC Educational Resources Information Center

Grace, Donna J.; Ku'ulei Serna, Alethea

2013-01-01

This study provides a brief overview of the history of early childhood education and care for Native Hawaiian children in Hawai'i. Data sources include a literature review, examination of archival documents, and interviews with a sample of Native Hawaiian parents and community members. We trace the emergence of outside-the-home early childhood…

The History of Hebrew Secondary Mathematics Education in Palestine during the First Half of the Twentieth Century

ERIC Educational Resources Information Center

Aricha-Metzer, Inbar

2013-01-01

This dissertation traces the history of mathematics education in Palestine Hebrew secondary schools from the foundation of the first Hebrew secondary school in 1905 until the establishment of the State of Israel in 1948. The study draws on primary sources from archives in Israel and analyzes curricula, textbooks, student notebooks, and…

Data archive for NO(y) from observations and construction and testing of airborne instrument for simultaneous measurement of NO, NO2, NO(y), and O3

NASA Technical Reports Server (NTRS)

Carroll, Mary Anne; Emmons, Louisa

1995-01-01

The compilation and archiving of NO(x) and NO(y) measurements began in mid-March 1994. Since the submission of the first report, data summaries have been obtained for the TROPOZ 2, STRATOZ 3, OCTA and TOR/Schauinsland campaigns, and the full data sets will become a part of this archive in the near future. Climatologies of NO(x) and NO(y) have been developed from these and previously archived data sets, including the available GTE campaigns (ABLE-2A, B, -3A, B, CITE-2, -3, TRACE-A, PEM WEST-A) and AASE 1 and 2. The data have been grouped by season and altitude (boundary layer and 3 km ranges in the free troposphere). Maps showing median values of midday NO, NO(x) and NO(y) have been produced for each season for the boundary layer and 3 km ranges of the free troposphere. The statistics of the data (median, mean, and standard deviation, central 67% and 90%) have also been determined, and are shown in representative figures included in this report.

Vaginal microbial flora analysis by next generation sequencing and microarrays; can microbes indicate vaginal origin in a forensic context?

PubMed

Benschop, Corina C G; Quaak, Frederike C A; Boon, Mathilde E; Sijen, Titia; Kuiper, Irene

2012-03-01

Forensic analysis of biological traces generally encompasses the investigation of both the person who contributed to the trace and the body site(s) from which the trace originates. For instance, for sexual assault cases, it can be beneficial to distinguish vaginal samples from skin or saliva samples. In this study, we explored the use of microbial flora to indicate vaginal origin. First, we explored the vaginal microbiome for a large set of clinical vaginal samples (n = 240) by next generation sequencing (n = 338,184 sequence reads) and found 1,619 different sequences. Next, we selected 389 candidate probes targeting genera or species and designed a microarray, with which we analysed a diverse set of samples; 43 DNA extracts from vaginal samples and 25 DNA extracts from samples from other body sites, including sites in close proximity of or in contact with the vagina. Finally, we used the microarray results and next generation sequencing dataset to assess the potential for a future approach that uses microbial markers to indicate vaginal origin. Since no candidate genera/species were found to positively identify all vaginal DNA extracts on their own, while excluding all non-vaginal DNA extracts, we deduce that a reliable statement about the cellular origin of a biological trace should be based on the detection of multiple species within various genera. Microarray analysis of a sample will then render a microbial flora pattern that is probably best analysed in a probabilistic approach.

Contribution of finger tracing to the recognition of Chinese characters.

PubMed

Yim-Ng, Y Y; Varley, R; Andrade, J

2000-01-01

Finger tracing is a simulation of the act of writing without the use of pen and paper. It is claimed to help in the processing of Chinese characters, possibly by providing additional motor coding. In this study, blindfolded subjects were equally good at identifying Chinese characters and novel visual stimuli through passive movements made with the index finger of the preferred hand and those made with the last finger of that hand. This suggests that finger tracing provides a relatively high level of coding specific to individual characters, but non-specific to motor effectors. Beginning each stroke from the same location, i.e. removing spatial information, impaired recognition of the familiar characters and the novel nonsense figures. Passively tracing the strokes in a random sequence also impaired recognition of the characters. These results therefore suggest that the beneficial effect of finger tracing on writing or recall of Chinese characters is mediated by sequence and spatial information embedded in the motor movements, and that proprioceptive channel may play a part in mediating visuo-spatial information. Finger tracing may be a useful strategy for remediation of Chinese language impairments.

Trace elements at the intersection of marine biological and geochemical evolution

USGS Publications Warehouse

Robbins, Leslie J.; Lalonde, Stefan V.; Planavsky, Noah J.; Partin, Camille A.; Reinhard, Christopher T.; Kendall, Brian; Scott, Clinton T.; Hardisty, Dalton S.; Gill, Benjamin C.; Alessi, Daniel S.; Dupont, Christopher L.; Saito, Mak A.; Crowe, Sean A.; Poulton, Simon W.; Bekker, Andrey; Lyons, Timothy W.; Konhauser, Kurt O.

2016-01-01

Life requires a wide variety of bioessential trace elements to act as structural components and reactive centers in metalloenzymes. These requirements differ between organisms and have evolved over geological time, likely guided in some part by environmental conditions. Until recently, most of what was understood regarding trace element concentrations in the Precambrian oceans was inferred by extrapolation, geochemical modeling, and/or genomic studies. However, in the past decade, the increasing availability of trace element and isotopic data for sedimentary rocks of all ages has yielded new, and potentially more direct, insights into secular changes in seawater composition – and ultimately the evolution of the marine biosphere. Compiled records of many bioessential trace elements (including Ni, Mo, P, Zn, Co, Cr, Se, and I) provide new insight into how trace element abundance in Earth's ancient oceans may have been linked to biological evolution. Several of these trace elements display redox-sensitive behavior, while others are redox-sensitive but not bioessential (e.g., Cr, U). Their temporal trends in sedimentary archives provide useful constraints on changes in atmosphere-ocean redox conditions that are linked to biological evolution, for example, the activity of oxygen-producing, photosynthetic cyanobacteria. In this review, we summarize available Precambrian trace element proxy data, and discuss how temporal trends in the seawater concentrations of specific trace elements may be linked to the evolution of both simple and complex life. We also examine several biologically relevant and/or redox-sensitive trace elements that have yet to be fully examined in the sedimentary rock record (e.g., Cu, Cd, W) and suggest several directions for future studies.

Environmental Mycobiome Modifiers of Inflammation and Fibrosis in Systemic Sclerosis

DTIC Science & Technology

2016-09-01

TUBB), and ribosomal proteins), while others are considered specific to SSc despite trace level detection in controls. For ex- ample, multiple SSc...Strong re- activity was seen against all five proteins in SSc with only trace levels detected in controls (Fig. 3a), indicating widespread immune...sequences in SSc RNA-seq data was used to detect microbial sequences in human tissues in an unbiased, quantitative manner. Our studies suggest that

An outbreak of respiratory tularemia caused by diverse clones of Francisella tularensis.

PubMed

Johansson, Anders; Lärkeryd, Adrian; Widerström, Micael; Mörtberg, Sara; Myrtännäs, Kerstin; Ohrman, Caroline; Birdsell, Dawn; Keim, Paul; Wagner, David M; Forsman, Mats; Larsson, Pär

2014-12-01

The bacterium Francisella tularensis is recognized for its virulence, infectivity, genetic homogeneity, and potential as a bioterrorism agent. Outbreaks of respiratory tularemia, caused by inhalation of this bacterium, are poorly understood. Such outbreaks are exceedingly rare, and F. tularensis is seldom recovered from clinical specimens. A localized outbreak of tularemia in Sweden was investigated. Sixty-seven humans contracted laboratory-verified respiratory tularemia. F. tularensis subspecies holarctica was isolated from the blood or pleural fluid of 10 individuals from July to September 2010. Using whole-genome sequencing and analysis of single-nucleotide polymorphisms (SNPs), outbreak isolates were compared with 110 archived global isolates. There were 757 SNPs among the genomes of the 10 outbreak isolates and the 25 most closely related archival isolates (all from Sweden/Finland). Whole genomes of outbreak isolates were >99.9% similar at the nucleotide level and clustered into 3 distinct genetic clades. Unexpectedly, high-sequence similarity grouped some outbreak and archival isolates that originated from patients from different geographic regions and up to 10 years apart. Outbreak and archival genomes frequently differed by only 1-3 of 1 585 229 examined nucleotides. The outbreak was caused by diverse clones of F. tularensis that occurred concomitantly, were widespread, and apparently persisted in the environment. Multiple independent acquisitions of F. tularensis from the environment over a short time period suggest that natural outbreaks of respiratory tularemia are triggered by environmental cues. The findings additionally caution against interpreting genome sequence identity for this pathogen as proof of a direct epidemiological link. © The Author 2014. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

AMPLIFICATION OF RIBOSOMAL RNA SEQUENCES

EPA Science Inventory

This book chapter offers an overview of the use of ribosomal RNA sequences. A history of the technology traces the evolution of techniques to measure bacterial phylogenetic relationships and recent advances in obtaining rRNA sequence information. The manual also describes procedu...

Extracting DNA from 'jaws': high yield and quality from archived tiger shark (Galeocerdo cuvier) skeletal material.

PubMed

Nielsen, E E; Morgan, J A T; Maher, S L; Edson, J; Gauthier, M; Pepperell, J; Holmes, B J; Bennett, M B; Ovenden, J R

2017-05-01

Archived specimens are highly valuable sources of DNA for retrospective genetic/genomic analysis. However, often limited effort has been made to evaluate and optimize extraction methods, which may be crucial for downstream applications. Here, we assessed and optimized the usefulness of abundant archived skeletal material from sharks as a source of DNA for temporal genomic studies. Six different methods for DNA extraction, encompassing two different commercial kits and three different protocols, were applied to material, so-called bio-swarf, from contemporary and archived jaws and vertebrae of tiger sharks (Galeocerdo cuvier). Protocols were compared for DNA yield and quality using a qPCR approach. For jaw swarf, all methods provided relatively high DNA yield and quality, while large differences in yield between protocols were observed for vertebrae. Similar results were obtained from samples of white shark (Carcharodon carcharias). Application of the optimized methods to 38 museum and private angler trophy specimens dating back to 1912 yielded sufficient DNA for downstream genomic analysis for 68% of the samples. No clear relationships between age of samples, DNA quality and quantity were observed, likely reflecting different preparation and storage methods for the trophies. Trial sequencing of DNA capture genomic libraries using 20 000 baits revealed that a significant proportion of captured sequences were derived from tiger sharks. This study demonstrates that archived shark jaws and vertebrae are potential high-yield sources of DNA for genomic-scale analysis. It also highlights that even for similar tissue types, a careful evaluation of extraction protocols can vastly improve DNA yield. © 2016 John Wiley & Sons Ltd.

The Gediz River fluvial archive: A benchmark for Quaternary research in Western Anatolia

NASA Astrophysics Data System (ADS)

Maddy, D.; Veldkamp, A.; Demir, T.; van Gorp, W.; Wijbrans, J. R.; van Hinsbergen, D. J. J.; Dekkers, M. J.; Schreve, D.; Schoorl, J. M.; Scaife, R.; Stemerdink, C.; van der Schriek, T.; Bridgland, D. R.; Aytaç, A. S.

2017-06-01

The Gediz River, one of the principal rivers of Western Anatolia, has an extensive Pleistocene fluvial archive that potentially offers a unique window into fluvial system behaviour on the western margins of Asia during the Quaternary. In this paper we review our work on the Quaternary Gediz River Project (2001-2010) and present new data which leads to a revised stratigraphical model for the Early Pleistocene development of this fluvial system. In previous work we confirmed the preservation of eleven buried Early Pleistocene fluvial terraces of the Gediz River (designated GT11, the oldest and highest, to GT1, the youngest and lowest) which lie beneath the basalt-covered plateaux of the Kula Volcanic Province. Deciphering the information locked in this fluvial archive requires the construction of a robust geochronology. Fortunately, the Gediz archive provides ample opportunity for age-constraint based upon age estimates derived from basaltic lava flows that repeatedly entered the palaeo-Gediz valley floors. In this paper we present, for the first time, our complete dataset of 40Ar/39Ar age estimates and associated palaeomagnetic measurements. These data, which can be directly related to the underlying fluvial deposits, provide age constraints critical to our understanding of this sequence. The new chronology establishes the onset of Quaternary volcanism at ∼1320ka (MIS42). This volcanism, which is associated with GT6, confirms a pre-MIS42 age for terraces GT11-GT7. Evidence from the colluvial sequences directly overlying these early terraces suggests that they formed in response to hydrological and sediment budget changes forced by climate-driven vegetation change. The cyclic formation of terraces and their timing suggests they represent the obliquity-driven climate changes of the Early Pleistocene. By way of contrast the GT5-GT1 terrace sequence, constrained by a lava flow with an age estimate of ∼1247ka, span the time-interval MIS42 - MIS38 and therefore do not match the frequency of climate change as previously suggested. The onset of volcanism breaks the simple linkage of terracing to climate-driven change. These younger terraces more likely reflect a localized terracing process triggered by base level changes forced by volcanic eruptions and associated reactivation of pre-existing faults, lava dam construction, landsliding and subsequent lava-dammed lake drainage. Establishing a firm stratigraphy and geochronology for the Early Pleistocene archive provides a secure framework for future exploitation of this part of the archive and sets the standard as we begin our work on the Middle-Late Pleistocene sequence. We believe this work forms a benchmark study for detailed Quaternary research in Turkey.

STRUCTURED MOLECULAR GAS REVEALS GALACTIC SPIRAL ARMS

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

Sawada, Tsuyoshi; Hasegawa, Tetsuo; Koda, Jin, E-mail: sawada.tsuyoshi@nao.ac.jp

We explore the development of structures in molecular gas in the Milky Way by applying the analysis of the brightness distribution function and the brightness distribution index (BDI) in the archival data from the Boston University-Five College Radio Astronomy Observatory {sup 13}CO J = 1-0 Galactic Ring Survey. The BDI measures the fractional contribution of spatially confined bright molecular emission over faint emission extended over large areas. This relative quantity is largely independent of the amount of molecular gas and of any conventional, pre-conceived structures, such as cores, clumps, or giant molecular clouds. The structured molecular gas traced by highermore » BDI is located continuously along the spiral arms in the Milky Way in the longitude-velocity diagram. This clearly indicates that molecular gas changes its structure as it flows through the spiral arms. Although the high-BDI gas generally coincides with H II regions, there is also some high-BDI gas with no/little signature of ongoing star formation. These results support a possible evolutionary sequence in which unstructured, diffuse gas transforms itself into a structured state on encountering the spiral arms, followed by star formation and an eventual return to the unstructured state after the spiral arm passage.« less

Database resources of the National Center for Biotechnology Information.

PubMed

Wheeler, David L; Barrett, Tanya; Benson, Dennis A; Bryant, Stephen H; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M; DiCuccio, Michael; Edgar, Ron; Federhen, Scott; Geer, Lewis Y; Kapustin, Yuri; Khovayko, Oleg; Landsman, David; Lipman, David J; Madden, Thomas L; Maglott, Donna R; Ostell, James; Miller, Vadim; Pruitt, Kim D; Schuler, Gregory D; Sequeira, Edwin; Sherry, Steven T; Sirotkin, Karl; Souvorov, Alexandre; Starchenko, Grigory; Tatusov, Roman L; Tatusova, Tatiana A; Wagner, Lukas; Yaschenko, Eugene

2007-01-01

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, the Entrez Programming Utilities, My NCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link(BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genome, Genome Project and related tools, the Trace and Assembly Archives, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs), Viral Genotyping Tools, Influenza Viral Resources, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART) and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

Database resources of the National Center for Biotechnology Information

PubMed Central

Wheeler, David L.; Barrett, Tanya; Benson, Dennis A.; Bryant, Stephen H.; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M.; DiCuccio, Michael; Edgar, Ron; Federhen, Scott; Feolo, Michael; Geer, Lewis Y.; Helmberg, Wolfgang; Kapustin, Yuri; Khovayko, Oleg; Landsman, David; Lipman, David J.; Madden, Thomas L.; Maglott, Donna R.; Miller, Vadim; Ostell, James; Pruitt, Kim D.; Schuler, Gregory D.; Shumway, Martin; Sequeira, Edwin; Sherry, Steven T.; Sirotkin, Karl; Souvorov, Alexandre; Starchenko, Grigory; Tatusov, Roman L.; Tatusova, Tatiana A.; Wagner, Lukas; Yaschenko, Eugene

2008-01-01

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data available through NCBI's web site. NCBI resources include Entrez, the Entrez Programming Utilities, My NCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link, Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genome, Genome Project and related tools, the Trace, Assembly, and Short Read Archives, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups, Influenza Viral Resources, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Entrez Probe, GENSAT, Database of Genotype and Phenotype, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool and the PubChem suite of small molecule databases. Augmenting the web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov. PMID:18045790

One-Dimensional Signal Extraction Of Paper-Written ECG Image And Its Archiving

NASA Astrophysics Data System (ADS)

Zhang, Zhi-ni; Zhang, Hong; Zhuang, Tian-ge

1987-10-01

A method for converting paper-written electrocardiograms to one dimensional (1-D) signals for archival storage on floppy disk is presented here. Appropriate image processing techniques were employed to remove the back-ground noise inherent to ECG recorder charts and to reconstruct the ECG waveform. The entire process consists of (1) digitization of paper-written ECGs with an image processing system via a TV camera; (2) image preprocessing, including histogram filtering and binary image generation; (3) ECG feature extraction and ECG wave tracing, and (4) transmission of the processed ECG data to IBM-PC compatible floppy disks for storage and retrieval. The algorithms employed here may also be used in the recognition of paper-written EEG or EMG and may be useful in robotic vision.

Trace element storage capacity of sediments in dead Posidonia oceanica mat from a chronically contaminated marine ecosystem.

PubMed

Di Leonardo, Rossella; Mazzola, Antonio; Cundy, Andrew B; Tramati, Cecilia Doriana; Vizzini, Salvatrice

2017-01-01

Posidonia oceanica mat is considered a long-term bioindicator of contamination. Storage and sequestration of trace elements and organic carbon (C org ) were assessed in dead P. oceanica mat and bare sediments from a highly polluted coastal marine area (Augusta Bay, central Mediterranean). Sediment elemental composition and sources of organic matter have been altered since the 1950s. Dead P. oceanica mat displayed a greater ability to bury and store trace elements and C org than nearby bare sediments, acting as a long-term contaminant sink over the past 120 yr. Trace elements, probably associated with the mineral fraction, were stabilized and trapped despite die-off of the overlying P. oceanica meadow. Mat deposits registered historic contamination phases well, confirming their role as natural archives for recording trace element trends in marine coastal environments. This sediment typology is enriched with seagrass-derived refractory organic matter, which acts mainly as a diluent of trace elements. Bare sediments showed evidence of inwash of contaminated sediments via reworking; more rapid and irregular sediment accumulation; and, because of the high proportions of labile organic matter, a greater capacity to store trace elements. Through different processes, both sediment typologies represent a repository for chemicals and may pose a risk to the marine ecosystem as a secondary source of contaminants in the case of sediment dredging or erosion. Environ Toxicol Chem 2017;36:49-58. © 2016 SETAC. © 2016 SETAC.

Immunity: Insect Immune Memory Goes Viral.

PubMed

Ligoxygakis, Petros

2017-11-20

Adaptive memory in insect immunity has been controversial. In this issue, Andino and co-workers propose that acquisition of viral sequences in the host genome gives rise to anti-sense, anti-viral piRNAs. Such sequences can be regarded as both a genomic archive of past infections and as an armour of potential heritable memory. Copyright © 2017 Elsevier Ltd. All rights reserved.

Cardiology-oriented PACS

NASA Astrophysics Data System (ADS)

Silva, Augusto F. d.; Costa, Carlos; Abrantes, Pedro; Gama, Vasco; Den Boer, Ad

1998-07-01

This paper describes an integrated system designed to provide efficient means for DICOM compliant cardiac imaging archival, transmission and visualization based on a communications backbone matching recent enabling telematic technologies like Asynchronous Transfer Mode (ATM) and switched Local Area Networks (LANs). Within a distributed client-server framework, the system was conceived on a modality based bottom-up approach, aiming ultrafast access to short term archives and seamless retrieval of cardiac video sequences throughout review stations located at the outpatient referral rooms, intensive and intermediate care units and operating theaters.

Dynamics of drug resistance-associated mutations in HIV-1 DNA reverse transcriptase sequence during effective ART.

PubMed

Nouchi, A; Nguyen, T; Valantin, M A; Simon, A; Sayon, S; Agher, R; Calvez, V; Katlama, C; Marcelin, A G; Soulie, C

2018-05-29

To investigate the dynamics of HIV-1 variants archived in cells harbouring drug resistance-associated mutations (DRAMs) to lamivudine/emtricitabine, etravirine and rilpivirine in patients under effective ART free from selective pressure on these DRAMs, in order to assess the possibility of recycling molecules with resistance history. We studied 25 patients with at least one DRAM to lamivudine/emtricitabine, etravirine and/or rilpivirine identified on an RNA sequence in their history and with virological control for at least 5 years under a regimen excluding all drugs from the resistant class. Longitudinal ultra-deep sequencing (UDS) and Sanger sequencing of the reverse transcriptase region were performed on cell-associated HIV-1 DNA samples taken over the 5 years of follow-up. Viral variants harbouring the analysed DRAMs were no longer detected by UDS over the 5 years in 72% of patients, with viruses susceptible to the molecules of interest found after 5 years in 80% of patients with UDS and in 88% of patients with Sanger. Residual viraemia with <50 copies/mL was detected in 52% of patients. The median HIV DNA level remained stable (2.4 at baseline versus 2.1 log10 copies/106 cells 5 years later). These results show a clear trend towards clearance of archived DRAMs to reverse transcriptase inhibitors in cell-associated HIV-1 DNA after a long period of virological control, free from therapeutic selective pressure on these DRAMs, reflecting probable residual replication in some reservoirs of the fittest viruses and leading to persistent evolution of the archived HIV-1 DNA resistance profile.

Archive of digital boomer seismic reflection data collected during USGS field activities 95LCA03 and 96LCA02 in the Peace River of West-Central Florida, 1995 and 1996

USGS Publications Warehouse

Calderon, Karynna; Dadisman, Shawn V.; Tihansky, Ann B.; Lewelling, Bill R.; Flocks, James G.; Wiese, Dana S.; Kindinger, Jack G.; Harrison, Arnell S.

2006-01-01

In October and November of 1995 and February of 1996, the U.S. Geological Survey, in cooperation with the Southwest Florida Water Management District, conducted geophysical surveys of the Peace River in west-central Florida from east of Bartow to west of Arcadia. This report serves as an archive of unprocessed digital boomer seismic reflection data, trackline maps, navigation files, GIS files, Field Activity Collection System (FACS) logs, observers' logbooks, and formal FGDC metadata. Filtered and gained digital images of the seismic profiles are also provided. Refer to the Acronyms page for expansion of acronyms and abbreviations used in this report. The archived trace data are in standard Society of Exploration Geophysicists (SEG) SEG-Y format (Barry and others, 1975) and may be downloaded and processed with commercial or public domain software such as Seismic Unix (SU). Example SU processing scripts and USGS software for viewing the SEG-Y files (Zihlman, 1992) are also provided.

Identification of extracellular miRNA in archived serum samples by next-generation sequencing from RNA extracted using multiple methods.

PubMed

Gautam, Aarti; Kumar, Raina; Dimitrov, George; Hoke, Allison; Hammamieh, Rasha; Jett, Marti

2016-10-01

miRNAs act as important regulators of gene expression by promoting mRNA degradation or by attenuating protein translation. Since miRNAs are stably expressed in bodily fluids, there is growing interest in profiling these miRNAs, as it is minimally invasive and cost-effective as a diagnostic matrix. A technical hurdle in studying miRNA dynamics is the ability to reliably extract miRNA as small sample volumes and low RNA abundance create challenges for extraction and downstream applications. The purpose of this study was to develop a pipeline for the recovery of miRNA using small volumes of archived serum samples. The RNA was extracted employing several widely utilized RNA isolation kits/methods with and without addition of a carrier. The small RNA library preparation was carried out using Illumina TruSeq small RNA kit and sequencing was carried out using Illumina platform. A fraction of five microliters of total RNA was used for library preparation as quantification is below the detection limit. We were able to profile miRNA levels in serum from all the methods tested. We found out that addition of nucleic acid based carrier molecules had higher numbers of processed reads but it did not enhance the mapping of any miRBase annotated sequences. However, some of the extraction procedures offer certain advantages: RNA extracted by TRIzol seemed to align to the miRBase best; extractions using TRIzol with carrier yielded higher miRNA-to-small RNA ratios. Nuclease free glycogen can be carrier of choice for miRNA sequencing. Our findings illustrate that miRNA extraction and quantification is influenced by the choice of methodologies. Addition of nucleic acid- based carrier molecules during extraction procedure is not a good choice when assaying miRNA using sequencing. The careful selection of an extraction method permits the archived serum samples to become valuable resources for high-throughput applications.

A Public Health Model for the Molecular Surveillance of HIV Transmission in San Diego, California

PubMed Central

May, Susanne; Tweeten, Samantha; Drumright, Lydia; Pacold, Mary E.; Kosakovsky Pond, Sergei L.; Pesano, Rick L.; Lie, Yolanda S.; Richman, Douglas D.; Frost, Simon D.W.; Woelk, Christopher H.; Little, Susan J.

2009-01-01

Background Current public health efforts often use molecular technologies to identify and contain communicable disease networks, but not for HIV. Here, we investigate how molecular epidemiology can be used to identify highly-related HIV networks within a population and how voluntary contact tracing of sexual partners can be used to selectively target these networks. Methods We evaluated the use of HIV-1 pol sequences obtained from participants of a community-recruited cohort (n=268) and a primary infection research cohort (n=369) to define highly related transmission clusters and the use of contact tracing to link other individuals (n=36) within these clusters. The presence of transmitted drug resistance was interpreted from the pol sequences (Calibrated Population Resistance v3.0). Results Phylogenetic clustering was conservatively defined when the genetic distance between any two pol sequences was <1%, which identified 34 distinct transmission clusters within the combined community-recruited and primary infection research cohorts containing 160 individuals. Although sequences from the epidemiologically-linked partners represented approximately 5% of the total sequences, they clustered with 60% of the sequences that clustered from the combined cohorts (O.R. 21.7; p=<0.01). Major resistance to at least one class of antiretroviral medication was found in 19% of clustering sequences. Conclusions Phylogenetic methods can be used to identify individuals who are within highly related transmission groups, and contact tracing of epidemiologically-linked partners of recently infected individuals can be used to link into previously-defined transmission groups. These methods could be used to implement selectively targeted prevention interventions. PMID:19098493

A gradient of radioactive contamination in Dolon village near the SNTS and comparison of computed dose values with instrumental estimates for the 29 August, 1949 nuclear test.

PubMed

Stepanenko, Valeriy F; Hoshi, Masaharu; Dubasov, Yuriy V; Sakaguchi, Aya; Yamamoto, Masayoshi; Orlov, Mark Y; Bailiff, Ian K; Ivannikov, Alexander I; Skvortsov, Valeriy G; Iaskova, Elena K; Kryukova, Irina G; Zhumadilov, Kassym S; Endo, Satoru; Tanaka, Kenichi; Apsalikov, Kazbek N; Gusev, Boris I

2006-02-01

Spatial distributions of soil contamination by 137Cs (89 sampling points) and 239+240Pu (76 points) near and within Dolon village were analyzed. An essential exponential decrease of contamination was found in Dolon village: the distance of a half reduction in contamination is about 0.87-1.25 km (in a northwest-southeast direction from the supposed centerline of the radioactive trace). This fact is in agreement with the available exposure rate measurements near Dolon (September 1949 archive data): on the basis of a few measurements the pattern of the trace was estimated to comprise a narrow 2 km corridor of maximum exposure rate. To compare computed external doses in air with local dose estimates by retrospective luminescence dosimetry (RLD) the gradient of radioactive soil contamination within the village was accounted for. The computed dose associated with the central axis of the trace was found to be equal to 2260 mGy (calculations based on archive exposure rate data). Local doses near the RLD sampling points (southeast of the village) were calculated to be in the range 466-780 mGy (averaged value: 645+/-70 mGy), which is comparable with RLD data (averaged value 460+/-92 mGy with range 380-618 mGy). A comparison of the computed mean dose in the settlement with dose estimates by ESR tooth enamel dosimetry makes it possible to estimate the "upper level" of the "shielding and behavior" factor in dose reduction for inhabitants of Dolon village which was found to be 0.28+/-0.068.

MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive.

PubMed

Bernstein, Matthew N; Doan, AnHai; Dewey, Colin N

2017-09-15

The NCBI's Sequence Read Archive (SRA) promises great biological insight if one could analyze the data in the aggregate; however, the data remain largely underutilized, in part, due to the poor structure of the metadata associated with each sample. The rules governing submissions to the SRA do not dictate a standardized set of terms that should be used to describe the biological samples from which the sequencing data are derived. As a result, the metadata include many synonyms, spelling variants and references to outside sources of information. Furthermore, manual annotation of the data remains intractable due to the large number of samples in the archive. For these reasons, it has been difficult to perform large-scale analyses that study the relationships between biomolecular processes and phenotype across diverse diseases, tissues and cell types present in the SRA. We present MetaSRA, a database of normalized SRA human sample-specific metadata following a schema inspired by the metadata organization of the ENCODE project. This schema involves mapping samples to terms in biomedical ontologies, labeling each sample with a sample-type category, and extracting real-valued properties. We automated these tasks via a novel computational pipeline. The MetaSRA is available at metasra.biostat.wisc.edu via both a searchable web interface and bulk downloads. Software implementing our computational pipeline is available at http://github.com/deweylab/metasra-pipeline. cdewey@biostat.wisc.edu. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Optimisation of solar synoptic observations

NASA Astrophysics Data System (ADS)

Klvaña, Miroslav; Sobotka, Michal; Švanda, Michal

2012-09-01

The development of instrumental and computer technologies is connected with steadily increasing needs for archiving of large data volumes. The current trend to meet this requirement includes the data compression and growth of storage capacities. This approach, however, has technical and practical limits. A further reduction of the archived data volume can be achieved by means of an optimisation of the archiving that consists in data selection without losing the useful information. We describe a method of optimised archiving of solar images, based on the selection of images that contain a new information. The new information content is evaluated by means of the analysis of changes detected in the images. We present characteristics of different kinds of image changes and divide them into fictitious changes with a disturbing effect and real changes that provide a new information. In block diagrams describing the selection and archiving, we demonstrate the influence of clouds, the recording of images during an active event on the Sun, including a period before the event onset, and the archiving of long-term history of solar activity. The described optimisation technique is not suitable for helioseismology, because it does not conserve the uniform time step in the archived sequence and removes the information about solar oscillations. In case of long-term synoptic observations, the optimised archiving can save a large amount of storage capacities. The actual capacity saving will depend on the setting of the change-detection sensitivity and on the capability to exclude the fictitious changes.

The ExoMars Science Data Archive: Status and Plans

NASA Astrophysics Data System (ADS)

Heather, David; Barbarisi, Isa; Brumfitt, Jon; Lim, Tanya; Metcalfe, Leo; Villacorta, Antonio

2017-04-01

The ExoMars program is a co-operation between ESA and Roscosmos comprising two missions: the first, launched on 14 March 2016, included the Trace Gas Orbiter and Schiaparelli lander; the second, due for launch in 2020, will be a Rover and Surface Platform (RSP). The archiving and management of the science data to be returned from ExoMars will require a significant development effort for the new Planetary Science Archive (PSA). These are the first data in the PSA to be formatted according to the new PDS4 Standards, and there are also significant differences in the way in which a scientist will want to query, retrieve, and use data from a suite of rover instruments as opposed to remote sensing instrumentation from an orbiter. NASA has a strong user community interaction for their rovers, and a similar approach to their 'Analysts Notebook' will be needed for the future PSA. In addition to the archiving interface itself, there are differences with the overall archiving process being followed for ExoMars compared to previous ESA planetary missions. The first level of data processing for the 2016 mission, from telemetry to raw, is completed by ESA at ESAC in Madrid, where the archive itself resides. Data continuously flow direct to the PSA, where after the given proprietary period, they will be released to the community via the user interfaces. For the rover mission, the data pipelines are being developed by European industry, in close collaboration with ESA PSA experts and with the instrument teams. The first level of data processing will be carried out for all instruments at ALTEC in Turin where the pipelines are developed, and from where the rover operations will also be run. This presentation will focus on the challenges involved in archiving the data from the ExoMars Program, and will outline the plans and current status of the system being developed to respond to the needs of the missions.

Evaluation of positive Rift Valley fever virus formalin-fixed paraffin embedded samples as a source of sequence data for retrospective phylogenetic analysis.

PubMed

Mubemba, B; Thompson, P N; Odendaal, L; Coetzee, P; Venter, E H

2017-05-01

Rift Valley fever (RVF), caused by an arthropod borne Phlebovirus in the family Bunyaviridae, is a haemorrhagic disease that affects ruminants and humans. Due to the zoonotic nature of the virus, a biosafety level 3 laboratory is required for isolation of the virus. Fresh and frozen samples are the preferred sample type for isolation and acquisition of sequence data. However, these samples are scarce in addition to posing a health risk to laboratory personnel. Archived formalin-fixed, paraffin-embedded (FFPE) tissue samples are safe and readily available, however FFPE derived RNA is in most cases degraded and cross-linked in peptide bonds and it is unknown whether the sample type would be suitable as reference material for retrospective phylogenetic studies. A RT-PCR assay targeting a 490 nt portion of the structural G N glycoprotein encoding gene of the RVFV M-segment was applied to total RNA extracted from archived RVFV positive FFPE samples. Several attempts to obtain target amplicons were unsuccessful. FFPE samples were then analysed using next generation sequencing (NGS), i.e. Truseq ® (Illumina) and sequenced on the Miseq ® genome analyser (Illumina). Using reference mapping, gapped virus sequence data of varying degrees of shallow depth was aligned to a reference sequence. However, the NGS did not yield long enough contigs that consistently covered the same genome regions in all samples to allow phylogenetic analysis. Copyright © 2017 Elsevier B.V. All rights reserved.

A mid-twentieth century reduction in tropical upwelling inferred from coralline trace element proxies

NASA Astrophysics Data System (ADS)

Reuer, Matthew K.; Boyle, Edward A.; Cole, Julia E.

2003-05-01

The Cariaco Basin is an important archive of past climate variability given its response to inter- and extratropical climate forcing and the accumulation of annually laminated sediments within an anoxic water column. This study presents high-resolution surface coral trace element records ( Montastrea annularis and Siderastrea siderea) from Isla Tortuga, Venezuela, located within the upwelling center of this region. A two-fold reduction in Cd/Ca ratios (3.5-1.7 nmol/mol) is observed from 1946 to 1952 with no concurrent shift in Ba/Ca ratios. This reduction agrees with the hydrographic distribution of dissolved cadmium and barium and their expected response to upwelling. Significant anthropogenic variability is also observed from Pb/Ca analysis, observing three lead maxima since 1920. Kinetic control of trace element ratios is inferred from an interspecies comparison of Cd/Ca and Ba/Ca ratios (consistent with the Sr/Ca kinetic artifact), but these artifacts are smaller than the environmental signal and do not explain the Cd/Ca transition. The trace element records agree with historical climate data and differ from sedimentary faunal abundance records, suggesting a linear response to North Atlantic extratropical forcing cannot account for the observed historical variability in this region.

454 next generation-sequencing outperforms allele-specific PCR, Sanger sequencing, and pyrosequencing for routine KRAS mutation analysis of formalin-fixed, paraffin-embedded samples

PubMed Central

Altimari, Annalisa; de Biase, Dario; De Maglio, Giovanna; Gruppioni, Elisa; Capizzi, Elisa; Degiovanni, Alessio; D’Errico, Antonia; Pession, Annalisa; Pizzolitto, Stefano; Fiorentino, Michelangelo; Tallini, Giovanni

2013-01-01

Detection of KRAS mutations in archival pathology samples is critical for therapeutic appropriateness of anti-EGFR monoclonal antibodies in colorectal cancer. We compared the sensitivity, specificity, and accuracy of Sanger sequencing, ARMS-Scorpion (TheraScreen®) real-time polymerase chain reaction (PCR), pyrosequencing, chip array hybridization, and 454 next-generation sequencing to assess KRAS codon 12 and 13 mutations in 60 nonconsecutive selected cases of colorectal cancer. Twenty of the 60 cases were detected as wild-type KRAS by all methods with 100% specificity. Among the 40 mutated cases, 13 were discrepant with at least one method. The sensitivity was 85%, 90%, 93%, and 92%, and the accuracy was 90%, 93%, 95%, and 95% for Sanger sequencing, TheraScreen real-time PCR, pyrosequencing, and chip array hybridization, respectively. The main limitation of Sanger sequencing was its low analytical sensitivity, whereas TheraScreen real-time PCR, pyrosequencing, and chip array hybridization showed higher sensitivity but suffered from the limitations of predesigned assays. Concordance between the methods was k = 0.79 for Sanger sequencing and k > 0.85 for the other techniques. Tumor cell enrichment correlated significantly with the abundance of KRAS-mutated deoxyribonucleic acid (DNA), evaluated as ΔCt for TheraScreen real-time PCR (P = 0.03), percentage of mutation for pyrosequencing (P = 0.001), ratio for chip array hybridization (P = 0.003), and percentage of mutation for 454 next-generation sequencing (P = 0.004). Also, 454 next-generation sequencing showed the best cross correlation for quantification of mutation abundance compared with all the other methods (P < 0.001). Our comparison showed the superiority of next-generation sequencing over the other techniques in terms of sensitivity and specificity. Next-generation sequencing will replace Sanger sequencing as the reference technique for diagnostic detection of KRAS mutation in archival tumor tissues. PMID:23950653

Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample

PubMed Central

Gilks, William P.; Pennell, Tanya M.; Flis, Ilona; Webster, Matthew T.; Morrow, Edward H.

2016-01-01

As part of a study into the molecular genetics of sexually dimorphic complex traits, we used high-throughput sequencing to obtain data on genomic variation in an outbred laboratory-adapted fruit fly ( Drosophila melanogaster) population. We successfully resequenced the whole genome of 220 hemiclonal females that were heterozygous for the same Berkeley reference line genome (BDGP6/dm6), and a unique haplotype from the outbred base population (LH M). The use of a static and known genetic background enabled us to obtain sequences from whole-genome phased haplotypes. We used a BWA-Picard-GATK pipeline for mapping sequence reads to the dm6 reference genome assembly, at a median depth-of coverage of 31X, and have made the resulting data publicly-available in the NCBI Short Read Archive (Accession number SRP058502). We used Haplotype Caller to discover and genotype 1,726,931 small genomic variants (SNPs and indels, <200bp). Additionally we detected and genotyped 167 large structural variants (1-100Kb in size) using GenomeStrip/2.0. Sequence and genotype data are publicly-available at the corresponding NCBI databases: Short Read Archive, dbSNP and dbVar (BioProject PRJNA282591). We have also released the unfiltered genotype data, and the code and logs for data processing and summary statistics ( https://zenodo.org/communities/sussex_drosophila_sequencing/). PMID:27928499

Octafluoropropane Concentration Dynamics on Board the International Space Station

NASA Technical Reports Server (NTRS)

Perry, J. L.

2003-01-01

Since activating the International Space Station s (IS9 Service Module in November 2000, archival air quality samples have shown highly variable concentrations of octafluoropropane in the cabin. This variability has been directly linked to leakage from air conditioning systems on board the Service Module, Zvezda. While octafluoro- propane is not highly toxic, it presents a significant chal- lenge to the trace contaminant control systems. A discussion of octafluoropropane concentration dynamics is presented and the ability of on board trace contami- nant control systems to effectively remove octafluoropro- pane from the cabin atmosphere is assessed. Consideration is given to operational and logistics issues that may arise from octafluoropropane and other halo- carbon challenges to the contamination control systems as well as the potential for effecting cabin air quality.

Molecular Tracing of Hepatitis C Virus Genotype 1 Isolates in Iran: A NS5B Phylogenetic Analysis with Systematic Review.

PubMed

Hesamizadeh, Khashayar; Alavian, Seyed Moayed; Najafi Tireh Shabankareh, Azar; Sharafi, Heidar

2016-12-01

Hepatitis C virus (HCV) is characterized by a high degree of genetic heterogeneity and classified into 7 genotypes and different subtypes. It heterogeneously distributed through various risk groups and geographical regions. A well-established phylogenetic relationship can simplify the tracing of HCV hierarchical strata into geographical regions. The current study aimed to find genetic phylogeny of subtypes 1a and 1b of HCV isolates based on NS5B nucleotide sequences in Iran and other members of Eastern Mediterranean regional office of world health organization, as well as other Middle Eastern countries, with a systematic review of available published and unpublished studies. The phylogenetic analyses were performed based on the nucleotide sequences of NS5B gene of HCV genotype 1 (HCV-1), which were registered in the GenBank database. The literature review was performed in two steps: 1) searching studies evaluating the NS5B sequences of HCV-1, on PubMed, Scopus, and Web of Science, and 2) Searching sequences of unpublished studies registered in the GenBank database. In this study, 442 sequences from HCV-1a and 232 from HCV-1b underwent phylogenetic analysis. Phylogenetic analysis of all sequences revealed different clusters in the phylogenetic trees. The results showed that the proportion of HCV-1a and -1b isolates from Iranian patients probably originated from domestic sources. Moreover, the HCV-1b isolates from Iranian patients may have similarities with the European ones. In this study, phylogenetic reconstruction of HCV-1 sequences clearly indicated for molecular tracing and ancestral relationships of the HCV genotypes in Iran, and showed the likelihood of domestic origin for HCV-1a and various origin for HCV-1b.

Persistence of Mycoplasma hyopneumoniae sequence types in spite of a control program for enzootic pneumonia in pigs.

PubMed

Overesch, Gudrun; Kuhnert, Peter

2017-09-15

Enzootic pneumonia (EP) in pigs caused by Mycoplasma (M.) hyopneumoniae has successfully been combatted in Switzerland. A control program was fully implemented in 2004 which is based on total depopulation strategies of affected fattening farms as well as partial depopulation on breeding farms. Thereby, the number of cases has dropped drastically from more than 200 in 2003 to two cases in 2013. Currently monitoring is done based on clinical observation and subsequent diagnostic of coughing pigs. Moreover, in case of more than 10% gross pathological lesions per slaughter batch laboratory confirmation for EP is compulsory. Despite these strict measures it was not possible to eliminate M. hyopneumoniae from Swiss pig production. In fact, during the last few years the number of EP cases has slightly increased. Therefore, genotyping of the involved M. hyopneumoniae strains was conducted in order to elucidate possible sources and routes of infection. All available and typeable samples from totally 22 cases during the period 2014-2016 were investigated by extended multilocus sequence typing (MLST). A total of 16 cases, including eight from 2014, five from 2015 and three from 2016 could thereby be included in the study. MLST revealed that the majority of cases in 2014/2015 were due to two major spread scenarios, i.e. two M. hyopneumoniae sequence types, each scenario involving six individual production farms in five to six different Cantons (states), respectively. Moreover, by comparison of archived sequences some sequence types were observed over ten years demonstrating their persistence over a long time and the possible partial failure of elimination measures in Switzerland. Insufficient sanitation on affected farms and subsequent animal transport of symptomless infected pigs could lead to recurrent cases. Wild boar harbor identical strains found with EP but solid data are missing to assign a role as reservoir to this wild animal. Implementing a monitoring scheme for M. hyopneumoniae in wild boar in combination with genotyping of all available samples from domestic pigs could direct responsible authorities to possible gaps and deficiencies of control measures taken for combating enzootic pneumonia. With the newly installed PubMLST database sequence types for M. hyopneumoniae are now available and allow tracing back strains on the international level. Copyright © 2017 Elsevier B.V. All rights reserved.

Molecular Characterization of Corynebacterium diphtheriae Outbreak Isolates, South Africa, March-June 2015.

PubMed

du Plessis, Mignon; Wolter, Nicole; Allam, Mushal; de Gouveia, Linda; Moosa, Fahima; Ntshoe, Genevie; Blumberg, Lucille; Cohen, Cheryl; Smith, Marshagne; Mutevedzi, Portia; Thomas, Juno; Horne, Valentino; Moodley, Prashini; Archary, Moherndran; Mahabeer, Yesholata; Mahomed, Saajida; Kuhn, Warren; Mlisana, Koleka; McCarthy, Kerrigan; von Gottberg, Anne

2017-08-01

In 2015, a cluster of respiratory diphtheria cases was reported from KwaZulu-Natal Province in South Africa. By using whole-genome analysis, we characterized 21 Corynebacterium diphtheriae isolates collected from 20 patients and contacts during the outbreak (1 patient was infected with 2 variants of C. diphtheriae). In addition, we included 1 cutaneous isolate, 2 endocarditis isolates, and 2 archived clinical isolates (ca. 1980) for comparison. Two novel lineages were identified, namely, toxigenic sequence type (ST) ST-378 (n = 17) and nontoxigenic ST-395 (n = 3). One archived isolate and the cutaneous isolate were ST-395, suggesting ongoing circulation of this lineage for >30 years. The absence of preexisting molecular sequence data limits drawing conclusions pertaining to the origin of these strains; however, these findings provide baseline genotypic data for future cases and outbreaks. Neither ST has been reported in any other country; this ST appears to be endemic only in South Africa.

Space plasma physics research

NASA Technical Reports Server (NTRS)

Comfort, Richard H.; Horwitz, James L.

1993-01-01

During the course of this grant, work was performed on a variety of topics and there were a number of significant accomplishments. A summary of these accomplishments is included. The topics studied include empirical model data base, data reduction for archiving, semikinetic modeling of low energy plasma in the inner terrestrial magnetosphere and ionosphere, O(+) outflows, equatorial plasma trough, and plasma wave ray-tracing studies. A list of publications and presentations which have resulted from this research is also included.

Strain-specific and pooled genome sequences for populations of Drosophila melanogaster from three continents.

PubMed Central

Bergman, Casey M.; Haddrill, Penelope R.

2015-01-01

To contribute to our general understanding of the evolutionary forces that shape variation in genome sequences in nature, we have sequenced genomes from 50 isofemale lines and six pooled samples from populations of Drosophila melanogaster on three continents. Analysis of raw and reference-mapped reads indicates the quality of these genomic sequence data is very high. Comparison of the predicted and experimentally-determined Wolbachia infection status of these samples suggests that strain or sample swaps are unlikely to have occurred in the generation of these data. Genome sequences are freely available in the European Nucleotide Archive under accession ERP009059. Isofemale lines can be obtained from the Drosophila Species Stock Center. PMID:25717372

Strain-specific and pooled genome sequences for populations of Drosophila melanogaster from three continents.

PubMed

Bergman, Casey M; Haddrill, Penelope R

2015-01-01

To contribute to our general understanding of the evolutionary forces that shape variation in genome sequences in nature, we have sequenced genomes from 50 isofemale lines and six pooled samples from populations of Drosophila melanogaster on three continents. Analysis of raw and reference-mapped reads indicates the quality of these genomic sequence data is very high. Comparison of the predicted and experimentally-determined Wolbachia infection status of these samples suggests that strain or sample swaps are unlikely to have occurred in the generation of these data. Genome sequences are freely available in the European Nucleotide Archive under accession ERP009059. Isofemale lines can be obtained from the Drosophila Species Stock Center.

Classification and Lineage Tracing of SH2 Domains Throughout Eukaryotes.

PubMed

Liu, Bernard A

2017-01-01

Today there exists a rapidly expanding number of sequenced genomes. Cataloging protein interaction domains such as the Src Homology 2 (SH2) domain across these various genomes can be accomplished with ease due to existing algorithms and predictions models. An evolutionary analysis of SH2 domains provides a step towards understanding how SH2 proteins integrated with existing signaling networks to position phosphotyrosine signaling as a crucial driver of robust cellular communication networks in metazoans. However organizing and tracing SH2 domain across organisms and understanding their evolutionary trajectory remains a challenge. This chapter describes several methodologies towards analyzing the evolutionary trajectory of SH2 domains including a global SH2 domain classification system, which facilitates annotation of new SH2 sequences essential for tracing the lineage of SH2 domains throughout eukaryote evolution. This classification utilizes a combination of sequence homology, protein domain architecture and the boundary positions between introns and exons within the SH2 domain or genes encoding these domains. Discrete SH2 families can then be traced across various genomes to provide insight into its origins. Furthermore, additional methods for examining potential mechanisms for divergence of SH2 domains from structural changes to alterations in the protein domain content and genome duplication will be discussed. Therefore a better understanding of SH2 domain evolution may enhance our insight into the emergence of phosphotyrosine signaling and the expansion of protein interaction domains.

AXAF FITS standard for ray trace interchange

NASA Astrophysics Data System (ADS)

Hsieh, Paul F.

1993-07-01

A standard data format for the archival and transport of x-ray events generated by ray trace models is described. Upon review and acceptance by the Advanced X-ray Astrophysics Facility (AXAF) Software Systems Working Group (SSWG), this standard shall become the official AXAF data format for ray trace events. The Flexible Image Transport System (FITS) is well suited for the purposes of the standard and was selected to be the basis of the standard. FITS is both flexible and efficient and is also widely used within the astronomical community for storage and transfer of data. In addition, software to read and write FITS format files are widely available. In selecting quantities to be included within the ray trace standard, the AXAF Mission Support team, Science Instruments team, and the other contractor teams were surveyed. From the results of this survey, the following requirements were established: (1) for the scientific needs, each photon should have associated with it: position, direction, energy, and statistical weight; the standard must also accommodate path length (relative phase), and polarization. (2) a unique photon identifier is necessary for bookkeeping purposes; (3) a log of individuals, organizations, and software packages that have modified the data must be maintained in order to create an audit trail; (4) a mechanism for extensions to the basic kernel should be provided; and (5) the ray trace standard should integrate with future AXAF data product standards.

AXAF FITS standard for ray trace interchange

NASA Technical Reports Server (NTRS)

Hsieh, Paul F.

1993-01-01

A standard data format for the archival and transport of x-ray events generated by ray trace models is described. Upon review and acceptance by the Advanced X-ray Astrophysics Facility (AXAF) Software Systems Working Group (SSWG), this standard shall become the official AXAF data format for ray trace events. The Flexible Image Transport System (FITS) is well suited for the purposes of the standard and was selected to be the basis of the standard. FITS is both flexible and efficient and is also widely used within the astronomical community for storage and transfer of data. In addition, software to read and write FITS format files are widely available. In selecting quantities to be included within the ray trace standard, the AXAF Mission Support team, Science Instruments team, and the other contractor teams were surveyed. From the results of this survey, the following requirements were established: (1) for the scientific needs, each photon should have associated with it: position, direction, energy, and statistical weight; the standard must also accommodate path length (relative phase), and polarization. (2) a unique photon identifier is necessary for bookkeeping purposes; (3) a log of individuals, organizations, and software packages that have modified the data must be maintained in order to create an audit trail; (4) a mechanism for extensions to the basic kernel should be provided; and (5) the ray trace standard should integrate with future AXAF data product standards.

Critical issues in trace gas biogeochemistry and global change.

PubMed

Beerling, David J; Nicholas Hewitt, C; Pyle, John A; Raven, John A

2007-07-15

The atmospheric composition of trace gases and aerosols is determined by the emission of compounds from the marine and terrestrial biospheres, anthropogenic sources and their chemistry and deposition processes. Biogenic emissions depend upon physiological processes and climate, and the atmospheric chemistry is governed by climate and feedbacks involving greenhouse gases themselves. Understanding and predicting the biogeochemistry of trace gases in past, present and future climates therefore demands an interdisciplinary approach integrating across physiology, atmospheric chemistry, physics and meteorology. Here, we highlight critical issues raised by recent findings in all of these key areas to provide a framework for better understanding the past and possible future evolution of the atmosphere. Incorporating recent experimental and observational findings, especially the influence of CO2 on trace gas emissions from marine algae and terrestrial plants, into earth system models remains a major research priority. As we move towards this goal, archives of the concentration and isotopes of N2O and CH4 from polar ice cores extending back over 650,000 years will provide a valuable benchmark for evaluating such models. In the Pre-Quaternary, synthesis of theoretical modelling with geochemical and palaeontological evidence is also uncovering the roles played by trace gases in episodes of abrupt climatic warming and ozone depletion. Finally, observations and palaeorecords across a range of timescales allow assessment of the Earth's climate sensitivity, a metric influencing our ability to decide what constitutes 'dangerous' climate change.

Sedimentary chronology reinterpreted from Changshou Lake of the Three Gorges Reservoir Area reveals natural and anthropogenic controls on sediment production.

PubMed

Anjum, Raheel; Tang, Qiang; Collins, Adrian L; Gao, Jinzhang; Long, Yi; Zhang, Xinbao; He, Xiubin; Shi, Zhonglin; Wen, Anbang; Wei, Jie

2018-04-17

Sedimentary archives preserved in geomorphic sinks provide records of historical sediment dynamics and its related natural and anthropogenic controls. This study reinterpreted sedimentary processes in Changshou Lake of the Three Gorges Reservoir Area in China by combining a rainfall erosivity index with multiple tracing proxies, and the impacts of natural and anthropogenic drivers on sediment production were also explored. Erosive rainfalls with low frequency and large magnitude in the rainy season contribute to a substantial proportion of annual total rainfall, which thus can be used to infer erosion and sediment yield events. The sedimentary chronology was determined by comparing rainfall erosivity index with depth distribution of 137 Cs and absolute particle size, which revealed annual sedimentation rates ranging from 1.1 to 2.3 cm a -1 . The multi-proxy dating index and variation of sedimentation rate divided the sediment profile into three major periods. The reference period (1956-1982) displays low variability of TOC, TN, trace metal concentrations, and mean sedimentation rate. In the stressed period (1982-1998), industrial and sewerage discharge led to input and deposition of TOC, TN, and trace metals (e.g., Cd, Co, Cu, Cr, and Ni). The highest annual sediment accumulation rate of 2.3 cm a -1 may be ascribed to the 1982 big flood event. In the present period (1998-2013), increased TOC, TN and decreased trace metals in the top layers of the sediment core indicated changes in lake ecology. Fish farming promoted algal growth and primary productivity which caused eutrophication until 2004-2005. The reduced mean sedimentation rate of 1.7 cm a -1 between 1998 and 2004, and thereafter, may be attributed to soil and water conservation and reforestation policies implemented in the Longxi catchment. Human activities such as deforestation, cultural and industrial revolution, and lake eutrophication associated with fish farming since 1989, therefore led to appreciable limnological variations. Overall, the dated sedimentary profile from Changshou Lake displays high consistency with archived historical events and reflects the impact of both natural and anthropogenic controls on sediment production.

Metaphor as a Possible Pathway to More Formal Understanding of the Definition of Sequence Convergence

ERIC Educational Resources Information Center

Dawkins, Paul Christian

2012-01-01

This study presents how the introduction of a metaphor for sequence convergence constituted an experientially real context in which an undergraduate real analysis student developed a property-based definition of sequence convergence. I use elements from Zandieh and Rasmussen's (2010) Defining as a Mathematical Activity framework to trace the…

Direct Formalin Fixation Induces Widespread Genomic Effects in Archival Tissues

EPA Science Inventory

Recent advances in next generation sequencing have dramatically improved transcriptional analysis of degraded RNA from formalin-fixed paraffin-embedded (FFPE) samples. However, little is known about potential genomic artifacts induced by formalin fixation, which could affect toxi...

Compendium of NASA data base for the Global Tropospheric Experiment's Arctic Boundary Layer Experiments ABLE-3A and ABLE-3B

NASA Technical Reports Server (NTRS)

Gregory, Gerald L.; Scott, A. Donald, Jr.

1994-01-01

The report provides a compendium of NASA aircraft data that are available from NASA's Global Tropospheric Experiment's (GTE) Arctic Boundary Layer Experiments (ABLE) conducted in July and August of 1988 (ABLE-3A) and 1990 (ABLE-3B). ABLE-3A flight experiments were based at Barrow and Bethel, Alaska, and included survey/transit flights to Thule, Greenland. ABLE-3B flight experiments were based at North Bay (Ontario) and Goose Bay, Canada, and included flights northward to Frobisher Bay, Canada. The primary purposes of the experiments were (1) the measurement of the flux of various trace gases from high-arctic ecosystems, (2) the elucidation of factors important to the production and destruction of ozone, and (3) the documentation of source and chemical signature of air common to and transported into the regions. The report provides a representation, in the form of selected data plots, of aircraft data that are available in archived format via NASA Langley's Distributed Active Archive Center. The archived data bases include data for other species measured on the aircraft as well as numerous supporting data, including meteorological observations/products, results from surface studies, satellite observations, and sondes releases.

Archive of digital Boomer seismic reflection data collected during USGS Cruises 94CCT01 and 95CCT01, eastern Texas and western Louisiana, 1994 and 1995

USGS Publications Warehouse

Calderon, Karynna; Dadisman, Shawn V.; Kindinger, Jack G.; Flocks, James G.; Morton, Robert A.; Wiese, Dana S.

2004-01-01

In June of 1994 and August and September of 1995, the U.S. Geological Survey, in cooperation with the University of Texas Bureau of Economic Geology, conducted geophysical surveys of the Sabine and Calcasieu Lake areas and the Gulf of Mexico offshore eastern Texas and western Louisiana. This report serves as an archive of unprocessed digital boomer seismic reflection data, trackline maps, navigation files, observers' logbooks, GIS information, and formal FGDC metadata. In addition, a filtered and gained GIF image of each seismic profile is provided. The archived trace data are in standard Society of Exploration Geophysicists (SEG) SEG-Y format (Barry and others, 1975) and may be downloaded and processed with commercial or public domain software such as Seismic Unix (SU). Examples of SU processing scripts and in-house (USGS) software for viewing SEG-Y files (Zihlman, 1992) are also provided. Processed profile images, trackline maps, navigation files, and formal metadata may be viewed with a web browser. Scanned handwritten logbooks and Field Activity Collection System (FACS) logs may be viewed with Adobe Reader.

Archive of digital Boomer and Chirp seismic reflection data collected during USGS Cruises 01RCE05 and 02RCE01 in the Lower Atchafalaya River, Mississippi River Delta, and offshore southeastern Louisiana, October 23-30, 2001, and August 18-19, 2002

USGS Publications Warehouse

Calderon, Karynna; Dadisman, Shawn V.; Kindinger, Jack G.; Flocks, James G.; Ferina, Nicholas F.; Wiese, Dana S.

2004-01-01

In October of 2001 and August of 2002, the U.S. Geological Survey conducted geophysical surveys of the Lower Atchafalaya River, the Mississippi River Delta, Barataria Bay, and the Gulf of Mexico south of East Timbalier Island, Louisiana. This report serves as an archive of unprocessed digital marine seismic reflection data, trackline maps, navigation files, observers' logbooks, GIS information, and formal FGDC metadata. In addition, a filtered and gained GIF image of each seismic profile is provided. The archived trace data are in standard Society of Exploration Geophysicists (SEG) SEG-Y format (Barry and othes, 1975) and may be downloaded and processed with commercial or public domain software such as Seismic Unix (SU). Examples of SU processing scripts and in-house (USGS) software for viewing SEG-Y files (Zihlman, 1992) are also provided. Processed profile images, trackline maps, navigation files, and formal metadata may be viewed with a web browser. Scanned handwritten logbooks and Field Activity Collection System (FACS) logs may be viewed with Adobe Reader.

Next-generation digital information storage in DNA.

PubMed

Church, George M; Gao, Yuan; Kosuri, Sriram

2012-09-28

Digital information is accumulating at an astounding rate, straining our ability to store and archive it. DNA is among the most dense and stable information media known. The development of new technologies in both DNA synthesis and sequencing make DNA an increasingly feasible digital storage medium. We developed a strategy to encode arbitrary digital information in DNA, wrote a 5.27-megabit book using DNA microchips, and read the book by using next-generation DNA sequencing.

FDSTools: A software package for analysis of massively parallel sequencing data with the ability to recognise and correct STR stutter and other PCR or sequencing noise.

PubMed

Hoogenboom, Jerry; van der Gaag, Kristiaan J; de Leeuw, Rick H; Sijen, Titia; de Knijff, Peter; Laros, Jeroen F J

2017-03-01

Massively parallel sequencing (MPS) is on the advent of a broad scale application in forensic research and casework. The improved capabilities to analyse evidentiary traces representing unbalanced mixtures is often mentioned as one of the major advantages of this technique. However, most of the available software packages that analyse forensic short tandem repeat (STR) sequencing data are not well suited for high throughput analysis of such mixed traces. The largest challenge is the presence of stutter artefacts in STR amplifications, which are not readily discerned from minor contributions. FDSTools is an open-source software solution developed for this purpose. The level of stutter formation is influenced by various aspects of the sequence, such as the length of the longest uninterrupted stretch occurring in an STR. When MPS is used, STRs are evaluated as sequence variants that each have particular stutter characteristics which can be precisely determined. FDSTools uses a database of reference samples to determine stutter and other systemic PCR or sequencing artefacts for each individual allele. In addition, stutter models are created for each repeating element in order to predict stutter artefacts for alleles that are not included in the reference set. This information is subsequently used to recognise and compensate for the noise in a sequence profile. The result is a better representation of the true composition of a sample. Using Promega Powerseq™ Auto System data from 450 reference samples and 31 two-person mixtures, we show that the FDSTools correction module decreases stutter ratios above 20% to below 3%. Consequently, much lower levels of contributions in the mixed traces are detected. FDSTools contains modules to visualise the data in an interactive format allowing users to filter data with their own preferred thresholds. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

GTSO: Global Trace Synchronization and Ordering Mechanism for Wireless Sensor Network Monitoring Platforms

PubMed Central

Bonastre, Alberto; Ors, Rafael

2017-01-01

Monitoring is one of the best ways to evaluate the behavior of computer systems. When the monitored system is a distributed system—such as a wireless sensor network (WSN)—the monitoring operation must also be distributed, providing a distributed trace for further analysis. The temporal sequence of occurrence of the events registered by the distributed monitoring platform (DMP) must be correctly established to provide cause-effect relationships between them, so the logs obtained in different monitor nodes must be synchronized. Many of synchronization mechanisms applied to DMPs consist in adjusting the internal clocks of the nodes to the same value as a reference time. However, these mechanisms can create an incoherent event sequence. This article presents a new method to achieve global synchronization of the traces obtained in a DMP. It is based on periodic synchronization signals that are received by the monitor nodes and logged along with the recorded events. This mechanism processes all traces and generates a global post-synchronized trace by scaling all times registered proportionally according with the synchronization signals. It is intended to be a simple but efficient offline mechanism. Its application in a WSN-DMP demonstrates that it guarantees a correct ordering of the events, avoiding the aforementioned issues. PMID:29295494

Dispersion model on PM₂.₅ fugitive dust and trace metals levels in Kuwait Governorates.

PubMed

Bu-Olayan, A H; Thomas, B V

2012-03-01

Frequent dust storms and recent environmental changes were found to affect the human health especially in residents of arid countries. Investigations on the PM(2.5) fugitive dust in six Kuwait Governorate areas using dispersion Gaussian plume modeling revealed significant relationship between low rate of pollutant emission, low wind velocity, and stable weather conditions' matrix causing high rate of dust deposition in summer than in winter. The rate of dust deposition and trace metals levels in PM(2.5) were in the sequence of G-VI > G-I > G-II > G-V > G-III > G-IV. Trace metals were observed in the sequence of Al > Fe > Zn > Ni > Pb > Cd irrespective of the Governorate areas and the two seasons. The high rate of dust deposition and trace metals in PM(2.5) was reflected by the vast open area, wind velocity, and rapid industrialization besides natural and anthropogenic sources. A combination of air dispersion modeling and nephalometric and gravimetric studies of this kind not only determines the seasonal qualitative and quantitative analyses on the PM(2.5) dust deposition besides trace metals apportionment in six Kuwait Governorate areas, but also characterizes air pollution factors that could be used by environmentalist to deduce preventive measures.

GTSO: Global Trace Synchronization and Ordering Mechanism for Wireless Sensor Network Monitoring Platforms.

PubMed

Navia, Marlon; Campelo, José Carlos; Bonastre, Alberto; Ors, Rafael

2017-12-23

Monitoring is one of the best ways to evaluate the behavior of computer systems. When the monitored system is a distributed system-such as a wireless sensor network (WSN)-the monitoring operation must also be distributed, providing a distributed trace for further analysis. The temporal sequence of occurrence of the events registered by the distributed monitoring platform (DMP) must be correctly established to provide cause-effect relationships between them, so the logs obtained in different monitor nodes must be synchronized. Many of synchronization mechanisms applied to DMPs consist in adjusting the internal clocks of the nodes to the same value as a reference time. However, these mechanisms can create an incoherent event sequence. This article presents a new method to achieve global synchronization of the traces obtained in a DMP. It is based on periodic synchronization signals that are received by the monitor nodes and logged along with the recorded events. This mechanism processes all traces and generates a global post-synchronized trace by scaling all times registered proportionally according with the synchronization signals. It is intended to be a simple but efficient offline mechanism. Its application in a WSN-DMP demonstrates that it guarantees a correct ordering of the events, avoiding the aforementioned issues.

Compendium of NASA data base for the global tropospheric experiment's Transport and Atmospheric Chemistry Near the Equator-Atlantic (TRACE-A)

NASA Technical Reports Server (NTRS)

Gregory, Gerald L.; Scott, A. Donald, Jr.

1995-01-01

This compendium describes aircraft data that are available from NASA's Transport and Atmospheric Chemistry near the Equator - Atlantic (TRACE-A) conducted in September/October 1992. The broad objectives of TRACE-A were to study chemical processes and long-range transport associated with South American and African continental outflow during periods of widespread vegetation burning, and to understand the ozone enhancements observed from satellite data measured over the southern tropical Atlantic Ocean during the September/October time period. Flight experiments were conducted from Brazil, South Africa, Namibia, and the Ascension Island. This document provides a representation of aircraft data that are available from NASA Langley's Distributed Active Archive Center (DAAC). The data format of time series and altitude profile plots is not intended to support original analyses, but to assist the reader in identifying data that are of interest. This compendium is for only the NASA aircraft data. The DAAC data base includes numerous supporting data-meteorological products, results from surface studies, satellite observations, and data from sonde releases.

TraceContract: A Scala DSL for Trace Analysis

NASA Technical Reports Server (NTRS)

Barringer, Howard; Havelund, Klaus

2011-01-01

In this paper we describe TRACECONTRACT, an API for trace analysis, implemented in the SCALA programming language. We argue that for certain forms of trace analysis the best weapon is a high level programming language augmented with constructs for temporal reasoning. A trace is a sequence of events, which may for example be generated by a running program, instrumented appropriately to generate events. The API supports writing properties in a notation that combines an advanced form of data parameterized state machines with temporal logic. The implementation utilizes SCALA's support for defining internal Domain Specific Languages (DSLs). Furthermore SCALA's combination of object oriented and functional programming features, including partial functions and pattern matching, makes it an ideal host language for such an API.

The last Deglaciation in the Mediterranean region: a multi-archives synthesis

NASA Astrophysics Data System (ADS)

Bazin, Lucie; Siani, Giuseppe; Landais, Amaelle; Bassinot, Frank; Genty, Dominique; Govin, Aline; Michel, Elisabeth; Nomade, Sebastien; Waelbroeck, Claire

2016-04-01

Multiple proxies record past climatic changes in different climate archives. These proxies are influenced by different component of the climate system and bring complementary information on past climate variability. The major limitation when combining proxies from different archives comes from the coherency of their chronologies. Indeed, each climate archives possess their own dating methods, not necessarily coherent with each other's. Consequently, when we want to assess the latitudinal changes and mechanisms behind a climate event, we often have to rely on assumptions of synchronisation between the different archives, such as synchronous temperature changes during warming events (Austin and Hibbert 2010). Recently, a dating method originally developed to produce coherent chronologies for ice cores (Datice,Lemieux-Dudon et al., 2010) has been adapted in order to integrate different climate archives (ice cores, sediment cores and speleothems (Lemieux-Dudon et al., 2015, Bazin et al., in prep)). In this presentation we present the validation of this multi-archives dating tool with a first application covering the last Deglaciation in the Mediterranean region. For this experiment, we consider the records from Monticchio, the MD90-917, Tenaghi Philippon and Lake Orhid sediment cores as well as continuous speleothems from Sofular, Soreq and La Mine caves. Using the Datice dating tool, and with the identification of common tephra layers between the cores considered, we are able to produce a multi-archives coherent chronology for this region, independently of any climatic assumption. Using this common chronological framework, we show that the usual climatic synchronisation assumptions are not valid over this region for the last glacial-interglacial transition. Finally, we compare our coherent Mediterranean chronology with Greenland ice core records in order to discuss the sequence of events of the last Deglaciation between these two regions.

The abundance and relative volatility of refractory trace elements in Allende Ca,Al-rich inclusions - Implications for chemical and physical processes in the solar nebula

NASA Technical Reports Server (NTRS)

Kornacki, Alan S.; Fegley, Bruce, Jr.

1986-01-01

The relative volatilities of lithophile refractory trace elements (LRTE) were determined using calculated 50-percent condensation temperatures. Then, the refractory trace-element abundances were measured in about 100 Allende inclusions. The abundance patterns found in Allende Ca,Al-rich inclusions (CAIs) and ultrarefractory inclusions were used to empirically modify the calculated LRTE volatility sequence. In addition, the importance of crystal-chemical effects, diffusion constraints, and grain transport for the origin of the trace-element chemistry of Allende CAIs (which have important implications for chemical and physical processes in the solar nebula) is discussed.

Sequencing of bimaxillary surgery in the correction of vertical maxillary excess: retrospective study.

PubMed

Salmen, F S; de Oliveira, T F M; Gabrielli, M A C; Pereira Filho, V A; Real Gabrielli, M F

2018-06-01

The aim of this study was to evaluate the precision of bimaxillary surgery performed to correct vertical maxillary excess, when the procedure is sequenced with mandibular surgery first or maxillary surgery first. Thirty-two patients, divided into two groups, were included in this retrospective study. Group 1 comprised patients who received bimaxillary surgery following the classical sequence with repositioning of the maxilla first. Patients in group 2 received bimaxillary surgery, but the mandible was operated on first. The precision of the maxillomandibular repositioning was determined by comparison of the digital prediction and postoperative tracings superimposed on the cranial base. The data were tabulated and analyzed statistically. In this sample, both surgical sequences provided adequate clinical accuracy. The classical sequence, repositioning the maxilla first, resulted in greater accuracy for A-point and the upper incisor edge vertical position. Repositioning the mandible first allowed greater precision in the vertical position of pogonion. In conclusion, although both surgical sequences may be used, repositioning the mandible first will result in greater imprecision in relation to the predictive tracing than repositioning the maxilla first. The classical sequence resulted in greater accuracy in the vertical position of the maxilla, which is key for aesthetics. Copyright © 2017 International Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

Major and trace element abundances in volcanic rocks of orogenic areas.

NASA Technical Reports Server (NTRS)

Jakes, P.; White, A. J. R.

1972-01-01

The composition of recent island-arc volcanic rocks in relation to their geographic and stratigraphic relations is discussed. The differences in composition between volcanic rocks and those in continental margins are pointed out. Trace elements and major elements are shown to suggest a continuous gradational sequence from tholeiites through calc-alkaline rocks to shoshonites.

A single mini-barcode test to screen for Australian mammalian predators from environmental samples

PubMed Central

MacDonald, Anna J; Sarre, Stephen D

2017-01-01

Abstract Identification of species from trace samples is now possible through the comparison of diagnostic DNA fragments against reference DNA sequence databases. DNA detection of animals from non-invasive samples, such as predator faeces (scats) that contain traces of DNA from their species of origin, has proved to be a valuable tool for the management of elusive wildlife. However, application of this approach can be limited by the availability of appropriate genetic markers. Scat DNA is often degraded, meaning that longer DNA sequences, including standard DNA barcoding markers, are difficult to recover. Instead, targeted short diagnostic markers are required to serve as diagnostic mini-barcodes. The mitochondrial genome is a useful source of such trace DNA markers because it provides good resolution at the species level and occurs in high copy numbers per cell. We developed a mini-barcode based on a short (178 bp) fragment of the conserved 12S ribosomal ribonucleic acid mitochondrial gene sequence, with the goal of discriminating amongst the scats of large mammalian predators of Australia. We tested the sensitivity and specificity of our primers and can accurately detect and discriminate amongst quolls, cats, dogs, foxes, and devils from trace DNA samples. Our approach provides a cost-effective, time-efficient, and non-invasive tool that enables identification of all 8 medium-large mammal predators in Australia, including native and introduced species, using a single test. With modification, this approach is likely to be of broad applicability elsewhere. PMID:28810700

Postretrieval new learning does not reliably induce human memory updating via reconsolidation.

PubMed

Hardwicke, Tom E; Taqi, Mahdi; Shanks, David R

2016-05-10

Reconsolidation theory proposes that retrieval can destabilize an existing memory trace, opening a time-dependent window during which that trace is amenable to modification. Support for the theory is largely drawn from nonhuman animal studies that use invasive pharmacological or electroconvulsive interventions to disrupt a putative postretrieval restabilization ("reconsolidation") process. In human reconsolidation studies, however, it is often claimed that postretrieval new learning can be used as a means of "updating" or "rewriting" existing memory traces. This proposal warrants close scrutiny because the ability to modify information stored in the memory system has profound theoretical, clinical, and ethical implications. The present study aimed to replicate and extend a prominent 3-day motor-sequence learning study [Walker MP, Brakefield T, Hobson JA, Stickgold R (2003) Nature 425(6958):616-620] that is widely cited as a convincing demonstration of human reconsolidation. However, in four direct replication attempts (n = 64), we did not observe the critical impairment effect that has previously been taken to indicate disruption of an existing motor memory trace. In three additional conceptual replications (n = 48), we explored the broader validity of reconsolidation-updating theory by using a declarative recall task and sequences similar to phone numbers or computer passwords. Rather than inducing vulnerability to interference, memory retrieval appeared to aid the preservation of existing sequence knowledge relative to a no-retrieval control group. These findings suggest that memory retrieval followed by new learning does not reliably induce human memory updating via reconsolidation.

Tracing Males From Different Continents by Genotyping JC Polyomavirus in DNA From Semen Samples.

PubMed

Rotondo, John Charles; Candian, Tommaso; Selvatici, Rita; Mazzoni, Elisa; Bonaccorsi, Gloria; Greco, Pantaleo; Tognon, Mauro; Martini, Fernanda

2017-05-01

The human JC polyomavirus (JCPyV) is an ubiquitous viral agent infecting approximately 60% of humans. Recently, JCPyV sequences have been detected in semen samples. The aim of this investigation was to test whether semen JCPyV genotyping can be employed to trace the origin continent of males. Semen DNA samples (n = 170) from males of different Continents were investigated by PCR for the polymorphic JCPyV viral capsid protein 1 (VP1) sequences, followed by DNA sequencing. JCPyV sequences were detected with an overall prevalence of 27.6% (47/170). DNA sequencing revealed that European males carried JCPyV types 1A (71.4%), 4 (11.4%), 2B (2.9%), 2D1 (2.9%), and 3A (2.9%). Asians JCPyV type 2D1 (66.7%) and Africans JCPyV types 3A (33.3%) and 1A (33.3%). In 10.6% of males, two different JCPyV genotypes were detected, suggesting that the second JCPyV genotype was acquired in the destination country. This study indicates that the majority of semen samples found to be JCPyV-positive, were infected with the JCPyV genotype found in the geographic area of male origin. Therefore, semen JCPyV genotyping could be employed to trace the origin continent of males. Our findings could be applied to forensic investigations, in case of for instance sexual crimes. Indeed, JCPyV genotyping should enable investigators to make additional detailed profiling of the offender. J. Cell. Physiol. 232: 982-985, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Tracing marine cryptotephras in the North Atlantic during the last glacial period: Improving the North Atlantic marine tephrostratigraphic framework

NASA Astrophysics Data System (ADS)

Abbott, Peter M.; Griggs, Adam J.; Bourne, Anna J.; Chapman, Mark R.; Davies, Siwan M.

2018-06-01

Tephrochronology is increasingly being recognised as a key tool for the correlation of disparate palaeoclimatic archives, underpinning chronological models and facilitating climatically independent comparisons of climate proxies. Tephra frameworks integrating both distal and proximal tephra occurrences are essential to these investigations providing key details on their spatial distributions, geochemical signatures, eruptive sources as well as any available chronological and/or stratigraphic information. Frameworks also help to avoid mis-correlation of horizons and provide important information on volcanic history. Here we present a comprehensive chronostratigraphic framework of 14 tephra horizons from North Atlantic marine sequences spanning 60-25 cal ka BP. Horizons previously discovered as visible or coarse-grained deposits have been combined with 11 newly recognised volcanic deposits, identified through the application of cryptotephra identification and characterisation methods to a wide network of marine sequences. Their isochronous integrity has been assessed using their physical characteristics. All horizons originated from Iceland with the vast majority having a basaltic composition sourced from the Grímsvötn, Kverkfjöll, Hekla/Vatnafjöll and Katla volcanic systems. New occurrences, improved stratigraphic placements and a refinement of the geochemical signature of the NAAZ II are reported and the range of the FMAZ IV has been extended. In addition, several significant geochemical populations that further investigations could show to be isochronous are reported. This tephra framework provides the foundation for the correlation and synchronisation of these marine records to the Greenland ice-cores and European terrestrial records to investigate the phasing, rate, timing and mechanisms controlling rapid climate changes that characterised the last glacial period.

Sequence of events from the onset to the demise of the Last Interglacial: Evaluating strengths and limitations of chronologies used in climatic archives

NASA Astrophysics Data System (ADS)

Govin, A.; Capron, E.; Tzedakis, P. C.; Verheyden, S.; Ghaleb, B.; Hillaire-Marcel, C.; St-Onge, G.; Stoner, J. S.; Bassinot, F.; Bazin, L.; Blunier, T.; Combourieu-Nebout, N.; El Ouahabi, A.; Genty, D.; Gersonde, R.; Jimenez-Amat, P.; Landais, A.; Martrat, B.; Masson-Delmotte, V.; Parrenin, F.; Seidenkrantz, M.-S.; Veres, D.; Waelbroeck, C.; Zahn, R.

2015-12-01

The Last Interglacial (LIG) represents an invaluable case study to investigate the response of components of the Earth system to global warming. However, the scarcity of absolute age constraints in most archives leads to extensive use of various stratigraphic alignments to different reference chronologies. This feature sets limitations to the accuracy of the stratigraphic assignment of the climatic sequence of events across the globe during the LIG. Here, we review the strengths and limitations of the methods that are commonly used to date or develop chronologies in various climatic archives for the time span (∼140-100 ka) encompassing the penultimate deglaciation, the LIG and the glacial inception. Climatic hypotheses underlying record alignment strategies and the interpretation of tracers are explicitly described. Quantitative estimates of the associated absolute and relative age uncertainties are provided. Recommendations are subsequently formulated on how best to define absolute and relative chronologies. Future climato-stratigraphic alignments should provide (1) a clear statement of climate hypotheses involved, (2) a detailed understanding of environmental parameters controlling selected tracers and (3) a careful evaluation of the synchronicity of aligned paleoclimatic records. We underscore the need to (1) systematically report quantitative estimates of relative and absolute age uncertainties, (2) assess the coherence of chronologies when comparing different records, and (3) integrate these uncertainties in paleoclimatic interpretations and comparisons with climate simulations. Finally, we provide a sequence of major climatic events with associated age uncertainties for the period 140-105 ka, which should serve as a new benchmark to disentangle mechanisms of the Earth system's response to orbital forcing and evaluate transient climate simulations.

Development and Validation of an Ultradeep Next-Generation Sequencing Assay for Testing of Plasma Cell-Free DNA from Patients with Advanced Cancer.

PubMed

Janku, Filip; Zhang, Shile; Waters, Jill; Liu, Li; Huang, Helen J; Subbiah, Vivek; Hong, David S; Karp, Daniel D; Fu, Siqing; Cai, Xuyu; Ramzanali, Nishma M; Madwani, Kiran; Cabrilo, Goran; Andrews, Debra L; Zhao, Yue; Javle, Milind; Kopetz, E Scott; Luthra, Rajyalakshmi; Kim, Hyunsung J; Gnerre, Sante; Satya, Ravi Vijaya; Chuang, Han-Yu; Kruglyak, Kristina M; Toung, Jonathan; Zhao, Chen; Shen, Richard; Heymach, John V; Meric-Bernstam, Funda; Mills, Gordon B; Fan, Jian-Bing; Salathia, Neeraj S

2017-09-15

Purpose: Tumor-derived cell-free DNA (cfDNA) in plasma can be used for molecular testing and provide an attractive alternative to tumor tissue. Commonly used PCR-based technologies can test for limited number of alterations at the time. Therefore, novel ultrasensitive technologies capable of testing for a broad spectrum of molecular alterations are needed to further personalized cancer therapy. Experimental Design: We developed a highly sensitive ultradeep next-generation sequencing (NGS) assay using reagents from TruSeqNano library preparation and NexteraRapid Capture target enrichment kits to generate plasma cfDNA sequencing libraries for mutational analysis in 61 cancer-related genes using common bioinformatics tools. The results were retrospectively compared with molecular testing of archival primary or metastatic tumor tissue obtained at different points of clinical care. Results: In a study of 55 patients with advanced cancer, the ultradeep NGS assay detected 82% (complete detection) to 87% (complete and partial detection) of the aberrations identified in discordantly collected corresponding archival tumor tissue. Patients with a low variant allele frequency (VAF) of mutant cfDNA survived longer than those with a high VAF did ( P = 0.018). In patients undergoing systemic therapy, radiological response was positively associated with changes in cfDNA VAF ( P = 0.02), and compared with unchanged/increased mutant cfDNA VAF, decreased cfDNA VAF was associated with longer time to treatment failure (TTF; P = 0.03). Conclusions: Ultradeep NGS assay has good sensitivity compared with conventional clinical mutation testing of archival specimens. A high VAF in mutant cfDNA corresponded with shorter survival. Changes in VAF of mutated cfDNA were associated with TTF. Clin Cancer Res; 23(18); 5648-56. ©2017 AACR . ©2017 American Association for Cancer Research.

Complementary concept for an image archive and communication system in a cardiological department based on CD-medical, an online archive, and networking facilities

NASA Astrophysics Data System (ADS)

Oswald, Helmut; Mueller-Jones, Kay; Builtjes, Jan; Fleck, Eckart

1998-07-01

The developments in information technologies -- computer hardware, networking and storage media -- has led to expectations that these advances make it possible to replace 35 mm film completely by digital techniques in the catheter laboratory. Besides the role of an archival medium, cine film is used as the major image review and exchange medium in cardiology. None of the today technologies can fulfill completely the requirements to replace cine film. One of the major drawbacks of cine film is the single access in time and location. For the four catheter laboratories in our institutions we have designed a complementary concept combining the CD-R, also called CD-medical, as a single patient storage and exchange medium, and a digital archive for on-line access and image review of selected frames or short sequences on adequate medical workstations. The image data from various modalities as well as all digital documents regarding to a patient are part of an electronic patient record. The access, the processing and the display of documents is supported by an integrated medical application.

Retrospective MicroRNA Sequencing: Complementary DNA Library Preparation Protocol Using Formalin-fixed Paraffin-embedded RNA Specimens.

PubMed

Loudig, Olivier; Liu, Christina; Rohan, Thomas; Ben-Dov, Iddo Z

2018-05-05

-Archived, clinically classified formalin-fixed paraffin-embedded (FFPE) tissues can provide nucleic acids for retrospective molecular studies of cancer development. By using non-invasive or pre-malignant lesions from patients who later develop invasive disease, gene expression analyses may help identify early molecular alterations that predispose to cancer risk. It has been well described that nucleic acids recovered from FFPE tissues have undergone severe physical damage and chemical modifications, which make their analysis difficult and generally requires adapted assays. MicroRNAs (miRNAs), however, which represent a small class of RNA molecules spanning only up to ~18-24 nucleotides, have been shown to withstand long-term storage and have been successfully analyzed in FFPE samples. Here we present a 3' barcoded complementary DNA (cDNA) library preparation protocol specifically optimized for the analysis of small RNAs extracted from archived tissues, which was recently demonstrated to be robust and highly reproducible when using archived clinical specimens stored for up to 35 years. This library preparation is well adapted to the multiplex analysis of compromised/degraded material where RNA samples (up to 18) are ligated with individual 3' barcoded adapters and then pooled together for subsequent enzymatic and biochemical preparations prior to analysis. All purifications are performed by polyacrylamide gel electrophoresis (PAGE), which allows size-specific selections and enrichments of barcoded small RNA species. This cDNA library preparation is well adapted to minute RNA inputs, as a pilot polymerase chain reaction (PCR) allows determination of a specific amplification cycle to produce optimal amounts of material for next-generation sequencing (NGS). This approach was optimized for the use of degraded FFPE RNA from specimens archived for up to 35 years and provides highly reproducible NGS data.

Neuropeptidomics of the Mosquito Aedes Aegypti

DTIC Science & Technology

2010-01-01

translational processing ( pyroglutamate formation) was detected for AST-C and CAPA-PVK-2. For the first time in insects, we succeeded in the direct...hormones, trace DNA sequences generated by TIGR and the Broad Institute were first searched by TBLASTN24 using amino acid sequences of candidate peptides...previously described.1 TBLASTN searches, using the amino acid sequences of putative Ae. aegypti neuropeptide and peptide hormone orthologs identified in

The Pacific Exploratory Mission-West Phase B: February-March, 1994

NASA Astrophysics Data System (ADS)

Hoell, J. M.; Davis, D. D.; Liu, S. C.; Newell, R. E.; Akimoto, H.; McNeal, R. J.; Bendura, R. J.

1997-12-01

The NASA Pacific Exploratory Mission in the Western Pacific Ocean (PEM-West) is a major component of the East Asia/North Pacific Regional Study (APARE), a project within the International Global Atmospheric Chemistry (IGAC) Program. The broad objectives of the PEM-West/APARE initiative are to study chemical processes and long-range transport of atmospheric trace species over the north-west Pacific Ocean and to estimate the magnitude of the human impact on these species over this region. The first phase of PEM-West (PEM-West A) was conducted in September-October 1991, a period characterized by minimum outflow from the Asian continent. The second phase of this mission, PEM-West B, was conducted during February-March 1994, a period characterized by enhanced outflow from the Asian continent. Both field campaigns of PEM-West included intensive airborne measurements of trace gases and aerosols from the NASA DC-8 aircraft coordinated with measurements at surface sites. This paper reports the experimental design for PEM-West B and provides a brief summary of the salient results of the PEM-West B campaign with particular emphases on the difference/similarities between phases A and B. Results from the two campaigns clearly quantify, from a trace gas perspective, the seasonal differences in the continental outflow that were qualitatively anticipated based upon meteorological considerations, and show the impact of major meteorological features within the region on the quality of tropospheric air over the North Pacific Ocean regions. The PEM-West database provides a "baseline" tool by which future assessments of a continuing impact of Asian emissions on remote Pacific regions can be judged. [These data are currently available through the Global Troposhperic Experiment Data Archive at NASA's Langley Research Center (http://www-gte.larc.nasa.gov) and the Langley Distributed Archive Center (http://eosdis.larc.nasa.gov)].

The bark of the branches of holm oak (Quercus ilex L.) for a retrospective study of trace elements in the atmosphere.

PubMed

Drava, Giuliana; Brignole, Daniele; Giordani, Paolo; Minganti, Vincenzo

2017-04-01

Tree bark has proved to be a useful bioindicator for trace elements in the atmosphere, however it reflects an exposure occurring during an unidentified period of time, so it provides spatial information about the distribution of contaminants in a certain area, but it cannot be used to detect temporal changes or trends, which is an important achievement in environmental studies. In order to obtain information about a known period of time, the bark collected from the annual segments of tree branches can be used, allowing analyses going back 10-15 years with annual resolution. In the present study, the concentrations of As, Cd, Co, Cu, Fe, Mn, Ni, Pb, V and Zn were measured by atomic emission spectrometry in a series of samples covering the period from 2001 to 2013 in an urban environment. Downward time trends were significant for Cd, Pb and Zn. The only trace element showing an upward time trend was V. The concentrations of the remaining six trace elements were constant over time, showing that their presence in bark is not simply proportional to the duration of exposure. This approach, which is simple, reliable and widely applicable at a low cost, allows the "a posteriori" reconstruction of atmospheric trace element deposition when or where no monitoring programme is in progress and no other natural archives are available. Copyright © 2017 Elsevier Inc. All rights reserved.

The proactive historian: Methodological opportunities presented by the new archives documenting genomics.

PubMed

García-Sancho, Miguel

2016-02-01

In this paper, I propose a strategy for navigating newly available archives in the study of late-twentieth century genomics. I demonstrate that the alleged 'explosion of data' characteristic of genomics-and of contemporary science in general-is not a new problem and that historians of earlier periods have dealt with information overload by relying on the 'perspective of time': the filtering effect the passage of time naturally exerts on both sources and memories. I argue that this reliance on the selective capacity of time results in inheriting archives curated by others and, consequently, poses the risk of reifying ahistorical scientific discourses. Through a preliminary examination of archives documenting early attempts at mapping and sequencing the human genome, I propose an alternative approach, in which historians proactively problematize and improve available sources. This approach provides historians with a voice in the socio-political management of scientific heritage and advances methodological innovations in the use of oral histories. It also provides a narrative framework in which to address big science initiatives by following second order administrators, rather than individual scientists. The new genomic archives thus represent an opportunity for historians to take an active role in current debates concerning 'big data' and critically embed the humanities in pressing global problems. Copyright © 2015 Elsevier Ltd. All rights reserved.

Basic Book Repair Methods.

ERIC Educational Resources Information Center

Schechter, Abraham A.

This book addresses some common preservation techniques that invariably become necessary in library and archival collections of any size. The procedures are described in chronological sequence, and photographs show the techniques from the viewpoint of the person actually doing the work. The recommended repair methods can be accomplished using…

The metagenomic data life-cycle: standards and best practices

PubMed Central

ten Hoopen, Petra; Finn, Robert D.; Bongo, Lars Ailo; Corre, Erwan; Meyer, Folker; Mitchell, Alex; Pelletier, Eric; Pesole, Graziano; Santamaria, Monica; Willassen, Nils Peder

2017-01-01

Abstract Metagenomics data analyses from independent studies can only be compared if the analysis workflows are described in a harmonized way. In this overview, we have mapped the landscape of data standards available for the description of essential steps in metagenomics: (i) material sampling, (ii) material sequencing, (iii) data analysis, and (iv) data archiving and publishing. Taking examples from marine research, we summarize essential variables used to describe material sampling processes and sequencing procedures in a metagenomics experiment. These aspects of metagenomics dataset generation have been to some extent addressed by the scientific community, but greater awareness and adoption is still needed. We emphasize the lack of standards relating to reporting how metagenomics datasets are analysed and how the metagenomics data analysis outputs should be archived and published. We propose best practice as a foundation for a community standard to enable reproducibility and better sharing of metagenomics datasets, leading ultimately to greater metagenomics data reuse and repurposing. PMID:28637310

The metagenomic data life-cycle: standards and best practices

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

ten Hoopen, Petra; Finn, Robert D.; Bongo, Lars Ailo

Metagenomics data analyses from independent studies can only be compared if the analysis workflows are described in a harmonised way. In this overview, we have mapped the landscape of data standards available for the description of essential steps in metagenomics: (1) material sampling, (2) material sequencing (3) data analysis and (4) data archiving & publishing. Taking examples from marine research, we summarise essential variables used to describe material sampling processes and sequencing procedures in a metagenomics experiment. These aspects of metagenomics dataset generation have been to some extent addressed by the scientific community but greater awareness and adoption is stillmore » needed. We emphasise the lack of standards relating to reporting how metagenomics datasets are analysed and how the metagenomics data analysis outputs should be archived and published. We propose best practice as a foundation for a community standard to enable reproducibility and better sharing of metagenomics datasets, leading ultimately to greater metagenomics data reuse and repurposing.« less

Mantle-derived trace element variability in olivines and their melt inclusions

NASA Astrophysics Data System (ADS)

Neave, David A.; Shorttle, Oliver; Oeser, Martin; Weyer, Stefan; Kobayashi, Katsura

2018-02-01

Trace element variability in oceanic basalts is commonly used to constrain the physics of mantle melting and the chemistry of Earth's deep interior. However, the geochemical properties of mantle melts are often overprinted by mixing and crystallisation processes during ascent and storage. Studying primitive melt inclusions offers one solution to this problem, but the fidelity of the melt-inclusion archive to bulk magma chemistry has been repeatedly questioned. To provide a novel check of the melt inclusion record, we present new major and trace element analyses from olivine macrocrysts in the products of two geographically proximal, yet compositionally distinct, primitive eruptions from the Reykjanes Peninsula of Iceland. By combining these macrocryst analyses with new and published melt inclusion analyses we demonstrate that olivines have similar patterns of incompatible trace element (ITE) variability to the inclusions they host, capturing chemical systematics on intra- and inter-eruption scales. ITE variability (element concentrations, ratios, variances and variance ratios) in olivines from the ITE-enriched Stapafell eruption is best accounted for by olivine-dominated fractional crystallisation. In contrast, ITE variability in olivines and inclusions from the ITE-depleted Háleyjabunga eruption cannot be explained by crystallisation alone, and must have originated in the mantle. Compatible trace element (CTE) variability is best described by crystallisation processes in both eruptions. Modest correlations between host and inclusion ITE contents in samples from Háleyjabunga suggest that melt inclusions can be faithful archives of melting and magmatic processes. It also indicates that degrees of ITE enrichment can be estimated from olivines directly when melt inclusion and matrix glass records of geochemical variability are poor or absent. Inter-eruption differences in olivine ITE systematics between Stapafell and Háleyjabunga mirror differences in melt inclusion suites, and confirm that the Stapafell eruption was fed by lower degree melts from greater depths within the melting region than the Háleyjabunga eruption. Although olivine macrocrysts from Stapafell are slightly richer in Ni than those from Háleyjabunga, their overall CTE systematics (e.g., Ni/(Mg/Fe), Fe/Mn and Zn/Fe) are inconsistent with being derived from olivine-free pyroxenites. However, the major element systematics of Icelandic basalts require lithological heterogeneity in their mantle source in the form of Fe-rich and hence fusible domains. We thus conclude that enriched heterogeneities in the Icelandic mantle are composed of modally enriched, yet nonetheless olivine-bearing, lithologies and that olivine CTE contents provide an incomplete record of lithological heterogeneity in the mantle. Modally enriched peridotites may therefore play a more important role in oceanic magma genesis than previously inferred.

Data security in genomics: A review of Australian privacy requirements and their relation to cryptography in data storage.

PubMed

Schlosberg, Arran

2016-01-01

The advent of next-generation sequencing (NGS) brings with it a need to manage large volumes of patient data in a manner that is compliant with both privacy laws and long-term archival needs. Outside of the realm of genomics there is a need in the broader medical community to store data, and although radiology aside the volume may be less than that of NGS, the concepts discussed herein are similarly relevant. The relation of so-called "privacy principles" to data protection and cryptographic techniques is explored with regards to the archival and backup storage of health data in Australia, and an example implementation of secure management of genomic archives is proposed with regards to this relation. Readers are presented with sufficient detail to have informed discussions - when implementing laboratory data protocols - with experts in the fields.

Data security in genomics: A review of Australian privacy requirements and their relation to cryptography in data storage

PubMed Central

Schlosberg, Arran

2016-01-01

The advent of next-generation sequencing (NGS) brings with it a need to manage large volumes of patient data in a manner that is compliant with both privacy laws and long-term archival needs. Outside of the realm of genomics there is a need in the broader medical community to store data, and although radiology aside the volume may be less than that of NGS, the concepts discussed herein are similarly relevant. The relation of so-called “privacy principles” to data protection and cryptographic techniques is explored with regards to the archival and backup storage of health data in Australia, and an example implementation of secure management of genomic archives is proposed with regards to this relation. Readers are presented with sufficient detail to have informed discussions – when implementing laboratory data protocols – with experts in the fields. PMID:26955504

ENDEMIC INFECTION OF STRANDED SOUTHERN SEA OTTERS (ENHYDRA LUTRIS NEREIS) WITH NOVEL PARVOVIRUS, POLYOMAVIRUS, AND ADENOVIRUS.

PubMed

Siqueira, Juliana D; Ng, Terry F; Miller, Melissa; Li, Linlin; Deng, Xutao; Dodd, Erin; Batac, Francesca; Delwart, Eric

2017-07-01

Over the past century, the southern sea otter (SSO; Enhydra lutris nereis) population has been slowly recovering from near extinction due to overharvest. The SSO is a threatened subspecies under federal law and a fully protected species under California law, US. Through a multiagency collaborative program, stranded animals are rehabilitated and released, while deceased animals are necropsied and tissues are cryopreserved to facilitate scientific study. Here, we processed archival tissues to enrich particle-associated viral nucleic acids, which we randomly amplified and deeply sequenced to identify viral genomes through sequence similarities. Anelloviruses and endogenous retroviral sequences made up over 50% of observed viral sequences. Polyomavirus, parvovirus, and adenovirus sequences made up most of the remaining reads. We characterized and phylogenetically analyzed the full genome of sea otter polyomavirus 1 and the complete coding sequence of sea otter parvovirus 1 and found that the closest known viruses infect primates and domestic pigs ( Sus scrofa domesticus), respectively. We tested archived tissues from 69 stranded SSO necropsied over 14 yr (2000-13) by PCR. Polyomavirus, parvovirus, and adenovirus infections were detected in 51, 61, and 29% of examined animals, respectively, with no significant increase in frequency over time, suggesting endemic infection. We found that 80% of tested SSO were infected with at least one of the three DNA viruses, whose tissue distribution we determined in 261 tissue samples. Parvovirus DNA was most frequently detected in mesenteric lymph node, polyomavirus DNA in spleen, and adenovirus DNA in multiple tissues (spleen, retropharyngeal and mesenteric lymph node, lung, and liver). This study describes the virome in tissues of a threatened species and shows that stranded SSO are frequently infected with multiple viruses, warranting future research to investigate associations between these infections and observed lesions.

Differential transferability of EST-SSR primers developed from diploid species Pseudoroegneria spicata, Thinopyrum bessarabicum, and Th. elongatum

USDA-ARS?s Scientific Manuscript database

Simple sequence repeat technology based on expressed sequence tag (EST-SSR) is a useful genomic tool for genome mapping, characterizing plant species relationships, elucidating genome evolution, and tracing genes on alien chromosome segments. EST-SSR primers developed from three perennial diploid T...

A Contextualized, Differential Sequence Mining Method to Derive Students' Learning Behavior Patterns

ERIC Educational Resources Information Center

Kinnebrew, John S.; Loretz, Kirk M.; Biswas, Gautam

2013-01-01

Computer-based learning environments can produce a wealth of data on student learning interactions. This paper presents an exploratory data mining methodology for assessing and comparing students' learning behaviors from these interaction traces. The core algorithm employs a novel combination of sequence mining techniques to identify deferentially…

Inquiry-Based Learning of Molecular Phylogenetics

ERIC Educational Resources Information Center

Campo, Daniel; Garcia-Vazquez, Eva

2008-01-01

Reconstructing phylogenies from nucleotide sequences is a challenge for students because it strongly depends on evolutionary models and computer tools that are frequently updated. We present here an inquiry-based course aimed at learning how to trace a phylogeny based on sequences existing in public databases. Computer tools are freely available…

Airborne Measurements of Formaldehyde Employing a Tunable Diode Laser Absorption Spectrometer During TRACE-P

NASA Technical Reports Server (NTRS)

Fried, Alan; Drummond, James

2003-01-01

This final report summarizes the progress achieved over the entire 3-year proposal period including two extensions spanning 1 year. These activities include: 1) Preparation for and participation in the NASA 2001 TRACE-P campaign using our airborne tunable diode laser system to acquire measurements of formaldehyde (CH2O); 2) Comprehensive data analysis and data submittal to the NASA archive; 3) Follow up data interpretation working with NASA modelers to place our ambient CH2O measurements into a broader photochemical context; 4) Publication of numerous JGR papers using this data; 5) Extensive follow up laboratory tests on the selectivity and efficiency of our CH20 scrubbing system; and 6) An extensive follow up effort to assess and study the mechanical stability of our entire optical system, particularly the multipass absorption cell, with aircraft changes in cabin pressure.

ExoMars Trace Gas Orbiter (TGO) Science Ground Segment (SGS)

NASA Astrophysics Data System (ADS)

Metcalfe, L.; Aberasturi, M.; Alonso, E.; Álvarez, R.; Ashman, M.; Barbarisi, I.; Brumfitt, J.; Cardesín, A.; Coia, D.; Costa, M.; Fernández, R.; Frew, D.; Gallegos, J.; García Beteta, J. J.; Geiger, B.; Heather, D.; Lim, T.; Martin, P.; Muñoz Crego, C.; Muñoz Fernandez, M.; Villacorta, A.; Svedhem, H.

2018-06-01

The ExoMars Trace Gas Orbiter (TGO) Science Ground Segment (SGS), comprised of payload Instrument Team, ESA and Russian operational centres, is responsible for planning the science operations of the TGO mission and for the generation and archiving of the scientific data products to levels meeting the scientific aims and criteria specified by the ESA Project Scientist as advised by the Science Working Team (SWT). The ExoMars SGS builds extensively upon tools and experience acquired through earlier ESA planetary missions like Mars and Venus Express, and Rosetta, but also is breaking ground in various respects toward the science operations of future missions like BepiColombo or JUICE. A productive interaction with the Russian partners in the mission facilitates broad and effective collaboration. This paper describes the global organisation and operation of the SGS, with reference to its principal systems, interfaces and operational processes.

In-depth investigation of archival and prospectively collected samples reveals no evidence for XMRV infection in prostate cancer.

PubMed

Lee, Deanna; Das Gupta, Jaydip; Gaughan, Christina; Steffen, Imke; Tang, Ning; Luk, Ka-Cheung; Qiu, Xiaoxing; Urisman, Anatoly; Fischer, Nicole; Molinaro, Ross; Broz, Miranda; Schochetman, Gerald; Klein, Eric A; Ganem, Don; Derisi, Joseph L; Simmons, Graham; Hackett, John; Silverman, Robert H; Chiu, Charles Y

2012-01-01

XMRV, or xenotropic murine leukemia virus (MLV)-related virus, is a novel gammaretrovirus originally identified in studies that analyzed tissue from prostate cancer patients in 2006 and blood from patients with chronic fatigue syndrome (CFS) in 2009. However, a large number of subsequent studies failed to confirm a link between XMRV infection and CFS or prostate cancer. On the contrary, recent evidence indicates that XMRV is a contaminant originating from the recombination of two mouse endogenous retroviruses during passaging of a prostate tumor xenograft (CWR22) in mice, generating laboratory-derived cell lines that are XMRV-infected. To confirm or refute an association between XMRV and prostate cancer, we analyzed prostate cancer tissues and plasma from a prospectively collected cohort of 39 patients as well as archival RNA and prostate tissue from the original 2006 study. Despite comprehensive microarray, PCR, FISH, and serological testing, XMRV was not detected in any of the newly collected samples or in archival tissue, although archival RNA remained XMRV-positive. Notably, archival VP62 prostate tissue, from which the prototype XMRV strain was derived, tested negative for XMRV on re-analysis. Analysis of viral genomic and human mitochondrial sequences revealed that all previously characterized XMRV strains are identical and that the archival RNA had been contaminated by an XMRV-infected laboratory cell line. These findings reveal no association between XMRV and prostate cancer, and underscore the conclusion that XMRV is not a naturally acquired human infection.

Actionable mutations in canine hemangiosarcoma

PubMed Central

Wang, Guannan; Wu, Ming; Maloneyhuss, Martha A.; Wojcik, John; Durham, Amy C.; Mason, Nicola J.

2017-01-01

Background Angiosarcomas (AS) are rare in humans, but they are a deadly subtype of soft tissue sarcoma. Discovery sequencing in AS, especially the visceral form, is hampered by the rarity of cases. Most diagnostic material exists as archival formalin fixed, paraffin embedded tissue which serves as a poor source of high quality DNA for genome-wide sequencing. We approached this problem through comparative genomics. We hypothesized that exome sequencing a histologically similar tumor, hemangiosarcoma (HSA), that occurs in approximately 50,000 dogs per year, may lead to the identification of potential oncogenic drivers and druggable targets that could also occur in angiosarcoma. Methods Splenic hemangiosarcomas are common in dogs, which allowed us to collect a cohort of archived matched tumor and normal tissue samples suitable for whole exome sequencing. Mapping of the reads to the latest canine reference genome (Canfam3) demonstrated that >99% of the targeted exomal regions were covered, with >80% at 20X coverage and >90% at 10X coverage. Results and conclusions Sequence analysis of 20 samples identified somatic mutations in PIK3CA, TP53, PTEN, and PLCG1, all of which correspond to well-known tumor drivers in human cancer, in more than half of the cases. In one case, we identified a mutation in PLCG1 identical to a mutation observed previously in this gene in human visceral AS. Activating PIK3CA mutations present novel therapeutic targets, and clinical trials of targeted inhibitors are underway in human cancers. Our results lay a foundation for similar clinical trials in canine HSA, enabling a precision medicine approach to this disease. PMID:29190660

Actionable mutations in canine hemangiosarcoma.

PubMed

Wang, Guannan; Wu, Ming; Maloneyhuss, Martha A; Wojcik, John; Durham, Amy C; Mason, Nicola J; Roth, David B

2017-01-01

Angiosarcomas (AS) are rare in humans, but they are a deadly subtype of soft tissue sarcoma. Discovery sequencing in AS, especially the visceral form, is hampered by the rarity of cases. Most diagnostic material exists as archival formalin fixed, paraffin embedded tissue which serves as a poor source of high quality DNA for genome-wide sequencing. We approached this problem through comparative genomics. We hypothesized that exome sequencing a histologically similar tumor, hemangiosarcoma (HSA), that occurs in approximately 50,000 dogs per year, may lead to the identification of potential oncogenic drivers and druggable targets that could also occur in angiosarcoma. Splenic hemangiosarcomas are common in dogs, which allowed us to collect a cohort of archived matched tumor and normal tissue samples suitable for whole exome sequencing. Mapping of the reads to the latest canine reference genome (Canfam3) demonstrated that >99% of the targeted exomal regions were covered, with >80% at 20X coverage and >90% at 10X coverage. Sequence analysis of 20 samples identified somatic mutations in PIK3CA, TP53, PTEN, and PLCG1, all of which correspond to well-known tumor drivers in human cancer, in more than half of the cases. In one case, we identified a mutation in PLCG1 identical to a mutation observed previously in this gene in human visceral AS. Activating PIK3CA mutations present novel therapeutic targets, and clinical trials of targeted inhibitors are underway in human cancers. Our results lay a foundation for similar clinical trials in canine HSA, enabling a precision medicine approach to this disease.

A sparse differential clustering algorithm for tracing cell type changes via single-cell RNA-sequencing data

PubMed Central

Barron, Martin; Zhang, Siyuan

2018-01-01

Abstract Cell types in cell populations change as the condition changes: some cell types die out, new cell types may emerge and surviving cell types evolve to adapt to the new condition. Using single-cell RNA-sequencing data that measure the gene expression of cells before and after the condition change, we propose an algorithm, SparseDC, which identifies cell types, traces their changes across conditions and identifies genes which are marker genes for these changes. By solving a unified optimization problem, SparseDC completes all three tasks simultaneously. SparseDC is highly computationally efficient and demonstrates its accuracy on both simulated and real data. PMID:29140455

NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

PubMed Central

Pruitt, Kim D.; Tatusova, Tatiana; Maglott, Donna R.

2005-01-01

The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database (http://www.ncbi.nlm.nih.gov/RefSeq/) provides a non-redundant collection of sequences representing genomic data, transcripts and proteins. Although the goal is to provide a comprehensive dataset representing the complete sequence information for any given species, the database pragmatically includes sequence data that are currently publicly available in the archival databases. The database incorporates data from over 2400 organisms and includes over one million proteins representing significant taxonomic diversity spanning prokaryotes, eukaryotes and viruses. Nucleotide and protein sequences are explicitly linked, and the sequences are linked to other resources including the NCBI Map Viewer and Gene. Sequences are annotated to include coding regions, conserved domains, variation, references, names, database cross-references, and other features using a combined approach of collaboration and other input from the scientific community, automated annotation, propagation from GenBank and curation by NCBI staff. PMID:15608248

NCBI GEO: archive for functional genomics data sets--update.

PubMed

Barrett, Tanya; Wilhite, Stephen E; Ledoux, Pierre; Evangelista, Carlos; Kim, Irene F; Tomashevsky, Maxim; Marshall, Kimberly A; Phillippy, Katherine H; Sherman, Patti M; Holko, Michelle; Yefanov, Andrey; Lee, Hyeseung; Zhang, Naigong; Robertson, Cynthia L; Serova, Nadezhda; Davis, Sean; Soboleva, Alexandra

2013-01-01

The Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) is an international public repository for high-throughput microarray and next-generation sequence functional genomic data sets submitted by the research community. The resource supports archiving of raw data, processed data and metadata which are indexed, cross-linked and searchable. All data are freely available for download in a variety of formats. GEO also provides several web-based tools and strategies to assist users to query, analyse and visualize data. This article reports current status and recent database developments, including the release of GEO2R, an R-based web application that helps users analyse GEO data.

The bark of the branches of holm oak (Quercus ilex L.) for a retrospective study of trace elements in the atmosphere

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

Drava, Giuliana, E-mail: drava@difar.unige.it; Bri

Tree bark has proved to be a useful bioindicator for trace elements in the atmosphere, however it reflects an exposure occurring during an unidentified period of time, so it provides spatial information about the distribution of contaminants in a certain area, but it cannot be used to detect temporal changes or trends, which is an important achievement in environmental studies. In order to obtain information about a known period of time, the bark collected from the annual segments of tree branches can be used, allowing analyses going back 10–15 years with annual resolution. In the present study, the concentrations ofmore » As, Cd, Co, Cu, Fe, Mn, Ni, Pb, V and Zn were measured by atomic emission spectrometry in a series of samples covering the period from 2001 to 2013 in an urban environment. Downward time trends were significant for Cd, Pb and Zn. The only trace element showing an upward time trend was V. The concentrations of the remaining six trace elements were constant over time, showing that their presence in bark is not simply proportional to the duration of exposure. This approach, which is simple, reliable and widely applicable at a low cost, allows the “a posteriori” reconstruction of atmospheric trace element deposition when or where no monitoring programme is in progress and no other natural archives are available. - Highlights: • Branch bark allows the historical reconstruction of atmospheric trace elements. • This approach is simple, reliable, widely applicable and “a posteriori”. • Downward time trends were found for Cd, Pb and Zn; upward trend for V.« less

The DFVLR wind-energy test facility 'Ulrich Huetter' on Schnittlinger Berg

NASA Astrophysics Data System (ADS)

Kussmann, Alfred

1986-11-01

The DFVLR test facility for wind-energy systems (named after Ulrich Huetter, the designer of the 100-kW GFRP-rotor W 34 wind turbine first manufactured and tested in the 1950s) is described and illustrated with photographs. The history of the facility is traced, and current operations in gathering, archiving, processing, interpreting, and documenting performance-test data are outlined. The facility includes instrumentation for rotor telemetry, gondola motion measurements, and ground measurements and provides testing services to private users on both contract and leasing bases.

Nature and origins of virtual environments - A bibliographical essay

NASA Technical Reports Server (NTRS)

Ellis, S. R.

1991-01-01

Virtual environments presented via head-mounted, computer-driven displays provide a new media for communication. They may be analyzed by considering: (1) what may be meant by an environment; (2) what is meant by the process of virtualization; and (3) some aspects of human performance that constrain environmental design. Their origins are traced from previous work in vehicle simulation and multimedia research. Pointers are provided to key technical references, in the dispersed, archival literature, that are relevant to the development and evaluation of virtual-environment interface systems.

1-Tochtli, 2-Acatl Survivals of the New Fire Ceremony 1558/1559; 1610/1611

NASA Astrophysics Data System (ADS)

Lebeuf, Arnold

2016-11-01

In pre-Hispanic Mexico great ceremonies were celebrated every 52 years at the congruency of the two basic calendar cycles, of 365 and of 260 days. All ritual and domestic fires, were extinguished for five days. Then a new fire was lit on the chest of a victim. The evangelization of Mexico was accompanied by syncretism of the local faith, its feasts and places of cult. We find in the archives of the XVI and XVII centuries traces of the survivals of the New Fire Ceremony.

Making Sense of the 'Chemical Revolution'. Patients' Voices on the Introduction of Neuroleptics in the 1950s.

PubMed

Majerus, Benoît

2016-01-01

The so-called chemical revolution has produced a vast historiographical corpus. Yet the patient's voice remains surprisingly absent from these stories. Based on the archives of the Institut de Psychiatrie (Brussels), this paper traces the introduction of Largactil as recounted in patient letters, physician records and nurse notes. The paper thus contributes to the history of therapies from below, but also participates in the historiographical debate about whether the introduction of neuroleptics can indeed be considered a revolution.

Making Sense of the ‘Chemical Revolution’. Patients’ Voices on the Introduction of Neuroleptics in the 1950s

PubMed Central

Majerus, Benoît

2016-01-01

The so-called chemical revolution has produced a vast historiographical corpus. Yet the patient’s voice remains surprisingly absent from these stories. Based on the archives of the Institut de Psychiatrie (Brussels), this paper traces the introduction of Largactil as recounted in patient letters, physician records and nurse notes. The paper thus contributes to the history of therapies from below, but also participates in the historiographical debate about whether the introduction of neuroleptics can indeed be considered a revolution. PMID:26651188

A Team Taught Interdisciplinary Approach To Physics and Calculus Education.

ERIC Educational Resources Information Center

Johnson, David B.

The Special Intensive Program for Scientists and Engineers (SIPSE) at Diablo Valley College in California replaces the traditional engineering calculus and physics sequences with a single sequence that combines the two subjects into an integrated whole. The project report provides an overview of SIPSE, a section that traces the project from…

Identifying Learning Behaviors by Contextualizing Differential Sequence Mining with Action Features and Performance Evolution

ERIC Educational Resources Information Center

Kinnebrew, John S.; Biswas, Gautam

2012-01-01

Our learning-by-teaching environment, Betty's Brain, captures a wealth of data on students' learning interactions as they teach a virtual agent. This paper extends an exploratory data mining methodology for assessing and comparing students' learning behaviors from these interaction traces. The core algorithm employs sequence mining techniques to…

Geochemistry of volcanic rocks from the Wawa greenstone belt

NASA Technical Reports Server (NTRS)

Schulz, K. J.; Sylvester, P. J.; Attoh, K.

1983-01-01

The Wawa greenstone belt is located in the District of Algoma and extends east-northeast from Lake Superior to the western part of the Sudbury District in Ontario, Canada. Recent mapping by Attoh has shown that an unconformity at the base of the Dore' Formation and equivalent sedimentary rocks marks a significant stratigraphic break which can be traced throughout the volcanic belt. This break has been used to subdivide the volcanic-sedimentary into pre- and post-Dore' sequences. The pre-Dore' sequence includes at least two cycles of mafic-to-felsic volcanism, each capped by an iron-formation unit. The post-Dore' sequence includes an older mafic-to-felsic unit, which directly overlies sedimentary rocks correlated with the Dore' Formation, and a younger felsic breccia unit interpreted to have formed as debris flows from a felsic volcanic center. In the present study, samples of both the pre-and post-Dore' volcanic sequences were analyzed for major and trace elements, incuding rare earths (REE). This preliminary study is part of an ongoing program to assess the petrogenesis of the volcanic rocks of the Wawa greenstone belt.

Archiving, sharing, processing and publishing historical earthquakes data: the IT point of view

NASA Astrophysics Data System (ADS)

Locati, Mario; Rovida, Andrea; Albini, Paola

2014-05-01

Digital tools devised for seismological data are mostly designed for handling instrumentally recorded data. Researchers working on historical seismology are forced to perform their daily job using a general purpose tool and/or coding their own to address their specific tasks. The lack of out-of-the-box tools expressly conceived to deal with historical data leads to a huge amount of time lost in performing tedious task to search for the data and, to manually reformat it in order to jump from one tool to the other, sometimes causing a loss of the original data. This reality is common to all activities related to the study of earthquakes of the past centuries, from the interpretations of past historical sources, to the compilation of earthquake catalogues. A platform able to preserve the historical earthquake data, trace back their source, and able to fulfil many common tasks was very much needed. In the framework of two European projects (NERIES and SHARE) and one global project (Global Earthquake History, GEM), two new data portals were designed and implemented. The European portal "Archive of Historical Earthquakes Data" (AHEAD) and the worldwide "Global Historical Earthquake Archive" (GHEA), are aimed at addressing at least some of the above mentioned issues. The availability of these new portals and their well-defined standards makes it easier than before the development of side tools for archiving, publishing and processing the available historical earthquake data. The AHEAD and GHEA portals, their underlying technologies and the developed side tools are presented.

The Mungo Mega-Lake Event, Semi-Arid Australia: Non-Linear Descent into the Last Ice Age, Implications for Human Behaviour

PubMed Central

Fitzsimmons, Kathryn E.; Stern, Nicola; Murray-Wallace, Colin V.; Truscott, William; Pop, Cornel

2015-01-01

The Willandra Lakes complex is one of the few locations in semi-arid Australia to preserve both paleoenvironmental and Paleolithic archeological archives at high resolution. The stratigraphy of transverse lunette dunes on the lakes’ downwind margins record a late Quaternary sequence of wetting and drying. Within the Willandra system, the Lake Mungo lunette is best known for its preservation of the world’s oldest known ritual burials, and high densities of archeological traces documenting human adaptation to changing environmental conditions over the last 45 ka. Here we identify evidence at Lake Mungo for a previously unrecognised short-lived, very high lake filling phase at 24 ka, just prior to the Last Glacial Maximum. Mega-lake Mungo was up to 5 m deeper than preceding or subsequent lake full events and represented a lake volume increase of almost 250%. Lake Mungo was linked with neighboring Lake Leaghur at two overflow points, creating an island from the northern part of the Mungo lunette. This event was most likely caused by a pulse of high catchment rainfall and runoff, combined with neotectonic activity which may have warped the lake basin. It indicates a non-linear transition to more arid ice age conditions. The mega-lake restricted mobility for people living in the area, yet archeological traces indicate that humans rapidly adapted to the new conditions. People repeatedly visited the island, transporting stone tools across water and exploiting food resources stranded there. They either swam or used watercraft to facilitate access to the island and across the lake. Since there is no evidence for watercraft use in Australia between initial colonization of the continent prior to 45 ka and the mid-Holocene, repeated visits to the island may represent a resurrection of waterfaring technologies following a hiatus of at least 20 ky. PMID:26083665

Identification and validation of differentially expressed transcripts by RNA-sequencing of formalin-fixed, paraffin-embedded (FFPE) lung tissue from patients with Idiopathic Pulmonary Fibrosis.

PubMed

Vukmirovic, Milica; Herazo-Maya, Jose D; Blackmon, John; Skodric-Trifunovic, Vesna; Jovanovic, Dragana; Pavlovic, Sonja; Stojsic, Jelena; Zeljkovic, Vesna; Yan, Xiting; Homer, Robert; Stefanovic, Branko; Kaminski, Naftali

2017-01-12

Idiopathic Pulmonary Fibrosis (IPF) is a lethal lung disease of unknown etiology. A major limitation in transcriptomic profiling of lung tissue in IPF has been a dependence on snap-frozen fresh tissues (FF). In this project we sought to determine whether genome scale transcript profiling using RNA Sequencing (RNA-Seq) could be applied to archived Formalin-Fixed Paraffin-Embedded (FFPE) IPF tissues. We isolated total RNA from 7 IPF and 5 control FFPE lung tissues and performed 50 base pair paired-end sequencing on Illumina 2000 HiSeq. TopHat2 was used to map sequencing reads to the human genome. On average ~62 million reads (53.4% of ~116 million reads) were mapped per sample. 4,131 genes were differentially expressed between IPF and controls (1,920 increased and 2,211 decreased (FDR < 0.05). We compared our results to differentially expressed genes calculated from a previously published dataset generated from FF tissues analyzed on Agilent microarrays (GSE47460). The overlap of differentially expressed genes was very high (760 increased and 1,413 decreased, FDR < 0.05). Only 92 differentially expressed genes changed in opposite directions. Pathway enrichment analysis performed using MetaCore confirmed numerous IPF relevant genes and pathways including extracellular remodeling, TGF-beta, and WNT. Gene network analysis of MMP7, a highly differentially expressed gene in both datasets, revealed the same canonical pathways and gene network candidates in RNA-Seq and microarray data. For validation by NanoString nCounter® we selected 35 genes that had a fold change of 2 in at least one dataset (10 discordant, 10 significantly differentially expressed in one dataset only and 15 concordant genes). High concordance of fold change and FDR was observed for each type of the samples (FF vs FFPE) with both microarrays (r = 0.92) and RNA-Seq (r = 0.90) and the number of discordant genes was reduced to four. Our results demonstrate that RNA sequencing of RNA obtained from archived FFPE lung tissues is feasible. The results obtained from FFPE tissue are highly comparable to FF tissues. The ability to perform RNA-Seq on archived FFPE IPF tissues should greatly enhance the availability of tissue biopsies for research in IPF.

Sequencing degraded DNA from non-destructively sampled museum specimens for RAD-tagging and low-coverage shotgun phylogenetics.

PubMed

Tin, Mandy Man-Ying; Economo, Evan Philip; Mikheyev, Alexander Sergeyevich

2014-01-01

Ancient and archival DNA samples are valuable resources for the study of diverse historical processes. In particular, museum specimens provide access to biotas distant in time and space, and can provide insights into ecological and evolutionary changes over time. However, archival specimens are difficult to handle; they are often fragile and irreplaceable, and typically contain only short segments of denatured DNA. Here we present a set of tools for processing such samples for state-of-the-art genetic analysis. First, we report a protocol for minimally destructive DNA extraction of insect museum specimens, which produced sequenceable DNA from all of the samples assayed. The 11 specimens analyzed had fragmented DNA, rarely exceeding 100 bp in length, and could not be amplified by conventional PCR targeting the mitochondrial cytochrome oxidase I gene. Our approach made these samples amenable to analysis with commonly used next-generation sequencing-based molecular analytic tools, including RAD-tagging and shotgun genome re-sequencing. First, we used museum ant specimens from three species, each with its own reference genome, for RAD-tag mapping. Were able to use the degraded DNA sequences, which were sequenced in full, to identify duplicate reads and filter them prior to base calling. Second, we re-sequenced six Hawaiian Drosophila species, with millions of years of divergence, but with only a single available reference genome. Despite a shallow coverage of 0.37 ± 0.42 per base, we could recover a sufficient number of overlapping SNPs to fully resolve the species tree, which was consistent with earlier karyotypic studies, and previous molecular studies, at least in the regions of the tree that these studies could resolve. Although developed for use with degraded DNA, all of these techniques are readily applicable to more recent tissue, and are suitable for liquid handling automation.

Robustness of fossil fish teeth for seawater neodymium isotope reconstructions under variable redox conditions in an ancient shallow marine setting

NASA Astrophysics Data System (ADS)

Huck, Claire E.; van de Flierdt, Tina; Jiménez-Espejo, Francisco J.; Bohaty, Steven M.; Röhl, Ursula; Hammond, Samantha J.

2016-03-01

Fossil fish teeth from pelagic open ocean settings are considered a robust archive for preserving the neodymium (Nd) isotopic composition of ancient seawater. However, using fossil fish teeth as an archive to reconstruct seawater Nd isotopic compositions in different sedimentary redox environments and in terrigenous-dominated, shallow marine settings is less proven. To address these uncertainties, fish tooth and sediment samples from a middle Eocene section deposited proximal to the East Antarctic margin at Integrated Ocean Drilling Program Site U1356 were analyzed for major and trace element geochemistry, and Nd isotopes. Major and trace element analyses of the sediments reveal changing redox conditions throughout deposition in a shallow marine environment. However, variations in the Nd isotopic composition and rare earth element (REE) patterns of the associated fish teeth do not correspond to redox changes in the sediments. REE patterns in fish teeth at Site U1356 carry a typical mid-REE-enriched signature. However, a consistently positive Ce anomaly marks a deviation from a pure authigenic origin of REEs to the fish tooth. Neodymium isotopic compositions of cleaned and uncleaned fish teeth fall between modern seawater and local sediments and hence could be authigenic in nature, but could also be influenced by sedimentary fluxes. We conclude that the fossil fish tooth Nd isotope proxy is not sensitive to moderate changes in pore water oxygenation. However, combined studies on sediments, pore waters, fish teeth, and seawater are needed to fully understand processes driving the reconstructed signature from shallow marine sections in proximity to continental sources.

Effective removal of hazardous trace metals from recovery boiler fly ashes.

PubMed

Kinnarinen, Teemu; Golmaei, Mohammad; Jernström, Eeva; Häkkinen, Antti

2018-02-15

The objective of this study is to introduce a treatment sequence enabling straightforward and effective recovery of hazardous trace elements from recovery boiler fly ash (RBFA) by a novel method, and to demonstrate the subsequent removal of Cl and K with the existing crystallization technology. The treatment sequence comprises two stages: dissolution of most other RBFA components than the hazardous trace elements in water in Step 1 of the treatment, and crystallization of the process chemicals in Step 2. Solid-liquid separation has an important role in the treatment, due to the need to separate first the small solid residue containing the trace elements, and to separate the valuable crystals, containing Na and S, from the liquid rich in Cl and K. According to the results, nearly complete recovery of cadmium, lead and zinc can be reached even without pH adjustment. Some other metals, such as Mg and Mn, are removed together with the hazardous metals. Regarding the removal of Cl and K from the process, in this non-optimized case the removal efficiency was satisfactory: 60-70% for K when 80% of sodium was recovered, and close to 70% for Cl when 80% of sulfate was recovered. Copyright © 2017 Elsevier B.V. All rights reserved.

Archive of Digital Boomer Seismic Reflection Data Collected During USGS Field Activities 93LCA01 and 94LCA01 in Kingsley, Orange, and Lowry Lakes, Northeast Florida, 1993 and 1994

USGS Publications Warehouse

Calderon, Karynna; Dadisman, Shawn V.; Kindinger, Jack G.; Davis, Jeffrey B.; Flocks, James G.; Wiese, Dana S.

2004-01-01

In August and September of 1993 and January of 1994, the U.S. Geological Survey, under a cooperative agreement with the St. Johns River Water Management District (SJRWMD), conducted geophysical surveys of Kingsley Lake, Orange Lake, and Lowry Lake in northeast Florida. This report serves as an archive of unprocessed digital boomer seismic reflection data, trackline maps, navigation files, GIS information, observer's logbook, Field Activity Collection System (FACS) logs, and formal FGDC metadata. A filtered and gained GIF image of each seismic profile is also provided. Refer to the Acronyms page for expansion of acronyms and abbreviations used in this report. The archived trace data are in standard Society of Exploration Geophysicists (SEG) SEG-Y format (Barry and others, 1975) and may be downloaded and processed with commercial or public domain software such as Seismic Unix (SU). Examples of SU processing scripts and in-house (USGS) software for viewing SEG-Y files (Zihlman, 1992) are also provided. The data archived here were collected under a cooperative agreement with the St. Johns River Water Management District as part of the USGS Lakes and Coastal Aquifers (LCA) Project. For further information about this study, refer to http://coastal.er.usgs.gov/stjohns, Kindinger and others (1994), and Kindinger and others (2000). The USGS Florida Integrated Science Center (FISC) - Coastal and Watershed Studies in St. Petersburg, Florida, assigns a unique identifier to each cruise or field activity. For example, 93LCA01 tells us the data were collected in 1993 for the Lakes and Coastal Aquifers (LCA) Project and the data were collected during the first field activity for that project in that calendar year. For a detailed description of the method used to assign the field activity ID, see http://walrus.wr.usgs.gov/infobank/programs/html/definition/activity.html. The boomer is an acoustic energy source that consists of capacitors charged to a high voltage and discharged through a transducer in the water. The transducer is towed on a sled at the sea surface and when discharged emits a short acoustic pulse, or shot, that propagates through the water and sediment column. The acoustic energy is reflected at density boundaries (such as the seafloor or sediment layers beneath the seafloor), detected by the receiver, and recorded by a PC-based seismic acquisition system. This process is repeated at timed intervals (e.g., 0.5 s) and recorded for specific intervals of time (e.g., 100 ms). In this way, a two-dimensional vertical image of the shallow geologic structure beneath the ship track is produced. Acquisition geometery for 94LCA01 is recorded in the operations logbook. No logbook exists for 93LCA01. Table 1 displays acquisition parameters for both field activities. For more information about the acquisition equipment used, refer to the FACS equipment logs. The unprocessed seismic data are stored in SEG-Y format (Barry and others, 1975). For a detailed description of the data format, refer to the SEG-Y Format page. See the How To Download SEG-Y Data page for more information about these files. Processed profiles can be viewed as GIF images from the Profiles page. Refer to the Software page for details about the processing and examples of the processing scripts. Detailed information about the navigation systems used for each field activity can be found in Table 1 and the FACS equipment logs. To view the trackline maps and navigation files, and for more information about these items, see the Navigation page. The original trace files were recorded in nonstandard ELICS format and later converted to standard SEG-Y format. The original trace files for 94LCA01 lines ORJ127_1, ORJ127_3, and ORJ131_1 were divided into two or more trace files (e.g., ORJ127_1 became ORJ127_1a and ORJ127_1b) because the original total number of traces exceeded the maximum allowed by the processing system. Digital data were not recoverable for 93LCA

Products and Services Available from the Southern California Earthquake Data Center (SCEDC) and the Southern California Seismic Network (SCSN)

NASA Astrophysics Data System (ADS)

Yu, E.; Bhaskaran, A.; Chen, S.; Chowdhury, F. R.; Meisenhelter, S.; Hutton, K.; Given, D.; Hauksson, E.; Clayton, R. W.

2010-12-01

Currently the SCEDC archives continuous and triggered data from nearly 5000 data channels from 425 SCSN recorded stations, processing and archiving an average of 12,000 earthquakes each year. The SCEDC provides public access to these earthquake parametric and waveform data through its website www.data.scec.org and through client applications such as STP and DHI. This poster will describe the most significant developments at the SCEDC in the past year. Updated hardware: ● The SCEDC has more than doubled its waveform file storage capacity by migrating to 2 TB disks. New data holdings: ● Waveform data: Beginning Jan 1, 2010 the SCEDC began continuously archiving all high-sample-rate strong-motion channels. All seismic channels recorded by SCSN are now continuously archived and available at SCEDC. ● Portable data from El Mayor Cucapah 7.2 sequence: Seismic waveforms from portable stations installed by researchers (contributed by Elizabeth Cochran, Jamie Steidl, and Octavio Lazaro-Mancilla) have been added to the archive and are accessible through STP either as continuous data or associated with events in the SCEDC earthquake catalog. This additional data will help SCSN analysts and researchers improve event locations from the sequence. ● Real time GPS solutions from El Mayor Cucapah 7.2 event: Three component 1Hz seismograms of California Real Time Network (CRTN) GPS stations, from the April 4, 2010, magnitude 7.2 El Mayor-Cucapah earthquake are available in SAC format at the SCEDC. These time series were created by Brendan Crowell, Yehuda Bock, the project PI, and Mindy Squibb at SOPAC using data from the CRTN. The El Mayor-Cucapah earthquake demonstrated definitively the power of real-time high-rate GPS data: they measure dynamic displacements directly, they do not clip and they are also able to detect the permanent (coseismic) surface deformation. ● Triggered data from the Quake Catcher Network (QCN) and Community Seismic Network (CSN): The SCEDC in cooperation with QCN and CSN is exploring ways to archive and distribute data from high density low cost networks. As a starting point the SCEDC will store a dataset from QCN and CSN and distribute it through a separate STP client. New archival methods: ● The SCEDC is exploring the feasibility of archiving and distributing waveform data using cloud computing such as Google Apps. A month of continuous data from the SCEDC archive will be stored in Google Apps and a client developed to access it in a manner similar to STP. XML formats: ● The SCEDC is now distributing earthquake parameter data through web services in QuakeML format. ● The SCEDC in collaboration with the Northern California Earthquake Data Center (NCEDC) and USGS Golden has reviewed and revised the StationXML format to produce version 2.0. The new version includes a rules on extending the schema, use of named complex types, and greater consistency in naming conventions. Based on this work we plan to develop readers and writers of the StationXML format.

The HIPPO Project Archive: Carbon Cycle and Greenhouse Gas Data

NASA Astrophysics Data System (ADS)

Christensen, S. W.; Aquino, J.; Hook, L.; Williams, S. F.

2012-12-01

The HIAPER (NSF/NCAR Gulfstream V Aircraft) Pole-to-Pole Observations (HIPPO) project measured a comprehensive suite of atmospheric trace gases and aerosols pertinent to understanding the global carbon cycle from the surface to the tropopause and approximately pole-to-pole over the Pacific Ocean. Flights took place over five missions during different seasons from 2009 to 2011. Data and documentation are available to the public from two archives: (1) NCAR's Earth Observing Laboratory (EOL) provides complete aircraft and flight operational data, and (2) the U.S. DOE's Carbon Dioxide Information Analysis Center (CDIAC) provides integrated measurement data products. The integrated products are more generally useful for secondary analyses. Data processing is nearing completion, although improvements to the data will continue to evolve and analyses will continue many years into the future. Periodic new releases of integrated measurement (merged) products will be generated by EOL when individual measurement data have been updated as directed by the Lead Principal Investigator. The EOL and CDIAC archives will share documentation and supplemental links and will ensure that the latest versions of data products are available to users of both archives. The EOL archive (http://www.eol.ucar.edu/projects/hippo/) provides the underlying investigator-provided data, including supporting data sets (e.g. operational satellite, model output, global observations, etc.), and ancillary flight operational information including field catalogs, data quality reports, software, documentation, publications, photos/imagery, and other detailed information about the HIPPO missions. The CDIAC archive provides integrated measurement data products, user documentation, and metadata through the HIPPO website (http://hippo.ornl.gov). These merged products were derived by consistently combining the aircraft state parameters for position, time, temperature, pressure, and wind speed with meteorological, atmospheric chemistry and aerosol measurements made by several teams of investigators. Files are in ASCII text format. Selected data products have been loaded into a relational database for customized data subsetting and export formatting. We anticipate adding model-generated products to the archive. Metadata records have been compiled into a searchable CDIAC index and have been submitted to climate change research metadata clearinghouses (e.g., GCMD). Each data product is given a complete bibliographic citation and a persistent identifier (DOI) to facilitate attribution and access. A data policy was adopted that balances the needs of the project investigators with the interests of the scientific user community.

Epstein-Barr Virus, Human Papillomavirus and Mouse Mammary Tumour Virus as Multiple Viruses in Breast Cancer

PubMed Central

Glenn, Wendy K.; Heng, Benjamin; Delprado, Warick; Iacopetta, Barry; Whitaker, Noel J.; Lawson, James S.

2012-01-01

Background The purpose of this investigation is to determine if Epstein Barr virus (EBV), high risk human papillomavirus (HPV), and mouse mammary tumour viruses (MMTV) co-exist in some breast cancers. Materials and Methods All the specimens were from women residing in Australia. For investigations based on standard PCR, we used fresh frozen DNA extracts from 50 unselected invasive breast cancers. For normal breast specimens, we used DNA extracts from epithelial cells from milk donated by 40 lactating women. For investigations based on in situ PCR we used 27 unselected archival formalin fixed breast cancer specimens and 18 unselected archival formalin fixed normal breast specimens from women who had breast reduction surgery. Thirteen of these fixed breast cancer specimens were ductal carcinoma in situ (dcis) and 14 were predominantly invasive ductal carcinomas (idc). Results EBV sequences were identified in 68%, high risk HPV sequences in 50%, and MMTV sequences in 78% of DNA extracted from 50 invasive breast cancer specimens. These same viruses were identified in selected normal and breast cancer specimens by in situ PCR. Sequences from more than one viral type were identified in 72% of the same breast cancer specimens. Normal controls showed these viruses were also present in epithelial cells in human milk – EBV (35%), HPV, 20%) and MMTV (32%) of 40 milk samples from normal lactating women, with multiple viruses being identified in 13% of the same milk samples. Conclusions We conclude that (i) EBV, HPV and MMTV gene sequences are present and co-exist in many human breast cancers, (ii) the presence of these viruses in breast cancer is associated with young age of diagnosis and possibly an increased grade of breast cancer. PMID:23183846

Epstein-Barr virus, human papillomavirus and mouse mammary tumour virus as multiple viruses in breast cancer.

PubMed

Glenn, Wendy K; Heng, Benjamin; Delprado, Warick; Iacopetta, Barry; Whitaker, Noel J; Lawson, James S

2012-01-01

The purpose of this investigation is to determine if Epstein Barr virus (EBV), high risk human papillomavirus (HPV), and mouse mammary tumour viruses (MMTV) co-exist in some breast cancers. All the specimens were from women residing in Australia. For investigations based on standard PCR, we used fresh frozen DNA extracts from 50 unselected invasive breast cancers. For normal breast specimens, we used DNA extracts from epithelial cells from milk donated by 40 lactating women. For investigations based on in situ PCR we used 27 unselected archival formalin fixed breast cancer specimens and 18 unselected archival formalin fixed normal breast specimens from women who had breast reduction surgery. Thirteen of these fixed breast cancer specimens were ductal carcinoma in situ (dcis) and 14 were predominantly invasive ductal carcinomas (idc). EBV sequences were identified in 68%, high risk HPV sequences in 50%, and MMTV sequences in 78% of DNA extracted from 50 invasive breast cancer specimens. These same viruses were identified in selected normal and breast cancer specimens by in situ PCR. Sequences from more than one viral type were identified in 72% of the same breast cancer specimens. Normal controls showed these viruses were also present in epithelial cells in human milk - EBV (35%), HPV, 20%) and MMTV (32%) of 40 milk samples from normal lactating women, with multiple viruses being identified in 13% of the same milk samples. We conclude that (i) EBV, HPV and MMTV gene sequences are present and co-exist in many human breast cancers, (ii) the presence of these viruses in breast cancer is associated with young age of diagnosis and possibly an increased grade of breast cancer.

Database Resources of the BIG Data Center in 2018

PubMed Central

Xu, Xingjian; Hao, Lili; Zhu, Junwei; Tang, Bixia; Zhou, Qing; Song, Fuhai; Chen, Tingting; Zhang, Sisi; Dong, Lili; Lan, Li; Wang, Yanqing; Sang, Jian; Hao, Lili; Liang, Fang; Cao, Jiabao; Liu, Fang; Liu, Lin; Wang, Fan; Ma, Yingke; Xu, Xingjian; Zhang, Lijuan; Chen, Meili; Tian, Dongmei; Li, Cuiping; Dong, Lili; Du, Zhenglin; Yuan, Na; Zeng, Jingyao; Zhang, Zhewen; Wang, Jinyue; Shi, Shuo; Zhang, Yadong; Pan, Mengyu; Tang, Bixia; Zou, Dong; Song, Shuhui; Sang, Jian; Xia, Lin; Wang, Zhennan; Li, Man; Cao, Jiabao; Niu, Guangyi; Zhang, Yang; Sheng, Xin; Lu, Mingming; Wang, Qi; Xiao, Jingfa; Zou, Dong; Wang, Fan; Hao, Lili; Liang, Fang; Li, Mengwei; Sun, Shixiang; Zou, Dong; Li, Rujiao; Yu, Chunlei; Wang, Guangyu; Sang, Jian; Liu, Lin; Li, Mengwei; Li, Man; Niu, Guangyi; Cao, Jiabao; Sun, Shixiang; Xia, Lin; Yin, Hongyan; Zou, Dong; Xu, Xingjian; Ma, Lina; Chen, Huanxin; Sun, Yubin; Yu, Lei; Zhai, Shuang; Sun, Mingyuan; Zhang, Zhang; Zhao, Wenming; Xiao, Jingfa; Bao, Yiming; Song, Shuhui; Hao, Lili; Li, Rujiao; Ma, Lina; Sang, Jian; Wang, Yanqing; Tang, Bixia; Zou, Dong; Wang, Fan

2018-01-01

Abstract The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides freely open access to a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of omics data generated at ever-greater scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big-data integration and value-added curation, including BioCode (a repository archiving bioinformatics tool codes), BioProject (a biological project library), BioSample (a biological sample library), Genome Sequence Archive (GSA, a data repository for archiving raw sequence reads), Genome Warehouse (GWH, a centralized resource housing genome-scale data), Genome Variation Map (GVM, a public repository of genome variations), Gene Expression Nebulas (GEN, a database of gene expression profiles based on RNA-Seq data), Methylation Bank (MethBank, an integrated databank of DNA methylomes), and Science Wikis (a series of biological knowledge wikis for community annotations). In addition, three featured web services are provided, viz., BIG Search (search as a service; a scalable inter-domain text search engine), BIG SSO (single sign-on as a service; a user access control system to gain access to multiple independent systems with a single ID and password) and Gsub (submission as a service; a unified submission service for all relevant resources). All of these resources are publicly accessible through the home page of the BIG Data Center at http://bigd.big.ac.cn. PMID:29036542

EBI metagenomics--a new resource for the analysis and archiving of metagenomic data.

PubMed

Hunter, Sarah; Corbett, Matthew; Denise, Hubert; Fraser, Matthew; Gonzalez-Beltran, Alejandra; Hunter, Christopher; Jones, Philip; Leinonen, Rasko; McAnulla, Craig; Maguire, Eamonn; Maslen, John; Mitchell, Alex; Nuka, Gift; Oisel, Arnaud; Pesseat, Sebastien; Radhakrishnan, Rajesh; Rocca-Serra, Philippe; Scheremetjew, Maxim; Sterk, Peter; Vaughan, Daniel; Cochrane, Guy; Field, Dawn; Sansone, Susanna-Assunta

2014-01-01

Metagenomics is a relatively recently established but rapidly expanding field that uses high-throughput next-generation sequencing technologies to characterize the microbial communities inhabiting different ecosystems (including oceans, lakes, soil, tundra, plants and body sites). Metagenomics brings with it a number of challenges, including the management, analysis, storage and sharing of data. In response to these challenges, we have developed a new metagenomics resource (http://www.ebi.ac.uk/metagenomics/) that allows users to easily submit raw nucleotide reads for functional and taxonomic analysis by a state-of-the-art pipeline, and have them automatically stored (together with descriptive, standards-compliant metadata) in the European Nucleotide Archive.

EBI metagenomics—a new resource for the analysis and archiving of metagenomic data

PubMed Central

Hunter, Sarah; Corbett, Matthew; Denise, Hubert; Fraser, Matthew; Gonzalez-Beltran, Alejandra; Hunter, Christopher; Jones, Philip; Leinonen, Rasko; McAnulla, Craig; Maguire, Eamonn; Maslen, John; Mitchell, Alex; Nuka, Gift; Oisel, Arnaud; Pesseat, Sebastien; Radhakrishnan, Rajesh; Rocca-Serra, Philippe; Scheremetjew, Maxim; Sterk, Peter; Vaughan, Daniel; Cochrane, Guy; Field, Dawn; Sansone, Susanna-Assunta

2014-01-01

Metagenomics is a relatively recently established but rapidly expanding field that uses high-throughput next-generation sequencing technologies to characterize the microbial communities inhabiting different ecosystems (including oceans, lakes, soil, tundra, plants and body sites). Metagenomics brings with it a number of challenges, including the management, analysis, storage and sharing of data. In response to these challenges, we have developed a new metagenomics resource (http://www.ebi.ac.uk/metagenomics/) that allows users to easily submit raw nucleotide reads for functional and taxonomic analysis by a state-of-the-art pipeline, and have them automatically stored (together with descriptive, standards-compliant metadata) in the European Nucleotide Archive. PMID:24165880

NCBI GEO: archive for functional genomics data sets—update

PubMed Central

Barrett, Tanya; Wilhite, Stephen E.; Ledoux, Pierre; Evangelista, Carlos; Kim, Irene F.; Tomashevsky, Maxim; Marshall, Kimberly A.; Phillippy, Katherine H.; Sherman, Patti M.; Holko, Michelle; Yefanov, Andrey; Lee, Hyeseung; Zhang, Naigong; Robertson, Cynthia L.; Serova, Nadezhda; Davis, Sean; Soboleva, Alexandra

2013-01-01

The Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) is an international public repository for high-throughput microarray and next-generation sequence functional genomic data sets submitted by the research community. The resource supports archiving of raw data, processed data and metadata which are indexed, cross-linked and searchable. All data are freely available for download in a variety of formats. GEO also provides several web-based tools and strategies to assist users to query, analyse and visualize data. This article reports current status and recent database developments, including the release of GEO2R, an R-based web application that helps users analyse GEO data. PMID:23193258

PDBe: Protein Data Bank in Europe

PubMed Central

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

2012-01-01

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

Trace fossil evidence for late Permian shallow water condition in Guryul ravine, Kashmir, India

NASA Astrophysics Data System (ADS)

Parcha, Suraj; Horacek, Micha; Krystyn, Leopold; Pandey, Shivani

2015-04-01

The present study is focused on the Late Permian (Changhsingian) succession, present in the Guryul ravine, Kashmir Basin. The basin has a complete Cambro-Triassic sequence and thus contains a unique position in the geology of Himalaya. The Guryul Ravine Permian mainly comprises of mixed siliciclastic-carbonate sediments deposited in a shallow-shelf or ramp setting. The present assemblage of Ichnofossils is the first significant report of trace fossils in the Guryul ravine since early reports in the 1970s. The Ichnofossils reported from this section include: Diplichnites, Dimorphichnus, Monomorphichnus, Planolites, Skolithos along with burrow, scratch marks and annelid worm traces?. The ichnofossils are mainly preserved in medium grain sandstone-mudstone facies. The Ichnofossils are widely distributed throughout the section and are mostly belonging to arthropods and annelid origin, showing behavioral activity, mainly dwelling and feeding, and evidence the dominant presence of deposit feeders. The vertical to slightly inclined biogenic structures are commonly recognized from semi-consolidated substrate which are characteristic features of the near shore/foreshore marine environment, with moderate to high energy conditions. The topmost layer of silty shale contains trace fossils like Skolithos and poorly preserved burrows. The burrow material filled is same as that of host rock. The studied Zewan C and D sequence represents the early to late part of the Changhsingian stage, from 40 to 5 m below the top of Zewan D member with bioturbation still evident in some limestone layers till 2 metres above. No trace fossils could be recognized in the topmost 3 m beds of Zewan D due to their gliding related amalgamated structure. The widespread distribution of traces and their in situ nature will be useful for interpretation of the paleoecological and paleoenvironmental conditions during the late Permian in the Guryul ravine of Kashmir.

TraceContract

NASA Technical Reports Server (NTRS)

Kavelund, Klaus; Barringer, Howard

2012-01-01

TraceContract is an API (Application Programming Interface) for trace analysis. A trace is a sequence of events, and can, for example, be generated by a running program, instrumented appropriately to generate events. An event can be any data object. An example of a trace is a log file containing events that a programmer has found important to record during a program execution. Trace - Contract takes as input such a trace together with a specification formulated using the API and reports on any violations of the specification, potentially calling code (reactions) to be executed when violations are detected. The software is developed as an internal DSL (Domain Specific Language) in the Scala programming language. Scala is a relatively new programming language that is specifically convenient for defining such internal DSLs due to a number of language characteristics. This includes Scala s elegant combination of object-oriented and functional programming, a succinct notation, and an advanced type system. The DSL offers a combination of data-parameterized state machines and temporal logic, which is novel. As an extension of Scala, it is a very expressive and convenient log file analysis framework.

Whole-organism clone tracing using single-cell sequencing.

PubMed

Alemany, Anna; Florescu, Maria; Baron, Chloé S; Peterson-Maduro, Josi; van Oudenaarden, Alexander

2018-04-05

Embryonic development is a crucial period in the life of a multicellular organism, during which limited sets of embryonic progenitors produce all cells in the adult body. Determining which fate these progenitors acquire in adult tissues requires the simultaneous measurement of clonal history and cell identity at single-cell resolution, which has been a major challenge. Clonal history has traditionally been investigated by microscopically tracking cells during development, monitoring the heritable expression of genetically encoded fluorescent proteins and, more recently, using next-generation sequencing technologies that exploit somatic mutations, microsatellite instability, transposon tagging, viral barcoding, CRISPR-Cas9 genome editing and Cre-loxP recombination. Single-cell transcriptomics provides a powerful platform for unbiased cell-type classification. Here we present ScarTrace, a single-cell sequencing strategy that enables the simultaneous quantification of clonal history and cell type for thousands of cells obtained from different organs of the adult zebrafish. Using ScarTrace, we show that a small set of multipotent embryonic progenitors generate all haematopoietic cells in the kidney marrow, and that many progenitors produce specific cell types in the eyes and brain. In addition, we study when embryonic progenitors commit to the left or right eye. ScarTrace reveals that epidermal and mesenchymal cells in the caudal fin arise from the same progenitors, and that osteoblast-restricted precursors can produce mesenchymal cells during regeneration. Furthermore, we identify resident immune cells in the fin with a distinct clonal origin from other blood cell types. We envision that similar approaches will have major applications in other experimental systems, in which the matching of embryonic clonal origin to adult cell type will ultimately allow reconstruction of how the adult body is built from a single cell.

Gradient-Induced Voltages on 12-Lead ECGs during High Duty-Cycle MRI Sequences and a Method for Their Removal considering Linear and Concomitant Gradient Terms

PubMed Central

Zhang, Shelley HuaLei; Ho Tse, Zion Tsz; Dumoulin, Charles L.; Kwong, Raymond Y.; Stevenson, William G.; Watkins, Ronald; Ward, Jay; Wang, Wei; Schmidt, Ehud J.

2015-01-01

Purpose To restore 12-lead ECG signal fidelity inside MRI by removing magnetic-field gradient induced-voltages during high gradient-duty-cycle sequences. Theory and Methods A theoretical equation was derived, providing first- and second-order electrical fields induced at individual ECG electrode as a function of gradient fields. Experiments were performed at 3T on healthy volunteers, using a customized acquisition system which captured full amplitude and frequency response of ECGs, or a commercial recording system. The 19 equation coefficients were derived by linear regression of data from accelerated sequences, and used to compute induced-voltages in real-time during full-resolution sequences to remove ECG artifacts. Restored traces were evaluated relative to ones acquired without imaging. Results Measured induced-voltages were 0.7V peak-to-peak during balanced Steady-State Free Precession (bSSFP) with heart at the isocenter. Applying the equation during gradient echo sequencing, three-dimensional fast spin echo and multi-slice bSSFP imaging restored nonsaturated traces and second-order concomitant terms showed larger contributions in electrodes farther from the magnet isocenter. Equation coefficients are evaluated with high repeatability (ρ = 0.996) and are subject, sequence, and slice-orientation dependent. Conclusion Close agreement between theoretical and measured gradient-induced voltages allowed for real-time removal. Prospective estimation of sequence-periods where large induced-voltages occur may allow hardware removal of these signals. PMID:26101951

myPhyloDB: a local web server for the storage and analysis of metagenomics data

USDA-ARS?s Scientific Manuscript database

myPhyloDB is a user-friendly personal database with a browser-interface designed to facilitate the storage, processing, analysis, and distribution of metagenomics data. MyPhyloDB archives raw sequencing files, and allows for easy selection of project(s)/sample(s) of any combination from all availab...

myPhyloDB: a local web-server and database for the storage and analysis of metagenomics data

USDA-ARS?s Scientific Manuscript database

The advent of next-generation sequencing has resulted in an explosion of metagenomics data associated with microbial communities from a variety of ecosystems. However, no database and/or analytical software is currently available that allows for archival and cross-study comparison of such data. my...

Assessing the prevalence of mycoplasma contamination in cell culture via a survey of NCBI's RNA-seq archive

PubMed Central

Olarerin-George, Anthony O.; Hogenesch, John B.

2015-01-01

Mycoplasmas are notorious contaminants of cell culture and can have profound effects on host cell biology by depriving cells of nutrients and inducing global changes in gene expression. Over the last two decades, sentinel testing has revealed wide-ranging contamination rates in mammalian culture. To obtain an unbiased assessment from hundreds of labs, we analyzed sequence data from 9395 rodent and primate samples from 884 series in the NCBI Sequence Read Archive. We found 11% of these series were contaminated (defined as ≥100 reads/million mapping to mycoplasma in one or more samples). Ninety percent of mycoplasma-mapped reads aligned to ribosomal RNA. This was unexpected given 37% of contaminated series used poly(A)-selection for mRNA enrichment. Lastly, we examined the relationship between mycoplasma contamination and host gene expression in a single cell RNA-seq dataset and found 61 host genes (P < 0.001) were significantly associated with mycoplasma-mapped read counts. In all, this study suggests mycoplasma contamination is still prevalent today and poses substantial risk to research quality. PMID:25712092

Tracing cell lineages in videos of lens-free microscopy.

PubMed

Rempfler, Markus; Stierle, Valentin; Ditzel, Konstantin; Kumar, Sanjeev; Paulitschke, Philipp; Andres, Bjoern; Menze, Bjoern H

2018-06-05

In vitro experiments with cultured cells are essential for studying their growth and migration pattern and thus, for gaining a better understanding of cancer progression and its treatment. Recent progress in lens-free microscopy (LFM) has rendered it an inexpensive tool for label-free, continuous live cell imaging, yet there is only little work on analysing such time-lapse image sequences. We propose (1) a cell detector for LFM images based on fully convolutional networks and residual learning, and (2) a probabilistic model based on moral lineage tracing that explicitly handles multiple detections and temporal successor hypotheses by clustering and tracking simultaneously. (3) We benchmark our method in terms of detection and tracking scores on a dataset of three annotated sequences of several hours of LFM, where we demonstrate our method to produce high quality lineages. (4) We evaluate its performance on a somewhat more challenging problem: estimating cell lineages from the LFM sequence as would be possible from a corresponding fluorescence microscopy sequence. We present experiments on 16 LFM sequences for which we acquired fluorescence microscopy in parallel and generated annotations from them. Finally, (5) we showcase our methods effectiveness for quantifying cell dynamics in an experiment with skin cancer cells. Copyright © 2018 Elsevier B.V. All rights reserved.

Brunhes-Matuyama Magnetic Polarity Reversal Tracing using Chinese loess10Be

NASA Astrophysics Data System (ADS)

Zhou, W.; Beck, W.; Kong, X.; An, Z.; Qiang, X.; Wu, Z.; Xian, F.; Ao, H.

2014-12-01

The geomagnetic polarity reversal is generally considered to occur synchronously around the world, and is commonly used as a time marker. However, in the case of the most recent reversal, the Brunhes-Matuyama (B-M) reversal (~780 ka), comparison of paleomagnetic studies in Chinese loess-paleosol sequences versus marine sediments revealed a marked discrepancy in timing of this event (Tauxe et al., 1996; Zhou and Shackleton, 1999), leading to the debate on uncertainties of paleoclimatic correlation between the Chinese loess-paleosol sequences and marine sediments (Wang et al., 2006; Liu et al., 2008; Jin and Liu, 2011). Based on this issue, here we propose to use the cosmogenic 10Be to address this conundrum. 10Be is a long-lived radionuclide produced in the atmosphere by cosmic ray spallation reactions and carried to the ground attached to aerosols. Its atmospheric production rate is inversely proportional to the geomagnetic field intensity (Masarik and Beer, 1999). This allows us to reconstruct past geomagnetic field intensity variations using 10Be concentrations recorded in different sedimentary archives. We carried out the 10Be studies in Luochuan and Xifeng sections in Chinese Loess Plateau, both loess profiles show that 10Be production rate was at a maximum-an indication of the dipole field reversal-at ca. 780 ± 3 ka BP., in paleosol unit S7corresponding to MIS 19. These results have proven that the timing of B-M reversal recorded in Chinese loess is synchronous with that seen in marine records (Tauxe et al., 1996) and reaffirmed the conventional paleoclimatic correlation of loess-paleosol sequences with marine isotope stages and the standard loess timescale as correct. However, it is ~25 ka younger than the age (depth) of the magnetic polarity reversal recorded in these same Chinese loess-paleosol sequences, demonstrating that loess magnetic overprinting has occurred. 1.Jin, C.S.,et al., 2011,PALAEOGEOGR PALAEOCL, 299, 309-3172.Liu, Q.S., et al., 2008, EARTH PLANET SC LETT, 275, 1-2,102-1103.Masarik, J., and Beer, J., 1999, Jounal of Geophysical Research, 104, 12099-12111.4.Tauxe, L., et al., 1996, EARTH PLANET SC LETT, 140, 133-1465.Wang, X.S., et al., 2006,PHYS EARTH PLANET IN, 159, 109-1176.Zhou, L.P., and Shackleton, 1999,EARTH PLANET SC LETT, 168,117-130

Sanger and Next-Generation Sequencing data for characterization of CTL epitopes in archived HIV-1 proviral DNA.

PubMed

Tumiotto, Camille; Riviere, Lionel; Bellecave, Pantxika; Recordon-Pinson, Patricia; Vilain-Parce, Alice; Guidicelli, Gwenda-Line; Fleury, Hervé

2017-01-01

One of the strategies for curing viral HIV-1 is a therapeutic vaccine involving the stimulation of cytotoxic CD8-positive T cells (CTL) that are Human Leucocyte Antigen (HLA)-restricted. The lack of efficiency of previous vaccination strategies may have been due to the immunogenic peptides used, which could be different from a patient's virus epitopes and lead to a poor CTL response. To counteract this lack of specificity, conserved epitopes must be targeted. One alternative is to gather as many data as possible from a large number of patients on their HIV-1 proviral archived epitope variants, taking into account their genetic background to select the best presented CTL epitopes. In order to process big data generated by Next-Generation Sequencing (NGS) of the DNA of HIV-infected patients, we have developed a software package called TutuGenetics. This tool combines an alignment derived either from Sanger or NGS files, HLA typing, target gene and a CTL epitope list as input files. It allows automatic translation after correction of the alignment obtained between the HxB2 reference and the reads, followed by automatic calculation of the MHC IC50 value for each epitope variant and the HLA allele of the patient by using NetMHCpan 3.0, resulting in a csv file as output result. We validated this new tool by comparing Sanger and NGS (454, Roche) sequences obtained from the proviral DNA of patients at success of ART included in the Provir Latitude 45 study and showed a 90% correlation between the quantitative results of NGS and Sanger. This automated analysis combined with complementary samples should yield more data regarding the archived CTL epitopes according to the patients' HLA alleles and will be useful for screening epitopes that in theory are presented efficiently to the HLA groove, thus constituting promising immunogenic peptides for a therapeutic vaccine.

The Spectral Energy Distribution of the Earliest Phases of Massive Star Formation from the Spizter and Herschel Archives

NASA Astrophysics Data System (ADS)

Klein, Randolf; Looney, Leslie; Henning, Thomas; Chakrabarti, Sukanya; Shenoy, Sachin

2015-08-01

Infrared Dark Clouds (IRDCs) are very good candidates for the earliest phases of massive star formation, but can only be found in regions with high infrared background. We have searched for early phases among cold and massive (M>100M⊙) cloud cores by selecting cores from millimeter continuum surveys (Faundez et al. 2004, Sridharan et al. 2005, Klein et al. 2005, Beltran et al. 2006) without associations at short wavelengths. We compared the millimeter continuum peak positions with IR and radio catalogs (2MASS, MSX, IRAS, and NVSS) and excluded cores that had sources associated with the cores' peaks. We compiled a list of 173 cores in over 117 regions that are candidates for very early phases of Massive Star Formation (MSF). Now with the Spitzer and Herschel archives, these cores can be characterized further. The GLIMPSE and MIPSGAL programs alone covered 86 of these regions. The Herschel Archive adds even longer wavelengths. We are compiling this data set to construct the complete spectral energy distribution (SED) in the mid- and far-infrared with good spatial resolution and broad spectral coverage. This allow us to disentangle the complex regions and model the SED of the deeply embedded protostars/clusters.We will be presenting the IR properties of all cores and their embedded source, attempt a characterization, and order the cores in an evolutionary sequence. The resulting properties can be compared to e.g. IRDCs, a class of objects suggested to be the earliest stages of MSF. With the relative large number of cores, we can try to answer questions like: How homogeneous or diverse are our regions in terms of their evolutionary stage? Where do our embedded sources fit in the evolutionary sequence of IRDCs, hot molecular cores, ultra-compact HII regions, etc? How is the MSF shaping the environment and vice versa? Can we extrapolate to the initial conditions of MSF using our evolutionary sequence?

Tracing Forest Change through 40 Years on Two Continents with the BULC Algorithm and Google Earth Engine

NASA Astrophysics Data System (ADS)

Cardille, J. A.; Crowley, M.; Fortin, J. A.; Lee, J.; Perez, E.; Sleeter, B. M.; Thau, D.

2016-12-01

With the opening of the Landsat archive, researchers have a vast new data source teeming with imagery and potential. Beyond Landsat, data from other sensors is newly available as well: these include ALOS/PALSAR, Sentinel-1 and -2, MERIS, and many more. Google Earth Engine, developed to organize and provide analysis tools for these immense data sets, is an ideal platform for researchers trying to sift through huge image stacks. It offers nearly unlimited processing power and storage with a straightforward programming interface. Yet labeling land-cover change through time remains challenging given the current state of the art for interpreting remote sensing image sequences. Moreover, combining data from very different image platforms remains quite difficult. To address these challenges, we developed the BULC algorithm (Bayesian Updating of Land Cover), designed for the continuous updating of land-cover classifications through time in large data sets. The algorithm ingests data from any of the wide variety of earth-resources sensors; it maintains a running estimate of land-cover probabilities and the most probable class at all time points along a sequence of events. Here we compare BULC results from two study sites that witnessed considerable forest change in the last 40 years: the Pacific Northwest of the United States and the Mato Grosso region of Brazil. In Brazil, we incorporated rough classifications from more than 100 images of varying quality, mixing imagery from more than 10 different sensors. In the Pacific Northwest, we used BULC to identify forest changes due to logging and urbanization from 1973 to the present. Both regions had classification sequences that were better than many of the component days, effectively ignoring clouds and other unwanted noise while fusing the information contained on several platforms. As we leave remote sensing's data-poor era and enter a period with multiple looks at Earth's surface from multiple sensors over a short period of time, the BULC algorithm can help to sift through images of varying quality in Google Earth Engine to extract the most useful information for mapping the state and history of Earth's land cover.

Tracing Forest Change through 40 Years on Two Continents with the BULC Algorithm and Google Earth Engine

NASA Astrophysics Data System (ADS)

Cardille, J. A.

2015-12-01

With the opening of the Landsat archive, researchers have a vast new data source teeming with imagery and potential. Beyond Landsat, data from other sensors is newly available as well: these include ALOS/PALSAR, Sentinel-1 and -2, MERIS, and many more. Google Earth Engine, developed to organize and provide analysis tools for these immense data sets, is an ideal platform for researchers trying to sift through huge image stacks. It offers nearly unlimited processing power and storage with a straightforward programming interface. Yet labeling forest change through time remains challenging given the current state of the art for interpreting remote sensing image sequences. Moreover, combining data from very different image platforms remains quite difficult. To address these challenges, we developed the BULC algorithm (Bayesian Updating of Land Cover), designed for the continuous updating of land-cover classifications through time in large data sets. The algorithm ingests data from any of the wide variety of earth-resources sensors; it maintains a running estimate of land-cover probabilities and the most probable class at all time points along a sequence of events. Here we compare BULC results from two study sites that witnessed considerable forest change in the last 40 years: the Pacific Northwest of the United States and the Mato Grosso region of Brazil. In Brazil, we incorporated rough classifications from more than 100 images of varying quality, mixing imagery from more than 10 different sensors. In the Pacific Northwest, we used BULC to identify forest changes due to logging and urbanization from 1973 to the present. Both regions had classification sequences that were better than many of the component days, effectively ignoring clouds and other unwanted signal while fusing the information contained on several platforms. As we leave remote sensing's data-poor era and enter a period with multiple looks at Earth's surface from multiple sensors over a short period of time, this algorithm may help to sift through images of varying quality in Google Earth Engine to extract the most useful information for mapping.

Distribution of creep in the northern San Francisco Bay Area illuminated by repeating earthquakes and InSAR

NASA Astrophysics Data System (ADS)

Funning, G.; Shakibay Senobari, N.; Swiatlowski, J. L.

2017-12-01

Surface observations of fault creep in the region north of San Francisco Bay are sporadic. While there are long-standing instances of creep-affected infrastructure on the Maacama and Bartlett Springs faults, the lateral and depth extents of creep on these and other faults in the region remain a question. Here, we supplement this sparse existing observation set with additional information from repeating earthquake sequences (REs) and InSAR, to illuminate, and significantly improve our knowledge of, creep across the region. Repeating earthquakes have long been considered indicators of creep on faults. We present the results of an extensive similarity search through over 600,000 archived waveforms from 43,000 events using a fast algorithm; from this we can identify 39 periodic repeating sequences and over 80 nonperiodic repeated event groups. We compare these with decadal line-of-sight velocity measurements made by applying the StaMPS time series InSAR code to ERS and Envisat data covering the region, that can be used to identify surface creep on faults. On the Rodgers Creek, Maacama and Bartlett Springs faults, both InSAR and REs show corroborating evidence for creep at locations where it was previously inferred. The REs additionally provide information on its depth extent. On the Maacama fault, we find REs extending almost to the southern limit of the mapped fault trace, south of Cloverdale, suggesting that creep may be pervasive on the fault. We can also identify structural complexity both in the stepover region with the Rodgers Creek fault, and in the northern segment of the fault close to Willits, potentially indicating parallel and/or down-dip branching creeping structures in both locations. REs on the Bartlett Springs fault indicate creep that extends across the full down-dip width of the brittle fault; here the proximity of InSAR creep rate estimates and a shallow RE sequence may permit a calibration of the RE `creepmeter', allowing us to estimate creep rates directly from RE source characteristics.

Trace elements in fish from Taihu Lake, China: levels, associated risks, and trophic transfer.

PubMed

Hao, Ying; Chen, Liang; Zhang, Xiaolan; Zhang, Dongping; Zhang, Xinyu; Yu, Yingxin; Fu, Jiamo

2013-04-01

Concentrations of eight trace elements [iron (Fe), manganese (Mn), zinc (Zn), chromium (Cr), mercury (Hg), cadmium (Cd), lead (Pb), and arsenic (As)] were measured in a total of 198 samples covering 24 fish species collected from Taihu Lake, China, in September 2009. The trace elements were detected in all samples, and the total mean concentrations ranged from 18.2 to 215.8 μg/g dw (dry weight). The concentrations of the trace elements followed the sequence of Zn>Fe>Mn>Cr>As>Hg>Pb>Cd. The measured trace element concentrations in fish from Taihu Lake were similar to or lower than the reported values in fish around the world. The metal pollution index was used to compare the total trace element accumulation levels among various species. Toxabramis swinhonis (1.606) accumulated the highest level of the total trace elements, and Saurogobio dabryi (0.315) contained the lowest. The concentrations of human non-essential trace elements (Hg, Cd, Pb, and As) were lower than the allowable maximum levels in fish in China and the European Union. The relationships between the trace element concentrations and the δ(15)N values of fish species were used to investigate the trophic transfer potential of the trace elements. Of the trace elements, Hg might be biomagnified through the food chain in Taihu Lake if the significant level of p-value was set at 0.1. No biomagnification and biodilution were observed for other trace elements. Copyright © 2012 Elsevier Inc. All rights reserved.

The Physical Tourist Physics in Glasgow: A Heritage Tour

NASA Astrophysics Data System (ADS)

Johnston, Sean F.

2006-12-01

I trace the history of the physical and applied sciences, and particularly physics, in Glasgow. Among the notable individuals I discuss are Joseph Black (1728 1799), James Watt (1736 1819), William John Macquorn Rankine (1820 1872), William Thomson, Lord Kelvin (1824 1907), John Kerr (1824 1907), Frederick Soddy (1877 1956), John Logie Baird (1888 1946), and Ian Donald (1910 1987), as well as physics-related businesses.The locations, centering on the city center and University of Glasgow, include sites both recognizable today and transformed from past usage, as well as museums and archives related to the history and interpretation of physics.

Mining dynamic noteworthy functions in software execution sequences.

PubMed

Zhang, Bing; Huang, Guoyan; Wang, Yuqian; He, Haitao; Ren, Jiadong

2017-01-01

As the quality of crucial entities can directly affect that of software, their identification and protection become an important premise for effective software development, management, maintenance and testing, which thus contribute to improving the software quality and its attack-defending ability. Most analysis and evaluation on important entities like codes-based static structure analysis are on the destruction of the actual software running. In this paper, from the perspective of software execution process, we proposed an approach to mine dynamic noteworthy functions (DNFM)in software execution sequences. First, according to software decompiling and tracking stack changes, the execution traces composed of a series of function addresses were acquired. Then these traces were modeled as execution sequences and then simplified so as to get simplified sequences (SFS), followed by the extraction of patterns through pattern extraction (PE) algorithm from SFS. After that, evaluating indicators inner-importance and inter-importance were designed to measure the noteworthiness of functions in DNFM algorithm. Finally, these functions were sorted by their noteworthiness. Comparison and contrast were conducted on the experiment results from two traditional complex network-based node mining methods, namely PageRank and DegreeRank. The results show that the DNFM method can mine noteworthy functions in software effectively and precisely.

DNApod: DNA polymorphism annotation database from next-generation sequence read archives.

PubMed

Mochizuki, Takako; Tanizawa, Yasuhiro; Fujisawa, Takatomo; Ohta, Tazro; Nikoh, Naruo; Shimizu, Tokurou; Toyoda, Atsushi; Fujiyama, Asao; Kurata, Nori; Nagasaki, Hideki; Kaminuma, Eli; Nakamura, Yasukazu

2017-01-01

With the rapid advances in next-generation sequencing (NGS), datasets for DNA polymorphisms among various species and strains have been produced, stored, and distributed. However, reliability varies among these datasets because the experimental and analytical conditions used differ among assays. Furthermore, such datasets have been frequently distributed from the websites of individual sequencing projects. It is desirable to integrate DNA polymorphism data into one database featuring uniform quality control that is distributed from a single platform at a single place. DNA polymorphism annotation database (DNApod; http://tga.nig.ac.jp/dnapod/) is an integrated database that stores genome-wide DNA polymorphism datasets acquired under uniform analytical conditions, and this includes uniformity in the quality of the raw data, the reference genome version, and evaluation algorithms. DNApod genotypic data are re-analyzed whole-genome shotgun datasets extracted from sequence read archives, and DNApod distributes genome-wide DNA polymorphism datasets and known-gene annotations for each DNA polymorphism. This new database was developed for storing genome-wide DNA polymorphism datasets of plants, with crops being the first priority. Here, we describe our analyzed data for 679, 404, and 66 strains of rice, maize, and sorghum, respectively. The analytical methods are available as a DNApod workflow in an NGS annotation system of the DNA Data Bank of Japan and a virtual machine image. Furthermore, DNApod provides tables of links of identifiers between DNApod genotypic data and public phenotypic data. To advance the sharing of organism knowledge, DNApod offers basic and ubiquitous functions for multiple alignment and phylogenetic tree construction by using orthologous gene information.

DNApod: DNA polymorphism annotation database from next-generation sequence read archives

PubMed Central

Mochizuki, Takako; Tanizawa, Yasuhiro; Fujisawa, Takatomo; Ohta, Tazro; Nikoh, Naruo; Shimizu, Tokurou; Toyoda, Atsushi; Fujiyama, Asao; Kurata, Nori; Nagasaki, Hideki; Kaminuma, Eli; Nakamura, Yasukazu

2017-01-01

With the rapid advances in next-generation sequencing (NGS), datasets for DNA polymorphisms among various species and strains have been produced, stored, and distributed. However, reliability varies among these datasets because the experimental and analytical conditions used differ among assays. Furthermore, such datasets have been frequently distributed from the websites of individual sequencing projects. It is desirable to integrate DNA polymorphism data into one database featuring uniform quality control that is distributed from a single platform at a single place. DNA polymorphism annotation database (DNApod; http://tga.nig.ac.jp/dnapod/) is an integrated database that stores genome-wide DNA polymorphism datasets acquired under uniform analytical conditions, and this includes uniformity in the quality of the raw data, the reference genome version, and evaluation algorithms. DNApod genotypic data are re-analyzed whole-genome shotgun datasets extracted from sequence read archives, and DNApod distributes genome-wide DNA polymorphism datasets and known-gene annotations for each DNA polymorphism. This new database was developed for storing genome-wide DNA polymorphism datasets of plants, with crops being the first priority. Here, we describe our analyzed data for 679, 404, and 66 strains of rice, maize, and sorghum, respectively. The analytical methods are available as a DNApod workflow in an NGS annotation system of the DNA Data Bank of Japan and a virtual machine image. Furthermore, DNApod provides tables of links of identifiers between DNApod genotypic data and public phenotypic data. To advance the sharing of organism knowledge, DNApod offers basic and ubiquitous functions for multiple alignment and phylogenetic tree construction by using orthologous gene information. PMID:28234924

Eurytemora carolleeae in the Laurentian Great Lakes revealed by phylogenetic and morphological analysis

USGS Publications Warehouse

Vasquez, Adrian A.; Hudson, Patrick L.; Fujimoto, Masanori; Keeler, Kevin M.; Armenio, Patricia M.; Ram, Jeffrey L.

2016-01-01

In the Laurentian Great Lakes, specimens of Eurytemora have been reported asEurytemora affinis since its invasion in the late 1950s. During an intensive collection of aquatic invertebrates for morphological and molecular identification in Western Lake Erie in 2012-2013, several specimens of Eurytemora were collected. Analysis of these specimens identified them as the recently described species Eurytemora carolleeaeAlekseev and Souissi 2011. This result led us to assess E. carolleeae’s identifying features, geographic distribution and historical presence in the Laurentian Great Lakes in view of its recent description in 2011. Cytochrome oxidase I (COI) DNA sequences ofEurytemora specimens were identified as closer (2 - 4% different) to recently describedE. carolleeae than to most E. affinis sequences (14% different). Eurytemora from other areas of the Great Lakes and from North American rivers as far west as South Dakota (Missouri River) and east to Delaware (Christina River) also keyed to E. carolleeae. Morphological analysis of archival specimens from 1962 and from all the Great Lakes was identified as E. carolleeae. Additionally, Eurytemora drawings in previous publications were reassessed to determine if the species was E. carolleeae and are reported here. Additional morphological characters that may distinguish North AmericanE. carolleeae from other taxa are also described. We conclude that E. carolleeae is the correct name for the species of Eurytemora that has inhabited the Great Lakes since its invasion, as established by both morphological and COI sequence comparisons to reference keys and sequence databases in present and archival specimens.

Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index.

PubMed

Pandey, Prashant; Almodaresi, Fatemeh; Bender, Michael A; Ferdman, Michael; Johnson, Rob; Patro, Rob

2018-06-18

Sequence-level searches on large collections of RNA sequencing experiments, such as the NCBI Sequence Read Archive (SRA), would enable one to ask many questions about the expression or variation of a given transcript in a population. Existing approaches, such as the sequence Bloom tree, suffer from fundamental limitations of the Bloom filter, resulting in slow build and query times, less-than-optimal space usage, and potentially large numbers of false-positives. This paper introduces Mantis, a space-efficient system that uses new data structures to index thousands of raw-read experiments and facilitates large-scale sequence searches. In our evaluation, index construction with Mantis is 6× faster and yields a 20% smaller index than the state-of-the-art split sequence Bloom tree (SSBT). For queries, Mantis is 6-108× faster than SSBT and has no false-positives or -negatives. For example, Mantis was able to search for all 200,400 known human transcripts in an index of 2,652 RNA sequencing experiments in 82 min; SSBT took close to 4 days. Copyright © 2018 Elsevier Inc. All rights reserved.

Carbon Dioxide Information Analysis Center and World Data Center for Atmospheric Trace Gases, Fiscal Year 2002 Annual Report

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

Cushman, R.M.

2003-08-28

The Carbon Dioxide Information Analysis Center (CDIAC), which includes the World Data Center (WDC) for Atmospheric Trace Gases, is the primary global change data and information analysis center of the U.S. Department of Energy (DOE). More than just an archive of data sets and publications, CDIAC has, since its inception in 1982, enhanced the value of its holdings through intensive quality assurance, documentation, and integration. Whereas many traditional data centers are discipline-based (for example, meteorology or oceanography), CDIAC's scope includes potentially anything and everything that would be of value to users concerned with the greenhouse effect and global climate change,more » including atmospheric concentrations and atmospheric emissions of carbon dioxide (CO{sub 2}) and other radiatively active gases; the role of the terrestrial biosphere and the oceans in the biogeochemical cycles of greenhouse gases; long-term climate trends; the effects of elevated CO{sub 2} on vegetation; and the vulnerability of coastal areas to rising sea levels.« less

Impact of mineral fertility and bedrock erosion on single-mineral detrital studies: insights from trace-element and Nd-isotope systematics of detrital apatite from the Po River catchment

NASA Astrophysics Data System (ADS)

Malusa', Marco Giovanni; Wang, Jiangang; Garzanti, Eduardo; Villa, Igor M.; Wittman, Hella

2017-04-01

The detrital record provides an archive of mountain erosion that preserves key information for paleotectonic and paleoclimatic reconstructions. Detrital studies are often based on single-mineral analyses (e.g., geo/thermochronologic analyses on apatite and zircon). Their geologic interpretation can be challenging, because the impact of each eroding source on the detrital record is controlled by a range of factors including the rate of erosion and the fertility of chosen minerals in eroded bedrock. Here, we combine (i) a state-of-the art dataset of trace element and Nd isotope fingerprints of detrital apatite, (ii) a comprehensive dataset of apatite-fertility measurements (Malusà et al. 2016), (iii) fission-track data, and (iv) cosmogenic-derived erosion rates from the Po River catchment (Wittmann et al. 2016), to test the impact of mineral fertility and bedrock erosion on the single-mineral detrital signal preserved in the final sediment sink. Our results show that the information provided by accessory minerals, when complemented with accurate mineral fertility measurements, are fully consistent with information provided by the analysis of more abundant framework minerals. We found that trace element and Nd isotope analyses provide a reliable tool to disentangle the complex single-mineral record of orogenic erosion, and demonstrate that such a record is largely determined by high-fertility source rocks exposed within the drainage. Detrital thermochronology studies based on the lag-time approach should thus preferably include independent provenance discriminations and a full mineral fertility characterization of the potential source areas, in order to ensure a correct identification of the sediment sources and of the exogenic and endogenic processes monitored in the stratigraphic archive. Malusà M.G., Resentini A., Garzanti E., 2016. Hydraulic sorting and mineral fertility bias in detrital geochronology. Gondwana Res., 31, 1-19 Wittmann H., Malusà M.G., Resentini A., Garzanti E., Niedermann S., 2016. The cosmogenic record of mountain erosion transmitted across a foreland basin: Source-to-sink analysis of in situ 10Be, 26Al and 21Ne in sediment of the Po river catchment. Earth Planet. Sci. Lett. 452, 258-271

NABIC: A New Access Portal to Search, Visualize, and Share Agricultural Genomics Data.

PubMed

Seol, Young-Joo; Lee, Tae-Ho; Park, Dong-Suk; Kim, Chang-Kug

2016-01-01

The National Agricultural Biotechnology Information Center developed an access portal to search, visualize, and share agricultural genomics data with a focus on South Korean information and resources. The portal features an agricultural biotechnology database containing a wide range of omics data from public and proprietary sources. We collected 28.4 TB of data from 162 agricultural organisms, with 10 types of omics data comprising next-generation sequencing sequence read archive, genome, gene, nucleotide, DNA chip, expressed sequence tag, interactome, protein structure, molecular marker, and single-nucleotide polymorphism datasets. Our genomic resources contain information on five animals, seven plants, and one fungus, which is accessed through a genome browser. We also developed a data submission and analysis system as a web service, with easy-to-use functions and cutting-edge algorithms, including those for handling next-generation sequencing data.

Tracing the origin of disseminated tumor cells in breast cancer using single-cell sequencing.

PubMed

Demeulemeester, Jonas; Kumar, Parveen; Møller, Elen K; Nord, Silje; Wedge, David C; Peterson, April; Mathiesen, Randi R; Fjelldal, Renathe; Zamani Esteki, Masoud; Theunis, Koen; Fernandez Gallardo, Elia; Grundstad, A Jason; Borgen, Elin; Baumbusch, Lars O; Børresen-Dale, Anne-Lise; White, Kevin P; Kristensen, Vessela N; Van Loo, Peter; Voet, Thierry; Naume, Bjørn

2016-12-09

Single-cell micro-metastases of solid tumors often occur in the bone marrow. These disseminated tumor cells (DTCs) may resist therapy and lay dormant or progress to cause overt bone and visceral metastases. The molecular nature of DTCs remains elusive, as well as when and from where in the tumor they originate. Here, we apply single-cell sequencing to identify and trace the origin of DTCs in breast cancer. We sequence the genomes of 63 single cells isolated from six non-metastatic breast cancer patients. By comparing the cells' DNA copy number aberration (CNA) landscapes with those of the primary tumors and lymph node metastasis, we establish that 53% of the single cells morphologically classified as tumor cells are DTCs disseminating from the observed tumor. The remaining cells represent either non-aberrant "normal" cells or "aberrant cells of unknown origin" that have CNA landscapes discordant from the tumor. Further analyses suggest that the prevalence of aberrant cells of unknown origin is age-dependent and that at least a subset is hematopoietic in origin. Evolutionary reconstruction analysis of bulk tumor and DTC genomes enables ordering of CNA events in molecular pseudo-time and traced the origin of the DTCs to either the main tumor clone, primary tumor subclones, or subclones in an axillary lymph node metastasis. Single-cell sequencing of bone marrow epithelial-like cells, in parallel with intra-tumor genetic heterogeneity profiling from bulk DNA, is a powerful approach to identify and study DTCs, yielding insight into metastatic processes. A heterogeneous population of CNA-positive cells is present in the bone marrow of non-metastatic breast cancer patients, only part of which are derived from the observed tumor lineages.

SpaceOps 1992: Proceedings of the Second International Symposium on Ground Data Systems for Space Mission Operations

NASA Technical Reports Server (NTRS)

1993-01-01

The Second International Symposium featured 135 oral presentations in these 12 categories: Future Missions and Operations; System-Level Architectures; Mission-Specific Systems; Mission and Science Planning and Sequencing; Mission Control; Operations Automation and Emerging Technologies; Data Acquisition; Navigation; Operations Support Services; Engineering Data Analysis of Space Vehicle and Ground Systems; Telemetry Processing, Mission Data Management, and Data Archiving; and Operations Management. Topics focused on improvements in the productivity, effectiveness, efficiency, and quality of mission operations, ground systems, and data acquisition. Also emphasized were accomplishments in management of human factors; use of information systems to improve data retrieval, reporting, and archiving; design and implementation of logistics support for mission operations; and the use of telescience and teleoperations.

Placental fetal stem segmentation in a sequence of histology images

NASA Astrophysics Data System (ADS)

Athavale, Prashant; Vese, Luminita A.

2012-02-01

Recent research in perinatal pathology argues that analyzing properties of the placenta may reveal important information on how certain diseases progress. One important property is the structure of the placental fetal stems. Analysis of the fetal stems in a placenta could be useful in the study and diagnosis of some diseases like autism. To study the fetal stem structure effectively, we need to automatically and accurately track fetal stems through a sequence of digitized hematoxylin and eosin (H&E) stained histology slides. There are many problems in successfully achieving this goal. A few of the problems are: large size of images, misalignment of the consecutive H&E slides, unpredictable inaccuracies of manual tracing, very complicated texture patterns of various tissue types without clear characteristics, just to name a few. In this paper we propose a novel algorithm to achieve automatic tracing of the fetal stem in a sequence of H&E images, based on an inaccurate manual segmentation of a fetal stem in one of the images. This algorithm combines global affine registration, local non-affine registration and a novel 'dynamic' version of the active contours model without edges. We first use global affine image registration of all the images based on displacement, scaling and rotation. This gives us approximate location of the corresponding fetal stem in the image that needs to be traced. We then use the affine registration algorithm "locally" near this location. At this point, we use a fast non-affine registration based on L2-similarity measure and diffusion regularization to get a better location of the fetal stem. Finally, we have to take into account inaccuracies in the initial tracing. This is achieved through a novel dynamic version of the active contours model without edges where the coefficients of the fitting terms are computed iteratively to ensure that we obtain a unique stem in the segmentation. The segmentation thus obtained can then be used as an initial guess to obtain segmentation in the rest of the images in the sequence. This constitutes an important step in the extraction and understanding of the fetal stem vasculature.

Database Resources of the BIG Data Center in 2018.

PubMed

2018-01-04

The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides freely open access to a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of omics data generated at ever-greater scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big-data integration and value-added curation, including BioCode (a repository archiving bioinformatics tool codes), BioProject (a biological project library), BioSample (a biological sample library), Genome Sequence Archive (GSA, a data repository for archiving raw sequence reads), Genome Warehouse (GWH, a centralized resource housing genome-scale data), Genome Variation Map (GVM, a public repository of genome variations), Gene Expression Nebulas (GEN, a database of gene expression profiles based on RNA-Seq data), Methylation Bank (MethBank, an integrated databank of DNA methylomes), and Science Wikis (a series of biological knowledge wikis for community annotations). In addition, three featured web services are provided, viz., BIG Search (search as a service; a scalable inter-domain text search engine), BIG SSO (single sign-on as a service; a user access control system to gain access to multiple independent systems with a single ID and password) and Gsub (submission as a service; a unified submission service for all relevant resources). All of these resources are publicly accessible through the home page of the BIG Data Center at http://bigd.big.ac.cn. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Constructing storyboards based on hierarchical clustering analysis

NASA Astrophysics Data System (ADS)

Hasebe, Satoshi; Sami, Mustafa M.; Muramatsu, Shogo; Kikuchi, Hisakazu

2005-07-01

There are growing needs for quick preview of video contents for the purpose of improving accessibility of video archives as well as reducing network traffics. In this paper, a storyboard that contains a user-specified number of keyframes is produced from a given video sequence. It is based on hierarchical cluster analysis of feature vectors that are derived from wavelet coefficients of video frames. Consistent use of extracted feature vectors is the key to avoid a repetition of computationally-intensive parsing of the same video sequence. Experimental results suggest that a significant reduction in computational time is gained by this strategy.

Case-Based Plan Recognition Using Action Sequence Graphs

DTIC Science & Technology

2014-10-01

resized as necessary. Similarly, trace- based reasoning (Zarka et al., 2013) and episode -based reasoning (Sánchez-Marré, 2005) store fixed-length...is a goal state of Π, where satisfies has the same semantics as originally laid out in Ghallab, Nau & Traverso (2004). Action 0 is ...Although there are syntactic similarities between planning encoding graphs and action sequence graphs, important semantic differences exist because the

Mache: No-Loss Trace Compaction

DTIC Science & Technology

1988-09-15

Data Compression . IEEE Computer 176 (June 1984), 8-19. 10. ZIV , J. AND LEMPEL , A. A Universal Algorithm for Sequential Data Com- pression. IEEE... compression scheme which takes ad- vantage of repeating patterns in the sequence of bytes. I have used the Lempel - Ziv compression algorithm [9,10,11...Transactions on Information Theory 23 (1976), 75-81. 11. ZIV , J. AND LEMPEL , A. Compression of Individual Sequences via Variable-

Understanding the Calcium Isotope and Trace Metal Composition of Elasmobranch Teeth: Implications for Recreating the δ44/40Ca of Seawater

NASA Astrophysics Data System (ADS)

Akhtar, A.; Higgins, J. A.

2017-12-01

Non-traditional stable isotopes in marine fossils have the potential to act as archives of paleo-seawater chemistry, biological evolution, and ancient ecosystems. In particular, bioapatite in elasmobranch enamel has been shown to be a robust proxy for environmental, geochemical and ecological reconstructions through Earth history due to its temporal range (from Devonian to present day) and resistance to diagenetic alteration. Moreover, frequent replacement rates of teeth in individuals, and high species level diversity and global distribution ensure a sample suite that encompasses a wide range of geographies and ecosystems. Here we present δ44/40Ca, δ87/86Sr and trace element (e.g. Sr/Ca, Mg/Ca) data from a suite of 300 teeth spanning the Cretaceous to present day and representing primary, secondary and tertiary piscivores. Modern teeth analyzed as part of this study have an average δ44/40Ca value of -2.07±0.48‰ (2s, n = 80) and Sr/Ca ratio of 2.30±0.24 mmol/mol (2s, n = 40), both offset from present day seawater (0 permil and 8.6 mmol/mol, respectively) due to a combination of inorganic (e.g. mineral precipitation) and biological (e.g. ionic regulation) effects. The total range in δ44/40Ca values in modern teeth is 1.19‰, the same order as that expected for variations in the δ44/40Ca value of ancient seawater. Using results from synthetic apatite synthesis experiments, mathematical modeling, and measurements of shark soft-tissue (e.g. blood and flesh), we explore sources of Ca isotope variability in shark teeth and evaluate their potential as archives of ancient seawater chemistry.

Transformation of Air Quality Monitor Data from the International Space Station into Toxicological Effect Groups

NASA Technical Reports Server (NTRS)

James, John T.; Zalesak, Selina M.

2011-01-01

The primary reason for monitoring air quality aboard the International Space Station (ISS) is to determine whether air pollutants have collectively reached a concentration where the crew could experience adverse health effects. These effects could be near-real-time (e.g. headache, respiratory irritation) or occur late in the mission or even years later (e.g. cancer, liver toxicity). Secondary purposes for monitoring include discovery that a potentially harmful compound has leaked into the atmosphere or that air revitalization system performance has diminished. Typical ISS atmospheric trace pollutants consist of alcohols, aldehydes, aromatic compounds, halo-carbons, siloxanes, and silanols. Rarely, sulfur-containing compounds and alkanes are found at trace levels. Spacecraft Maximum Allowable Concentrations (SMACs) have been set in cooperation with a subcommittee of the National Research Council Committee on Toxicology. For each compound and time of exposure, the limiting adverse effect(s) has been identified. By factoring the analytical data from the Air Quality Monitor (AQM), which is in use as a prototype instrument aboard the ISS, through the array of compounds and SMACs, the risk of 16 specific adverse effects can be estimated. Within each adverse-effect group, we have used an additive model proportioned to each applicable 180-day SMAC to estimate risk. In the recent past this conversion has been performed using archival data, which can be delayed for months after an air sample is taken because it must be returned to earth for analysis. But with the AQM gathering in situ data each week, NASA is in a position to follow toxic-effect groups and correlate these with any reported crew symptoms. The AQM data are supplemented with data from real-time CO2 instruments aboard the ISS and from archival measurements of formaldehyde, which the AQM cannot detect.

Wandering Minds: Tracing Inner Worlds Through a Historical-Geographical Art Installation

PubMed Central

Powell, Hilary; Morrison, Hazel; Callard, Felicity

2018-01-01

The human act of wandering across landscapes and cityscapes has carved the research interests of scholars in cultural, urban, and historical geography, as well as in the humanities. Here we call for—and take the first steps toward—a historical geography of wandering that is pursued in the head rather than with the legs. We do so through analyzing how our audiovisual installation on mind wandering opened up epistemological and ontological questions facing historical geographies of the mind. This installation both modeled mind wandering as conceptualized at different historical moments and aimed to induce mental perambulation in its visitors. In so doing, it was intended both to stage and to disrupt relations between body and mind, the internal and external, attention and inattention, motion and stillness—and, importantly, between the archival and that which resists archival capture. We reflect on how we interspersed traditional scholarly historical and geographical enquiry with methods gleaned from creative practices. In particular, we consider the challenges that such practices pose for how we conceptualize archives—not least when the focus of attention comprises fugitive mental phenomena.

Efficient Unsteady Flow Visualization with High-Order Access Dependencies

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

Zhang, Jiang; Guo, Hanqi; Yuan, Xiaoru

We present a novel high-order access dependencies based model for efficient pathline computation in unsteady flow visualization. By taking longer access sequences into account to model more sophisticated data access patterns in particle tracing, our method greatly improves the accuracy and reliability in data access prediction. In our work, high-order access dependencies are calculated by tracing uniformly-seeded pathlines in both forward and backward directions in a preprocessing stage. The effectiveness of our proposed approach is demonstrated through a parallel particle tracing framework with high-order data prefetching. Results show that our method achieves higher data locality and hence improves the efficiencymore » of pathline computation.« less

ECG Electrocardiogram (For Parents)

MedlinePlus

... presented in a standard sequence. Now the ECG tracings are stored as computer files that can be ... of Use Notice of Nondiscrimination Visit the Nemours Web site. Note: All information on KidsHealth® is for ...

Early forest fire detection using principal component analysis of infrared video

NASA Astrophysics Data System (ADS)

Saghri, John A.; Radjabi, Ryan; Jacobs, John T.

2011-09-01

A land-based early forest fire detection scheme which exploits the infrared (IR) temporal signature of fire plume is described. Unlike common land-based and/or satellite-based techniques which rely on measurement and discrimination of fire plume directly from its infrared and/or visible reflectance imagery, this scheme is based on exploitation of fire plume temporal signature, i.e., temperature fluctuations over the observation period. The method is simple and relatively inexpensive to implement. The false alarm rate is expected to be lower that of the existing methods. Land-based infrared (IR) cameras are installed in a step-stare-mode configuration in potential fire-prone areas. The sequence of IR video frames from each camera is digitally processed to determine if there is a fire within camera's field of view (FOV). The process involves applying a principal component transformation (PCT) to each nonoverlapping sequence of video frames from the camera to produce a corresponding sequence of temporally-uncorrelated principal component (PC) images. Since pixels that form a fire plume exhibit statistically similar temporal variation (i.e., have a unique temporal signature), PCT conveniently renders the footprint/trace of the fire plume in low-order PC images. The PC image which best reveals the trace of the fire plume is then selected and spatially filtered via simple threshold and median filter operations to remove the background clutter, such as traces of moving tree branches due to wind.

Reactivation of the chloroplast CF1-ATPase beta subunit by trace amounts of the CF1 alpha subunit suggests a chaperonin-like activity for CF1 alpha.

PubMed

Avni, A; Avital, S; Gromet-Elhanan, Z

1991-04-25

Incubation of tobacco and lettuce thylakoids with 2 M LiCl in the presence of MgATP removes the beta subunit from their CF1-ATPase (CF1 beta) together with varying amounts of the CF1 alpha subunit (CF1 alpha). These 2 M LiCl extracts, as with the one obtained from spinach thylakoids (Avital, S., and Gromet-Elhanan, Z. (1991) J. Biol. Chem. 266, 7067-7072), could form active hybrid ATPases when reconstituted into inactive beta-less Rhodospirillum rubrum chromatophores. Pure CF1 beta fractions that have been isolated from these extracts could not form such active hybrids by themselves, but could do so when supplemented with trace amounts (less than 5%) of CF1 alpha. A mitochondrial F1-ATPase alpha subunit was recently reported to be a heat-shock protein, having two amino acid sequences that show a highly conserved identity with sequences found in molecular chaperones (Luis, A. M., Alconada, A., and Cuezva, J. M. (1990) J. Biol. Chem. 265, 7713-7716). These sequences are also conserved in CF1 alpha isolated from various plants, but not in F1 beta subunits. The above described reactivation of CF1 beta by trace amounts of CF1 alpha could thus be due to a chaperonin-like function of CF1 alpha, which involves the correct, active folding of isolated pure CF1 beta.

The Lagerlunda collision and the introduction of color vision testing.

PubMed

Mollon, J D; Cavonius, L R

2012-01-01

In histories of vision testing, the origins of occupational screening for color blindness are often traced to a fatal railroad accident that occurred in Sweden on the night of 14-15 November 1875. The scene of the accident was the estate of Baron Lagerfelt in Östergötland, but the critical events were played out at Linköping (the normal passing place for the northbound and southbound expresses) and at Bankeberg (a small station to which the passing place was reassigned at a few minutes' notice). First to arrive at Bankeberg, the northbound express slowed almost to a halt, but then inexplicably accelerated forwards towards the Lagerlunda estate, despite a sequence of signals from the stationmaster, Uno Björkelund, and a lineman, Oskar Johansson. Soon after the accident, the ophthalmologist Frithiof Holmgren suggested that the engineer of the northbound express, Andersson, or his oiler, Larsson, had been color blind. Neither survived to be tested. Using the records of the subsequent trial and other archival materials, we have re-examined the role of color blindness in the Lagerlunda incident and conclude that the accident cannot be attributed to color blindness alone. Yet the accident undoubtedly had a central role in the introduction of color vision testing by European and North American railroads. To persuade the railroad management to introduce universal screening of employees for color blindness, Holmgren used a dramatic coup de theatre and some unashamed subterfuge. Copyright © 2012 Elsevier Inc. All rights reserved.

Complete amino acid sequence of bovine colostrum low-Mr cysteine proteinase inhibitor.

PubMed

Hirado, M; Tsunasawa, S; Sakiyama, F; Niinobe, M; Fujii, S

1985-07-01

The complete amino acid sequence of bovine colostrum cysteine proteinase inhibitor was determined by sequencing native inhibitor and peptides obtained by cyanogen bromide degradation, Achromobacter lysylendopeptidase digestion and partial acid hydrolysis of reduced and S-carboxymethylated protein. Achromobacter peptidase digestion was successfully used to isolate two disulfide-containing peptides. The inhibitor consists of 112 amino acids with an Mr of 12787. Two disulfide bonds were established between Cys 66 and Cys 77 and between Cys 90 and Cys 110. A high degree of homology in the sequence was found between the colostrum inhibitor and human gamma-trace, human salivary acidic protein and chicken egg-white cystatin.

A Viral (Arc)hive for Metazoan Memory.

PubMed

Parrish, Nicholas F; Tomonaga, Keizo

2018-01-11

Arc, a master regulator of synaptic plasticity, contains sequence elements that are evolutionarily related to retrotransposon Gag genes. Two related papers in this issue of Cell show that Arc retains retroviral-like capsid-forming ability and can transmit mRNA between cells in the nervous system, a process that may be important for synaptic function. Copyright © 2017 Elsevier Inc. All rights reserved.

FBIS: A regional DNA barcode archival & analysis system for Indian fishes.

PubMed

Nagpure, Naresh Sahebrao; Rashid, Iliyas; Pathak, Ajey Kumar; Singh, Mahender; Singh, Shri Prakash; Sarkar, Uttam Kumar

2012-01-01

DNA barcode is a new tool for taxon recognition and classification of biological organisms based on sequence of a fragment of mitochondrial gene, cytochrome c oxidase I (COI). In view of the growing importance of the fish DNA barcoding for species identification, molecular taxonomy and fish diversity conservation, we developed a Fish Barcode Information System (FBIS) for Indian fishes, which will serve as a regional DNA barcode archival and analysis system. The database presently contains 2334 sequence records of COI gene for 472 aquatic species belonging to 39 orders and 136 families, collected from available published data sources. Additionally, it contains information on phenotype, distribution and IUCN Red List status of fishes. The web version of FBIS was designed using MySQL, Perl and PHP under Linux operating platform to (a) store and manage the acquisition (b) analyze and explore DNA barcode records (c) identify species and estimate genetic divergence. FBIS has also been integrated with appropriate tools for retrieving and viewing information about the database statistics and taxonomy. It is expected that FBIS would be useful as a potent information system in fish molecular taxonomy, phylogeny and genomics. The database is available for free at http://mail.nbfgr.res.in/fbis/

From Field to Laboratory: A New Database Approach for Linking Microbial Field Ecology with Laboratory Studies

NASA Technical Reports Server (NTRS)

Bebout, Leslie; Keller, R.; Miller, S.; Jahnke, L.; DeVincenzi, D. (Technical Monitor)

2002-01-01

The Ames Exobiology Culture Collection Database (AECC-DB) has been developed as a collaboration between microbial ecologists and information technology specialists. It allows for extensive web-based archiving of information regarding field samples to document microbial co-habitation of specific ecosystem micro-environments. Documentation and archiving continues as pure cultures are isolated, metabolic properties determined, and DNA extracted and sequenced. In this way metabolic properties and molecular sequences are clearly linked back to specific isolates and the location of those microbes in the ecosystem of origin. Use of this database system presents a significant advancement over traditional bookkeeping wherein there is generally little or no information regarding the environments from which microorganisms were isolated. Generally there is only a general ecosystem designation (i.e., hot-spring). However within each of these there are a myriad of microenvironments with very different properties and determining exactly where (which microenvironment) a given microbe comes from is critical in designing appropriate isolation media and interpreting physiological properties. We are currently using the database to aid in the isolation of a large number of cyanobacterial species and will present results by PI's and students demonstrating the utility of this new approach.

The BIG Data Center: from deposition to integration to translation

PubMed Central

2017-01-01

Biological data are generated at unprecedentedly exponential rates, posing considerable challenges in big data deposition, integration and translation. The BIG Data Center, established at Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, provides a suite of database resources, including (i) Genome Sequence Archive, a data repository specialized for archiving raw sequence reads, (ii) Gene Expression Nebulas, a data portal of gene expression profiles based entirely on RNA-Seq data, (iii) Genome Variation Map, a comprehensive collection of genome variations for featured species, (iv) Genome Warehouse, a centralized resource housing genome-scale data with particular focus on economically important animals and plants, (v) Methylation Bank, an integrated database of whole-genome single-base resolution methylomes and (vi) Science Wikis, a central access point for biological wikis developed for community annotations. The BIG Data Center is dedicated to constructing and maintaining biological databases through big data integration and value-added curation, conducting basic research to translate big data into big knowledge and providing freely open access to a variety of data resources in support of worldwide research activities in both academia and industry. All of these resources are publicly available and can be found at http://bigd.big.ac.cn. PMID:27899658

NABIC: A New Access Portal to Search, Visualize, and Share Agricultural Genomics Data

PubMed Central

Seol, Young-Joo; Lee, Tae-Ho; Park, Dong-Suk; Kim, Chang-Kug

2016-01-01

The National Agricultural Biotechnology Information Center developed an access portal to search, visualize, and share agricultural genomics data with a focus on South Korean information and resources. The portal features an agricultural biotechnology database containing a wide range of omics data from public and proprietary sources. We collected 28.4 TB of data from 162 agricultural organisms, with 10 types of omics data comprising next-generation sequencing sequence read archive, genome, gene, nucleotide, DNA chip, expressed sequence tag, interactome, protein structure, molecular marker, and single-nucleotide polymorphism datasets. Our genomic resources contain information on five animals, seven plants, and one fungus, which is accessed through a genome browser. We also developed a data submission and analysis system as a web service, with easy-to-use functions and cutting-edge algorithms, including those for handling next-generation sequencing data. PMID:26848255

The Impact of Mutation and Gene Conversion on the Local Diversification of Antigen Genes in African Trypanosomes

PubMed Central

Gjini, Erida; Haydon, Daniel T.; Barry, J. David; Cobbold, Christina A.

2012-01-01

Patterns of genetic diversity in parasite antigen gene families hold important information about their potential to generate antigenic variation within and between hosts. The evolution of such gene families is typically driven by gene duplication, followed by point mutation and gene conversion. There is great interest in estimating the rates of these processes from molecular sequences for understanding the evolution of the pathogen and its significance for infection processes. In this study, a series of models are constructed to investigate hypotheses about the nucleotide diversity patterns between closely related gene sequences from the antigen gene archive of the African trypanosome, the protozoan parasite causative of human sleeping sickness in Equatorial Africa. We use a hidden Markov model approach to identify two scales of diversification: clustering of sequence mismatches, a putative indicator of gene conversion events with other lower-identity donor genes in the archive, and at a sparser scale, isolated mismatches, likely arising from independent point mutations. In addition to quantifying the respective probabilities of occurrence of these two processes, our approach yields estimates for the gene conversion tract length distribution and the average diversity contributed locally by conversion events. Model fitting is conducted using a Bayesian framework. We find that diversifying gene conversion events with lower-identity partners occur at least five times less frequently than point mutations on variant surface glycoprotein (VSG) pairs, and the average imported conversion tract is between 14 and 25 nucleotides long. However, because of the high diversity introduced by gene conversion, the two processes have almost equal impact on the per-nucleotide rate of sequence diversification between VSG subfamily members. We are able to disentangle the most likely locations of point mutations and conversions on each aligned gene pair. PMID:22735079

Mini-DNA barcode in identification of the ornamental fish: A case study from Northeast India.

PubMed

Dhar, Bishal; Ghosh, Sankar Kumar

2017-09-05

The ornamental fishes were exported under the trade names or generic names, thus creating problems in species identification. In this regard, DNA barcoding could effectively elucidate the actual species status. However, the problem arises if the specimen is having taxonomic disputes, falsified by trade/generic names, etc., On the other hand, barcoding the archival museum specimens would be of greater benefit to address such issues as it would create firm, error-free reference database for rapid identification of any species. This can be achieved only by generating short sequences as DNA from chemically preserved are mostly degraded. Here we aimed to identify a short stretch of informative sites within the full-length barcode segment, capable of delineating diverse group of ornamental fish species, commonly traded from NE India. We analyzed 287 full-length barcode sequences from the major fish orders and compared the interspecific K2P distance with nucleotide substitutions patterns and found a strong correlation of interspecies distance with transversions (0.95, p<0.001). We, therefore, proposed a short stretch of 171bp (transversion rich) segment as mini-barcode. The proposed segment was compared with the full-length barcodes and found to delineate the species effectively. Successful PCR amplification and sequencing of the 171bp segment using designed primers for different orders validated it as mini-barcodes for ornamental fishes. Thus, our findings would be helpful in strengthening the global database with the sequence of archived fish species as well as an effective identification tool of the traded ornamental fish species, as a less time consuming, cost effective field-based application. Copyright © 2017 Elsevier B.V. All rights reserved.

Use of Archived Information by the United States National Data Center

NASA Astrophysics Data System (ADS)

Junek, W. N.; Pope, B. M.; Roman-Nieves, J. I.; VanDeMark, T. F.; Ichinose, G. A.; Poffenberger, A.; Woods, M. T.

2012-12-01

The United States National Data Center (US NDC) is responsible for monitoring international compliance to nuclear test ban treaties, acquiring data and data products from the International Data Center (IDC), and distributing data according to established policy. The archive of automated and reviewed event solutions residing at the US NDC is a valuable resource for assessing and improving the performance of signal detection, event formation, location, and discrimination algorithms. Numerous research initiatives are currently underway that are focused on optimizing these processes using historic waveform data and alphanumeric information. Identification of optimum station processing parameters is routinely performed through the analysis of archived waveform data. Station specific detector tuning studies produce and compare receiver operating characteristics for multiple detector configurations (e.g., detector type, filter passband) to identify an optimum set of processing parameters with an acceptable false alarm rate. Large aftershock sequences can inundate automated phase association algorithms with numerous detections that are closely spaced in time, which increases the number of false and/or mixed associations in automated event solutions and increases analyst burden. Archived waveform data and alphanumeric information are being exploited to develop an aftershock processor that will construct association templates to assist the Global Association (GA) application, reduce the number of false and merged phase associations, and lessen analyst burden. Statistical models are being developed and evaluated for potential use by the GA application for identifying and rejecting unlikely preliminary event solutions. Other uses of archived data at the US NDC include: improved event locations using empirical travel time corrections and discrimination via a statistical framework known as the event classification matrix (ECM).

Mining dynamic noteworthy functions in software execution sequences

PubMed Central

Huang, Guoyan; Wang, Yuqian; He, Haitao; Ren, Jiadong

2017-01-01

As the quality of crucial entities can directly affect that of software, their identification and protection become an important premise for effective software development, management, maintenance and testing, which thus contribute to improving the software quality and its attack-defending ability. Most analysis and evaluation on important entities like codes-based static structure analysis are on the destruction of the actual software running. In this paper, from the perspective of software execution process, we proposed an approach to mine dynamic noteworthy functions (DNFM)in software execution sequences. First, according to software decompiling and tracking stack changes, the execution traces composed of a series of function addresses were acquired. Then these traces were modeled as execution sequences and then simplified so as to get simplified sequences (SFS), followed by the extraction of patterns through pattern extraction (PE) algorithm from SFS. After that, evaluating indicators inner-importance and inter-importance were designed to measure the noteworthiness of functions in DNFM algorithm. Finally, these functions were sorted by their noteworthiness. Comparison and contrast were conducted on the experiment results from two traditional complex network-based node mining methods, namely PageRank and DegreeRank. The results show that the DNFM method can mine noteworthy functions in software effectively and precisely. PMID:28278276

The perils of pathogen discovery: origin of a novel parvovirus-like hybrid genome traced to nucleic acid extraction spin columns.

PubMed

Naccache, Samia N; Greninger, Alexander L; Lee, Deanna; Coffey, Lark L; Phan, Tung; Rein-Weston, Annie; Aronsohn, Andrew; Hackett, John; Delwart, Eric L; Chiu, Charles Y

2013-11-01

Next-generation sequencing was used for discovery and de novo assembly of a novel, highly divergent DNA virus at the interface between the Parvoviridae and Circoviridae. The virus, provisionally named parvovirus-like hybrid virus (PHV), is nearly identical by sequence to another DNA virus, NIH-CQV, previously detected in Chinese patients with seronegative (non-A-E) hepatitis. Although we initially detected PHV in a wide range of clinical samples, with all strains sharing ∼99% nucleotide and amino acid identity with each other and with NIH-CQV, the exact origin of the virus was eventually traced to contaminated silica-binding spin columns used for nucleic acid extraction. Definitive confirmation of the origin of PHV, and presumably NIH-CQV, was obtained by in-depth analyses of water eluted through contaminated spin columns. Analysis of environmental metagenome libraries detected PHV sequences in coastal marine waters of North America, suggesting that a potential association between PHV and diatoms (algae) that generate the silica matrix used in the spin columns may have resulted in inadvertent viral contamination during manufacture. The confirmation of PHV/NIH-CQV as laboratory reagent contaminants and not bona fide infectious agents of humans underscores the rigorous approach needed to establish the validity of new viral genomes discovered by next-generation sequencing.

Efficient use of single molecule time traces to resolve kinetic rates, models and uncertainties

NASA Astrophysics Data System (ADS)

Schmid, Sonja; Hugel, Thorsten

2018-03-01

Single molecule time traces reveal the time evolution of unsynchronized kinetic systems. Especially single molecule Förster resonance energy transfer (smFRET) provides access to enzymatically important time scales, combined with molecular distance resolution and minimal interference with the sample. Yet the kinetic analysis of smFRET time traces is complicated by experimental shortcomings—such as photo-bleaching and noise. Here we recapitulate the fundamental limits of single molecule fluorescence that render the classic, dwell-time based kinetic analysis unsuitable. In contrast, our Single Molecule Analysis of Complex Kinetic Sequences (SMACKS) considers every data point and combines the information of many short traces in one global kinetic rate model. We demonstrate the potential of SMACKS by resolving the small kinetic effects caused by different ionic strengths in the chaperone protein Hsp90. These results show an unexpected interrelation between conformational dynamics and ATPase activity in Hsp90.

1. PLAN OF MOXHAM, JOHNSTOWN, PENNA. ALL REGULAR LOTS 40 ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

1. PLAN OF MOXHAM, JOHNSTOWN, PENNA. ALL REGULAR LOTS 40 FT BY 120 FT. TRACED FROM DRAWING 10742 (dated February 1, 1892). THE JOHNSON COMPANY, SCALE 1 INCH - 160 FT, SEPT. 19TH 1898. DRAWING NUMBER 29781. Original plan for the Town of Moxham drafted in 1887-88, company archives contain several revised blueprints of the original plan. This revision reflects the subdivision of the Von Lunch Grove into residential lots, but still indicates the 'Moxham Block' on which the original Moxham Estate was built in 1888-89. (Photograph of drawing held at the Johnstown Corporation General Office, Johnstown, PA) - Borough of Moxham, Johnstown, Cambria County, PA

Behavior within fortuitous environments: The entwined history of Division 28 and the fields of behavioral pharmacology and toxicology.

PubMed

Campbell, Nancy D

2016-08-01

Behavioral pharmacology emerged in the early to mid-20th century as an experimental and observational science, helping to consolidate an empirically based psychological science of behavior. Behavioral psychologists came to play significant roles in toxicology, neuropharmacology, and psychopharmacology. This article traces the first 3 decades of American Psychological Association Division 28. Sources include the Division 28 Oral History Project; formal interviews conducted by the author in the early 2000s with behavioral, experimental, and clinical pharmacologists; and the archived newsletters of Division 28. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

RNA sequencing and pathway analysis identify tumor necrosis factor alpha driven small proline-rich protein dysregulation in chronic rhinosinusitis.

PubMed

Ramakrishnan, Vijay R; Gonzalez, Joseph R; Cooper, Sarah E; Barham, Henry P; Anderson, Catherine B; Larson, Eric D; Cool, Carlyne D; Diller, John D; Jones, Kenneth; Kinnamon, Sue C

2017-09-01

Chronic rhinosinusitis (CRS) is a heterogeneous inflammatory disorder in which many pathways contribute to end-organ disease. Small proline-rich proteins (SPRR) are polypeptides that have recently been shown to contribute to epithelial biomechanical properties relevant in T-helper type 2 inflammation. There is evidence that genetic polymorphism in SPRR genes may predict the development of asthma in children with atopy and, correlatively, that expression of SPRRs is increased under allergic conditions, which leads to epithelial barrier dysfunction in atopic disease. RNAs from uncinate tissue specimens from patients with CRS and control subjects were compared by RNA sequencing by using Ingenuity Pathway Analysis (n = 4 each), and quantitative polymerase chain reaction (PCR) (n = 15). A separate cohort of archived sinus tissue was examined by immunohistochemistry (n = 19). A statistically significant increase of SPRR expression in CRS sinus tissue was identified that was not a result of atopic presence. SPRR1 and SPRR2A expressions were markedly increased in patients with CRS (p < 0.01) on RNA sequencing, with confirmation by using real-time PCR. Immunohistochemistry of archived surgical samples demonstrated staining of SPRR proteins within squamous epithelium of both groups. Pathway analysis indicated tumor necrosis factor (TNF) alpha as a master regulator of the SPRR gene products. Expression of SPRR1 and of SPRR2A is increased in mucosal samples from patients with CRS and appeared as a downstream result of TNF alpha modulation, which possibly resulted in epithelial barrier dysfunction.

High-Throughput Sequencing and Copy Number Variation Detection Using Formalin Fixed Embedded Tissue in Metastatic Gastric Cancer

PubMed Central

Hong, Min Eui; Do, In-Gu; Kang, So Young; Ha, Sang Yun; Kim, Seung Tae; Park, Se Hoon; Kang, Won Ki; Choi, Min-Gew; Lee, Jun Ho; Sohn, Tae Sung; Bae, Jae Moon; Kim, Sung; Kim, Duk-Hwan; Kim, Kyoung-Mee

2014-01-01

In the era of targeted therapy, mutation profiling of cancer is a crucial aspect of making therapeutic decisions. To characterize cancer at a molecular level, the use of formalin-fixed paraffin-embedded tissue is important. We tested the Ion AmpliSeq Cancer Hotspot Panel v2 and nCounter Copy Number Variation Assay in 89 formalin-fixed paraffin-embedded gastric cancer samples to determine whether they are applicable in archival clinical samples for personalized targeted therapies. We validated the results with Sanger sequencing, real-time quantitative PCR, fluorescence in situ hybridization and immunohistochemistry. Frequently detected somatic mutations included TP53 (28.17%), APC (10.1%), PIK3CA (5.6%), KRAS (4.5%), SMO (3.4%), STK11 (3.4%), CDKN2A (3.4%) and SMAD4 (3.4%). Amplifications of HER2, CCNE1, MYC, KRAS and EGFR genes were observed in 8 (8.9%), 4 (4.5%), 2 (2.2%), 1 (1.1%) and 1 (1.1%) cases, respectively. In the cases with amplification, fluorescence in situ hybridization for HER2 verified gene amplification and immunohistochemistry for HER2, EGFR and CCNE1 verified the overexpression of proteins in tumor cells. In conclusion, we successfully performed semiconductor-based sequencing and nCounter copy number variation analyses in formalin-fixed paraffin-embedded gastric cancer samples. High-throughput screening in archival clinical samples enables faster, more accurate and cost-effective detection of hotspot mutations or amplification in genes. PMID:25372287

CARGO: effective format-free compressed storage of genomic information

PubMed Central

Roguski, Łukasz; Ribeca, Paolo

2016-01-01

The recent super-exponential growth in the amount of sequencing data generated worldwide has put techniques for compressed storage into the focus. Most available solutions, however, are strictly tied to specific bioinformatics formats, sometimes inheriting from them suboptimal design choices; this hinders flexible and effective data sharing. Here, we present CARGO (Compressed ARchiving for GenOmics), a high-level framework to automatically generate software systems optimized for the compressed storage of arbitrary types of large genomic data collections. Straightforward applications of our approach to FASTQ and SAM archives require a few lines of code, produce solutions that match and sometimes outperform specialized format-tailored compressors and scale well to multi-TB datasets. All CARGO software components can be freely downloaded for academic and non-commercial use from http://bio-cargo.sourceforge.net. PMID:27131376

Tidying Up International Nucleotide Sequence Databases: Ecological, Geographical and Sequence Quality Annotation of ITS Sequences of Mycorrhizal Fungi

PubMed Central

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

2011-01-01

Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS) region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD) are, however, unfiltered for quality and are often poorly annotated with metadata. To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/) for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/), the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi. PMID:21949797

In situ molecular identification of the Influenza A (H1N1) 2009 Neuraminidase in patients with severe and fatal infections during a pandemic in Mexico City

PubMed Central

2013-01-01

Background In April 2009, public health surveillance detected an increased number of influenza-like illnesses in Mexico City’s hospitals. The etiological agent was subsequently determined to be a spread of a worldwide novel influenza A (H1N1) triple reassortant. The purpose of the present study was to demonstrate that molecular detection of pandemic influenza A (H1N1) 2009 strains is possible in archival material such as paraffin-embedded lung samples. Methods In order to detect A (H1N1) virus sequences in archived biological samples, eight paraffin-embedded lung samples from patients who died of pneumonia and respiratory failure were tested for influenza A (H1N1) Neuraminidase (NA) RNA using in situ RT-PCR. Results We detected NA transcripts in 100% of the previously diagnosed A (H1N1)-positive samples as a cytoplasmic signal. No expression was detected by in situ RT-PCR in two Influenza-like Illness A (H1N1)-negative patients using standard protocols nor in a non-related cervical cell line. In situ relative transcription levels correlated with those obtained when in vitro RT-PCR assays were performed. Partial sequences of the NA gene from A (H1N1)-positive patients were obtained by the in situ RT-PCR-sequencing method. Sequence analysis showed 98% similarity with influenza viruses reported previously in other places. Conclusions We have successfully amplified specific influenza A (H1N1) NA sequences using stored clinical material; results suggest that this strategy could be useful when clinical RNA samples are quantity limited, or when poor quality is obtained. Here, we provide a very sensitive method that specifically detects the neuraminidase viral RNA in lung samples from patients who died from pneumonia caused by Influenza A (H1N1) outbreak in Mexico City. PMID:23327529

Sequencing the Unknown

NASA Image and Video Library

2017-12-19

Being able to identify microbes in real time aboard the International Space Station, without having to send them back to Earth for identification first, would be revolutionary for the world of microbiology and space exploration, and the Genes in Space-3 team turned that possibility into a reality this year when it completed the first-ever sample-to-sequence process entirely aboard the space station. This advance could aid in the ability to diagnose and treat astronaut ailments in real time, as well as assisting in the identification of DNA-based life on other planets. It could also benefit other experiments aboard the orbiting laboratory. HD Download: https://archive.org/details/jsc2017m001160_Sequencing_the_Unknown _______________________________________ FOLLOW THE SPACE STATION! Twitter: https://twitter.com/Space_Station Facebook: https://www.facebook.com/ISS Instagram: https://instagram.com/iss/

Interactions of trace metals with hydrogels and filter membranes used in DET and DGT techniques.

PubMed

Garmo, Oyvind A; Davison, William; Zhang, Hao

2008-08-01

Equilibrium partitioning of trace metals between bulk solution and hydrogels/filter was studied. Under some conditions, trace metal concentrations were higher in the hydrogels or filter membranes compared to bulk solution (enrichment). In synthetic soft water, enrichment of cationic trace metals in polyacrylamide hydrogels decreased with increasing trace metal concentration. Enrichment was little affected by Ca and Mg in the concentration range typically encountered in natural freshwaters, indicating high affinity but low capacity binding of trace metals to solid structure in polyacrylamide gels. The apparent binding strength decreased in the sequence: Cu > Pb > Ni approximately to Cd approximately to Co and a low concentration of cationic Cu eliminated enrichment of weakly binding trace metal cations. The polyacrylamide gels also had an affinity for fulvic acid and/or its trace metal complexes. Enrichment of cationic Cd in agarose gel and hydrophilic polyethersulfone filter was independent of concentration (10 nM to 5 microM) but decreased with increasing Ca/ Mg concentration and ionic strength, suggesting that it is mainly due to electrostatic interactions. However, Cu and Pb were enriched even after equilibration in seawater, indicating that these metals additionally bind to sites within the agarose gel and filter. Compared to the polyacrylamide gels, agarose gel had a lower affinity for metal-fulvic complexes. Potential biases in measurements made with the diffusive equilibration in thin-films (DET) technique, identified by this work, are discussed.

Piaget's Theory of Child Development

ERIC Educational Resources Information Center

Case, Robbie

1972-01-01

This article traces Piaget's theory of child development from its philosophic foundations in Kantian organization and then describes in sequence Piaget's four stages. (A follow-up article on Piaget and educational practice will appear in a later issue.) (JA)

Seven Salmonella Typhimurium Outbreaks in Australia Linked by Trace-Back and Whole Genome Sequencing.

PubMed

Ford, Laura; Wang, Qinning; Stafford, Russell; Ressler, Kelly-Anne; Norton, Sophie; Shadbolt, Craig; Hope, Kirsty; Franklin, Neil; Krsteski, Radomir; Carswell, Adrienne; Carter, Glen P; Seemann, Torsten; Howard, Peter; Valcanis, Mary; Castillo, Cristina Fabiola Sotomayor; Bates, John; Glass, Kathryn; Williamson, Deborah A; Sintchenko, Vitali; Howden, Benjamin P; Kirk, Martyn D

2018-05-01

Salmonella Typhimurium is a common cause of foodborne illness in Australia. We report on seven outbreaks of Salmonella Typhimurium multilocus variable-number tandem-repeat analysis (MLVA) 03-26-13-08-523 (European convention 2-24-12-7-0212) in three Australian states and territories investigated between November 2015 and March 2016. We identified a common egg grading facility in five of the outbreaks. While no Salmonella Typhimurium was detected at the grading facility and eggs could not be traced back to a particular farm, whole genome sequencing (WGS) of isolates from cases from all seven outbreaks indicated a common source. WGS was able to provide higher discriminatory power than MLVA and will likely link more Salmonella Typhimurium cases between states and territories in the future. National harmonization of Salmonella surveillance is important for effective implementation of WGS for Salmonella outbreak investigations.

Estimation of Dynamical Parameters in Atmospheric Data Sets

NASA Technical Reports Server (NTRS)

Wenig, Mark O.

2004-01-01

In this study a new technique is used to derive dynamical parameters out of atmospheric data sets. This technique, called the structure tensor technique, can be used to estimate dynamical parameters such as motion, source strengths, diffusion constants or exponential decay rates. A general mathematical framework was developed for the direct estimation of the physical parameters that govern the underlying processes from image sequences. This estimation technique can be adapted to the specific physical problem under investigation, so it can be used in a variety of applications in trace gas, aerosol, and cloud remote sensing. The fundamental algorithm will be extended to the analysis of multi- channel (e.g. multi trace gas) image sequences and to provide solutions to the extended aperture problem. In this study sensitivity studies have been performed to determine the usability of this technique for data sets with different resolution in time and space and different dimensions.

Metagenomics workflow analysis of endophytic bacteria from oil palm fruits

NASA Astrophysics Data System (ADS)

Tanjung, Z. A.; Aditama, R.; Sudania, W. M.; Utomo, C.; Liwang, T.

2017-05-01

Next-Generation Sequencing (NGS) has become a powerful sequencing tool for microbial study especially to lead the establishment of the field area of metagenomics. This study described a workflow to analyze metagenomics data of a Sequence Read Archive (SRA) file under accession ERP004286 deposited by University of Sao Paulo. It was a direct sequencing data generated by 454 pyrosequencing platform originated from oil palm fruits endophytic bacteria which were cultured using oil-palm enriched medium. This workflow used SortMeRNA to split ribosomal reads sequence, Newbler (GS Assembler and GS Mapper) to assemble and map reads into genome reference, BLAST package to identify and annotate contigs sequence, and QualiMap for statistical analysis. Eight bacterial species were identified in this study. Enterobacter cloacae was the most abundant species followed by Citrobacter koseri, Seratia marcescens, Latococcus lactis subsp. lactis, Klebsiella pneumoniae, Citrobacter amalonaticus, Achromobacter xylosoxidans, and Pseudomonas sp. respectively. All of these species have been reported as endophyte bacteria in various plant species and each has potential as plant growth promoting bacteria or another application in agricultural industries.

Rail-dbGaP: analyzing dbGaP-protected data in the cloud with Amazon Elastic MapReduce.

PubMed

Nellore, Abhinav; Wilks, Christopher; Hansen, Kasper D; Leek, Jeffrey T; Langmead, Ben

2016-08-15

Public archives contain thousands of trillions of bases of valuable sequencing data. More than 40% of the Sequence Read Archive is human data protected by provisions such as dbGaP. To analyse dbGaP-protected data, researchers must typically work with IT administrators and signing officials to ensure all levels of security are implemented at their institution. This is a major obstacle, impeding reproducibility and reducing the utility of archived data. We present a protocol and software tool for analyzing protected data in a commercial cloud. The protocol, Rail-dbGaP, is applicable to any tool running on Amazon Web Services Elastic MapReduce. The tool, Rail-RNA v0.2, is a spliced aligner for RNA-seq data, which we demonstrate by running on 9662 samples from the dbGaP-protected GTEx consortium dataset. The Rail-dbGaP protocol makes explicit for the first time the steps an investigator must take to develop Elastic MapReduce pipelines that analyse dbGaP-protected data in a manner compliant with NIH guidelines. Rail-RNA automates implementation of the protocol, making it easy for typical biomedical investigators to study protected RNA-seq data, regardless of their local IT resources or expertise. Rail-RNA is available from http://rail.bio Technical details on the Rail-dbGaP protocol as well as an implementation walkthrough are available at https://github.com/nellore/rail-dbgap Detailed instructions on running Rail-RNA on dbGaP-protected data using Amazon Web Services are available at http://docs.rail.bio/dbgap/ : anellore@gmail.com or langmea@cs.jhu.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Occurrence and characterization of mcr-1-harbouring Escherichia coli isolated from pigs in Great Britain from 2013 to 2015.

PubMed

Duggett, Nicholas A; Sayers, Ellie; AbuOun, Manal; Ellis, Richard J; Nunez-Garcia, Javier; Randall, Luke; Horton, Robert; Rogers, Jon; Martelli, Francesca; Smith, Richard P; Brena, Camilla; Williamson, Susanna; Kirchner, Miranda; Davies, Robert; Crook, Derrick; Evans, Sarah; Teale, Chris; Anjum, Muna F

2017-03-01

To determine the occurrence of mcr-1 -harbouring Escherichia coli in archived pig material originating in Great Britain (GB) from 2013 to 2015 and characterize mcr-1 plasmids. Enrichment and selective culture of 387 archived porcine caecal contents and recovery from archive of 1109 E. coli isolates to identify colistin-resistant bacteria by testing for the presence of mcr-1 by PCR and RT-PCR. mcr-1 -harbouring E. coli were characterized by WGS and compared with other available mcr-1 WGS. Using selective isolation following enrichment, the occurrence of mcr-1 E. coli in caeca from healthy pigs at slaughter from unique farms in GB was 0.6% (95% CI 0%-1.5%) in 2015. mcr-1 E. coli were also detected in isolates from two porcine veterinary diagnostic submissions in 2015. All isolates prior to 2015 were negative. WGS analysis of the four mcr-1 -positive E. coli indicated no other antimicrobial resistance (AMR) genes were linked to mcr-1 -plasmid-bearing contigs, despite all harbouring multiple AMR genes. The sequence similarity between mcr-1 -plasmid-bearing contigs identified and those found in GB, Chinese and South African human isolates and Danish, French and Estonian livestock-associated isolates was 90%-99%. mcr-1- harbouring plasmids were diverse, implying transposable elements are involved in mcr-1 transmission in GB. The low number of mcr-1 -positive E. coli isolates identified suggested mcr-1 is currently uncommon in E. coli from pigs within GB. The high sequence similarity between mcr-1 plasmid draft genomes identified in pig E. coli and plasmids found in human and livestock-associated isolates globally requires further investigation to understand the full implications. © Crown copyright 2016.

Revealing the Molecular Portrait of Triple Negative Breast Tumors in an Understudied Population through Omics Analysis of Formalin-Fixed and Paraffin-Embedded Tissues

PubMed Central

Vaca-Paniagua, Felipe; Alvarez-Gomez, Rosa María; Maldonado-Martínez, Hector Aquiles; Pérez-Plasencia, Carlos; Fragoso-Ontiveros, Veronica; Lasa-Gonsebatt, Federico; Herrera, Luis Alonso; Cantú, David; Bargallo-Rocha, Enrique; Mohar, Alejandro; Durand, Geoffroy; Forey, Nathalie; Voegele, Catherine; Vallée, Maxime; Le Calvez-Kelm, Florence; McKay, James; Ardin, Maude; Villar, Stéphanie; Zavadil, Jiri; Olivier, Magali

2015-01-01

Triple negative breast cancer (TNBC), defined by the lack of expression of the estrogen receptor, progesterone receptor and human epidermal receptor 2, is an aggressive form of breast cancer that is more prevalent in certain populations, in particular in low- and middle-income regions. The detailed molecular features of TNBC in these regions remain unexplored as samples are mostly accessible as formalin-fixed paraffin embedded (FFPE) archived tissues, a challenging material for advanced genomic and transcriptomic studies. Using dedicated reagents and analysis pipelines, we performed whole exome sequencing and miRNA and mRNA profiling of 12 FFPE tumor tissues collected from pathological archives in Mexico. Sequencing analyses of the tumor tissues and their blood pairs identified TP53 and RB1 genes as the most frequently mutated genes, with a somatic mutation load of 1.7 mutations/exome Mb on average. Transcriptional analyses revealed an overexpression of growth-promoting signals (EGFR, PDGFR, VEGF, PIK3CA, FOXM1), a repression of cell cycle control pathways (TP53, RB1), a deregulation of DNA-repair pathways, and alterations in epigenetic modifiers through miRNA:mRNA network de-regulation. The molecular programs identified were typical of those described in basal-like tumors in other populations. This work demonstrates the feasibility of using archived clinical samples for advanced integrated genomics analyses. It thus opens up opportunities for investigating molecular features of tumors from regions where only FFPE tissues are available, allowing retrospective studies on the search for treatment strategies or on the exploration of the geographic diversity of breast cancer. PMID:25961742

Ebola Virus Epidemiology and Evolution in Nigeria

DTIC Science & Technology

2016-10-04

the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of 10 Drosophila melanogaster strain w1118; iso-2; iso-3. Fly 2012...cases, and full-4 length Ebola virus (EBOV) genome sequences for 12 of the 20. The detailed contact data permits 5 nearly complete reconstruction of...two methods highlights the strengths of each, and the importance 16 of both contact tracing and genomic sequencing during an outbreak. 17 18

Tick-Borne Encephalitis with Hemorrhagic Syndrome, Novosibirsk Region, Russia, 1999

PubMed Central

Ternovoi, Vladimir A.; Kurzhukov, Gennady P.; Sokolov, Yuri V.; Ivanov, Gennady Y.; Ivanisenko, Vladimir A.; Loktev, Alexander V.; Ryder, Robert W.; Netesov, Sergey V.

2003-01-01

Eight fatal cases of tick-borne encephalitis with unusual hemorrhagic syndrome were identified in 1999 in the Novosibirsk Region, Russia. To study these strains, we sequenced cDNA fragments of protein E gene from six archival formalin-fixed brain samples. Phylogenetic analysis showed tick-borne encephalitis variants clustered with a Far Eastern subtype (homology 94.7%) but not with the Siberian subtype (82%). PMID:12781020

Trace fossils, storm beds, and depositional sequences in a clastic shelf setting, Upper Cretaceous of Utah

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

Frey, R.W.

In Coal Creek Canyon, Utah the Spring Canyon Member of the Blackhawk Formation is divisible into four regressive hemicycles of deposition each representing the downdip part of a nearshore-to-offshore sequence punctuated locally by hummocky cross-stratification. Bedding units span middle shoreface to lower offshore shelf lithofacies, the latter corresponding to a transgressive intertongue of the Mancos Shale. Trace fossil assemblage include 21 ichnospecies distributed among 17 ichnogenera: Ancorichnus, Aulichnites, Chondrites, Cylindrichnus, Ophiomorpha, Palaeophycus, Phoebichnus, Planolites, Rosselia, Schaubcylindrichnus, Scolicia, Skolithos, Taenidium, Teichichnus, Terebellina, Thalassinoides, and Uchirites. Distal deposits are typified by bioturbate textures; Cylindrichnus concentricus, Palaeophycus heberti, and Rosselia socialis otherwise aremore » prevalent throughout the lithofacies suite. Ophiomorpha irregulaire and Schaubcylindrichnus are most common in middle shoreface beds and Chondrites sp. in upper offshore beds; O. nodosa and O. annulata also are common in this part of the sequence. Planolites-type feeding burrows must have been predominant in many depositional settings but now remain inconspicuous and poorly preserved. Despite gradients in environmental distributions of trace fossils, all resident ichnofaunas are referable to the archetypical Cruziana ichnocoenose. Ichnofaunas in hummocky beds mainly represent either an archetypical Skolithos ichnocoenose or mixed Skolithos-Cruziana ichnocoenose. These post-storm ichnocoenoses correspond primarily to a sere of opportunistic pioneers and secondarily to ensuing seres of resilient resident populations. Differences in ichnofacies also are related to differences in post-storm rates of deposition: the slower the rate of sediment accumulation, the greater the degree of overprinting by burrows from subsequent seres or equilibrium communities.« less

Spatial Based Integrated Assessment of Bedrock and Ground Motions, Fault Offsets, and Their Effects for the October-November 2002 Earthquake Sequence on the Denali Fault, Alaska

NASA Astrophysics Data System (ADS)

Vinson, T. S.; Carlson, R.; Hansen, R.; Hulsey, L.; Ma, J.; White, D.; Barnes, D.; Shur, Y.

2003-12-01

A National Science Foundation (NSF) Small Grant Exploratory Research Grant was awarded to the University of Alaska Fairbanks to archive bedrock and ground motions and fault offsets and their effects for the October-November 2002 earthquake sequence on the Denali Fault, Alaska. The scope of work included the accumulation of all strong motion records, satellite imagery, satellite remote sensing data, aerial and ground photographs, and structural response (both measured and anecdotal) that would be useful to achieve the objective. Several interesting data sets were archived including ice cover, lateral movement of stream channels, landslides, avalanches, glacial fracturing, "felt" ground motions, and changes in water quantity and quality. The data sources may be spatially integrated to provide a comprehensive assessment of the bedrock and ground motions and fault offsets for the October-November 2002 earthquake sequence. In the aftermath of the October-November 2002 earthquake sequence on the Denali fault, the Alaskan engineering community expressed a strong interest to understand why their structures and infrastructure were not substantially damaged by the ground motions they experienced during the October-November 2002 Earthquake Sequence on the Denali Fault. The research work proposed under this NSF Grant is a necessary prerequisite to this understanding. Furthermore, the proposed work will facilitate a comparison of Denali events with the Loma Prieta and recent Kocelli and Dozce events in Turkey, all of which were associated with strike-slip faulting. Finally, the spatially integrated data will provide the basis for research work that is truly innovative. For example, is may be possible to predict the observed (1) landsliding and avalanches, (2) changes in water quantity and quality, (3) glacial fracturing, and (4) the widespread liquefaction and lateral spreading, which occurred along the Tok cutoff and Northway airport, with the bedrock and ground motions and fault offsets extrapolated from the product of the research. An integrated assessment of the composite effects may be performed to better understand the bedrock and ground motions and fault offset regime that existed during the earthquake sequence.

Next-Generation Sequencing of the Chrysanthemum nankingense (Asteraceae) Transcriptome Permits Large-Scale Unigene Assembly and SSR Marker Discovery

PubMed Central

Wang, Haibin; Jiang, Jiafu; Chen, Sumei; Qi, Xiangyu; Peng, Hui; Li, Pirui; Song, Aiping; Guan, Zhiyong; Fang, Weimin; Liao, Yuan; Chen, Fadi

2013-01-01

Background Simple sequence repeats (SSRs) are ubiquitous in eukaryotic genomes. Chrysanthemum is one of the largest genera in the Asteraceae family. Only few Chrysanthemum expressed sequence tag (EST) sequences have been acquired to date, so the number of available EST-SSR markers is very low. Methodology/Principal Findings Illumina paired-end sequencing technology produced over 53 million sequencing reads from C. nankingense mRNA. The subsequent de novo assembly yielded 70,895 unigenes, of which 45,789 (64.59%) unigenes showed similarity to the sequences in NCBI database. Out of 45,789 sequences, 107 have hits to the Chrysanthemum Nr protein database; 679 and 277 sequences have hits to the database of Helianthus and Lactuca species, respectively. MISA software identified a large number of putative EST-SSRs, allowing 1,788 primer pairs to be designed from the de novo transcriptome sequence and a further 363 from archival EST sequence. Among 100 primer pairs randomly chosen, 81 markers have amplicons and 20 are polymorphic for genotypes analysis in Chrysanthemum. The results showed that most (but not all) of the assays were transferable across species and that they exposed a significant amount of allelic diversity. Conclusions/Significance SSR markers acquired by transcriptome sequencing are potentially useful for marker-assisted breeding and genetic analysis in the genus Chrysanthemum and its related genera. PMID:23626799

A simple algorithm for quantifying DNA methylation levels on multiple independent CpG sites in bisulfite genomic sequencing electropherograms.

PubMed

Leakey, Tatiana I; Zielinski, Jerzy; Siegfried, Rachel N; Siegel, Eric R; Fan, Chun-Yang; Cooney, Craig A

2008-06-01

DNA methylation at cytosines is a widely studied epigenetic modification. Methylation is commonly detected using bisulfite modification of DNA followed by PCR and additional techniques such as restriction digestion or sequencing. These additional techniques are either laborious, require specialized equipment, or are not quantitative. Here we describe a simple algorithm that yields quantitative results from analysis of conventional four-dye-trace sequencing. We call this method Mquant and we compare it with the established laboratory method of combined bisulfite restriction assay (COBRA). This analysis of sequencing electropherograms provides a simple, easily applied method to quantify DNA methylation at specific CpG sites.

Provenance of Earth Science Datasets - How Deep Should One Go?

NASA Astrophysics Data System (ADS)

Ramapriyan, H.; Manipon, G. J. M.; Aulenbach, S.; Duggan, B.; Goldstein, J.; Hua, H.; Tan, D.; Tilmes, C.; Wilson, B. D.; Wolfe, R.; Zednik, S.

2015-12-01

For credibility of scientific research, transparency and reproducibility are essential. This fundamental tenet has been emphasized for centuries, and has been receiving increased attention in recent years. The Office of Management and Budget (2002) addressed reproducibility and other aspects of quality and utility of information from federal agencies. Specific guidelines from NASA (2002) are derived from the above. According to these guidelines, "NASA requires a higher standard of quality for information that is considered influential. Influential scientific, financial, or statistical information is defined as NASA information that, when disseminated, will have or does have clear and substantial impact on important public policies or important private sector decisions." For information to be compliant, "the information must be transparent and reproducible to the greatest possible extent." We present how the principles of transparency and reproducibility have been applied to NASA data supporting the Third National Climate Assessment (NCA3). The depth of trace needed of provenance of data used to derive conclusions in NCA3 depends on how the data were used (e.g., qualitatively or quantitatively). Given that the information is diligently maintained in the agency archives, it is possible to trace from a figure in the publication through the datasets, specific files, algorithm versions, instruments used for data collection, and satellites, as well as the individuals and organizations involved in each step. Such trace back permits transparency and reproducibility.

Characterizing marine particles and their impact on biogeochemical cycles in the GEOTRACES program

NASA Astrophysics Data System (ADS)

Anderson, Robert F.; Hayes, Christopher T.

2015-04-01

Trace elements and their isotopes (TEIs) are of priority interest in several subdisciplines of oceanography. For example, the vital role of trace element micronutrients in regulating the growth of marine organisms, which, in turn, may influence the structure and composition of marine ecosystems, is now well established (Morel and Price, 2003; Twining and Baines, 2013). Natural distributions of some TEIs have been severely impacted by anthropogenic emissions, leading to substantial perturbations of natural ocean inventories. Pb and Hg, for example, (Lamborg et al., 2002; Schaule and Patterson, 1981), may represent a significant threat to human food supply. Furthermore, much of our knowledge of past variability in the ocean environment, including the ocean's role in climate change, has been developed using TEI proxies archived in marine substrates such as sediments, corals and microfossils. Research in each of these areas relies on a comprehensive knowledge of the distributions of TEIs in the ocean, and on the sensitivity of these distributions to changing environmental conditions. With numerous processes affecting the regional supply and removal of TEIs in the ocean, a comprehensive understanding of the marine biogeochemical cycles of TEIs can be attained only by a global, coordinated, international effort. GEOTRACES, an international program designed to study the marine biogeochemical cycles of trace elements and their isotopes (Anderson et al., 2014; Henderson et al., 2007), aims to achieve these goals.

Observations of the Infrared Solar Spectrum from Space by the ATMOS Experiment

NASA Technical Reports Server (NTRS)

Abrams, M. C.; Goldman, A.; Gunson, M. R.; Rinsland, C. P.; Zander, R.

1999-01-01

The final flight of the Atmospheric Trace Molecule Spectroscopy experiment as part of the Atmospheric na Laboratory for Applications and Science (ATLAS-3) Space Shuttle mission in 1994 provided a new opportunity to measure broadband 625-4800/ cm, 2.1 - 16 micron infrared solar spectra at an unapodized resolution of 0.0l/ cm from space. The majority of the observations were obtained as exoatmospheric, of near Sun center, absorption spectra, which were later ratioed to grazing atmospheric measurements to compute the atmospheric transmission of the Earth's atmosphere and analyzed for vertical profiles of minor and trace gases. Relative to the SPACELAB-3 mission that produced 4800 high Sun spectra (which were averaged into four grand average spectra), the ATLAS-3 mission produced some 40,000 high Sun spectra (which have been similarly averaged) with an improvement in signal-to-noise ratio of a factor of 3-4 in the spectral region between 1000 and 4800/ cm. A brief description of the spectral calibration and spectral quality is given as well as the location of electronic archives of these spectra.

Withdrawal from Weihui: China missions and the silencing of missionary nursing, 1888-1947.

PubMed

Grypma, Sonya

2007-12-01

The shift of missionary nursing from the center to the margins of nursing practice can be traced to the unceremonious closure of China as a mission field in the late 1940s. Building on a larger study of Canadian missionary nursing at the United Church of Canada North China Mission between 1888 and 1947, this paper traces Clara Preston's experiences during the last tumultuous days of the mission during the height of China's civil war. Drawing on rich data from the United Church of Canada/ Victoria University Archives, private family collections (photos, letters, memoirs) as well as from three on-site visits to the Weihui Hospital in Henan, China, this paper focuses on the questions 'what happened during the last days of Canadian missionary nursing in China?' and 'why is so little known about missionary nursing?' According to this study, three issues contributed to the silencing of missionary nursing after 1947: the self-censorship of repatriated missionaries, the mission identity crises catalyzed by the 'failure' of the missionary enterprise in China, and the equating of the missionary movement with colonialism and imperialism in academic discourse.

Thallium as a tracer for preindustrial volcanic eruptions in an ice core record from Illimani, Bolivia.

PubMed

Kellerhals, Thomas; Tobler, Leonhard; Brütsch, Sabina; Sigl, Michael; Wacker, Lukas; Gäggeler, Heinz W; Schwikowski, Margit

2010-02-01

Trace element records from glacier and ice sheet archives provide insights into biogeochemical cycles, atmospheric circulation changes, and anthropogenic pollution history. We present the first continuous high-resolution thallium (Tl) record, derived from an accurately dated ice core from tropical South America, and discuss Tl as a tracer for volcanic eruptions. We identify four prominent Tl peaks and propose that they represent signals from the massive explosive eruptions of the "unknown 1258" A.D. volcano, of Kuwae ( approximately 1450 A.D.), Tambora (1815 A.D.), and Krakatoa (1883 A.D.). The highly resolved record was obtained with an improved setup for the continuous analysis of trace elements in ice with inductively coupled plasma sector field mass spectrometry (ICP-SFMS). The new setup allowed for a stronger initial acidification of the meltwater and shorter tubing length, thereby reducing the risk of memory effects and losses of analytes to the capillary walls. With a comparison of the continuous method to the established conventional decontamination and analysis procedure for discrete samples, we demonstrate the accuracy of the continuous method for Tl analyses.

Primer development to obtain complete coding sequence of HA and NA genes of influenza A/H3N2 virus.

PubMed

Agustiningsih, Agustiningsih; Trimarsanto, Hidayat; Setiawaty, Vivi; Artika, I Made; Muljono, David Handojo

2016-08-30

Influenza is an acute respiratory illness and has become a serious public health problem worldwide. The need to study the HA and NA genes in influenza A virus is essential since these genes frequently undergo mutations. This study describes the development of primer sets for RT-PCR to obtain complete coding sequence of Hemagglutinin (HA) and Neuraminidase (NA) genes of influenza A/H3N2 virus from Indonesia. The primers were developed based on influenza A/H3N2 sequence worldwide from Global Initiative on Sharing All Influenza Data (GISAID) and further tested using Indonesian influenza A/H3N2 archived samples of influenza-like illness (ILI) surveillance from 2008 to 2009. An optimum RT-PCR condition was acquired for all HA and NA fragments designed to cover complete coding sequence of HA and NA genes. A total of 71 samples were successfully sequenced for complete coding sequence both of HA and NA genes out of 145 samples of influenza A/H3N2 tested. The developed primer sets were suitable for obtaining complete coding sequences of HA and NA genes of Indonesian samples from 2008 to 2009.

Measuring the Evolution of Stellar Populations And Gas Metallicity in Galaxies with Far-Infrared Space Spectroscopy

NASA Astrophysics Data System (ADS)

Stacey, Gordon

We propose a study of the evolution of stellar populations and gas metallicities in about 80 nearby star forming galaxies based on mining the NASA data archives for observations of the [NIII] 57 µm, [OIII] 52 µm and/or 88 µm, [NII] 122 and [CII] 158 µm far-infrared (FIR) fine- structure lines and other archives for thermal radio continuum. These lines are powerful probes of both stellar populations and gas properties and our primary science derives from these tracers. For sources that show both signs of active galactic nuclei (AGN) and star formation, we will take advantage of the readily available NASA Spitzer IRS data base that includes mid-IR [NeII] 12.8 µm, [NeIII] 15.6 µm and [NeV] 14.3 µm, [OIV] 25.9 µm and PAH observations. These complementary data reveal the relative fractions of the FIR line emission that might arise from star formation and the narrow line regions (NLR) associated with an AGN, thereby providing a robust set of observations to compare with star formation models. Subsets of the FIR lines have been detected from hundreds of nearby galaxies. From both theoretical studies and the results of these pioneering observations we know that these lines can be powerful probes of stellar populations and star formation in galaxies. Here we plan to use various combinations of the lines to constrain (1) the age of the stellar populations (through lines that trace the hardness of the stellar radiation fields, hence stellar spectral type), (2) the degree of processing of the interstellar medium (through lines that trace growth of secondary to primary element abundances for example, the N/O ratio), (3) the efficiency of star formation (through growth in absolute abundances of N and O, the N/H and O/H ratios), and (4) the current day mass function of upper main sequence stars. Surprisingly, there has been no systematic study of the large sample of these line detections made with PACS on Herschel in order to truly assess and calibrate their diagnostic power. The rich Herschel/PACS data set is particularly attractive for this study due to its sensitivity and calibration uniformity. We propose to undertake such a study here. An initial search of the Herschel Archive reveals that there are at least 80 galaxies that have been observed in the [NII] 122 µm, [OIII] 52 and/or 88 µm and the [CII] 158 µm line. The primary goal of this proposal is to use these emission lines to study the star formation properties (age, metallicity, initial mass function (IMF) and star formation efficiency) in galaxies in the local Universe. This line of study ties into our overarching research objective which is to understand the evolution of star and galaxy formation over cosmic time. We have begun studying star formation in the early Universe by detecting these lines at high redshifts with our grating spectrometer ZEUS-2 on the APEX telescope, and through ALMA programs. The study we propose here will allow us to confidently apply these spectral probes to studies of high-z galaxies while also providing new insights into the characteristic and process of star-formation of galaxies in the nearby Universe. We will utilize NASA s space astrophysics archives to explore the evolution of stellar populations and the elements over cosmic time. The proposed work is therefore highly relevant to NASA s Strategic goal 1: Expand the frontiers of knowledge, capability, and opportunity in space. , Objective 1.6 Discover how the Universe works, explore how it began and evolved, and search for life on planets around other stars. Since the program involves both graduate and undergraduate students at a research university, we also address Strategic Goal 2 via Objective 2.4: Advance the Nation s STEM education and workforce pipeline by working collaborative with other agencies to engage students, teachers, and faculty in NASA s missions and unique assets.

Key Role of Sequencing to Trace Hepatitis A Viruses Circulating in Italy During a Large Multi-Country European Foodborne Outbreak in 2013

PubMed Central

Bruni, Roberto; Taffon, Stefania; Equestre, Michele; Chionne, Paola; Madonna, Elisabetta; Rizzo, Caterina; Tosti, Maria Elena; Alfonsi, Valeria; Ricotta, Lara; De Medici, Dario; Di Pasquale, Simona; Scavia, Gaia; Pavoni, Enrico; Losio, Marina Nadia; Romanò, Luisa; Zanetti, Alessandro Remo; Morea, Anna; Pacenti, Monia; Palù, Giorgio; Capobianchi, Maria Rosaria; Chironna, Maria; Pompa, Maria Grazia; Ciccaglione, Anna Rita

2016-01-01

Background Foodborne Hepatitis A Virus (HAV) outbreaks are being recognized as an emerging public health problem in industrialized countries. In 2013 three foodborne HAV outbreaks occurred in Europe and one in USA. During the largest of the three European outbreaks, most cases occurred in Italy (>1,200 cases as of March 31, 2014). A national Task Force was established at the beginning of the outbreak by the Ministry of Health. Mixed frozen berries were early demonstrated to be the source of infection by the identity of viral sequences in patients and in food. In the present study the molecular characterization of HAV isolates from 355 Italian cases is reported. Methods Molecular characterization was carried out by PCR/sequencing (VP1/2A region), comparison with reference strains and phylogenetic analysis. Results A unique strain was responsible for most characterized cases (235/355, 66.1%). Molecular data had a key role in tracing this outbreak, allowing 110 out of the 235 outbreak cases (46.8%) to be recognized in absence of any other link. The data also showed background circulation of further unrelated strains, both autochthonous and travel related, whose sequence comparison highlighted minor outbreaks and small clusters, most of them unrecognized on the basis of epidemiological data. Phylogenetic analysis showed most isolates from travel related cases clustering with reference strains originating from the same geographical area of travel. Conclusions In conclusion, the study documents, in a real outbreak context, the crucial role of molecular analysis in investigating an old but re-emerging pathogen. Improving the molecular knowledge of HAV strains, both autochthonous and circulating in countries from which potentially contaminated foods are imported, will become increasingly important to control outbreaks by supporting trace back activities, aiming to identify the geographical source(s) of contaminated food, as well as public health interventions. PMID:26901877

Key Role of Sequencing to Trace Hepatitis A Viruses Circulating in Italy During a Large Multi-Country European Foodborne Outbreak in 2013.

PubMed

Bruni, Roberto; Taffon, Stefania; Equestre, Michele; Chionne, Paola; Madonna, Elisabetta; Rizzo, Caterina; Tosti, Maria Elena; Alfonsi, Valeria; Ricotta, Lara; De Medici, Dario; Di Pasquale, Simona; Scavia, Gaia; Pavoni, Enrico; Losio, Marina Nadia; Romanò, Luisa; Zanetti, Alessandro Remo; Morea, Anna; Pacenti, Monia; Palù, Giorgio; Capobianchi, Maria Rosaria; Chironna, Maria; Pompa, Maria Grazia; Ciccaglione, Anna Rita

2016-01-01

Foodborne Hepatitis A Virus (HAV) outbreaks are being recognized as an emerging public health problem in industrialized countries. In 2013 three foodborne HAV outbreaks occurred in Europe and one in USA. During the largest of the three European outbreaks, most cases occurred in Italy (>1,200 cases as of March 31, 2014). A national Task Force was established at the beginning of the outbreak by the Ministry of Health. Mixed frozen berries were early demonstrated to be the source of infection by the identity of viral sequences in patients and in food. In the present study the molecular characterization of HAV isolates from 355 Italian cases is reported. Molecular characterization was carried out by PCR/sequencing (VP1/2A region), comparison with reference strains and phylogenetic analysis. A unique strain was responsible for most characterized cases (235/355, 66.1%). Molecular data had a key role in tracing this outbreak, allowing 110 out of the 235 outbreak cases (46.8%) to be recognized in absence of any other link. The data also showed background circulation of further unrelated strains, both autochthonous and travel related, whose sequence comparison highlighted minor outbreaks and small clusters, most of them unrecognized on the basis of epidemiological data. Phylogenetic analysis showed most isolates from travel related cases clustering with reference strains originating from the same geographical area of travel. In conclusion, the study documents, in a real outbreak context, the crucial role of molecular analysis in investigating an old but re-emerging pathogen. Improving the molecular knowledge of HAV strains, both autochthonous and circulating in countries from which potentially contaminated foods are imported, will become increasingly important to control outbreaks by supporting trace back activities, aiming to identify the geographical source(s) of contaminated food, as well as public health interventions.

Products and Services Available from the Southern California Earthquake Data Center (SCEDC) and the Southern California Seismic Network (SCSN)

NASA Astrophysics Data System (ADS)

Chen, S. E.; Yu, E.; Bhaskaran, A.; Chowdhury, F. R.; Meisenhelter, S.; Hutton, K.; Given, D.; Hauksson, E.; Clayton, R. W.

2011-12-01

Currently, the SCEDC archives continuous and triggered data from nearly 8400 data channels from 425 SCSN recorded stations, processing and archiving an average of 6.4 TB of continuous waveforms and 12,000 earthquakes each year. The SCEDC provides public access to these earthquake parametric and waveform data through its website www.data.scec.org and through client applications such as STP and DHI. This poster will describe the most significant developments at the SCEDC during 2011. New website design: ? The SCEDC has revamped its website. The changes make it easier for users to search the archive, discover updates and new content. These changes also improve our ability to manage and update the site. New data holdings: ? Post processing on El Mayor Cucapah 7.2 sequence continues. To date there have been 11847 events reviewed. Updates are available in the earthquake catalog immediately. ? A double difference catalog (Hauksson et. al 2011) spanning 1981 to 6/30/11 will be available for download at www.data.scec.org and available via STP. ? A focal mechanism catalog determined by Yang et al. 2011 is available for distribution at www.data.scec.org. ? Waveforms from Southern California NetQuake stations are now being stored in the SCEDC archive and available via STP as event associated waveforms. Amplitudes from these stations are also being stored in the archive and used by ShakeMap. ? As part of a NASA/AIST project in collaboration with JPL and SIO, the SCEDC will receive real time 1 sps streams of GPS displacement solutions from the California Real Time Network (http://sopac.ucsd.edu/projects/realtime; Genrich and Bock, 2006, J. Geophys. Res.). These channels will be archived at the SCEDC as miniSEED waveforms, which then can be distributed to the user community via applications such as STP. Improvements in the user tool STP: ? STP sac output now includes picks from the SCSN. New archival methods: ? The SCEDC is exploring the feasibility of archiving and distributing waveform data using cloud computing such as Google Apps. A month of continuous data from the SCEDC archive will be stored in Google Apps and a client developed to access it in a manner similar to STP. The data is stored in miniseed format with gzip compression. Time gaps between time series were padded with null values, which substantially increases search efficiency by make the records uniform in length.

Aura Atmospheric Data Products and Their Availability from NASA Goddard Earth Sciences DAAC

NASA Technical Reports Server (NTRS)

Ahmad, S.; Johnson, J.; Gopalan, A.; Smith, P.; Leptoukh, G.; Kempler, S.

2004-01-01

NASA's EOS-Aura spacecraft was launched successfully on July 15, 2004. The four instruments onboard the spacecraft are the Microwave Limb Sounder (MLS), the Ozone Monitoring Instrument (OMI), the Tropospheric Emission Spectrometer (TES), and the High Resolution Dynamics Limb Sounder (HBDLS). The Aura instruments are designed to gather earth sciences measurements across the ultraviolet, visible, infra-red, thermal and microwave regions of the electromagnetic spectrum. Aura will provide over 70 distinct standard atmospheric data products for use in ozone layer and surface UV-B monitoring, air quality forecast, and atmospheric chemistry and climate change studies (http://eosaura.gsfc.nasa.gov/). These products include earth-atmosphere radiances and solar spectral irradiances; total column, tropospheric, and profiles of ozone and other trace gases, surface W-B flux; clouds and aerosol characteristics; and temperature, geopotential height, and water vapor profiles. The MLS, OMI, and HIRDLS data products will be archived at the NASA Goddard Earth Sciences (GES) Distributed Active Archive Center (DAAC), while data from TES will be archived at NASA Langley Research Center DAAC. Some of the standard products which have gone through quick preliminary checks are already archived at the GES DAAC (http://daac.nsfc.nasa.gov/) and are available to the Aura science team and data validation team members for data validation; and to the application and visualization software developers, for testing their application modules. Once data are corrected for obvious calibration problems and partially validated using in-situ observations, they would be made available to the broader user community. This presentation will provide details of the whole suite of Aura atmospheric data products, and the time line of the availability of the rest of the preliminary products and of the partially validated provisional products. Software and took available for data access, visualization, and data mining will also be discussed.

Supersize me: how whole-genome sequencing and big data are transforming epidemiology.

PubMed

Kao, Rowland R; Haydon, Daniel T; Lycett, Samantha J; Murcia, Pablo R

2014-05-01

In epidemiology, the identification of 'who infected whom' allows us to quantify key characteristics such as incubation periods, heterogeneity in transmission rates, duration of infectiousness, and the existence of high-risk groups. Although invaluable, the existence of many plausible infection pathways makes this difficult, and epidemiological contact tracing either uncertain, logistically prohibitive, or both. The recent advent of next-generation sequencing technology allows the identification of traceable differences in the pathogen genome that are transforming our ability to understand high-resolution disease transmission, sometimes even down to the host-to-host scale. We review recent examples of the use of pathogen whole-genome sequencing for the purpose of forensic tracing of transmission pathways, focusing on the particular problems where evolutionary dynamics must be supplemented by epidemiological information on the most likely timing of events as well as possible transmission pathways. We also discuss potential pitfalls in the over-interpretation of these data, and highlight the manner in which a confluence of this technology with sophisticated mathematical and statistical approaches has the potential to produce a paradigm shift in our understanding of infectious disease transmission and control. Copyright © 2014 Elsevier Ltd. All rights reserved.

Isolating Viral and Host RNA Sequences from Archival Material and Production of cDNA Libraries for High-Throughput DNA Sequencing

PubMed Central

Xiao, Yongli; Sheng, Zong-Mei; Taubenberger, Jeffery K.

2015-01-01

The vast majority of surgical biopsy and post-mortem tissue samples are formalin-fixed and paraffin-embedded (FFPE), but this process leads to RNA degradation that limits gene expression analysis. As an example, the viral RNA genome of the 1918 pandemic influenza A virus was previously determined in a 9-year effort by overlapping RT-PCR from post-mortem samples. Using the protocols described here, the full genome of the 1918 virus at high coverage was determined in one high-throughput sequencing run of a cDNA library derived from total RNA of a 1918 FFPE sample after duplex-specific nuclease treatments. This basic methodological approach should assist in the analysis of FFPE tissue samples isolated over the past century from a variety of infectious diseases. PMID:26344216

Peat bogs and their organic soils: Archives of atmospheric change and global environmentalsignificance (Philippe Duchaufour Medal Lecture)

NASA Astrophysics Data System (ADS)

Shotyk, William

2013-04-01

A bog is much more than a waterlogged ecosystem where organic matter accumulates as peat. Peatlands such as bogs represent a critical link between the atmosphere, hydrosphere, and biosphere. Plants growing at the surface of ombrotrophic bogs receive nutrients exclusively from the atmosphere. Despite the variations in redox status caused by seasonal fluctuations in depth to water table, the low pHof the waters, and abundance of dissolved organic matter, bogs preserve a remarkably reproducible history of atmospheric pollution, climate change, landscape evolution and human history. For example, peat cores from bogs in Europe and North America have provided detailed reconstructions of the changing rates and sources of Ag, Cd, Hg, Pb, Sb, and Tl, providing new insights into the geochemical cycles of these elements, including the massive perturbations induced by human activities beginning many thousands of years ago. Despite the low pH, and perhaps because of the abundance of dissolved organic matter, bogs preserve many silicate and aluminosilicate minerals which renders them valuable archives of atmospheric dust deposition and the climate changes which drive them. In the deeper, basal peat layers of the bog, in the minerotrophic zone where pore waters are affected bymineral-water interactions in the underlying and surrounding soils and sediments, peat serves as animportant link to the hydrosphere, efficiently removing from the imbibed groundwaters such trace elements as As, Cu, Mo, Ni, Se, V, and U. These removal processes, while incompletely understood, are so effective that measuring the dissolved fraction of trace elements in the pore waters becomes a considerable challenge even for the most sophisticated analytical laboratories. While the trace elements listed above are removed from groundwaters (along with P and S), elements such as Fe and Mn are added to the waters because of reductive dissolution, an important first step in the formation of lacustrine Fe and Mn nodules. While these important chemical reactions have taken place silently and imperceptibly over millenia acrossthe Earth wherever climate and water allow bogs to form, at the same time, peat bogs represent an important component of the biosphere and provide a home to many unique plants and animals, thereby contributing to the vast biodiversity found on Earth.

Serial-order learning impairment and hypersensitivity-to-interference in dyscalculia.

PubMed

De Visscher, Alice; Szmalec, Arnaud; Van Der Linden, Lize; Noël, Marie-Pascale

2015-11-01

In the context of heterogeneity, the different profiles of dyscalculia are still hypothetical. This study aims to link features of mathematical difficulties to certain potential etiologies. First, we wanted to test the hypothesis of a serial-order learning deficit in adults with dyscalculia. For this purpose we used a Hebb repetition learning task. Second, we wanted to explore a recent hypothesis according to which hypersensitivity-to-interference hampers the storage of arithmetic facts and leads to a particular profile of dyscalculia. We therefore used interfering and non-interfering repeated sequences in the Hebb paradigm. A final test was used to assess the memory trace of the non-interfering sequence and the capacity to manipulate it. In line with our predictions, we observed that people with dyscalculia who show good conceptual knowledge in mathematics but impaired arithmetic fluency suffer from increased sensitivity-to-interference compared to controls. Secondly, people with dyscalculia who show a deficit in a global mathematical test suffer from a serial-order learning deficit characterized by a slow learning and a quick degradation of the memory trace of the repeated sequence. A serial-order learning impairment could be one of the explanations for a basic numerical deficit, since it is necessary for the number-word sequence acquisition. Among the different profiles of dyscalculia, this study provides new evidence and refinement for two particular profiles. Copyright © 2015 Elsevier B.V. All rights reserved.

The Perils of Pathogen Discovery: Origin of a Novel Parvovirus-Like Hybrid Genome Traced to Nucleic Acid Extraction Spin Columns

PubMed Central

Naccache, Samia N.; Greninger, Alexander L.; Lee, Deanna; Coffey, Lark L.; Phan, Tung; Rein-Weston, Annie; Aronsohn, Andrew; Hackett, John; Delwart, Eric L.

2013-01-01

Next-generation sequencing was used for discovery and de novo assembly of a novel, highly divergent DNA virus at the interface between the Parvoviridae and Circoviridae. The virus, provisionally named parvovirus-like hybrid virus (PHV), is nearly identical by sequence to another DNA virus, NIH-CQV, previously detected in Chinese patients with seronegative (non-A-E) hepatitis. Although we initially detected PHV in a wide range of clinical samples, with all strains sharing ∼99% nucleotide and amino acid identity with each other and with NIH-CQV, the exact origin of the virus was eventually traced to contaminated silica-binding spin columns used for nucleic acid extraction. Definitive confirmation of the origin of PHV, and presumably NIH-CQV, was obtained by in-depth analyses of water eluted through contaminated spin columns. Analysis of environmental metagenome libraries detected PHV sequences in coastal marine waters of North America, suggesting that a potential association between PHV and diatoms (algae) that generate the silica matrix used in the spin columns may have resulted in inadvertent viral contamination during manufacture. The confirmation of PHV/NIH-CQV as laboratory reagent contaminants and not bona fide infectious agents of humans underscores the rigorous approach needed to establish the validity of new viral genomes discovered by next-generation sequencing. PMID:24027301

Multi-proxies Approach of Climatic Records In Terrestrial Mollusks Shells

NASA Astrophysics Data System (ADS)

Labonne, M.; Rousseau, D. D.; Ben Othman, D.; Luck, J. M.; Metref, S.

Fossil land snails shells constitute a valuable source of information for the study of Quaternary deposits as they are commonly preserved in many regions and notably in loess sequences. The use of stable isotope composition of the carbonate in the shells was previously applied to reconstruct past climate or environnements but the technic was not widely exploited and compared with other proxies from the same sequence. In this study, we have analysed stables isotopes, trace elements and Sr isotopes from both shells of land snails Vertigo modesta and the sediment from the Eustis upper Pleistocene loess sequence (Nebraska, USA). This serie developed during the last glaciation and records the last deglaciation between 18,000 and 12,000 B.P. years. We compare the paleoclimatic information obtained by different proxies, such as mag- netic susceptibility, temperature and moisture estimated by land snails assemblage with geochemical data measured on land snails shells in order to validate the climatic information obtained with this proxy. Our study demonstrates that shell carbonate reflects environmental conditions estimated by other proxies. Carbon and oxygen iso- topes show cyclic variations (millenial cycles) along the profile which correlate with stratigraphic units and could be link with the retreat of the Laurentide ice sheet. Trace element and Sr isotopes in the shells indicate various origins for the eolian dusts in the two main loess units along the sequence.

Criteria for the recognition and correlation of sandstone units in the Precambrian and Paleozoic-Mesozoic clastic sequence in the near east

NASA Astrophysics Data System (ADS)

Weissbrod, T.; Perath, I.

A systematic study of the Precambrian and Paleozoic-Mesozoic clastic sequences (Nubian Sandstone) in Israel and Sinai, and a comparative analysis of its stratigraphy in neighbouring countries, has shown that besides the conventional criteria of subdivision (lithology, field appearance, photogeological features, fossil content), additional criteria can be applied, which singly or in mutual conjuction enable the recognition of widespread units and boundaries. These criteria show lateral constancy, and recurrence of a similar vertical sequence over great distances, and are therefore acceptable for the identification of synchronous, region-wide sedimentary units (and consequently, major unconformities). They also enable, once the units are established, to identify detached (not in situ) samples, samples from isolated or discontinous outcrops, borehole material or archive material. The following rock properties were tested and found to be usefuls in stratigraphic interpretation, throughout large distribution areas of the clastic sequence: Landscape, which is basically the response of a particular textural-chemic al aggregate to atmospheric weathering. Characteristic outcrop feature — styles of roundness or massivity, fissuring or fliatin, slope profile, bedding — express a basic uniformity of these platform-type clastics. Colors are often stratigraphically constant over hundreds of kilometers, through various climates and topographies, and express some intrinsic unity of the rock bodies. Grain size and sorting, when cross-plotted, enable to differentiate existing unit. The method requires the analysis of representative numbers of samples. Vertical trends of median grain size and sorting show reversals, typically across unconformities. Feldstar content diminishes from 15-50% in Precambrian-Paleozoic rocks to a mere 5% or less in Mesozoic sandstones — a distinctive regionwide time trend. Dominance of certain feldstar types characterizes Precambrian and Paleozoic units. Clay minerals, though subordinate, characterize certain units. Illite is usually the dominant clay mineral in the Precambrain-Paleozoic sediments, showing different degress of crystallization in different units. Kaolinite is the main, often the only clay mineral in Mesozoic units. Heavy minerals, whose species spectra reflect on parent rock and provenance terrain and whose differential response to degradation points to the sedimentary history of the deposit, show certain vertical regularities, such as the abrupt disappearance of species or whole assemblages at certain levels, indicating unconformities. Trace metals, which in places reach ore concentrations (e.g. copper), are often extensive, though of well-defined vertical distribution. They express adsorptive capacity of specific widespread lithologies, enabling the discrimination of units. Even though each of these criteria is not always by itself diagnostic, they may in conjuction with one or more other criteria amount to a petrographic fingerprint that enables fairly accurate identification of the age interval of the unit, and its relation both to the regional and the local stratigraphic sequence.

Identification and tracing of Enterococcus spp. by RAPD-PCR in traditional fermented sausages and meat environment.

PubMed

Martín, B; Corominas, L; Garriga, M; Aymerich, T

2009-01-01

Four local small-scale factories were studied to determine the sources of enterococci in traditional fermented sausages. Different points during the production of a traditional fermented sausage type (fuet) were evaluated. Randomly amplified polymorphic DNA (RAPD)-PCR was used to type 596 Enterococcus isolates from the final products, the initial meat batter, the casing, the workers' hands and the equipment. Species-specific PCR-multiplex and the partial sequencing of atpA gene and 16S rRNA gene sequencing allowed the identification of the isolates: Enterococcus faecalis (31.4%), Enterococcus faecium (30.7%), Enterococcus sanguinicola (14.9%), Enterococcus devriesei (9.7%), Enterococcus malodoratus (7.2%), Enterococcus gilvus (1.0%), Enterococcus gallinarum (1.3%), Enterococcus casseliflavus (3.4%), Enterococcus hermanniensis (0.2%), and Enterococcus durans (0.2%). A total of 92 different RAPD-PCR profiles were distributed among the different factories and samples evaluated. Most of the genotypes found in fuet samples were traced back to their source. The major sources of enterococci in the traditional fermented sausages studied were mainly the equipment followed by the raw ingredients, although a low proportion was traced back to human origin. This work contributes to determine the source of enterococcal contamination in fermented sausages and also to the knowledge of the meat environment.

Exploring the CO/CN line ratio in nearby galaxies with the ALMA archive

NASA Astrophysics Data System (ADS)

Wilson, Christine D.

2018-07-01

We describe an archival project using Cycle 0 data from the Atacama Large Millimeter/submillimeter Array to survey the CO/CN line ratio in 17 nearby galaxies. CN is an interesting molecule that traces dense gas exposed to ultraviolet radiation and its N = 1 - 0 lines can be observed simultaneously with the CO J = 1 - 0 line. We identify eight galaxies with distances <200 Mpc for which both lines are detected. Signal-to-noise ratio matched CO/CN ratios range from as low as 7 to as high as 65, while ratios using the total detected flux range from 20 to 140. Spatial variations greater than a factor of 3 are seen in several galaxies. These line ratio changes are likely due to changes in the [CN]/[H2] abundance ratio and/or the CN excitation. Additional measurements of the warm gas pressure and the CN excitation should help to distinguish between these two possibilities. Three of the four active galactic nuclei in our sample show CO/CN line ratios that are roughly a factor of 2-3 larger than those seen in starburst-dominated regions, which may be in conflict with models of molecular abundances in X-ray-dominated regions.

Cultural Heritage Reconstruction from Historical Photographs and Videos

NASA Astrophysics Data System (ADS)

Condorelli, F.; Rinaudo, F.

2018-05-01

Historical archives save invaluable treasures and play a critical role in the conservation of Cultural Heritage. Old photographs and videos, which have survived over time and stored in these archives, preserve traces of architecture and urban transformation and, in many cases, are the only evidence of buildings that no longer exist. They are a precious source of enormous informative potential in Cultural Heritage documentation and save invaluable treasures. Thanks to photogrammetric techniques it is possible to extract metric information from these sources useful for 3D virtual reconstructions of monuments and historic buildings. This paper explores the ways to search for, classify and group historical data by considering their possible use in metric documentation and aims to provide an overview of criticality and open issues of the methodologies that could be used to process these data. A practical example is described and presented as a case study. The video "Torino 1928", an old movie dating from the 1930s, was processed for reconstructing the temporary pavilions of the "Exposition" held in Turin in 1928. Despite the initial concerns relating to processing this kind of data, the experimental methodology used in this research has allowed to reach a quality of results of acceptable standard.

Marine bivalve shell geochemistry and ultrastructure from modern low pH environments: environmental effect versus experimental bias

NASA Astrophysics Data System (ADS)

Hahn, S.; Rodolfo-Metalpa, R.; Griesshaber, E.; Schmahl, W. W.; Buhl, D.; Hall-Spencer, J. M.; Baggini, C.; Fehr, K. T.; Immenhauser, A.

2012-05-01

Bivalve shells can provide excellent archives of past environmental change but have not been used to interpret ocean acidification events. We investigated carbon, oxygen and trace element records from different shell layers in the mussels Mytilus galloprovincialis combined with detailed investigations of the shell ultrastructure. Mussels from the harbour of Ischia (Mediterranean, Italy) were transplanted and grown in water with mean pHT 7.3 and mean pHT 8.1 near CO2 vents on the east coast of the island. Most prominently, the shells recorded the shock of transplantation, both in their shell ultrastructure, textural and geochemical record. Shell calcite, precipitated subsequently under acidified seawater responded to the pH gradient by an in part disturbed ultrastructure. Geochemical data from all test sites show a strong metabolic effect that exceeds the influence of the low-pH environment. These field experiments showed that care is needed when interpreting potential ocean acidification signals because various parameters affect shell chemistry and ultrastructure. Besides metabolic processes, seawater pH, factors such as salinity, water temperature, food availability and population density all affect the biogenic carbonate shell archive.

Time trends (1983-1999) for organochlorines and polybrominated diphenyl ethers in rainbow smelt (Osmerus mordax) from Lakes Michigan, Huron and Superior, USA

USGS Publications Warehouse

Chernyak, Sergei M.; Rice, Clifford P.; Quintal, Richard T.; Begnoche, Linda J.; Hickey, James P.; Vinyard, Bryan T.

2005-01-01

The U.S. Geological Service Great Lakes Science Center has archived rainbow smelt (Osmerus mordax) collected from the early 1980s to the present. These fish were collected to provide time- and site-dependent contaminant residue data needed by researchers and managers to fill critical data gaps regarding trends and behavior of persistent organic contaminants in the Great Lakes ecosystem. In the present study, data are presented for concentrations of several organochlorine (OC) contaminants in the archived smelt, including DDT, polychlorinated biphenyls (PCBs), toxaphene, and chlordanes in Lakes Michigan and Huron (MI, USA) and in Lake Superior (MN, USA). The trends for all the OCs were declining as a first-order decay over the sampled time series (1983/1985–1993/1999) with the exception of toxaphene in Lake Superior and PCBs at the Charlevoix/Little Traverse Bay site in Lake Michigan. Concentration of the emerging contaminant, polybrominated diphenyl ethers (PBDEs), also was traced from its apparent entry into this ecosystem in approximately 1980 until 1999. Time trends for the PBDEs were increasing exponentially at all sites, with concentration-doubling times varying from 1.58 to 2.94 years.

Expansion of the On-line Archive "Statistically Downscaled WCRP CMIP3 Climate Projections"

NASA Astrophysics Data System (ADS)

Brekke, L. D.; Pruitt, T.; Maurer, E. P.; Das, T.; Duffy, P.; White, K.

2009-12-01

Presentation highlights status and plans for a public-access archive of downscaled CMIP3 climate projections. Incorporating climate projection information into long-term evaluations of water and energy resources requires analysts to have access to projections at "basin-relevant" resolution. Such projections would ideally be bias-corrected to account for climate model tendencies to systematically simulate historical conditions different than observed. In 2007, the U.S. Bureau of Reclamation, Santa Clara University and Lawrence Livermore National Laboratory (LLNL) collaborated to develop an archive of 112 bias-corrected and spatially disaggregated (BCSD) CMIP3 temperature and precipitation projections. These projections were generated using 16 CMIP3 models to simulate three emissions pathways (A2, A1b, and B1) from one or more initializations (runs). Projections are specified on a monthly time step from 1950-2099 and at 0.125 degree spatial resolution within the North American Land Data Assimilation System domain (i.e. contiguous U.S., southern Canada and northern Mexico). Archive data are freely accessible at LLNL Green Data Oasis (url). Since being launched, the archive has served over 3500 data requests by nearly 500 users in support of a range of planning, research and educational activities. Archive developers continue to look for ways to improve the archive and respond to user needs. One request has been to serve the intermediate datasets generated during the BCSD procedure, helping users to interpret the relative influences of the bias-correction and spatial disaggregation on the transformed CMIP3 output. This request has been addressed with intermediate datasets now posted at the archive web-site. Another request relates closely to studying hydrologic and ecological impacts under climate change, where users are asking for projected diurnal temperature information (e.g., projected daily minimum and maximum temperature) and daily time step resolution. In response, archive developers are adding content in 2010, teaming with Scripps Institution of Oceanography (through their NOAA-RISA California-Nevada Applications Program and the California Climate Change Center) to apply a new daily downscaling technique to a sub-ensemble of the archive’s CMIP3 projections. The new technique, Bias-Corrected Constructed Analogs, combines the BC part of BCSD with a recently developed technique that preserves the daily sequencing structure of CMIP3 projections (Constructed Analogs, or CA). Such data will more easily serve hydrologic and ecological impacts assessments, and offer an opportunity to evaluate projection uncertainty associated with downscaling technique. Looking ahead to the arrival CMIP5 projections, archive collaborators have plans apply both BCSD and BCCA over the contiguous U.S. consistent with CMIP3 applications above, and also apply BCSD globally at a 0.5 degree spatial resolution. The latter effort involves collaboration with U.S. Army Corps of Engineers (USACE) and Climate Central.

Seasonally-resolved trace element concentrations in stalagmites from a shallow cave in New Mexico

NASA Astrophysics Data System (ADS)

Sekhon, N.; Banner, J.; Miller, N. R.; Carlson, P. E.; Breecker, D.

2017-12-01

High-resolution (sub-annual/seasonal) paleoclimate records extending beyond the instrumental period are required to test climate models and better understand how climate warming/cooling and wetting/drying are manifested seasonally. This is particularly the case for areas such as the southwest United States where precipitation and temperature seasonality dictate the regional climate. Study of a 20thcentury stalagmite (Carlson et al., in prep) documented (1) seasonal variation in trace element compositions of a stalagmite from a shallow, well-ventilated cave and (2) demonstrated the seasonal variation in stalagmite Mg to be in agreement with predicted temperature-dependent fractionation between water and calcite. The seasonal nature of variability was constrained by monitoring the cave on a monthly basis (Casteel and Banner, 2015; Carlson et al., in prep). Here we expand on using stalagmites from shallow, well-ventilated caves as archives of seasonally-resolved climate recorders by studying trace element variations in two coeval modern stalagmites (SBFC-1 and SBFC-2) cored from Sitting Bull Falls, southern New Mexico. Seasonal cycles will be confirmed by analyzing Mg, Ba, and Sr in in-situ calcite precipitated on artificial substrates as available (July, Sept., and Nov. 2017). The chronology is constrained by semi-automated peak counting and 14C bomb-peak. In addition, principal component analyses of trace element data identify two primary underlying modes of trace element variability for soil-derived elements (Cu, Zn, and Fe) and bedrock-derived elements (Mg, Sr, and Ba). We hypothesize that the soil-derived elements are transported by seasonal infiltration of organic colloids and the bedrock-derived elements are ­­controlled by variability in cave air temperature, drip water, and calcite growth rate. The two modes of variability will be calibrated against instrumental data over the 20th century. When complete, these new seasonally resolved proxy records will constrain the pattern and mechanism of the regional climate in southwest United States with a focus on drought indicators.

A Constraint Generation Approach to Learning Stable Linear Dynamical Systems

DTIC Science & Technology

2008-01-01

task of learning dynamic textures from image sequences as well as to modeling biosurveillance drug-sales data. The constraint generation approach...previous methods in our experiments. One application of LDSs in computer vision is learning dynamic textures from video data [8]. An advantage of...over-the-counter (OTC) drug sales for biosurveillance , and sunspot numbers from the UCR archive [9]. Comparison to the best alternative methods [7, 10

Comparative RNA-sequencing of the acarbose producer Actinoplanes sp. SE50/110 cultivated in different growth media.

PubMed

Schwientek, Patrick; Wendler, Sergej; Neshat, Armin; Eirich, Christina; Rückert, Christian; Klein, Andreas; Wehmeier, Udo F; Kalinowski, Jörn; Stoye, Jens; Pühler, Alfred

2013-08-20

Actinoplanes sp. SE50/110 is known as the producer of the alpha-glucosidase inhibitor acarbose, a potent drug in the treatment of type-2 diabetes mellitus. We conducted the first whole transcriptome analysis of Actinoplanes sp. SE50/110, using RNA-sequencing technology for comparative gene expression studies between cells grown in maltose minimal medium, maltose minimal medium with trace elements, and glucose complex medium. We first studied the behavior of Actinoplanes sp. SE50/110 cultivations in these three media and found that the different media had significant impact on growth rate and in particular on acarbose production. It was demonstrated that Actinoplanes sp. SE50/110 grew well in all three media, but acarbose biosynthesis was only observed in cultures grown in maltose minimal medium with and without trace elements. When comparing the expression profiles between the maltose minimal media with and without trace elements, only few significantly differentially expressed genes were found, which mainly code for uptake systems of metal ions provided in the trace element solution. In contrast, the comparison of expression profiles from maltose minimal medium and glucose complex medium revealed a large number of differentially expressed genes, of which the most conspicuous genes account for iron storage and uptake. Furthermore, the acarbose gene cluster was found to be highly expressed in maltose-containing media and almost silent in the glucose-containing medium. In addition, a putative antibiotic biosynthesis gene cluster was found to be similarly expressed as the acarbose cluster. Copyright © 2012 Elsevier B.V. All rights reserved.

Event-specific plasmid standards and real-time PCR methods for transgenic Bt11, Bt176, and GA21 maize and transgenic GT73 canola.

PubMed

Taverniers, Isabel; Windels, Pieter; Vaïtilingom, Marc; Milcamps, Anne; Van Bockstaele, Erik; Van den Eede, Guy; De Loose, Marc

2005-04-20

Since the 18th of April 2004, two new regulations, EC/1829/2003 on genetically modified food and feed products and EC/1830/2003 on traceability and labeling of GMOs, are in force in the EU. This new, comprehensive regulatory framework emphasizes the need of an adequate tracing system. Unique identifiers, such as the transgene genome junction region or a specific rearrangement within the transgene DNA, should form the basis of such a tracing system. In this study, we describe the development of event-specific tracing systems for transgenic maize lines Bt11, Bt176, and GA21 and for canola event GT73. Molecular characterization of the transgene loci enabled us to clone an event-specific sequence into a plasmid vector, to be used as a marker, and to develop line-specific primers. Primer specificity was tested through qualitative PCRs and dissociation curve analysis in SYBR Green I real-time PCRs. The primers were then combined with event-specific TaqMan probes in quantitative real-time PCRs. Calibration curves were set up both with genomic DNA samples and the newly synthesized plasmid DNA markers. It is shown that cloned plasmid GMO target sequences are perfectly suitable as unique identifiers and quantitative calibrators. Together with an event-specific primer pair and a highly specific TaqMan probe, the plasmid markers form crucial components of a unique and straighforward tracing system for Bt11, Bt176, and GA21 maize and GT73 canola events.

Optimizing exosomal RNA isolation for RNA-Seq analyses of archival sera specimens.

PubMed

Prendergast, Emily N; de Souza Fonseca, Marcos Abraão; Dezem, Felipe Segato; Lester, Jenny; Karlan, Beth Y; Noushmehr, Houtan; Lin, Xianzhi; Lawrenson, Kate

2018-01-01

Exosomes are endosome-derived membrane vesicles that contain proteins, lipids, and nucleic acids. The exosomal transcriptome mediates intercellular communication, and represents an understudied reservoir of novel biomarkers for human diseases. Next-generation sequencing enables complex quantitative characterization of exosomal RNAs from diverse sources. However, detailed protocols describing exosome purification for preparation of exosomal RNA-sequence (RNA-Seq) libraries are lacking. Here we compared methods for isolation of exosomes and extraction of exosomal RNA from human cell-free serum, as well as strategies for attaining equal representation of samples within pooled RNA-Seq libraries. We compared commercial precipitation with ultracentrifugation for exosome purification and confirmed the presence of exosomes via both transmission electron microscopy and immunoblotting. Exosomal RNA extraction was compared using four different RNA purification methods. We determined the minimal starting volume of serum required for exosome preparation and showed that high quality exosomal RNA can be isolated from sera stored for over a decade. Finally, RNA-Seq libraries were successfully prepared with exosomal RNAs extracted from human cell-free serum, cataloguing both coding and non-coding exosomal transcripts. This method provides researchers with strategic options to prepare RNA-Seq libraries and compare RNA-Seq data quantitatively from minimal volumes of fresh and archival human cell-free serum for disease biomarker discovery.

NCBI Epigenomics: a new public resource for exploring epigenomic data sets

PubMed Central

Fingerman, Ian M.; McDaniel, Lee; Zhang, Xuan; Ratzat, Walter; Hassan, Tarek; Jiang, Zhifang; Cohen, Robert F.; Schuler, Gregory D.

2011-01-01

The Epigenomics database at the National Center for Biotechnology Information (NCBI) is a new resource that has been created to serve as a comprehensive public resource for whole-genome epigenetic data sets (www.ncbi.nlm.nih.gov/epigenomics). Epigenetics is the study of stable and heritable changes in gene expression that occur independently of the primary DNA sequence. Epigenetic mechanisms include post-translational modifications of histones, DNA methylation, chromatin conformation and non-coding RNAs. It has been observed that misregulation of epigenetic processes has been associated with human disease. We have constructed the new resource by selecting the subset of epigenetics-specific data from general-purpose archives, such as the Gene Expression Omnibus, and Sequence Read Archives, and then subjecting them to further review, annotation and reorganization. Raw data is processed and mapped to genomic coordinates to generate ‘tracks’ that are a visual representation of the data. These data tracks can be viewed using popular genome browsers or downloaded for local analysis. The Epigenomics resource also provides the user with a unique interface that allows for intuitive browsing and searching of data sets based on biological attributes. Currently, there are 69 studies, 337 samples and over 1100 data tracks from five well-studied species that are viewable and downloadable in Epigenomics. PMID:21075792

NCBI Epigenomics: a new public resource for exploring epigenomic data sets.

PubMed

Fingerman, Ian M; McDaniel, Lee; Zhang, Xuan; Ratzat, Walter; Hassan, Tarek; Jiang, Zhifang; Cohen, Robert F; Schuler, Gregory D

2011-01-01

The Epigenomics database at the National Center for Biotechnology Information (NCBI) is a new resource that has been created to serve as a comprehensive public resource for whole-genome epigenetic data sets (www.ncbi.nlm.nih.gov/epigenomics). Epigenetics is the study of stable and heritable changes in gene expression that occur independently of the primary DNA sequence. Epigenetic mechanisms include post-translational modifications of histones, DNA methylation, chromatin conformation and non-coding RNAs. It has been observed that misregulation of epigenetic processes has been associated with human disease. We have constructed the new resource by selecting the subset of epigenetics-specific data from general-purpose archives, such as the Gene Expression Omnibus, and Sequence Read Archives, and then subjecting them to further review, annotation and reorganization. Raw data is processed and mapped to genomic coordinates to generate 'tracks' that are a visual representation of the data. These data tracks can be viewed using popular genome browsers or downloaded for local analysis. The Epigenomics resource also provides the user with a unique interface that allows for intuitive browsing and searching of data sets based on biological attributes. Currently, there are 69 studies, 337 samples and over 1100 data tracks from five well-studied species that are viewable and downloadable in Epigenomics.

FBIS: A regional DNA barcode archival & analysis system for Indian fishes

PubMed Central

Nagpure, Naresh Sahebrao; Rashid, Iliyas; Pathak, Ajey Kumar; Singh, Mahender; Singh, Shri Prakash; Sarkar, Uttam Kumar

2012-01-01

DNA barcode is a new tool for taxon recognition and classification of biological organisms based on sequence of a fragment of mitochondrial gene, cytochrome c oxidase I (COI). In view of the growing importance of the fish DNA barcoding for species identification, molecular taxonomy and fish diversity conservation, we developed a Fish Barcode Information System (FBIS) for Indian fishes, which will serve as a regional DNA barcode archival and analysis system. The database presently contains 2334 sequence records of COI gene for 472 aquatic species belonging to 39 orders and 136 families, collected from available published data sources. Additionally, it contains information on phenotype, distribution and IUCN Red List status of fishes. The web version of FBIS was designed using MySQL, Perl and PHP under Linux operating platform to (a) store and manage the acquisition (b) analyze and explore DNA barcode records (c) identify species and estimate genetic divergence. FBIS has also been integrated with appropriate tools for retrieving and viewing information about the database statistics and taxonomy. It is expected that FBIS would be useful as a potent information system in fish molecular taxonomy, phylogeny and genomics. Availability The database is available for free at http://mail.nbfgr.res.in/fbis/ PMID:22715304

Helicobacter Species Identified in Captive Sooty Mangabeys (Cercocebus atys) with Metastatic Gastric Adenocarcinoma

PubMed Central

Esmail, Michael Y.; Bacon, Rebecca; Swennes, Alton G.; Feng, Yan; Shen, Zeli; Garcia, AnaPatricia; Sharma, Prachi; Cohen, Joyce; Fox, James G.

2016-01-01

Background Of all human cancers, gastric carcinoma is the one of the leading causes of death. Helicobacter pylori is considered a major etiologic agent of this disease. Spontaneously occurring gastric carcinoma is a rare diagnosis in nonhuman primates. A 2011 case report documented a high incidence of gastric adenocarcinoma in a closed colony of captive sooty mangabeys (Cercebus atys). However, H. pylori infection was not detected in these animals. Materials and Methods In this study, using archived formalin-fixed, paraffin-embedded stomach sections of these animals alternative methodologies were used to identify H. pylori and other non-H. pylori Helicobacter species. In addition, two additional cases of sooty mangabeys with metastatic gastric carcinoma are characterized. Results Using fluorescent in situ hybridization, we identified gastric H. suis in 75% of archived and new gastric carcinoma cases. In the two newly reported cases, H. suis and a novel Helicobacter species were detected via PCR and sequence analysis of the 16S rRNA gene. H. pylori was not identified in any of the gastric carcinoma cases via FISH and/or PCR and sequence analysis of Helicobacter spp. in DNA from of available tissues. Conclusions This report is the first to characterize Helicobacter species infection in spontaneous gastric carcinoma with metastatic potential in nonhuman primates. PMID:26477442

The BIG Data Center: from deposition to integration to translation.

PubMed

2017-01-04

Biological data are generated at unprecedentedly exponential rates, posing considerable challenges in big data deposition, integration and translation. The BIG Data Center, established at Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, provides a suite of database resources, including (i) Genome Sequence Archive, a data repository specialized for archiving raw sequence reads, (ii) Gene Expression Nebulas, a data portal of gene expression profiles based entirely on RNA-Seq data, (iii) Genome Variation Map, a comprehensive collection of genome variations for featured species, (iv) Genome Warehouse, a centralized resource housing genome-scale data with particular focus on economically important animals and plants, (v) Methylation Bank, an integrated database of whole-genome single-base resolution methylomes and (vi) Science Wikis, a central access point for biological wikis developed for community annotations. The BIG Data Center is dedicated to constructing and maintaining biological databases through big data integration and value-added curation, conducting basic research to translate big data into big knowledge and providing freely open access to a variety of data resources in support of worldwide research activities in both academia and industry. All of these resources are publicly available and can be found at http://bigd.big.ac.cn. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Tropical wetlands - problems and potentials as paleo-monsoon archives

NASA Astrophysics Data System (ADS)

Chabangborn, Akkaneewut; Chawchai, Sakonvan; Fritz, Sherilyn; Löwemark, Ludvig; Wohlfarth, Barbara

2014-05-01

Paleoclimatic and paleoenvironmental information is still scarce for Southeast Asia despite the fact that this large region is home to numerous natural lakes and wetlands that may contain long sedimentary archives. During the past years we have been surveying lakes and wetlands in different parts of Thailand to select the most promising and longest sedimentary sequences for paleoenvironmental studies. Our survey of more than 30 lakes shows that only very few lakes and wetlands still contain soft sediments. The sediments in the majority of the lakes and wetlands have been dredged and excavated during the past 10 years to provide open and clear water for fishing and recreation. Dredging and excavation using large caterpillars has disturbed and in some cases completely destroyed the sedimentary records. Stiff clays now drape most of the lake bottoms. Based on our extensive survey, we found five sites, from which we successfully obtained intact sediment sequences: Lakes Kumphawapi and Pa Kho in northeast Thailand, Nong Leng Sai in northern Thailand and Sam Roi Yod and Nong Thale Pron in southern Thailand. All of these sites contain a detailed sedimentary record covering the past 2000 years, two of the sites cover parts of or, the entire Holocene; and two sites have sediments covering the last Termination and MIS 3, respectively.

The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions

PubMed Central

Kwong, Waldan K.; McFrederick, Quinn; Anderson, Kirk E.; Barribeau, Seth Michael; Chandler, James Angus; Cornman, R. Scott; Dainat, Jacques; Doublet, Vincent; Emery, Olivier; Evans, Jay D.; Farinelli, Laurent; Flenniken, Michelle L.; Granberg, Fredrik; Grasis, Juris A.; Gauthier, Laurent; Hayer, Juliette; Koch, Hauke; Kocher, Sarah; Martinson, Vincent G.; Moran, Nancy; Munoz-Torres, Monica; Newton, Irene; Paxton, Robert J.; Powell, Eli; Sadd, Ben M.; Schmid-Hempel, Paul; Schmid-Hempel, Regula; Schwarz, Ryan S.; vanEngelsdorp, Dennis

2016-01-01

ABSTRACT As pollinators, bees are cornerstones for terrestrial ecosystem stability and key components in agricultural productivity. All animals, including bees, are associated with a diverse community of microbes, commonly referred to as the microbiome. The bee microbiome is likely to be a crucial factor affecting host health. However, with the exception of a few pathogens, the impacts of most members of the bee microbiome on host health are poorly understood. Further, the evolutionary and ecological forces that shape and change the microbiome are unclear. Here, we discuss recent progress in our understanding of the bee microbiome, and we present challenges associated with its investigation. We conclude that global coordination of research efforts is needed to fully understand the complex and highly dynamic nature of the interplay between the bee microbiome, its host, and the environment. High-throughput sequencing technologies are ideal for exploring complex biological systems, including host-microbe interactions. To maximize their value and to improve assessment of the factors affecting bee health, sequence data should be archived, curated, and analyzed in ways that promote the synthesis of different studies. To this end, the BeeBiome consortium aims to develop an online database which would provide reference sequences, archive metadata, and host analytical resources. The goal would be to support applied and fundamental research on bees and their associated microbes and to provide a collaborative framework for sharing primary data from different research programs, thus furthering our understanding of the bee microbiome and its impact on pollinator health. PMID:27118586

The bee microbiome: Impact on bee health and model for evolution and ecology of host-microbe interactions

USGS Publications Warehouse

Engel, Philipp; Kwong, Waldan K.; McFrederick, Quinn; Anderson, Kirk E.; Barribeau, Seth Michael; Chandler, James Angus; Cornman, Robert S.; Dainat, Jacques; de Miranda, Joachim R.; Doublet, Vincent; Emery, Olivier; Evans, Jay D.; Farinelli, Laurent; Flenniken, Michelle L.; Granberg, Fredrik; Grasis, Juris A.; Gauthier, Laurent; Hayer, Juliette; Koch, Hauke; Kocher, Sarah; Martinson, Vincent G.; Moran, Nancy; Munoz-Torres, Monica; Newton, Irene; Paxton, Robert J.; Powell, Eli; Sadd, Ben M.; Schmid-Hempel, Paul; Schmid-Hempel, Regula; Song, Se Jin; Schwarz, Ryan S.; vanEngelsdorp, Dennis; Dainat, Benjamin

2016-01-01

As pollinators, bees are cornerstones for terrestrial ecosystem stability and key components in agricultural productivity. All animals, including bees, are associated with a diverse community of microbes, commonly referred to as the microbiome. The bee microbiome is likely to be a crucial factor affecting host health. However, with the exception of a few pathogens, the impacts of most members of the bee microbiome on host health are poorly understood. Further, the evolutionary and ecological forces that shape and change the microbiome are unclear. Here, we discuss recent progress in our understanding of the bee microbiome, and we present challenges associated with its investigation. We conclude that global coordination of research efforts is needed to fully understand the complex and highly dynamic nature of the interplay between the bee microbiome, its host, and the environment. High-throughput sequencing technologies are ideal for exploring complex biological systems, including host-microbe interactions. To maximize their value and to improve assessment of the factors affecting bee health, sequence data should be archived, curated, and analyzed in ways that promote the synthesis of different studies. To this end, the BeeBiome consortium aims to develop an online database which would provide reference sequences, archive metadata, and host analytical resources. The goal would be to support applied and fundamental research on bees and their associated microbes and to provide a collaborative framework for sharing primary data from different research programs, thus furthering our understanding of the bee microbiome and its impact on pollinator health.

The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions.

PubMed

Engel, Philipp; Kwong, Waldan K; McFrederick, Quinn; Anderson, Kirk E; Barribeau, Seth Michael; Chandler, James Angus; Cornman, R Scott; Dainat, Jacques; de Miranda, Joachim R; Doublet, Vincent; Emery, Olivier; Evans, Jay D; Farinelli, Laurent; Flenniken, Michelle L; Granberg, Fredrik; Grasis, Juris A; Gauthier, Laurent; Hayer, Juliette; Koch, Hauke; Kocher, Sarah; Martinson, Vincent G; Moran, Nancy; Munoz-Torres, Monica; Newton, Irene; Paxton, Robert J; Powell, Eli; Sadd, Ben M; Schmid-Hempel, Paul; Schmid-Hempel, Regula; Song, Se Jin; Schwarz, Ryan S; vanEngelsdorp, Dennis; Dainat, Benjamin

2016-04-26

As pollinators, bees are cornerstones for terrestrial ecosystem stability and key components in agricultural productivity. All animals, including bees, are associated with a diverse community of microbes, commonly referred to as the microbiome. The bee microbiome is likely to be a crucial factor affecting host health. However, with the exception of a few pathogens, the impacts of most members of the bee microbiome on host health are poorly understood. Further, the evolutionary and ecological forces that shape and change the microbiome are unclear. Here, we discuss recent progress in our understanding of the bee microbiome, and we present challenges associated with its investigation. We conclude that global coordination of research efforts is needed to fully understand the complex and highly dynamic nature of the interplay between the bee microbiome, its host, and the environment. High-throughput sequencing technologies are ideal for exploring complex biological systems, including host-microbe interactions. To maximize their value and to improve assessment of the factors affecting bee health, sequence data should be archived, curated, and analyzed in ways that promote the synthesis of different studies. To this end, the BeeBiome consortium aims to develop an online database which would provide reference sequences, archive metadata, and host analytical resources. The goal would be to support applied and fundamental research on bees and their associated microbes and to provide a collaborative framework for sharing primary data from different research programs, thus furthering our understanding of the bee microbiome and its impact on pollinator health. Copyright © 2016 Engel et al.

Anchovies to Whales: tracking vertebrate biodiversity in Monterey Bay by metabarcoding environmental DNA (eDNA)

NASA Astrophysics Data System (ADS)

Closek, C. J.; Starks, H.; Walz, K.; Boehm, A. B.; Chavez, F.

2016-12-01

The oscillation between the dominance of Sardinops sagax (pacific sardine) and Engraulis mordax (northern anchovy) has been documented in the California Coastal Ecosystem for more than 100 years. These two species are strong drivers of trophic interactions in the region. As part of the Marine Biodiversity Observational Network (MBON) initiative, we used archived filtered seawater samples collected late-summer to mid-fall over a span of 8 years from Monterey Bay, CA to examine the change in marine vertebrate environmental DNA (eDNA). Water samples were collected from a nearshore location in Monterey Bay (C1) during the years of 2008-15. The water was then filtered, and the filter was archived at -80°C. DNA was extracted from the filters, and the 12S rRNA gene present in mitochondrial DNA was PCR amplification using primers designed to amplify 12s rRNA genes from marine vertebrates. The amplicons were subsequently sequenced with an Illumina MiSeq and the data processed using an analysis pipeline for sequence annotation. More than 20 fish genera were noted in the sequences from 2008-12, with Engraulis the dominant fish genus from 2013-15. Anchovy and Megaptera novaeangliae (humpback whale) were present in temporal patterns similar to those noted during visual observations where anchovy and humpback whale were more abundant during the years of 2013-2015 than the other years. This study demonstrates our ability to detect megafauna and fish species that are important to the Monterey Bay ecosystem from coastal water samples and determine community structural differences over time.

A paleomagnetic record in loess-paleosol sequences since late Pleistocene in the arid Central Asia

NASA Astrophysics Data System (ADS)

Li, Guanhua; Xia, Dunsheng; Appel, Erwin; Wang, Youjun; Jia, Jia; Yang, Xiaoqiang

2018-03-01

Geomagnetic excursions during Brunhes epoch have been brought to the forefront topic in paleomagnetic study, as they provide key information about Earth's interior dynamics and could serve as another tool for stratigraphic correlation among different lithology. Loess-paleosol sequences provide good archives for decoding geomagnetic excursions. However, the detailed pattern of these excursions was not sufficiently clarified due to pedogenic influence. In this study, paleomagnetic analysis was performed in loess-paleosol sequences on the northern piedmont of the Tianshan Mountains (northwestern China). By radiocarbon and luminance dating, the loess section was chronologically constrained to mainly the last c.130 ka, a period when several distinct geomagnetic excursions were involved. The rock magnetic properties in this loess section are dominated by magnetite and maghemite in a pseudo-single-domain state. The rock magnetic properties and magnetic anisotropy indicate weakly pedogenic influence for magnetic record. The stable component of remanent magnetization derived from thermal demagnetization revealed the presence of two intervals of directional anomalies with corresponding intensity lows in the Brunhes epoch. The age control in the key layers indicates these anomalies are likely associated with the Laschamp and Blake excursions, respectively. In addition, relative paleointensity in the loess section is basically compatible with other regional and global relative paleointensity records and indicates two low-paleointensity zones, possibly corresponding to the Blake and Laschamp excursions, respectively. As a result, this study suggests that the loess section may have the potential to record short-lived excursions, which largely reflect the variation of dipole components in the global archives.

[A collection of scientific instruments at the dawn of the modern hospital: Vincenzo Viviani's physical-mathematical instruments and Santa Maria Hospital in Florence (1871-1895)].

PubMed

Diana, Esther

2008-01-01

Around the second half of the nineteenth century, the collection of physics-mathematical instruments that Vincenzo Viviani (1622-1703) had bequeathed to the Santa Maria Nuova Hospital of Florence stirred new interest. The process of modernising the hospital was indeed to lead to the progressive alienation of the institution's rich historical patrimony, including the scientific collections. In tracing back the negotiations that led to the sale of the Viviani collection, archive documents have also brought to light the collection inventory, which is now proposed a new to help recount the history of how scientific instruments became museum collectibles in Florence.

Geographies of displacement: Latina/os, oral history, and the politics of gentrification in San Francisco's Mission District.

PubMed

Mirabal, Nancy Raquel

2009-05-01

During the 1990s and early 2000s, working-class and poor neighborhoods in San Francisco underwent dramatic economic and racial changes. One of the most heavily gentrified neighborhoods was the Mission District. As a result of local politics, housing and rental policies, real estate speculation, and development, thousands of Latina/o families were displaced. Using oral historical and ethnographic methodologies, print media, archival sources, and policy papers, this article traces the gentrification of the Mission District from the perspective of the Latina/o community. It also examines how gentrification was articulated as a positive turn within the larger public discourse on space and access.

Determination of the Prebomb Southern (Antartic) Ocean Radiocarbon in Organic Matter

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

Guilderson, T P

2001-02-26

The Southern Hemisphere is an important and unique region of the world's oceans for water-mass formation and mixing, upwelling, nutrient utilization, and carbon export. In fact, one of the primary interests of the oceanographic community is to decipher the climatic record of these processes in the source or sink terms for Southern Ocean surface waters in the CO{sub 2} balance of the atmosphere. Current coupled ocean-atmosphere modeling efforts to trace the input of CO{sub 2} into the ocean imply a strong sink of anthropogenic CO{sub 2} in the southern ocean. However, because of its relative inaccessibility and the difficulty inmore » directly measuring CO{sub 2} fluxes in the Southern Ocean, these results are controversial at best. An accepted diagnostic of the exchange of CO{sub 2} between the atmosphere and ocean is the prebomb distribution of radiocarbon in the ocean and its time-history since atmospheric nuclear testing. Such histories of {sup 14}C in the surface waters of the Southern Ocean do not currently exist, primarily because there are few continuous biological archives (e.g., in corals) such as those that have been used to monitor the {sup 14}C history of the tropics and subtropics. One of the possible long-term archives is the scallop Adamussium collbecki. Although not independently confirmed, relatively crude growth rate estimates of A. collbecki indicate that it has the potential to provide continuous 100 year time-series. We are exploring the suitability of this potential archive.« less

Trace elements records from vermetids aragonite as millennial paleo-oceanographic archives in the South-East Mediterranean

NASA Astrophysics Data System (ADS)

Jacobson, Yitzhak; Yam, Ruth; Shemesh, Aldo

2017-04-01

The Mediterranean Sea is a region under high anthropogenic stress, thus a hotspot for climate change studies. Natural conditions, such as SST, productivity, precipitation and dust fluxes along with human induced activity affect seawater chemistry. We study millennial variability of trace elements in East Mediterranean Sea high-resolution records, in attempt to connect them to environmental factors. The Mediterranean reef builder Vermetid, D. petraeum is a sessile gastropod, secreting its aragonite shells in tidal zones. Cores of Vermetid reefs from the South Eastern Mediterranean (Israel) were previously analyzed by Sisma?Ventura et al. (2014) to reconstruct seawater surface temperature (SST) and δ13C of dissolved inorganic carbon (DIC). In this study we analyzed trace elements of these vermetid cores, and reconstructed millennial records of elements to calcium (el/Ca) molar ratios. Vermetid trace element contents from recent decades are mostly in agreement with known values for marine biogenic aragonites from corals and mollusk. We divide vermetid trace element records into three element groups: 1) Sr and U are related to SST and DIC. These elements correlate with major climatic events of the last millennium, such as the Medieval Warm Period (900-1300 AD) and the Little Ice Age (1450-1850 AD). 2) Pb and Cd are related to anthropogenic pollution and demonstrate industrial sourced trends throughout the anthropocene (since 1750 AD). 3) Terrogenous elements, including Fe, Al, Mn and V. Al in seawater and sediments has been used to trace water masses and land derived sediment source. We observe a major change in average vermetid Al/Fe ratios from 0.5 to 2.5 over the recorded period (n=72). This vermetid Al/Fe change points at a possible shift from Nilotic sediments (0.1-0.5 Al/Fe molar ratio) to Saharan dust ratio (2-4 Al/Fe molar ratio). Mn and V show a similar variability to Fe. Understanding the variability of vermetid TE can help us interpret the relative dominance of different climate systems and anthropogenic processes on the East Mediterranean environment.

A Cost-Effective Transparency-Based Digital Imaging for Efficient and Accurate Wound Area Measurement

PubMed Central

Li, Pei-Nan; Li, Hong; Wu, Mo-Li; Wang, Shou-Yu; Kong, Qing-You; Zhang, Zhen; Sun, Yuan; Liu, Jia; Lv, De-Cheng

2012-01-01

Wound measurement is an objective and direct way to trace the course of wound healing and to evaluate therapeutic efficacy. Nevertheless, the accuracy and efficiency of the current measurement methods need to be improved. Taking the advantages of reliability of transparency tracing and the accuracy of computer-aided digital imaging, a transparency-based digital imaging approach is established, by which data from 340 wound tracing were collected from 6 experimental groups (8 rats/group) at 8 experimental time points (Day 1, 3, 5, 7, 10, 12, 14 and 16) and orderly archived onto a transparency model sheet. This sheet was scanned and its image was saved in JPG form. Since a set of standard area units from 1 mm2 to 1 cm2 was integrated into the sheet, the tracing areas in JPG image were measured directly, using the “Magnetic lasso tool” in Adobe Photoshop program. The pixel values/PVs of individual outlined regions were obtained and recorded in an average speed of 27 second/region. All PV data were saved in an excel form and their corresponding areas were calculated simultaneously by the formula of Y (PV of the outlined region)/X (PV of standard area unit) × Z (area of standard unit). It took a researcher less than 3 hours to finish area calculation of 340 regions. In contrast, over 3 hours were expended by three skillful researchers to accomplish the above work with traditional transparency-based method. Moreover, unlike the results obtained traditionally, little variation was found among the data calculated by different persons and the standard area units in different sizes and shapes. Given its accurate, reproductive and efficient properties, this transparency-based digital imaging approach would be of significant values in basic wound healing research and clinical practice. PMID:22666449

Dense Gas, Dynamical Equilibrium Pressure, and Star Formation in Nearby Star-forming Galaxies

NASA Astrophysics Data System (ADS)

Gallagher, Molly J.; Leroy, Adam K.; Bigiel, Frank; Cormier, Diane; Jiménez-Donaire, María J.; Ostriker, Eve; Usero, Antonio; Bolatto, Alberto D.; García-Burillo, Santiago; Hughes, Annie; Kepley, Amanda A.; Krumholz, Mark; Meidt, Sharon E.; Meier, David S.; Murphy, Eric J.; Pety, Jérôme; Rosolowsky, Erik; Schinnerer, Eva; Schruba, Andreas; Walter, Fabian

2018-05-01

We use new ALMA observations to investigate the connection between dense gas fraction, star formation rate (SFR), and local environment across the inner region of four local galaxies showing a wide range of molecular gas depletion times. We map HCN (1–0), HCO+ (1–0), CS (2–1), 13CO (1–0), and C18O (1–0) across the inner few kiloparsecs of each target. We combine these data with short-spacing information from the IRAM large program EMPIRE, archival CO maps, tracers of stellar structure and recent star formation, and recent HCN surveys by Bigiel et al. and Usero et al. We test the degree to which changes in the dense gas fraction drive changes in the SFR. {I}HCN}/{I}CO} (tracing the dense gas fraction) correlates strongly with I CO (tracing molecular gas surface density), stellar surface density, and dynamical equilibrium pressure, P DE. Therefore, {I}HCN}/{I}CO} becomes very low and HCN becomes very faint at large galactocentric radii, where ratios as low as {I}HCN}/{I}CO}∼ 0.01 become common. The apparent ability of dense gas to form stars, {{{Σ }}}SFR}/{{{Σ }}}dense} (where Σdense is traced by the HCN intensity and the star formation rate is traced by a combination of Hα and 24 μm emission), also depends on environment. {{{Σ }}}SFR}/{{{Σ }}}dense} decreases in regions of high gas surface density, high stellar surface density, and high P DE. Statistically, these correlations between environment and both {{{Σ }}}SFR}/{{{Σ }}}dense} and {I}HCN}/{I}CO} are stronger than that between apparent dense gas fraction ({I}HCN}/{I}CO}) and the apparent molecular gas star formation efficiency {{{Σ }}}SFR}/{{{Σ }}}mol}. We show that these results are not specific to HCN.

GenBank.

PubMed

Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Sayers, Eric W

2011-01-01

GenBank® is a comprehensive database that contains publicly available nucleotide sequences for more than 380,000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system that integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage: www.ncbi.nlm.nih.gov.

Simultaneous activation of parallel sensory pathways promotes a grooming sequence in Drosophila

PubMed Central

Hampel, Stefanie; McKellar, Claire E

2017-01-01

A central model that describes how behavioral sequences are produced features a neural architecture that readies different movements simultaneously, and a mechanism where prioritized suppression between the movements determines their sequential performance. We previously described a model whereby suppression drives a Drosophila grooming sequence that is induced by simultaneous activation of different sensory pathways that each elicit a distinct movement (Seeds et al., 2014). Here, we confirm this model using transgenic expression to identify and optogenetically activate sensory neurons that elicit specific grooming movements. Simultaneous activation of different sensory pathways elicits a grooming sequence that resembles the naturally induced sequence. Moreover, the sequence proceeds after the sensory excitation is terminated, indicating that a persistent trace of this excitation induces the next grooming movement once the previous one is performed. This reveals a mechanism whereby parallel sensory inputs can be integrated and stored to elicit a delayed and sequential grooming response. PMID:28887878

Dialog detection in narrative video by shot and face analysis

NASA Astrophysics Data System (ADS)

Kroon, B.; Nesvadba, J.; Hanjalic, A.

2007-01-01

The proliferation of captured personal and broadcast content in personal consumer archives necessitates comfortable access to stored audiovisual content. Intuitive retrieval and navigation solutions require however a semantic level that cannot be reached by generic multimedia content analysis alone. A fusion with film grammar rules can help to boost the reliability significantly. The current paper describes the fusion of low-level content analysis cues including face parameters and inter-shot similarities to segment commercial content into film grammar rule-based entities and subsequently classify those sequences into so-called shot reverse shots, i.e. dialog sequences. Moreover shot reverse shot specific mid-level cues are analyzed augmenting the shot reverse shot information with dialog specific descriptions.

gkmSVM: an R package for gapped-kmer SVM

PubMed Central

Ghandi, Mahmoud; Mohammad-Noori, Morteza; Ghareghani, Narges; Lee, Dongwon; Garraway, Levi; Beer, Michael A.

2016-01-01

Summary: We present a new R package for training gapped-kmer SVM classifiers for DNA and protein sequences. We describe an improved algorithm for kernel matrix calculation that speeds run time by about 2 to 5-fold over our original gkmSVM algorithm. This package supports several sequence kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel. Availability and Implementation: gkmSVM package is freely available through the Comprehensive R Archive Network (CRAN), for Linux, Mac OS and Windows platforms. The C ++ implementation is available at www.beerlab.org/gkmsvm Contact: mghandi@gmail.com or mbeer@jhu.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153639

Principles of Gestalt Psychology and Their Application to Teaching Junior High School Science

ERIC Educational Resources Information Center

Blosser, Patricia E.

1973-01-01

Discusses insightful learning, trace system,'' and laws of perception and Pragnanz in connection with problem solving and critical thinking in science teaching. Suggests 19 guidelines for sequencing curriculum and identifying activities for use in science classes. (CC)

Sampling solution traces for the problem of sorting permutations by signed reversals

PubMed Central

2012-01-01

Background Traditional algorithms to solve the problem of sorting by signed reversals output just one optimal solution while the space of all optimal solutions can be huge. A so-called trace represents a group of solutions which share the same set of reversals that must be applied to sort the original permutation following a partial ordering. By using traces, we therefore can represent the set of optimal solutions in a more compact way. Algorithms for enumerating the complete set of traces of solutions were developed. However, due to their exponential complexity, their practical use is limited to small permutations. A partial enumeration of traces is a sampling of the complete set of traces and can be an alternative for the study of distinct evolutionary scenarios of big permutations. Ideally, the sampling should be done uniformly from the space of all optimal solutions. This is however conjectured to be ♯P-complete. Results We propose and evaluate three algorithms for producing a sampling of the complete set of traces that instead can be shown in practice to preserve some of the characteristics of the space of all solutions. The first algorithm (RA) performs the construction of traces through a random selection of reversals on the list of optimal 1-sequences. The second algorithm (DFALT) consists in a slight modification of an algorithm that performs the complete enumeration of traces. Finally, the third algorithm (SWA) is based on a sliding window strategy to improve the enumeration of traces. All proposed algorithms were able to enumerate traces for permutations with up to 200 elements. Conclusions We analysed the distribution of the enumerated traces with respect to their height and average reversal length. Various works indicate that the reversal length can be an important aspect in genome rearrangements. The algorithms RA and SWA show a tendency to lose traces with high average reversal length. Such traces are however rare, and qualitatively our results show that, for testable-sized permutations, the algorithms DFALT and SWA produce distributions which approximate the reversal length distributions observed with a complete enumeration of the set of traces. PMID:22704580

A multi-archive coherent chronology: from Greenland to the Mediterranean sea

NASA Astrophysics Data System (ADS)

Bazin, Lucie; Landais, Amaelle; Lemieux-Dudon, Bénédicte; Siani, Giuseppe; Michel, Elisabeth; Combourieu-Nebout, Nathalie; Blamart, Dominique; Genty, Dominique

2015-04-01

Understanding the climate mechanisms requires a precise knowledge of the sequence of events during major climate changes. In order to provide precise relationships between changes in orbital and/or greenhouse gases concentration forcing, sea level changes and high vs low latitudes temperatures, a common chronological framework for different paleoclimatic archives is required. Coherent chronologies for ice cores have been recently produced using a bayesian dating tool, DATICE (Lemieux-Dudon et al., 2010, Bazin et al., 2013, Veres et al., 2013). Such tool has been recently developed to include marine cores and speleothems in addition to ice cores. This new development should enable one to test the coherency of different chronologies using absolute and stratigraphic links as well as to provide relationship between climatic changes recorded in different archives. We present here a first application of multi-archive coherent dating including paleoclimatic archives from (1) Greenland (NGRIP ice core), (2) Mediterranean sea (marine core MD90-917, 41° N17° E, 1010 m) and (3) speleothems from the South of France and North Tunisia (Chauvet, Villars and La Mine speleothems, Genty et al., 2006). Thanks to the good absolute chronological constraints from annual layer counting in NGRIP, 14C and tephra layers in MD90-917 and U-Th dating in speleothems, we can provide a precise chronological framework for the last 50 ka (ie. thousand years before present). Then, we present different tests on how to combine the records from the different archives and give the most plausible scenario for the sequence of events at different latitudes over the last deglaciation. Bazin, L., Landais, A. ; Lemieu¬-Dudon, B. ; Kele, H. T. M. ; Veres, D. ; Parrenin, F. ; Martinerie, P. ; Ritz, C. ; Capron, E. ; Lipenkov, V. ; Loutre, M.-F. ; Raynaud, D. ; Vinther, B. ; Svensson, A. ; Rasmussen, S. ; Severi, M. ; Blunier, T. ; Leuenberger, M. ; Fischer, H. ; Masson-¬-Delmotte, V. ; Chappellaz, J. & Wolff, E., An optimized multi-proxy, multi-site Antarctic ice and gas orbital chronology (AICC2012): 120-800 ka,Clim. Past 9, 1715-1731, 2013. Genty, D., Blamart, D., Ghaleb B., Plagnes, V., Causse, Ch., Bakalowicz, M., Zouari, K., Chkir, N., Hellstrom, J., Wainer, K., Bourges, F., Timing and dynamics of the last deglaciation from European and North African δ13C stalagmite profiles - comparison with Chinese ans South Hemisphere stalagmites, Quat. Sci. Rev. 25, 2118-2142, 2006. Lemieux-Dudon, B. ; Blayo, E. ; Petit, J.-R. ; Waelbroeck, C. ;Svensson, A. ; Ritz, C. ; Barnola, J.-M. ; Narcisi, B.M. ; Parrenin, F., Consitent dating for Antarctic and Greenland ice cores, Quat. Sci. Rev. 29(1-2), 2010. Veres, D. ; Bazin, L. ; Landais, A. ; Lemieux-Dudon, B. ; Parrenin, F. ; Martinerie, P. ; Toyé Mahamadou Kele, H. ; Capron, E. ; Chappellaz, J. ; Rasmussen, S. ; Severi, M. ; Svensson, A. ; Vinther, B. & Wolff, E., The Antarctic ice core chronology (AICC2012): an optimized multi-parameter and multi-site dating approach for the last 120 thousand years, Clim. Past, 9, 1733-1748, 2013.

Bamboo tea: reduction of taxonomic complexity and application of DNA diagnostics based on rbcL and matK sequence data

PubMed Central

Häser, Annette

2016-01-01

Background Names used in ingredient lists of food products are trivial and in their nature rarely precise. The most recent scientific interpretation of the term bamboo (Bambusoideae, Poaceae) comprises over 1,600 distinct species. In the European Union only few of these exotic species are well known sources for food ingredients (i.e., bamboo sprouts) and are thus not considered novel foods, which would require safety assessments before marketing of corresponding products. In contrast, the use of bamboo leaves and their taxonomic origin is mostly unclear. However, products containing bamboo leaves are currently marketed. Methods We analysed bamboo species and tea products containing bamboo leaves using anatomical leaf characters and DNA sequence data. To reduce taxonomic complexity associated with the term bamboo, we used a phylogenetic framework to trace the origin of DNA from commercially available bamboo leaves within the bambusoid subfamily. For authentication purposes, we introduced a simple PCR based test distinguishing genuine bamboo from other leaf components and assessed the diagnostic potential of rbcL and matK to resolve taxonomic entities within the bamboo subfamily and tribes. Results Based on anatomical and DNA data we were able to trace the taxonomic origin of bamboo leaves used in products to the genera Phyllostachys and Pseudosasa from the temperate “woody” bamboo tribe (Arundinarieae). Currently available rbcL and matK sequence data allow the character based diagnosis of 80% of represented bamboo genera. We detected adulteration by carnation in four of eight tea products and, after adapting our objectives, could trace the taxonomic origin of the adulterant to Dianthus chinensis (Caryophyllaceae), a well known traditional Chinese medicine with counter indications for pregnant women. PMID:27957401

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

Steele, Amy; Hughes, A. Meredith; Carpenter, John

The presence of debris disks around young main-sequence stars hints at the existence and structure of planetary systems. Millimeter-wavelength observations probe large grains that trace the location of planetesimal belts. The Formation and Evolution of Planetary Systems Spitzer Legacy survey of nearby young solar analogues yielded a sample of five debris disk-hosting stars with millimeter flux suitable for interferometric follow-up. We present observations with the Submillimeter Array (SMA) and the Combined Array for Research in Millimeter-wave Astronomy at ∼2″ resolution that spatially resolve the debris disks around these nearby (d ∼ 50 pc) stars. Two of the five disks (HDmore » 377, HD 8907) are spatially resolved for the first time and one (HD 104860) is resolved at millimeter wavelengths for the first time. We combine our new observations with archival SMA and Atacama Large Millimeter/Submillimeter Array data to enable a uniform analysis of the full five-object sample. We simultaneously model the broadband photometric data and resolved millimeter visibilities to constrain the dust temperatures and disk morphologies, and perform a Markov Chain Monte Carlo analysis to fit for basic structural parameters. We find that the radii and widths of the cold outer belts exhibit properties consistent with scaled-up versions of the Solar System's Kuiper Belt. All the disks exhibit characteristic grain sizes comparable to the blowout size, and all the resolved observations of emission from large dust grains are consistent with an axisymmetric dust distribution to within the uncertainties. These results are consistent with comparable studies carried out at infrared wavelengths.« less

Targeted or whole genome sequencing of formalin fixed tissue samples: potential applications in cancer genomics.

PubMed

Munchel, Sarah; Hoang, Yen; Zhao, Yue; Cottrell, Joseph; Klotzle, Brandy; Godwin, Andrew K; Koestler, Devin; Beyerlein, Peter; Fan, Jian-Bing; Bibikova, Marina; Chien, Jeremy

2015-09-22

Current genomic studies are limited by the poor availability of fresh-frozen tissue samples. Although formalin-fixed diagnostic samples are in abundance, they are seldom used in current genomic studies because of the concern of formalin-fixation artifacts. Better characterization of these artifacts will allow the use of archived clinical specimens in translational and clinical research studies. To provide a systematic analysis of formalin-fixation artifacts on Illumina sequencing, we generated 26 DNA sequencing data sets from 13 pairs of matched formalin-fixed paraffin-embedded (FFPE) and fresh-frozen (FF) tissue samples. The results indicate high rate of concordant calls between matched FF/FFPE pairs at reference and variant positions in three commonly used sequencing approaches (whole genome, whole exome, and targeted exon sequencing). Global mismatch rates and C · G > T · A substitutions were comparable between matched FF/FFPE samples, and discordant rates were low (<0.26%) in all samples. Finally, low-pass whole genome sequencing produces similar pattern of copy number alterations between FF/FFPE pairs. The results from our studies suggest the potential use of diagnostic FFPE samples for cancer genomic studies to characterize and catalog variations in cancer genomes.

Environmental and Ecological Risk Assessment of Trace Metal Contamination in Mangrove Ecosystems: A Case from Zhangjiangkou Mangrove National Nature Reserve, China

PubMed Central

Wang, Jun; Du, Huihong; Xu, Ye; Chen, Kai; Liang, Junhua; Ke, Hongwei; Cheng, Sha-Yen; Liu, Mengyang; Deng, Hengxiang; He, Tong; Wang, Wenqing

2016-01-01

Zhangjiangkou Mangrove National Nature Reserve is a subtropical wetland ecosystem in southeast coast of China, which is of dense population and rapid development. The concentrations, sources, and pollution assessment of trace metals (Cu, Cd, Pb, Cr, Zn, As, and Hg) in surface sediment from 29 sites and the biota specimen were investigated for better ecological risk assessment and environmental management. The ranges of trace metals in mg/kg sediment were as follows: Cu (10.79–26.66), Cd (0.03–0.19), Pb (36.71–59.86), Cr (9.67–134.51), Zn (119.69–157.84), As (15.65–31.60), and Hg (0.00–0.08). The sequences of the bioaccumulation of studied metals are Zn > Cu > As > Cr > Pb > Cd > Hg with few exceptions. Cluster analysis and principal component analysis revealed that the trace metals in the studied area mainly derived from anthropogenic activities, such as industrial effluents, agricultural waste, and domestic sewage. Pollution load index and geoaccumulation index were calculated for trace metals in surface sediments, which indicated unpolluted status in general except Pb, Cr, and As. PMID:27795956

Phylogenetic analysis and victim contact tracing of rabies virus from humans and dogs in Bali, Indonesia.

PubMed

Mahardika, G N K; Dibia, N; Budayanti, N S; Susilawathi, N M; Subrata, K; Darwinata, A E; Wignall, F S; Richt, J A; Valdivia-Granda, W A; Sudewi, A A R

2014-06-01

The emergence of human and animal rabies in Bali since November 2008 has attracted local, national and international interest. The potential origin and time of introduction of rabies virus to Bali is described. The nucleoprotein (N) gene of rabies virus from dog brain and human clinical specimens was sequenced using an automated DNA sequencer. Phylogenetic inference with Bayesian Markov Chain Monte Carlo (MCMC) analysis using the Bayesian Evolutionary Analysis by Sampling Trees (BEAST) v. 1.7.5 software confirmed that the outbreak of rabies in Bali was caused by an Indonesian lineage virus following a single introduction. The ancestor of Bali viruses was the descendant of a virus from Kalimantan. Contact tracing showed that the event most likely occurred in early 2008. The introduction of rabies into a large unvaccinated dog population in Bali clearly demonstrates the risk of disease transmission for government agencies and should lead to an increased preparedness and efforts for sustained risk reduction to prevent such events from occurring in future.

Trace level detection of compounds related to the chemical weapons convention by 1H-detected 13C NMR spectroscopy executed with a sensitivity-enhanced, cryogenic probehead.

PubMed

Cullinan, David B; Hondrogiannis, George; Henderson, Terry J

2008-04-15

Two-dimensional 1H-13C HSQC (heteronuclear single quantum correlation) and fast-HMQC (heteronuclear multiple quantum correlation) pulse sequences were implemented using a sensitivity-enhanced, cryogenic probehead for detecting compounds relevant to the Chemical Weapons Convention present in complex mixtures. The resulting methods demonstrated exceptional sensitivity for detecting the analytes at trace level concentrations. 1H-13C correlations of target analytes at < or = 25 microg/mL were easily detected in a sample where the 1H solvent signal was approximately 58,000-fold more intense than the analyte 1H signals. The problem of overlapping signals typically observed in conventional 1H spectroscopy was essentially eliminated, while 1H and 13C chemical shift information could be derived quickly and simultaneously from the resulting spectra. The fast-HMQC pulse sequences generated magnitude mode spectra suitable for detailed analysis in approximately 4.5 h and can be used in experiments to efficiently screen a large number of samples. The HSQC pulse sequences, on the other hand, required roughly twice the data acquisition time to produce suitable spectra. These spectra, however, were phase-sensitive, contained considerably more resolution in both dimensions, and proved to be superior for detecting analyte 1H-13C correlations. Furthermore, a HSQC spectrum collected with a multiplicity-edited pulse sequence provided additional structural information valuable for identifying target analytes. The HSQC pulse sequences are ideal for collecting high-quality data sets with overnight acquisitions and logically follow the use of fast-HMQC pulse sequences to rapidly screen samples for potential target analytes. Use of the pulse sequences considerably improves the performance of NMR spectroscopy as a complimentary technique for the screening, identification, and validation of chemical warfare agents and other small-molecule analytes present in complex mixtures and environmental samples.

Long-term observations of tropospheric ozone: GAW Measurement Guidelines

NASA Astrophysics Data System (ADS)

Tarasova, Oksana; Galbally, Ian E.; Schultz, Martin G.

2013-04-01

The Global Atmosphere Watch (GAW) Programme of the World Meteorological Organization (WMO) coordinates long-term observations of the chemical composition and physical properties of the atmosphere which are relevant for understanding of atmospheric chemistry and climate change. Atmospheric observations of reactive gases (tropospheric ozone, carbon monoxide, volatile organic compounds and nitrogen oxides) coordinated by the GAW Programme complement local and regional scale air quality monitoring efforts. As part of the GAW quality assurance (QA) system detailed measurement guidelines for atmospheric trace species are developed by international expert teams at irregular intervals. The most recent report focuses on continuous in-situ measurements of ozone in the troposphere, performed in particular at continental or island sites with altitudes ranging from sea level to mountain tops. Data Quality Objectives (DQOs) are defined for different applications of the data (e.g. trend analysis and verification of global model forecasts). These DQOs include a thorough discussion of the tolerable level of measurement uncertainty and data completeness. The guidelines present the best practices and practical arrangements adopted by the GAW Programme in order to enable the GAW station network to approach or achieve the defined tropospheric ozone DQOs. The document includes information on the selection of station and measurement locations, required skills and training of staff, recommendations on the measurement technique and the necessary equipment to perform highest quality measurements, rules for conducting the measurements, preparing the data and archiving them, and more. Much emphasis is given to discussions about how to ensure the quality of the data through tracing calibrations back to primary standards, proper calibration and data analysis, etc. In the GAW Programme the QA system is implemented through Central Facilities (Central Calibration Laboratories, World and Regional Calibration Centers and World Data Centers), Scientific Advisory Groups and GAW Training and Education Center. These bodies support primary standards, provide calibration and data archiving facilities, coordinate comparison campaigns, perform stations audit, provide documentation and training of personnel.

COMET Multimedia modules and objects in the digital library system

NASA Astrophysics Data System (ADS)

Spangler, T. C.; Lamos, J. P.

2003-12-01

Over the past ten years of developing Web- and CD-ROM-based training materials, the Cooperative Program for Operational Meteorology, Education and Training (COMET) has created a unique archive of almost 10,000 multimedia objects and some 50 web based interactive multimedia modules on various aspects of weather and weather forecasting. These objects and modules, containing illustrations, photographs, animations,video sequences, audio files, are potentially a valuable resource for university faculty and students, forecasters, emergency managers, public school educators, and other individuals and groups needing such materials for educational use. The COMET Modules are available on the COMET educational web site http://www.meted.ucar.edu, and the COMET Multimedia Database (MMDB) makes a collection of the multimedia objects available in a searchable online database for viewing and download over the Internet. Some 3200 objects are already available at the MMDB Website: http://archive.comet.ucar.edu/moria/

SeaWiFS Science Algorithm Flow Chart

NASA Technical Reports Server (NTRS)

Darzi, Michael

1998-01-01

This flow chart describes the baseline science algorithms for the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) Data Processing System (SDPS). As such, it includes only processing steps used in the generation of the operational products that are archived by NASA's Goddard Space Flight Center (GSFC) Distributed Active Archive Center (DAAC). It is meant to provide the reader with a basic understanding of the scientific algorithm steps applied to SeaWiFS data. It does not include non-science steps, such as format conversions, and places the greatest emphasis on the geophysical calculations of the level-2 processing. Finally, the flow chart reflects the logic sequences and the conditional tests of the software so that it may be used to evaluate the fidelity of the implementation of the scientific algorithm. In many cases however, the chart may deviate from the details of the software implementation so as to simplify the presentation.

EBI metagenomics in 2016 - an expanding and evolving resource for the analysis and archiving of metagenomic data

PubMed Central

Mitchell, Alex; Bucchini, Francois; Cochrane, Guy; Denise, Hubert; Hoopen, Petra ten; Fraser, Matthew; Pesseat, Sebastien; Potter, Simon; Scheremetjew, Maxim; Sterk, Peter; Finn, Robert D.

2016-01-01

EBI metagenomics (https://www.ebi.ac.uk/metagenomics/) is a freely available hub for the analysis and archiving of metagenomic and metatranscriptomic data. Over the last 2 years, the resource has undergone rapid growth, with an increase of over five-fold in the number of processed samples and consequently represents one of the largest resources of analysed shotgun metagenomes. Here, we report the status of the resource in 2016 and give an overview of new developments. In particular, we describe updates to data content, a complete overhaul of the analysis pipeline, streamlining of data presentation via the website and the development of a new web based tool to compare functional analyses of sequence runs within a study. We also highlight two of the higher profile projects that have been analysed using the resource in the last year: the oceanographic projects Ocean Sampling Day and Tara Oceans. PMID:26582919

DNA Data Bank of Japan

PubMed Central

Mashima, Jun; Kodama, Yuichi; Fujisawa, Takatomo; Katayama, Toshiaki; Okuda, Yoshihiro; Kaminuma, Eli; Ogasawara, Osamu; Okubo, Kousaku; Nakamura, Yasukazu; Takagi, Toshihisa

2017-01-01

The DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) has been providing public data services for thirty years (since 1987). We are collecting nucleotide sequence data from researchers as a member of the International Nucleotide Sequence Database Collaboration (INSDC, http://www.insdc.org), in collaboration with the US National Center for Biotechnology Information (NCBI) and European Bioinformatics Institute (EBI). The DDBJ Center also services Japanese Genotype-phenotype Archive (JGA), with the National Bioscience Database Center to collect human-subjected data from Japanese researchers. Here, we report our database activities for INSDC and JGA over the past year, and introduce retrieval and analytical services running on our supercomputer system and their recent modifications. Furthermore, with the Database Center for Life Science, the DDBJ Center improves semantic web technologies to integrate and to share biological data, for providing the RDF version of the sequence data. PMID:27924010

Segue: A Spectroscopic Survey of 240,000 Stars With g = 14-20

DTIC Science & Technology

2009-05-01

24 Research School of Astronomy and Astrophysics, Australian National University, Weston, ACT 2611, Australia 25 Lawrence Berkeley National...main-sequence and evolved objects, with the goal of studying the kinematics and populations of our Galaxy and its halo. The spectra are clustered in 212...SEGUE Survey is the subject of this paper . The pro- cessed, searchable data archive from SEGUE was made publicly available in the Fall of 2008 as part

Advanced Development of TIES-Enhancing Access to Tissue for Cancer Research | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

Archived human tissues are an essential resource for translational research. Formalin-fixed, paraffin embedded (FFPE) tissues from cancer patients are used in a wide range of assays, including RT-PCR, SNP profiling, multiplex biomarkers, imaging biomarkers, targeted exome, whole exome, and whole genome sequencing. Remainder FFPE tissues generated during patient care are ‘retrospective'; use of these tissues under specific conditions does not require consent.

Trace Elements Affect Methanogenic Activity and Diversity in Enrichments from Subsurface Coal Bed Produced Water

PubMed Central

Ünal, Burcu; Perry, Verlin Ryan; Sheth, Mili; Gomez-Alvarez, Vicente; Chin, Kuk-Jeong; Nüsslein, Klaus

2012-01-01

Microbial methane from coal beds accounts for a significant and growing percentage of natural gas worldwide. Our knowledge of physical and geochemical factors regulating methanogenesis is still in its infancy. We hypothesized that in these closed systems, trace elements (as micronutrients) are a limiting factor for methanogenic growth and activity. Trace elements are essential components of enzymes or cofactors of metabolic pathways associated with methanogenesis. This study examined the effects of eight trace elements (iron, nickel, cobalt, molybdenum, zinc, manganese, boron, and copper) on methane production, on mcrA transcript levels, and on methanogenic community structure in enrichment cultures obtained from coal bed methane (CBM) well produced water samples from the Powder River Basin, Wyoming. Methane production was shown to be limited both by a lack of additional trace elements as well as by the addition of an overly concentrated trace element mixture. Addition of trace elements at concentrations optimized for standard media enhanced methane production by 37%. After 7 days of incubation, the levels of mcrA transcripts in enrichment cultures with trace element amendment were much higher than in cultures without amendment. Transcript levels of mcrA correlated positively with elevated rates of methane production in supplemented enrichments (R2 = 0.95). Metabolically active methanogens, identified by clone sequences of mcrA mRNA retrieved from enrichment cultures, were closely related to Methanobacterium subterraneum and Methanobacterium formicicum. Enrichment cultures were dominated by M. subterraneum and had slightly higher predicted methanogenic richness, but less diversity than enrichment cultures without amendments. These results suggest that varying concentrations of trace elements in produced water from different subsurface coal wells may cause changing levels of CBM production and alter the composition of the active methanogenic community. PMID:22590465

Geoseq: a tool for dissecting deep-sequencing datasets.

PubMed

Gurtowski, James; Cancio, Anthony; Shah, Hardik; Levovitz, Chaya; George, Ajish; Homann, Robert; Sachidanandam, Ravi

2010-10-12

Datasets generated on deep-sequencing platforms have been deposited in various public repositories such as the Gene Expression Omnibus (GEO), Sequence Read Archive (SRA) hosted by the NCBI, or the DNA Data Bank of Japan (ddbj). Despite being rich data sources, they have not been used much due to the difficulty in locating and analyzing datasets of interest. Geoseq http://geoseq.mssm.edu provides a new method of analyzing short reads from deep sequencing experiments. Instead of mapping the reads to reference genomes or sequences, Geoseq maps a reference sequence against the sequencing data. It is web-based, and holds pre-computed data from public libraries. The analysis reduces the input sequence to tiles and measures the coverage of each tile in a sequence library through the use of suffix arrays. The user can upload custom target sequences or use gene/miRNA names for the search and get back results as plots and spreadsheet files. Geoseq organizes the public sequencing data using a controlled vocabulary, allowing identification of relevant libraries by organism, tissue and type of experiment. Analysis of small sets of sequences against deep-sequencing datasets, as well as identification of public datasets of interest, is simplified by Geoseq. We applied Geoseq to, a) identify differential isoform expression in mRNA-seq datasets, b) identify miRNAs (microRNAs) in libraries, and identify mature and star sequences in miRNAS and c) to identify potentially mis-annotated miRNAs. The ease of using Geoseq for these analyses suggests its utility and uniqueness as an analysis tool.

The ability of human nuclear DNA to cause false positive low-abundance heteroplasmy calls varies across the mitochondrial genome.

PubMed

Albayrak, Levent; Khanipov, Kamil; Pimenova, Maria; Golovko, George; Rojas, Mark; Pavlidis, Ioannis; Chumakov, Sergei; Aguilar, Gerardo; Chávez, Arturo; Widger, William R; Fofanov, Yuriy

2016-12-12

Low-abundance mutations in mitochondrial populations (mutations with minor allele frequency ≤ 1%), are associated with cancer, aging, and neurodegenerative disorders. While recent progress in high-throughput sequencing technology has significantly improved the heteroplasmy identification process, the ability of this technology to detect low-abundance mutations can be affected by the presence of similar sequences originating from nuclear DNA (nDNA). To determine to what extent nDNA can cause false positive low-abundance heteroplasmy calls, we have identified mitochondrial locations of all subsequences that are common or similar (one mismatch allowed) between nDNA and mitochondrial DNA (mtDNA). Performed analysis revealed up to a 25-fold variation in the lengths of longest common and longest similar (one mismatch allowed) subsequences across the mitochondrial genome. The size of the longest subsequences shared between nDNA and mtDNA in several regions of the mitochondrial genome were found to be as low as 11 bases, which not only allows using these regions to design new, very specific PCR primers, but also supports the hypothesis of the non-random introduction of mtDNA into the human nuclear DNA. Analysis of the mitochondrial locations of the subsequences shared between nDNA and mtDNA suggested that even very short (36 bases) single-end sequencing reads can be used to identify low-abundance variation in 20.4% of the mitochondrial genome. For longer (76 and 150 bases) reads, the proportion of the mitochondrial genome where nDNA presence will not interfere found to be 44.5 and 67.9%, when low-abundance mutations at 100% of locations can be identified using 417 bases long single reads. This observation suggests that the analysis of low-abundance variations in mitochondria population can be extended to a variety of large data collections such as NCBI Sequence Read Archive, European Nucleotide Archive, The Cancer Genome Atlas, and International Cancer Genome Consortium.

An improved chronology for the Lateglacial palaeoenvironmental record of Lake Haemelsee, Germany: challenges for independent site comparisons

NASA Astrophysics Data System (ADS)

Lane, Christine; Brauer, Achim; Ramsey Christopher, Bronk; Engels, Stefan; Haliuc, Aritina; Hoek, Wim; Hubay, Katalin; Jones, Gwydion; Sachse, Dirk; Staff, Richard; Turner, Falko; Wagner-Cremer, Frederike

2016-04-01

Exploring temporal and spatial variability of environmental response to climatic changes requires the comparison of widespread palaeoenvironmental sequences on their own, independently-derived, age models. High precision age-models can be constructed using statistical methods to combine absolute and relative age estimates measured using a range of techniques. Such an approach may help to highlight otherwise unrecognised uncertainties, where a single dating method has been applied in isolation. Radiocarbon dating, tephrochronology and varve counting have been combined within a Bayesian depositional model to build a chronology for a sediment sequence from Lake Haemelsee (Northern Germany) that continuously covers the entire Lateglacial and early Holocene. Each of the dating techniques used brought its own challenges. Radiocarbon dates provide the only absolute ages measured directly in the record, however a low macrofossil content led to small sample sizes and a limited number of low precision dates. A floating varved interval provided restricted but very precise relative dating for sediments covering the Allerød to Younger Dryas transition. Well-spaced, visible and crypto- tephra layers, including the widespread Laacher See , Vedde Ash, Askja-S and Saksunarvatn tephra layers, allow absolute ages for the tephra layers established in other locations to be imported into the Haemelsee sequence. These layers also provide multiple tie-lines that allow the Haemelsee sequences to be directly compared at particular moments in time, and within particular intervals, to other important Lateglacial archives. However, selecting the "best" published tephra ages to use in the Haemelsee age model is not simple and risks biasing comparison of the palaeoenvironmental record to fit one or another comparative archive. Here we investigate the use of multiple age models for the Haemelsee record, in order to retain an independent approach to investigating the environmental transitions of the Lateglacial to Early Holocene.

Intra-genotypic Diversity of Archival G4P[8] Human Rotaviruses from Washington, DC

PubMed Central

McDonald, Sarah M.; Davis, Kristin; McAllen, John K.; Spiro, David J.; Patton, John T.

2011-01-01

Group A human rotaviruses (RVs) remain the most frequently detected viral agents associated with acute gastroenteritis in infants and young children. Despite their medical importance, relatively few complete genome sequences have been determined for commonly circulating G/P-type strains (i.e., G1P[8], G2P[4], G3P[8], G4P[8], and G9P[8]). In the current study, we sequenced the genomes of 11 G4P[8] isolates from stool specimens that were collected in Washington, DC during the years of 1974-1991. We found that the VP7-VP4-VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5/6-encoding genes of all 11 G4P[8] RVs have the genotypes of G4-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1. By constructing phylogenetic trees for each gene, extensive intra-genotypic diversity was revealed among the G4P[8] RVs, and new sub-genotype gene alleles were identified. Several of these alleles are nearly identical to those of G3P[8] isolates previously sequenced from this same Washington, DC collection, strongly suggesting that the RVs underwent gene reassortment. On the other hand, we observed that some G4P[8] RVs exhibit completely different allele-based genome constellations, despite being collected during the same epidemic season; there was no evidence of gene reassortment between these strains. This observation extends our previous findings and supports the notion that stable, genetically-distinct clades of human RVs with the same G/P-type can co-circulate in a community. Interestingly, the sub-genotype gene alleles found in some of the DC RVs share a close evolutionary relationship with genes of more contemporary human strains. Thus, archival human RVs sequenced in this study might represent evolutionary precursors to modern-day strains. PMID:21712102

Distinguishing the genotype 1 genes and proteins of human Wa-like rotaviruses vs. porcine rotaviruses

PubMed Central

Silva, Fernanda D.F.; Gregori, F.; McDonald, Sarah M.

2016-01-01

Group A rotaviruses (RVAs) are 11-segmented, double-stranded RNA viruses and important causes of gastroenteritis in the young of many animal species. Previous studies have suggested that human Wa-like RVAs share a close evolutionary relationship with porcine RVAs. Specifically, the VP1-VP3 and NSP2-5/6 genes of these viruses are usually classified as genotype 1 with >81% nucleotide sequence identity. Yet, it remains unknown whether the genotype 1 genes and proteins of human Wa-like strains are distinguishable from those of porcine strains. To investigate this, we performed comprehensive bioinformatic analyses using all known genotype 1 gene sequences. The RVAs analyzed represent wildtype strains isolated from humans or pigs at various geographical locations during the years of 2004–2013, including 11 newly-sequenced porcine RVAs from Brazil. We also analyzed archival strains that were isolated during the years of 1977–1992 as well as atypical strains involved in inter-species transmission between humans and pigs. We found that, in general, the genotype 1 genes of typical modern human Wa-like RVAs clustered together in phylogenetic trees and were separate from those of typical modern porcine RVAs. The only exception was for the NSP5/6 gene, which showed no host-specific phylogenetic clustering. Using amino acid sequence alignments, we identified 34 positions that differentiated the VP1-VP3, NSP2, and NSP3 genotype 1 proteins of typical modern human Wa-like RVAs versus typical modern porcine RVAs and documented how these positions vary in the archival/unusual isolates. No host-specific amino acid positions were identified for NSP4, NSP5, or NSP6. Altogether, the results of this study support the notion that human Wa-like RVAs and porcine RVAs are evolutionarily related, but indicate that some of their genotype 1 genes and proteins have diverged over time possibly as a reflection of sequestered replication and protein co-adaptation in their respective hosts. PMID:27180895

Trace metal (Mg/Ca and Sr/Ca) analyses of single coccoliths by Secondary Ion Mass Spectrometry

NASA Astrophysics Data System (ADS)

Prentice, Katy; Jones, Tom Dunkley; Lees, Jackie; Young, Jeremy; Bown, Paul; Langer, Gerald; Fearn, Sarah; EIMF

2014-12-01

Here we present the first multi-species comparison of modern and fossil coccolith trace metal data obtained from single liths. We present both trace metal analyses (Sr, Ca, Mg and Al) and distribution maps of individual Paleogene fossil coccoliths obtained by Secondary Ion Mass Spectrometry (SIMS). We use this data to determine the effects of variable coccolith preservation and diagenetic calcite overgrowths on the recorded concentrations of strontium and magnesium in coccolith calcite. The analysis of coccoliths from deep-ocean sediments spanning the Eocene/Oligocene transition demonstrates that primary coccolith calcite is resistant to the neomorphism that is common in planktonic foraminifera from similar depositional environments. Instead, where present, diagenetic calcite forms distinct overgrowths over primary coccolith calcite rather than replacing this calcite. Diagenetic overgrowths on coccoliths are easily distinguished in SIMS analyses on the basis of relatively higher Mg and lower Sr concentrations than co-occurring primary coccolith calcite. This interpretation is confirmed by the comparable SIMS analyses of modern cultured coccoliths of Coccolithus braarudii. Further, with diagenetic calcite overgrowth being the principle source of bias in coccolith-based geochemical records, we infer that lithologies with lower carbonate content, deposited below the palaeo-lysocline, are more likely to produce geochemical records dominated by primary coccolith calcite than carbonate-rich sediments where overgrowth is ubiquitous. The preservation of primary coccolith carbonate in low-carbonate lithologies thus provides a reliable geochemical archive where planktonic foraminifera are absent or have undergone neomorphism.

Continuous, Large-Scale Processing of Seismic Archives for High-Resolution Monitoring of Seismic Activity and Seismogenic Properties

NASA Astrophysics Data System (ADS)

Waldhauser, F.; Schaff, D. P.

2012-12-01

Archives of digital seismic data recorded by seismometer networks around the world have grown tremendously over the last several decades helped by the deployment of seismic stations and their continued operation within the framework of monitoring earthquake activity and verification of the Nuclear Test-Ban Treaty. We show results from our continuing effort in developing efficient waveform cross-correlation and double-difference analysis methods for the large-scale processing of regional and global seismic archives to improve existing earthquake parameter estimates, detect seismic events with magnitudes below current detection thresholds, and improve real-time monitoring procedures. We demonstrate the performance of these algorithms as applied to the 28-year long seismic archive of the Northern California Seismic Network. The tools enable the computation of periodic updates of a high-resolution earthquake catalog of currently over 500,000 earthquakes using simultaneous double-difference inversions, achieving up to three orders of magnitude resolution improvement over existing hypocenter locations. This catalog, together with associated metadata, form the underlying relational database for a real-time double-difference scheme, DDRT, which rapidly computes high-precision correlation times and hypocenter locations of new events with respect to the background archive (http://ddrt.ldeo.columbia.edu). The DDRT system facilitates near-real-time seismicity analysis, including the ability to search at an unprecedented resolution for spatio-temporal changes in seismogenic properties. In areas with continuously recording stations, we show that a detector built around a scaled cross-correlation function can lower the detection threshold by one magnitude unit compared to the STA/LTA based detector employed at the network. This leads to increased event density, which in turn pushes the resolution capability of our location algorithms. On a global scale, we are currently building the computational framework for double-difference processing the combined parametric and waveform archives of the ISC, NEIC, and IRIS with over three million recorded earthquakes worldwide. Since our methods are scalable and run on inexpensive Beowulf clusters, periodic re-analysis of such archives may thus become a routine procedure to continuously improve resolution in existing global earthquake catalogs. Results from subduction zones and aftershock sequences of recent great earthquakes demonstrate the considerable social and economic impact that high-resolution images of active faults, when available in real-time, will have in the prompt evaluation and mitigation of seismic hazards. These results also highlight the need for consistent long-term seismic monitoring and archiving of records.

Frequency of the first feature in action sequences influences feature binding.

PubMed

Mattson, Paul S; Fournier, Lisa R; Behmer, Lawrence P

2012-10-01

We investigated whether binding among perception and action feature codes is a preliminary step toward creating a more durable memory trace of an action event. If so, increasing the frequency of a particular event (e.g., a stimulus requiring a movement with the left or right hand in an up or down direction) should increase the strength and speed of feature binding for this event. The results from two experiments, using a partial-repetition paradigm, confirmed that feature binding increased in strength and/or occurred earlier for a high-frequency (e.g., left hand moving up) than for a low-frequency (e.g., right hand moving down) event. Moreover, increasing the frequency of the first-specified feature in the action sequence alone (e.g., "left" hand) increased the strength and/or speed of action feature binding (e.g., between the "left" hand and movement in an "up" or "down" direction). The latter finding suggests an update to the theory of event coding, as not all features in the action sequence equally determine binding strength. We conclude that action planning involves serial binding of features in the order of action feature execution (i.e., associations among features are not bidirectional but are directional), which can lead to a more durable memory trace. This is consistent with physiological evidence suggesting that serial order is preserved in an action plan executed from memory and that the first feature in the action sequence may be critical in preserving this serial order.

Crystallochemistry and origin of pyroxenes in komatiites

NASA Astrophysics Data System (ADS)

Bouquain, Sebastien; Arndt, N. T.; Hellebrand, E.; Faure, F.

2009-11-01

We present a detailed mineralogical and major- and trace-element study of pyroxenes in two Archean komatiitic flows in Alexo, Canada. The pyroxenes in spinifex-textured lavas commonly are zoned with cores of magnesian pigeonite and rims of augite. Concentrations of incompatible trace elements are low in pigeonite and jump to higher values in the augite mantles, a variation that can be modelled using accepted partition coefficients and assuming crystallization from komatiitic liquids. Crystallization sequences are very different in different parts of both flows. In the flow top, the sequence is olivine followed by augite: deeper in the spinifex sequence, pigeonite crystallizes after olivine, followed by augite; in lower cumulates, orthopyroxene or augite accompany olivine. In spinifex lavas, pigeonite crystallizes sooner than would be predicted on the basis of equilibrium phase relations. We propose that contrasting crystallization sequences depend on the position in the flow and on the conditions of crystal growth. In the flowtop, rapid cooling causes quench crystallization. Deeper in the spinifex layer, constrained growth in a thermal gradient, perhaps augmented by Soret differentiation, accounts for the early crystallization of pigeonite. The cumulus minerals represent a near-equilibrium assemblage. Augites in Al-undepleted Archean komatiites in various localities in Canada and Zimbabwe have high moderate to high Wo contents but their Mg# (Mg/(Mg + Fe) are lower than in augites in komatiites from Barberton, South Africa. We attribute the combination of high Wo and high Mg# in Barberton rocks to the unusually high CaO/Al2O3 of these Al-depleted komatiites.

Incompleteness and limit of security theory of quantum key distribution

NASA Astrophysics Data System (ADS)

Hirota, Osamu; Murakami, Dan; Kato, Kentaro; Futami, Fumio

2012-10-01

It is claimed in the many papers that a trace distance: d guarantees the universal composition security in quantum key distribution (QKD) like BB84 protocol. In this introduction paper, at first, it is explicitly explained what is the main misconception in the claim of the unconditional security for QKD theory. In general terms, the cause of the misunderstanding on the security claim is the Lemma in the paper of Renner. It suggests that the generation of the perfect random key is assured by the probability (1-d), and its failure probability is d. Thus, it concludes that the generated key provides the perfect random key sequence when the protocol is success. So the QKD provides perfect secrecy to the one time pad. This is the reason for the composition claim. However, the quantity of the trace distance (or variational distance) is not the probability for such an event. If d is not small enough, always the generated key sequence is not uniform. Now one needs the reconstruction of the evaluation of the trace distance if one wants to use it. One should first go back to the indistinguishability theory in the computational complexity based, and to clarify the meaning of the value of the variational distance. In addition, the same analysis for the information theoretic case is necessary. The recent serial papers by H.P.Yuen have given the answer on such questions. In this paper, we show more concise description of Yuen's theory, and clarify that the upper bound theories for the trace distance by Tomamichel et al and Hayashi et al are constructed by the wrong reasoning of Renner and it is unsuitable as the security analysis. Finally, we introduce a new macroscopic quantum communication to replace Q-bit QKD.

Dakota sandstone facies, western Oklahoma panhandle

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

Atalik, E.; Mansfield, C.F.

The Cretaceous Dakota Sandstone in Cimarron County comprised three sandstone units and intervening mudrocks; it overlies the Kiowa Shale Member of the Purgatoire Formation. Deposits include shoreface, beach (foreshore) and dune, estuarine and tidal channel, marine marginal bay and swamp/marsh in a generally progradational sequences associated with marine regression in the Western Interior. The shoreface sand, characterized by ripple lamination, bioturbation and the trace fossils Teichichnus and Thalassinoides, is fine-grained, 5-10 m (15-30 ft) thick and grades into the underlying Kiowa Shale. Beach and associated dune deposits are 2-5 m (6-16 ft) thick, medium to fine-grained, medium to thick-bedded, tabular-planarmore » cross-bedded, and lenticular; cross-bed paleocurrent headings are northeasterly and northwesterly. Estuarine channel deposits are 3-5 m (10 to 16 ft) thick, trough to tabular-planar cross-bedded, and medium to coarse-grained with local conglomerate overlying the scoured base which commonly cuts into the Kiowa Shale or overlying shoreface sandstone; rip-up clasts and wood pieces are common but trace fossils are rare; southeasterly and southwesterly paleocurrents predominate. Tidal channel deposits are thinner (up to 2 m of 6 ft) and finer grained (medium to fine-grained) that the estuarine channel deposits; they occur within fine-grained sandstone and mudrock sequences, are trough cross-bedded, and commonly contain trace fossils (e.g., Skolithos) and wood fragments. Marine marginal (tidal flat or bay.) deposits comprise fine-grained sandstone, siltstone and interbedded shale, that are 1-3m (3-10 ft) thick with abundant burrows, small ripple marks, and parallel lamination. These grade into the fine to very fine-grained sandstones, siltstones, shales, and coals of the swamp/marsh deposits that are 1-5m (3-16 ft) thick and contain ripple marks, burrows, other trace fossils, and parallel lamination.« less

Ingestion of a carbonated beverage decreases lower esophageal sphincter pressure and increases frequency of transient lower esophageal sphincter relaxation in normal subjects.

PubMed

Shukla, Akash; Meshram, Megha; Gopan, Amrit; Ganjewar, Vaibhav; Kumar, Praveen; Bhatia, Shobna J

2012-06-01

Transient lower esophageal sphincter relaxation (tLESR) and decreased basal lower esophageal sphincter (LES) pressure are postulated mechanisms of gastroesophageal reflux (GER). There is conflicting evidence on the effect of carbonated drinks on lower esophageal sphincter function. This study was conducted to assess the effect of a carbonated beverage on tLESR and LES pressure. High resolution manometry tracings (16 channel water-perfused, Trace 1.2, Hebbard, Australia) were obtained in 18 healthy volunteers (6 men) for 30 min each at baseline, and after 200 mL of chilled potable water and 200 mL of chilled carbonated cola drink (Pepsi [Pepsico India Ltd]). The sequence of administration of the drinks was determined by random number method generated by a computer. The analysis of tracings was done using TRACE 1.2 software by a physician who was unaware of the sequence of administration of fluids. The mean (SD) age of the participant was 37.3 (12.9) years. The median (range) frequency of tLESr was higher after the carbonated beverage (10.5 [0-26]) as compared to baseline (0 [0-3], p = 0.005) as well as after water (1 [0-14], p = 0.010). The LES pressure decreased after ingestion of the carbonated beverage (18.5 [11-37] mmHg) compared to baseline (40.5 [25-66] mmHg, p = 0.0001) and after water (34 [15-67] mmHg, p = 0.003). Gastric pressure was not different in the three groups. Ingestion of a carbonated beverage increases tLESr and lowers LES pressure in healthy subjects.

Contour Tracking in Echocardiographic Sequences via Sparse Representation and Dictionary Learning

PubMed Central

Huang, Xiaojie; Dione, Donald P.; Compas, Colin B.; Papademetris, Xenophon; Lin, Ben A.; Bregasi, Alda; Sinusas, Albert J.; Staib, Lawrence H.; Duncan, James S.

2013-01-01

This paper presents a dynamical appearance model based on sparse representation and dictionary learning for tracking both endocardial and epicardial contours of the left ventricle in echocardiographic sequences. Instead of learning offline spatiotemporal priors from databases, we exploit the inherent spatiotemporal coherence of individual data to constraint cardiac contour estimation. The contour tracker is initialized with a manual tracing of the first frame. It employs multiscale sparse representation of local image appearance and learns online multiscale appearance dictionaries in a boosting framework as the image sequence is segmented frame-by-frame sequentially. The weights of multiscale appearance dictionaries are optimized automatically. Our region-based level set segmentation integrates a spectrum of complementary multilevel information including intensity, multiscale local appearance, and dynamical shape prediction. The approach is validated on twenty-six 4D canine echocardiographic images acquired from both healthy and post-infarct canines. The segmentation results agree well with expert manual tracings. The ejection fraction estimates also show good agreement with manual results. Advantages of our approach are demonstrated by comparisons with a conventional pure intensity model, a registration-based contour tracker, and a state-of-the-art database-dependent offline dynamical shape model. We also demonstrate the feasibility of clinical application by applying the method to four 4D human data sets. PMID:24292554

Using whole genome sequencing to study American foulbrood epidemiology in honeybees

PubMed Central

Ågren, Joakim; Schäfer, Marc Oliver

2017-01-01

American foulbrood (AFB), caused by Paenibacillus larvae, is a devastating disease in honeybees. In most countries, the disease is controlled through compulsory burning of symptomatic colonies causing major economic losses in apiculture. The pathogen is endemic to honeybees world-wide and is readily transmitted via the movement of hive equipment or bees. Molecular epidemiology of AFB currently largely relies on placing isolates in one of four ERIC-genotypes. However, a more powerful alternative is multi-locus sequence typing (MLST) using whole-genome sequencing (WGS), which allows for high-resolution studies of disease outbreaks. To evaluate WGS as a tool for AFB-epidemiology, we applied core genome MLST (cgMLST) on isolates from a recent outbreak of AFB in Sweden. The high resolution of the cgMLST allowed different bacterial clones involved in the disease outbreak to be identified and to trace the source of infection. The source was found to be a beekeeper who had sold bees to two other beekeepers, proving the epidemiological link between them. No such conclusion could have been made using conventional MLST or ERIC-typing. This is the first time that WGS has been used to study the epidemiology of AFB. The results show that the technique is very powerful for high-resolution tracing of AFB-outbreaks. PMID:29140998

Tori sequences as remnants of multiple accreting periods of Kerr SMBHs

NASA Astrophysics Data System (ADS)

Pugliese, D.; Stuchlík, Z.

2018-03-01

Super-massive black holes (SMBHs) hosted in active galactic nuclei (AGNs) can be characterized by multi-accreting periods as the attractors interact with the environment during their life-time. These multi-accretion episodes should leave traces in the matter orbiting the attractor. Counterrotating and even misaligned structures orbiting around the SMBHs would be consequences of these episodes. Our task in this work is to consider situations where such accretions occur and to trace their remnants represented by several toroidal accreting fluids, corotating or counterrotating relative to the central Kerr attractor, and created in various regimes during the evolution of matter configurations around SMBHs. We focus particularly on the emergence of matter instabilities, i.e., tori collisions, accretion onto the central Kerr black hole, or creation of jet-like structures (proto-jets). Each orbiting configuration is governed by the general relativistic hydrodynamic Boyer condition of equilibrium configurations of rotating perfect fluid. We prove that sequences of configurations and hot points, where an instability occurs, characterize the Kerr SMBHs, depending mainly on their spin-mass ratios. The occurrence of tori accretion or collision are strongly constrained by the fluid rotation with respect to the central black hole and the relative rotation with respect to each other. Our investigation provides characteristic of attractors where traces of multi-accreting episodes can be found and observed.

Reproducibility of Illumina platform deep sequencing errors allows accurate determination of DNA barcodes in cells.

PubMed

Beltman, Joost B; Urbanus, Jos; Velds, Arno; van Rooij, Nienke; Rohr, Jan C; Naik, Shalin H; Schumacher, Ton N

2016-04-02

Next generation sequencing (NGS) of amplified DNA is a powerful tool to describe genetic heterogeneity within cell populations that can both be used to investigate the clonal structure of cell populations and to perform genetic lineage tracing. For applications in which both abundant and rare sequences are biologically relevant, the relatively high error rate of NGS techniques complicates data analysis, as it is difficult to distinguish rare true sequences from spurious sequences that are generated by PCR or sequencing errors. This issue, for instance, applies to cellular barcoding strategies that aim to follow the amount and type of offspring of single cells, by supplying these with unique heritable DNA tags. Here, we use genetic barcoding data from the Illumina HiSeq platform to show that straightforward read threshold-based filtering of data is typically insufficient to filter out spurious barcodes. Importantly, we demonstrate that specific sequencing errors occur at an approximately constant rate across different samples that are sequenced in parallel. We exploit this observation by developing a novel approach to filter out spurious sequences. Application of our new method demonstrates its value in the identification of true sequences amongst spurious sequences in biological data sets.

Salt lake Laguna de Fuente de Piedra (S-Spain) as Late Quaternary palaeoenvironmental archive

NASA Astrophysics Data System (ADS)

Höbig, Nicole; Melles, Martin; Reicherter, Klaus

2014-05-01

This study deals with Late Quaternary palaeoenvironmental variability in Iberia reconstructed from terrestrial archives. In southern Iberia, endorheic basins of the Betic Cordilleras are relatively common and contain salt or fresh-water lakes due to subsurface dissolution of Triassic evaporites. Such precipitation or ground-water fed lakes (called Lagunas in Spanish) are vulnerable to changes in hydrology, climate or anthropogenic modifications. The largest Spanish salt lake, Laguna de Fuente de Piedra (Antequera region, S-Spain), has been investigated and serves as a palaeoenvironmental archive for the Late Pleistocene to Holocene time interval. Several sediment cores taken during drilling campaigns in 2012 and 2013 have revealed sedimentary sequences (up to 14 m length) along the shoreline. A multi-proxy study, including sedimentology, geochemistry and physical properties (magnetic susceptibility) has been performed on the cores. The sedimentary history is highly variable: several decimetre thick silty variegated clay deposits, laminated evaporites, and even few-centimetre thick massive gypsum crystals (i.e., selenites). XRF analysis was focussed on valuable palaeoclimatic proxies (e.g., S, Zr, Ti, and element ratios) to identify the composition and provenance of the sediments and to delineate palaeoenvironmental conditions. First age control has been realized by AMS-radiocarbon dating. The records start with approximately 2-3 m Holocene deposits and reach back to the middle of MIS 3 (GS-3). The sequences contain changes in sedimentation rates as well as colour changes, which can be summarized as brownish-beige deposits at the top and more greenish-grey deposits below as well as highly variegated lamination and selenites below ca. 6 m depth. The Younger Dryas, Bølling/Allerød, and the so-called Mystery Interval/Last Glacial Maximum have presumably been identified in the sediment cores and aligned to other climate records. In general, the cores of the Laguna de Fuente de Piedra show cyclic deposition including evaporitic sequences throughout the Holocene and Late Pleistocene, indicating higher fluxes and reworking of organic/inorganic carbon as well as other indicative proxy elements like Ti, Zr and Ca/Sr ratio during Late Pleistocene times. In order to achieve a better understanding of the palaeoenvironmental history in the study area further studies are planned which encompass biological/palaeontological indicators (e.g., pollen, diatoms) as well as another geochemical isotopic techniques on evaporitic deposits such as fluid inclusion analysis.

funRNA: a fungi-centered genomics platform for genes encoding key components of RNAi.

PubMed

Choi, Jaeyoung; Kim, Ki-Tae; Jeon, Jongbum; Wu, Jiayao; Song, Hyeunjeong; Asiegbu, Fred O; Lee, Yong-Hwan

2014-01-01

RNA interference (RNAi) is involved in genome defense as well as diverse cellular, developmental, and physiological processes. Key components of RNAi are Argonaute, Dicer, and RNA-dependent RNA polymerase (RdRP), which have been functionally characterized mainly in model organisms. The key components are believed to exist throughout eukaryotes; however, there is no systematic platform for archiving and dissecting these important gene families. In addition, few fungi have been studied to date, limiting our understanding of RNAi in fungi. Here we present funRNA http://funrna.riceblast.snu.ac.kr/, a fungal kingdom-wide comparative genomics platform for putative genes encoding Argonaute, Dicer, and RdRP. To identify and archive genes encoding the abovementioned key components, protein domain profiles were determined from reference sequences obtained from UniProtKB/SwissProt. The domain profiles were searched using fungal, metazoan, and plant genomes, as well as bacterial and archaeal genomes. 1,163, 442, and 678 genes encoding Argonaute, Dicer, and RdRP, respectively, were predicted. Based on the identification results, active site variation of Argonaute, diversification of Dicer, and sequence analysis of RdRP were discussed in a fungus-oriented manner. funRNA provides results from diverse bioinformatics programs and job submission forms for BLAST, BLASTMatrix, and ClustalW. Furthermore, sequence collections created in funRNA are synced with several gene family analysis portals and databases, offering further analysis opportunities. funRNA provides identification results from a broad taxonomic range and diverse analysis functions, and could be used in diverse comparative and evolutionary studies. It could serve as a versatile genomics workbench for key components of RNAi.

Lateglacial-Holocene abrupt vegetation changes at Lago Trifoglietti in Calabria, Southern Italy: The setting of ecosystems in a refugial zone

NASA Astrophysics Data System (ADS)

Beaulieu, Jacques-Louis de; Brugiapaglia, Elisabetta; Joannin, Sébastien; Guiter, Frédéric; Zanchetta, Giovanni; Wulf, Sabine; Peyron, Odile; Bernardo, Liliana; Didier, Julien; Stock, Agnès; Rius, Damien; Magny, Michel

2017-02-01

Retrospective science such as palaeoecology deeply depends on the preservation of archives in sensitive places. As an example, mountains of medium altitude from Mediterranean peninsulas have long been identified by biogeographers as refuges zones allowing the survival of European temperate taxa during the ice ages, but archives to validate this hypothesis are scarce, especially in Southern Italy. Here we present a new sequence from Lago Trifoglietti (1048 m a.s.l.) in the Calabrian Mountains, which covers the Late Glacial Interstadial (LGI, corresponding to the Bölling-Alleröd period in northern-central Europe) and the transition to the Holocene. The independent chronology based on seven radiocarbon dates is supported by the evidence of three tephra layers already identified in other regional sequences. During the LGI, besides the high diversity of non arboreal pollen grains, a great number of pollens of temperate forest trees are present or abundant (mostly deciduous oaks and fir). These assemblages suggest that the site was above but not far from the upper limit of diversified woodland stands. They confirm a local survival during the last glacial. The Younger Dryas is not marked by major changes, and oak percentages are even higher, suggesting a resilient expansion at lower altitude. Surprisingly the site remains above the timberline until an aridity crisis centered at 11,100 cal 14C yr PB, which is correlated with the Preboreal Oscillation (PBO). This event is immediately followed by the local settlement of a dense fir and beech forest around the lake. A comparison with other Italian key sequences aims at explaining the climate forcing factors that governed this original vegetation dynamic. Further investigations using additional proxies are needed for a more robust climate reconstruction.

VizieR Online Data Catalog: Far-UV spectral atlas of O-type stars (Smith, 2012)

NASA Astrophysics Data System (ADS)

Smith, M. A.

2012-10-01

In this paper, we present a spectral atlas covering the wavelength interval 930-1188Å for O2-O9.5 stars using Far-Ultraviolet Spectroscopic Explorer archival data. The stars selected for the atlas were drawn from three populations: Galactic main-sequence (classes III-V) stars, supergiants, and main-sequence stars in the Magellanic Clouds, which have low metallicities. For several of these stars, we have prepared FITS files comprised of pairs of merged spectra for user access via the Multimission Archive at Space Telescope (MAST). We chose spectra from the first population with spectral types O4, O5, O6, O7, O8, and O9.5 and used them to compile tables and figures with identifications of all possible atmospheric and interstellar medium lines in the region 949-1188Å. Our identified line totals for these six representative spectra are 821 (500), 992 (663), 1077 (749), 1178 (847), 1359 (1001), and 1798 (1392) lines, respectively, where the numbers in parentheses are the totals of lines formed in the atmospheres, according to spectral synthesis models. The total number of unique atmospheric identifications for the six main-sequence O-star template spectra is 1792, whereas the number of atmospheric lines in common to these spectra is 300. The number of identified lines decreases toward earlier types (increasing effective temperature), while the percentages of "missed" features (unknown lines not predicted from our spectral syntheses) drop from a high of 8% at type B0.2, from our recently published B-star far-UV atlas (Cat. J/ApJS/186/175), to 1%-3% for type O spectra. The percentages of overpredicted lines are similar, despite their being much higher for B-star spectra. (4 data files).

Chemically Dissected Rotation Curves of the Galactic Bulge from Main-sequence Proper Motions

NASA Astrophysics Data System (ADS)

Clarkson, William I.; Calamida, Annalisa; Sahu, Kailash C.; Brown, Thomas M.; Gennaro, Mario; Avila, Roberto J.; Valenti, Jeff; Debattista, Victor P.; Rich, R. Michael; Minniti, Dante; Zoccali, Manuela; Aufdemberge, Emily R.

2018-05-01

We report results from an exploratory study implementing a new probe of Galactic evolution using archival Hubble Space Telescope imaging observations. Precise proper motions are combined with photometric relative metallicity and temperature indices, to produce the proper-motion rotation curves of the Galactic bulge separately for metal-poor and metal-rich main-sequence samples. This provides a “pencil-beam” complement to large-scale wide-field surveys, which to date have focused on the more traditional bright giant branch tracers. We find strong evidence that the Galactic bulge rotation curves drawn from “metal-rich” and “metal-poor” samples are indeed discrepant. The “metal-rich” sample shows greater rotation amplitude and a steeper gradient against line-of-sight distance, as well as possibly a stronger central concentration along the line of sight. This may represent a new detection of differing orbital anisotropy between metal-rich and metal-poor bulge objects. We also investigate selection effects that would be implied for the longitudinal proper-motion cut often used to isolate a “pure-bulge” sample. Extensive investigation of synthetic stellar populations suggests that instrumental and observational artifacts are unlikely to account for the observed rotation curve differences. Thus, proper-motion-based rotation curves can be used to probe chemodynamical correlations for main-sequence tracer stars, which are orders of magnitude more numerous in the Galactic bulge than the bright giant branch tracers. We discuss briefly the prospect of using this new tool to constrain detailed models of Galactic formation and evolution. Based on observations made with the NASA/ESA Hubble Space Telescope and obtained from the data archive at the Space Telescope Science Institute. STScI is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555.

High quality methylome-wide investigations through next-generation sequencing of DNA from a single archived dry blood spot

PubMed Central

Aberg, Karolina A.; Xie, Lin Y.; Nerella, Srilaxmi; Copeland, William E.; Costello, E. Jane; van den Oord, Edwin J.C.G.

2013-01-01

The potential importance of DNA methylation in the etiology of complex diseases has led to interest in the development of methylome-wide association studies (MWAS) aimed at interrogating all methylation sites in the human genome. When using blood as biomaterial for a MWAS the DNA is typically extracted directly from fresh or frozen whole blood that was collected via venous puncture. However, DNA extracted from dry blood spots may also be an alternative starting material. In the present study, we apply a methyl-CpG binding domain (MBD) protein enrichment-based technique in combination with next generation sequencing (MBD-seq) to assess the methylation status of the ~27 million CpGs in the human autosomal reference genome. We investigate eight methylomes using DNA from blood spots. This data are compared with 1,500 methylomes previously assayed with the same MBD-seq approach using DNA from whole blood. When investigating the sequence quality and the enrichment profile across biological features, we find that DNA extracted from blood spots gives comparable results with DNA extracted from whole blood. Only if the amount of starting material is ≤ 0.5µg DNA we observe a slight decrease in the assay performance. In conclusion, we show that high quality methylome-wide investigations using MBD-seq can be conducted in DNA extracted from archived dry blood spots without sacrificing quality and without bias in enrichment profile as long as the amount of starting material is sufficient. In general, the amount of DNA extracted from a single blood spot is sufficient for methylome-wide investigations with the MBD-seq approach. PMID:23644822

High quality methylome-wide investigations through next-generation sequencing of DNA from a single archived dry blood spot.

PubMed

Aberg, Karolina A; Xie, Lin Y; Nerella, Srilaxmi; Copeland, William E; Costello, E Jane; van den Oord, Edwin J C G

2013-05-01

The potential importance of DNA methylation in the etiology of complex diseases has led to interest in the development of methylome-wide association studies (MWAS) aimed at interrogating all methylation sites in the human genome. When using blood as biomaterial for a MWAS the DNA is typically extracted directly from fresh or frozen whole blood that was collected via venous puncture. However, DNA extracted from dry blood spots may also be an alternative starting material. In the present study, we apply a methyl-CpG binding domain (MBD) protein enrichment-based technique in combination with next generation sequencing (MBD-seq) to assess the methylation status of the ~27 million CpGs in the human autosomal reference genome. We investigate eight methylomes using DNA from blood spots. This data are compared with 1,500 methylomes previously assayed with the same MBD-seq approach using DNA from whole blood. When investigating the sequence quality and the enrichment profile across biological features, we find that DNA extracted from blood spots gives comparable results with DNA extracted from whole blood. Only if the amount of starting material is ≤ 0.5µg DNA we observe a slight decrease in the assay performance. In conclusion, we show that high quality methylome-wide investigations using MBD-seq can be conducted in DNA extracted from archived dry blood spots without sacrificing quality and without bias in enrichment profile as long as the amount of starting material is sufficient. In general, the amount of DNA extracted from a single blood spot is sufficient for methylome-wide investigations with the MBD-seq approach.

Robustness of Next Generation Sequencing on Older Formalin-Fixed Paraffin-Embedded Tissue

PubMed Central

Carrick, Danielle Mercatante; Mehaffey, Michele G.; Sachs, Michael C.; Altekruse, Sean; Camalier, Corinne; Chuaqui, Rodrigo; Cozen, Wendy; Das, Biswajit; Hernandez, Brenda Y.; Lih, Chih-Jian; Lynch, Charles F.; Makhlouf, Hala; McGregor, Paul; McShane, Lisa M.; Phillips Rohan, JoyAnn; Walsh, William D.; Williams, Paul M.; Gillanders, Elizabeth M.; Mechanic, Leah E.; Schully, Sheri D.

2015-01-01

Next Generation Sequencing (NGS) technologies are used to detect somatic mutations in tumors and study germ line variation. Most NGS studies use DNA isolated from whole blood or fresh frozen tissue. However, formalin-fixed paraffin-embedded (FFPE) tissues are one of the most widely available clinical specimens. Their potential utility as a source of DNA for NGS would greatly enhance population-based cancer studies. While preliminary studies suggest FFPE tissue may be used for NGS, the feasibility of using archived FFPE specimens in population based studies and the effect of storage time on these specimens needs to be determined. We conducted a study to determine whether DNA in archived FFPE high-grade ovarian serous adenocarcinomas from Surveillance, Epidemiology and End Results (SEER) registries Residual Tissue Repositories (RTR) was present in sufficient quantity and quality for NGS assays. Fifty-nine FFPE tissues, stored from 3 to 32 years, were obtained from three SEER RTR sites. DNA was extracted, quantified, quality assessed, and subjected to whole exome sequencing (WES). Following DNA extraction, 58 of 59 specimens (98%) yielded DNA and moved on to the library generation step followed by WES. Specimens stored for longer periods of time had significantly lower coverage of the target region (6% lower per 10 years, 95% CI: 3-10%) and lower average read depth (40x lower per 10 years, 95% CI: 18-60), although sufficient quality and quantity of WES data was obtained for data mining. Overall, 90% (53/59) of specimens provided usable NGS data regardless of storage time. This feasibility study demonstrates FFPE specimens acquired from SEER registries after varying lengths of storage time and under varying storage conditions are a promising source of DNA for NGS. PMID:26222067

Deep sequencing in library selection projects: what insight does it bring?

PubMed

Glanville, J; D'Angelo, S; Khan, T A; Reddy, S T; Naranjo, L; Ferrara, F; Bradbury, A R M

2015-08-01

High throughput sequencing is poised to change all aspects of the way antibodies and other binders are discovered and engineered. Millions of available sequence reads provide an unprecedented sampling depth able to guide the design and construction of effective, high quality naïve libraries containing tens of billions of unique molecules. Furthermore, during selections, high throughput sequencing enables quantitative tracing of enriched clones and position-specific guidance to amino acid variation under positive selection during antibody engineering. Successful application of the technologies relies on specific PCR reagent design, correct sequencing platform selection, and effective use of computational tools and statistical measures to remove error, identify antibodies, estimate diversity, and extract signatures of selection from the clone down to individual structural positions. Here we review these considerations and discuss some of the remaining challenges to the widespread adoption of the technology. Copyright © 2015 Elsevier Ltd. All rights reserved.

Deep sequencing in library selection projects: what insight does it bring?

PubMed Central

Glanville, J; D’Angelo, S; Khan, T.A.; Reddy, S. T.; Naranjo, L.; Ferrara, F.; Bradbury, A.R.M.

2015-01-01

High throughput sequencing is poised to change all aspects of the way antibodies and other binders are discovered and engineered. Millions of available sequence reads provide an unprecedented sampling depth able to guide the design and construction of effective, high quality naïve libraries containing tens of billions of unique molecules. Furthermore, during selections, high throughput sequencing enables quantitative tracing of enriched clones and position-specific guidance to amino acid variation under positive selection during antibody engineering. Successful application of the technologies relies on specific PCR reagent design, correct sequencing platform selection, and effective use of computational tools and statistical measures to remove error, identify antibodies, estimate diversity, and extract signatures of selection from the clone down to individual structural positions. Here we review these considerations and discuss some of the remaining challenges to the widespread adoption of the technology. PMID:26451649

Stratigraphy and depositional environments of Fox Hills Formation in Williston basin

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

Daly, D.J.

The Fox Hills Formation (Maestrichtian), representing part of a regressive wedge deposited during the withdrawal of the sea from the Western Interior at the close of the Cretaceous, consists of marginal marine strata transitional between the offshore deposits of the underlying Pierre Shale and the terrestrial deltaic and coastal deposits of the overlying Hell Creek Formation. An investigation of outcrops of the Fox Hills Formation along the western and southern flanks of the Williston basin and study of over 300 oil and gas well logs from the central part of the basin indicate that the formation can be divided bothmore » stratigraphically and areally. Stratigraphically, the Fox Hills can be divided into lower and upper sequences; the lower includes the Trail City and Timber Lake Members, and the upper sequence includes the Colgate Member in the west and the Iron Lightning and Linton Members in the east. Areally, the formation can be divided into a northeastern and western part, where the strata are 30-45 m thick and are dominated by the lower sequence, and into a southeastern area where both the lower and upper sequences are well developed in a section 80-130 m thick. Typically, the lower Fox Hills consists of upward-coarsening shoreface or delta-front sequences containing hummocky bedding and a limited suite of trace fossils, most notably Ophiomorpha. In the southeast, however, these strata are dominated by bar complexes, oriented northeast-southwest, composed of cross-bedded medium to very fine-grained sand with abundant trace and body fossils. The upper Fox Hills represents a variety of shoreface, deltaic, and channel environments. The strata of the Fox Hills Formation exhibit facies similar to those reported for Upper Cretaceous gas reservoirs in the northern Great Plains.« less

Core Genome Multilocus Sequence Typing Scheme for High-Resolution Typing of Enterococcus faecium

PubMed Central

de Been, Mark; Pinholt, Mette; Top, Janetta; Bletz, Stefan; van Schaik, Willem; Brouwer, Ellen; Rogers, Malbert; Kraat, Yvette; Bonten, Marc; Corander, Jukka; Westh, Henrik; Harmsen, Dag

2015-01-01

Enterococcus faecium, a common inhabitant of the human gut, has emerged in the last 2 decades as an important multidrug-resistant nosocomial pathogen. Since the start of the 21st century, multilocus sequence typing (MLST) has been used to study the molecular epidemiology of E. faecium. However, due to the use of a small number of genes, the resolution of MLST is limited. Whole-genome sequencing (WGS) now allows for high-resolution tracing of outbreaks, but current WGS-based approaches lack standardization, rendering them less suitable for interlaboratory prospective surveillance. To overcome this limitation, we developed a core genome MLST (cgMLST) scheme for E. faecium. cgMLST transfers genome-wide single nucleotide polymorphism (SNP) diversity into a standardized and portable allele numbering system that is far less computationally intensive than SNP-based analysis of WGS data. The E. faecium cgMLST scheme was built using 40 genome sequences that represented the diversity of the species. The scheme consists of 1,423 cgMLST target genes. To test the performance of the scheme, we performed WGS analysis of 103 outbreak isolates from five different hospitals in the Netherlands, Denmark, and Germany. The cgMLST scheme performed well in distinguishing between epidemiologically related and unrelated isolates, even between those that had the same sequence type (ST), which denotes the higher discriminatory power of this cgMLST scheme over that of conventional MLST. We also show that in terms of resolution, the performance of the E. faecium cgMLST scheme is equivalent to that of an SNP-based approach. In conclusion, the cgMLST scheme developed in this study facilitates rapid, standardized, and high-resolution tracing of E. faecium outbreaks. PMID:26400782

Core Genome Multilocus Sequence Typing Scheme for High- Resolution Typing of Enterococcus faecium.

PubMed

de Been, Mark; Pinholt, Mette; Top, Janetta; Bletz, Stefan; Mellmann, Alexander; van Schaik, Willem; Brouwer, Ellen; Rogers, Malbert; Kraat, Yvette; Bonten, Marc; Corander, Jukka; Westh, Henrik; Harmsen, Dag; Willems, Rob J L

2015-12-01

Enterococcus faecium, a common inhabitant of the human gut, has emerged in the last 2 decades as an important multidrug-resistant nosocomial pathogen. Since the start of the 21st century, multilocus sequence typing (MLST) has been used to study the molecular epidemiology of E. faecium. However, due to the use of a small number of genes, the resolution of MLST is limited. Whole-genome sequencing (WGS) now allows for high-resolution tracing of outbreaks, but current WGS-based approaches lack standardization, rendering them less suitable for interlaboratory prospective surveillance. To overcome this limitation, we developed a core genome MLST (cgMLST) scheme for E. faecium. cgMLST transfers genome-wide single nucleotide polymorphism(SNP) diversity into a standardized and portable allele numbering system that is far less computationally intensive than SNP-based analysis of WGS data. The E. faecium cgMLST scheme was built using 40 genome sequences that represented the diversity of the species. The scheme consists of 1,423 cgMLST target genes. To test the performance of the scheme, we performed WGS analysis of 103 outbreak isolates from five different hospitals in the Netherlands, Denmark, and Germany. The cgMLST scheme performed well in distinguishing between epidemiologically related and unrelated isolates, even between those that had the same sequence type (ST), which denotes the higher discriminatory power of this cgMLST scheme over that of conventional MLST. We also show that in terms of resolution, the performance of the E. faecium cgMLST scheme is equivalent to that of an SNP-based approach. In conclusion, the cgMLST scheme developed in this study facilitates rapid, standardized, and high-resolution tracing of E. faecium outbreaks.

Ultraviolet spectral morphology of the O stars. IV - The OB supergiant sequence

NASA Technical Reports Server (NTRS)

Walborn, Nolan R.; Nichols-Bohlin, Joy

1987-01-01

An atlas of 25 O3-B8 supergiant spectra in the wavelength ranges 1320-1580 A and 1620-1880 A is presented, based on high-resolution data from the IUE archives. The remarkably detailed relationship between the stellar-wind profiles and the optical spectral classifications throughout this sequence is emphasized. For instance, the (Si IV)/(C IV) ratio reverses between O4 and O6.5; and the B0, B0.5, and B0.7 Ia wind characteristics are each qualitatively unique and distinct from one another. The systematic behavior of nine stellar-wind features with ionization potentials ranging from 114 to 19 eV is summarized as a function of advancing spectral type.

Molecular evidence of simian virus 40 infections in children

NASA Technical Reports Server (NTRS)

Butel, J. S.; Arrington, A. S.; Wong, C.; Lednicky, J. A.; Finegold, M. J.

1999-01-01

Recent studies have detected simian virus 40 (SV40) DNA in certain human tumors and normal tissues. The significance of human infections by SV40, which was first discovered as a contaminant of poliovirus vaccines used between 1955 and 1963, remains unknown. The occurrence of SV40 infections in unselected hospitalized children was evaluated. Polymerase chain reaction and DNA sequence analyses were done on archival tissue specimens from patients positive for SV40 neutralizing antibody. SV40 DNA was identified in samples from 4 of 20 children (1 Wilms' tumor, 3 transplanted kidney samples). Sequence variation among SV40 regulatory regions ruled out laboratory contamination of specimens. This study shows the presence of SV40 infections in pediatric patients born after 1982.

gkmSVM: an R package for gapped-kmer SVM.

PubMed

Ghandi, Mahmoud; Mohammad-Noori, Morteza; Ghareghani, Narges; Lee, Dongwon; Garraway, Levi; Beer, Michael A

2016-07-15

We present a new R package for training gapped-kmer SVM classifiers for DNA and protein sequences. We describe an improved algorithm for kernel matrix calculation that speeds run time by about 2 to 5-fold over our original gkmSVM algorithm. This package supports several sequence kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel. gkmSVM package is freely available through the Comprehensive R Archive Network (CRAN), for Linux, Mac OS and Windows platforms. The C ++ implementation is available at www.beerlab.org/gkmsvm mghandi@gmail.com or mbeer@jhu.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Rationale and Methods for Archival Sampling and Analysis of Atmospheric Trace Chemical Contaminants On Board Mir and Recommendations for the International Space Station

NASA Technical Reports Server (NTRS)

Perry, J. L.; James, J. T.; Cole, H. E.; Limero, T. F.; Beck, S. W.

1997-01-01

Collection and analysis of spacecraft cabin air samples are necessary to assess the cabin air quality with respect to crew health. Both toxicology and engineering disciplines work together to achieve an acceptably clean cabin atmosphere. Toxicology is concerned with limiting the risk to crew health from chemical sources, setting exposure limits, and analyzing air samples to determine how well these limits are met. Engineering provides the means for minimizing the contribution of the various contaminant generating sources by providing active contamination control equipment on board spacecraft and adhering to a rigorous material selection and control program during the design and construction of the spacecraft. A review of the rationale and objectives for sampling spacecraft cabin atmospheres is provided. The presently-available sampling equipment and methods are reviewed along with the analytical chemistry methods employed to determine trace contaminant concentrations. These methods are compared and assessed with respect to actual cabin air quality monitoring needs. Recommendations are presented with respect to the basic sampling program necessary to ensure an acceptably clean spacecraft cabin atmosphere. Also, rationale and recommendations for expanding the scope of the basic monitoring program are discussed.

Milgram's Obedience to Authority experiments: origins and early evolution.

PubMed

Russell, Nestar John Charles

2011-03-01

Stanley Milgram's Obedience to Authority experiments remain one of the most inspired contributions in the field of social psychology. Although Milgram undertook more than 20 experimental variations, his most (in)famous result was the first official trial run - the remote condition and its 65% completion rate. Drawing on many unpublished documents from Milgram's personal archive at Yale University, this article traces the historical origins and early evolution of the obedience experiments. Part 1 presents the previous experiences that led to Milgram's conception of his rudimentary research idea and then details the role of his intuition in its refinement. Part 2 traces the conversion of Milgram's evolving idea into a reality, paying particular attention to his application of the exploratory method of discovery during several pilot studies. Both parts illuminate Milgram's ad hoc introduction of various manipulative techniques and subtle tension-resolving refinements. The procedural adjustments continued until Milgram was confident that the first official experiment would produce a high completion rate, a result contrary to expectations of people's behaviour. Showing how Milgram conceived of, then arrived at, this first official result is important because the insights gained may help others to determine theoretically why so many participants completed this experiment. ©2010 The British Psychological Society.

Comparison of Absolute Apparent Diffusion Coefficient (ADC) Values in ADC Maps Generated Across Different Postprocessing Software: Reproducibility in Endometrial Carcinoma.

PubMed

Ghosh, Adarsh; Singh, Tulika; Singla, Veenu; Bagga, Rashmi; Khandelwal, Niranjan

2017-12-01

Apparent diffusion coefficient (ADC) maps are usually generated by builtin software provided by the MRI scanner vendors; however, various open-source postprocessing software packages are available for image manipulation and parametric map generation. The purpose of this study is to establish the reproducibility of absolute ADC values obtained using different postprocessing software programs. DW images with three b values were obtained with a 1.5-T MRI scanner, and the trace images were obtained. ADC maps were automatically generated by the in-line software provided by the vendor during image generation and were also separately generated on postprocessing software. These ADC maps were compared on the basis of ROIs using paired t test, Bland-Altman plot, mountain plot, and Passing-Bablok regression plot. There was a statistically significant difference in the mean ADC values obtained from the different postprocessing software programs when the same baseline trace DW images were used for the ADC map generation. For using ADC values as a quantitative cutoff for histologic characterization of tissues, standardization of the postprocessing algorithm is essential across processing software packages, especially in view of the implementation of vendor-neutral archiving.

A SEARCH FOR MAGNESIUM IN EUROPA'S ATMOSPHERE

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

Hoerst, S. M.; Brown, M. E., E-mail: sarah.horst@colorado.edu

Europa's tenuous atmosphere results from sputtering of the surface. The trace element composition of its atmosphere is therefore related to the composition of Europa's surface. Magnesium salts are often invoked to explain Galileo Near Infrared Mapping Spectrometer spectra of Europa's surface, thus magnesium may be present in Europa's atmosphere. We have searched for magnesium emission in the Hubble Space Telescope Faint Object Spectrograph archival spectra of Europa's atmosphere. Magnesium was not detected and we calculate an upper limit on the magnesium column abundance. This upper limit indicates that either Europa's surface is depleted in magnesium relative to sodium and potassium,more » or magnesium is not sputtered as efficiently resulting in a relative depletion in its atmosphere.« less

Statistical tables and charts showing geochemical variation in the Mesoproterozoic Big Creek, Apple Creek, and Gunsight formations, Lemhi group, Salmon River Mountains and Lemhi Range, central Idaho

USGS Publications Warehouse

Lindsey, David A.; Tysdal, Russell G.; Taggart, Joseph E.

2002-01-01

The principal purpose of this report is to provide a reference archive for results of a statistical analysis of geochemical data for metasedimentary rocks of Mesoproterozoic age of the Salmon River Mountains and Lemhi Range, central Idaho. Descriptions of geochemical data sets, statistical methods, rationale for interpretations, and references to the literature are provided. Three methods of analysis are used: R-mode factor analysis of major oxide and trace element data for identifying petrochemical processes, analysis of variance for effects of rock type and stratigraphic position on chemical composition, and major-oxide ratio plots for comparison with the chemical composition of common clastic sedimentary rocks.

A few laced genes: women's standpoint in the feminist ancestry of Dorothy E. Smith.

PubMed

Smythe, Deirdre

2009-04-01

This article looks at the feminist activism of particular women in the ancestry of the eminent Canadian sociologist, Dorothy E. Smith, and at the archival data that confirm the traces of their influence found in her theory-building. Using the method of interpretative historical sociology and a conceptual framework drawn from Marx called the "productive forces," the article examines the feminist theology of her Quaker ancestor, Margaret Fell, and the militant suffrage activism of her mother and her grandmother, Dorothy Foster Place and Lucy Ellison Abraham, respectively. The article argues that the household labour of the remarkable women in her family line became a "productive force" that facilitated her imagining of the feminist theory, "the standpoint of women".

Disability and Depression.

PubMed

Cvetkovich, A; Wilkerson, A

2016-12-01

Here, Ann Cvetkovich, interviewed by Abby Wilkerson, brings Cvetkovich's influential cultural studies analysis of depression explicitly into conversation with disability studies. Cvetkovich understands "feeling bad" (a term she prefers to "depression") as a defining affective state under neoliberalism. Drawing on a distinctive historical/cultural archive, she challenges the atomism of the neoliberal medical model that frames depression and affective distress more generally as the result of faulty brain chemistry-individual organisms gone awry. Instead, she traces these common experiences to sociopolitical phenomena ranging from current neoliberal demands for productivity as exemplified in university life, to histories of colonization, slavery, and displacement. The conversation considers the value of disability frameworks for understanding mental health diagnoses and the intersections of social institutions, bodily practices, and everyday affective life.

Development of the Plant Growth Facility for Use in the Shuttle Middeck and Test Units for Ground-Based Experiments

NASA Technical Reports Server (NTRS)

Chapman, David K.; Wells, H. William

1996-01-01

The plant growth facility (PGF), currently under development as a Space Shuttle middeck facility for the support of research on higher plants in microgravity, is presented. The PGF provides controlled fluorescent lighting and the active control of temperature, relative humidity and CO2 concentration. These parameters are designed to be centrally controlled by a dedicated microprocessor. The status of the experiment can be displayed for onboard analysis, and will be automatically archived for post-flight analysis. The facility is designed to operate for 15 days and will provide air filtration to remove ethylene and trace organics with replaceable potassium permanganate filters. Similar ground units will be available for pre-flight experimentation.

The "cholera cloud" in the nineteenth-century "British World": history of an object-without-an-essence.

PubMed

Mukharji, Projit Bihari

2012-01-01

The "cholera cloud" is one of the most persistent presences in the archives of nineteenth-century cholera in the "British World." Yet it has seldom received anything more than a passing acknowledgment from historians of cholera. Tracing the history of the cholera cloud as an object promises to open up a new dimension of the historically contingent experience of cholera, as well as make a significant contribution to the emergent literature on "thing theory." By conceptualizing the cholera cloud as an object-without-an-essence, this article demonstrates how global cholera pandemics in the nineteenth century produced globalized objects in which a near-universal recognizability and an utterly context-specific set of meanings, visions, and realities could ironically cohabit.

Fluvial deposits as an archive of early human activity: Progress during the 20 years of the Fluvial Archives Group

NASA Astrophysics Data System (ADS)

Chauhan, Parth R.; Bridgland, David R.; Moncel, Marie-Hélène; Antoine, Pierre; Bahain, Jean-Jacques; Briant, Rebecca; Cunha, Pedro P.; Despriée, Jackie; Limondin-Lozouet, Nicole; Locht, Jean-Luc; Martins, Antonio A.; Schreve, Danielle C.; Shaw, Andrew D.; Voinchet, Pierre; Westaway, Rob; White, Mark J.; White, Tom S.

2017-06-01

Fluvial sedimentary archives are important repositories for Lower and Middle Palaeolithic artefacts throughout the 'Old World', especially in Europe, where the beginning of their study coincided with the realisation that early humans were of great antiquity. Now that many river terrace sequences can be reliably dated and correlated with the globally valid marine isotope record, potentially useful patterns can be recognized in the distribution of the find-spots of the artefacts that constitute the large collections that were assembled during the years of manual gravel extraction. This paper reviews the advances during the past two decades in knowledge of hominin occupation based on artefact occurrences in fluvial contexts, in Europe, Asia and Africa. As such it is an update of a comparable review in 2007, at the end of IGCP Project no. 449, which had instigated the compilation of fluvial records from around the world during 2000-2004, under the auspices of the Fluvial Archives Group. An overarching finding is the confirmation of the well-established view that in Europe there is a demarcation between handaxe making in the west and flake-core industries in the east, although on a wider scale that pattern is undermined by the increased numbers of Lower Palaeolithic bifaces now recognized in East Asia. It is also apparent that, although it seems to have appeared at different places and at different times in the later Lower Palaeolithic, the arrival of Levallois technology as a global phenomenon was similarly timed across the area occupied by Middle Pleistocene hominins, at around 0.3 Ma.

MIDG-Emerging grid technologies for multi-site preclinical molecular imaging research communities.

PubMed

Lee, Jasper; Documet, Jorge; Liu, Brent; Park, Ryan; Tank, Archana; Huang, H K

2011-03-01

Molecular imaging is the visualization and identification of specific molecules in anatomy for insight into metabolic pathways, tissue consistency, and tracing of solute transport mechanisms. This paper presents the Molecular Imaging Data Grid (MIDG) which utilizes emerging grid technologies in preclinical molecular imaging to facilitate data sharing and discovery between preclinical molecular imaging facilities and their collaborating investigator institutions to expedite translational sciences research. Grid-enabled archiving, management, and distribution of animal-model imaging datasets help preclinical investigators to monitor, access and share their imaging data remotely, and promote preclinical imaging facilities to share published imaging datasets as resources for new investigators. The system architecture of the Molecular Imaging Data Grid is described in a four layer diagram. A data model for preclinical molecular imaging datasets is also presented based on imaging modalities currently used in a molecular imaging center. The MIDG system components and connectivity are presented. And finally, the workflow steps for grid-based archiving, management, and retrieval of preclincial molecular imaging data are described. Initial performance tests of the Molecular Imaging Data Grid system have been conducted at the USC IPILab using dedicated VMware servers. System connectivity, evaluated datasets, and preliminary results are presented. The results show the system's feasibility, limitations, direction of future research. Translational and interdisciplinary research in medicine is increasingly interested in cellular and molecular biology activity at the preclinical levels, utilizing molecular imaging methods on animal models. The task of integrated archiving, management, and distribution of these preclinical molecular imaging datasets at preclinical molecular imaging facilities is challenging due to disparate imaging systems and multiple off-site investigators. A Molecular Imaging Data Grid design, implementation, and initial evaluation is presented to demonstrate the secure and novel data grid solution for sharing preclinical molecular imaging data across the wide-area-network (WAN).

Archive of digital boomer seismic reflection data collected during USGS cruises 94GFP01, 95GFP01, 96GFP01, 97GFP01, and 98GFP02 in Lakes Pontchartrain, Borgne, and Maurepas, Louisiana, 1994-1998

USGS Publications Warehouse

Calderon, Karynna; Dadisman, Shawn V.; Kindinger, Jack G.; Williams, S. Jeffress; Flocks, James G.; Penland, Shea; Wiese, Dana S.

2003-01-01

The U.S. Geological Survey, in cooperation with the University of New Orleans, the Lake Pontchartrain Basin Foundation, the National Oceanic and Atmospheric Administration, the Coalition to Restore Coastal Louisiana, the U.S. Army Corps of Engineers, the Environmental Protection Agency, and the University of Georgia, conducted five geophysical surveys of Lakes Pontchartrain, Borgne, and Maurepas in Louisiana from 1994 to 1998. This report serves as an archive of unprocessed digital boomer seismic reflection data, trackline maps, navigation files, observers' logbooks, GIS information, and formal FGDC metadata. In addition, a filtered and gained digital GIF image of each seismic profile is provided. Refer to the Acronyms page for expansion of acronyms and abbreviations used in this report. The archived trace data are in standard Society of Exploration Geophysicists (SEG) SEG-Y format (Barry and others, 1975) and may be downloaded and processed with commercial or public domain software such as Seismic Unix (SU). Examples of SU processing scripts and in-house (USGS) software for viewing SEG-Y headers (Zihlman, 1992) are also provided. Processed profile images, trackline maps, navigation files, and formal metadata may be viewed with a web browser, and scanned handwritten logbooks may be viewed with Adobe Reader. To access the information contained on these discs, open the file 'index.htm' located at the top level of the discs using a web browser. This report also contains hyperlinks to USGS collaborators and other agencies. These links are only accessible if access to the Internet is available while viewing these documents.

Lyman Limit Absorbers in GALEX Spectra

NASA Astrophysics Data System (ADS)

Williger, Gerard M.; Haberzettl, Lutz G.; Ribaudo, Joseph; Kuchner, Marc J.; Burchett, Joseph; Clowes, Roger G.; Lauroesch, James T.; Mills, Brianna; Borden, Jeremy

2018-01-01

We describe the method and early results for crowdsourcing a search for low-redshift partial and complete Lyman Limit Systems (pLLSs and LLSs) in the GALEX spectral archive. LLSs have been found in large numbers at z>3 and traced to lower redshift through a relatively small number of QSO spectra from spaced-based telescopes. From a sample of 44 pLLSs and 11 LLSs at 0.1 = -0.32 +/- 0.07 and the low-metallicity portion centered at <[X/H]> = -1.87 +/- 0.11.The GALEX spectral archive offers a vast dataset potentially containing hundreds of LLSs, which may be leveraged to search for such a bimodality and track its evolution within the unconstrained near-UV gap at 1

Campylobacter multi-locus sequence typing subtypes detected on chicken livers available at retail.

USDA-ARS?s Scientific Manuscript database

Foodborne campylobacteriosis has been traced to undercooked chicken liver. It is not known what prevalence of Campylobacter to expect on fresh chicken livers available at retail. The objectives of this study were to measure prevalence of Campylobacter associated with chicken livers at retail and d...

The Agh Band loess-palaeosol sequence in Northern Iran - a detailed archive for climate and environmental change during the last and penultimate glacial - interglacial cycles

NASA Astrophysics Data System (ADS)

Lauer, Tobias; Frechen, Manfred; Vlaminck, Stefan; Kehl, Martin; Sharifi, Jafar; Rolf, Christian; Khormali, Farhad

2016-04-01

The northern Iranian loess profiles host important information on quaternary climate and palaeoenvironmental changes in the region. Furthermore, they build an important link to correlate European and Central Asian archives. Due to a significant climatic gradient with decreasing precipitation from the west to the east and from the south to the north, loess-palaeosol sequences which were formed synchronously under different climatic conditions can be studied. The Agh Band profile is located in the so called Iranian "Loess Plateau", a semi-arid region with about 300 mm annual precipitation. The loess deposits reach a thickness of > 60 meters and are subdivided by several weak soil horizons in the more upper part and by a pedo-complex of 3 Bw(y) horizons in the lower part of the loess. The Agh Band profile was sampled in 2 cm intervals for multi-proxy analyses (e.g. magnetic susceptibility and grain size measurements). Furthermore, samples for palaeomangentic studies and luminescence dating were collected and a pIRIR290 approach was applied to fine-grain polyminerals. The results show that the Agh Band profile yields a climate archive reaching from MIS 7 to MIS 2. Several chronological hiatuses of some 10 ka show that periods of intense loess accumulation were interrupted by phases of only minor loess sedimentation and/or erosion. The Agh Band profile hosts an extraordinary good temporal resolution for MIS 4 and MIS 5. The pedocomplex at the bottom part of the profile indicates a period of increased humidity and landscape stability during late MIS 7 and MIS 6 following the luminescence ages. The loess-profile is also subdivided by several shifts in grain-size distribution. The coarsening- and fining up trends correlate with increasing and decreasing wind- velocity, respectively.

The Fluvial Archives Group: 20 years of research connecting fluvial geomorphology and palaeoenvironments

NASA Astrophysics Data System (ADS)

Cordier, Stéphane; Briant, Becky; Bridgland, David; Herget, Jürgen; Maddy, Darrel; Mather, Anne; Vandenberghe, Jef

2017-06-01

The Fluvial Archives Group (FLAG) was formed in 1996 under the auspices of the British Quaternary Research Association (QRA). The rationale for its creation was the desire to bring together those working across timescales encompassing the last few million years to the Holocene and even modern process studies. The principles of uniformitarianism are important in the validation of this grouping of interests, with the modern and recent providing analogues from which the older and longer-timescale sequences can be more readily interpreted. The creation of FLAG occurred in the context of improved understanding of terrestrially-based Quaternary sequences and at a time when knowledge of the environmental significance of river systems had also seen great advances, following several decades of engineering experience and research into the management of such systems. This field was subsequently transformed in the European Union by the Water Framework Directive (WFD, 2000), which promoted a strategy for the re-naturalization of rivers. Above all, the WFD implied the (re-)establishment of an initial, pre-anthropogenic, reference state, the recovery of which was a prime aim. This would be a demanding task, considering that rivers are characterized by constant change, even without anthropogenic intervention. The evidence for and understanding of such change, observable at various timescales, is very much the business of FLAG (see below, section 6).

An ion microprobe study of the intra-crystalline behavior of REE and selected trace elements in pyroxene from mare basalts with different cooling and crystallization histories

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

Shearer, C.K.; Papike, J.J.; Simon, S.B.

1989-05-01

To study the effects of crystallization sequence and rate on trace element zoning characteristics of pyroxenes, the authors used combined electron microprobe-ion microprobe techniques on four nearly isochemical Apollo 12 and 15 pigeonite basalts with different cooling rates and crystallization histories. Major and minor element zoning characteristics are nearly identical to those reported in the literature. All the pyroxenes have similar chondrite-normalized REE patterns: negative Eu anomalies, positive slopes as defined by Yb/Ce, and slopes of REE patterns from Ce to Sm much steeper than from Gd to Yb. These trace element zoning characteristics in pyroxene and the partitioning ofmore » trace elements between pyroxene and the melt are intimately related to the interplay among the efficiency of the crystallization process, the kinetics at the crystal-melt interface, the kinetics of plagioclase nucleation and the characteristics of the crystal chemical substitutions within both the pyroxene and the associated crystallizing phases (i.e. plagioclase).« less

Phenotypic and genotypic analysis of Borrelia burgdorferi isolates from various sources.

PubMed Central

Adam, T; Gassmann, G S; Rasiah, C; Göbel, U B

1991-01-01

A total of 17 B. burgdorferi isolates from various sources were characterized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis of whole-cell proteins, restriction enzyme analysis, Southern hybridization with probes complementary to unique regions of evolutionarily conserved genes (16S rRNA and fla), and direct sequencing of in vitro polymerase chain reaction-amplified fragments of the 16S rRNA gene. Three groups were distinguished on the basis of phenotypic and genotypic traits, the latter traced to the nucleotide sequence level. Images PMID:1649797

Ciliates and the rare biosphere: a review.

PubMed

Dunthorn, Micah; Stoeck, Thorsten; Clamp, John; Warren, Alan; Mahé, Frédéric

2014-01-01

Here we provide a brief review of the rare biosphere from the perspective of ciliates and other microbial eukaryotes. We trace research on rarity from its lack of much in-depth focus in morphological and Sanger sequencing projects, to its central importance in analyses using high throughput sequencing strategies. The problem that the rare biosphere is potentially comprised of mostly errors is then discussed in the light of asking community-comparative, novel-diversity, and ecosystem-functioning questions. © 2014 The Author(s) Journal of Eukaryotic Microbiology © 2014 International Society of Protistologists.

Marine bivalve geochemistry and shell ultrastructure from modern low pH environments

NASA Astrophysics Data System (ADS)

Hahn, S.; Rodolfo-Metalpa, R.; Griesshaber, E.; Schmahl, W. W.; Buhl, D.; Hall-Spencer, J. M.; Baggini, C.; Fehr, K. T.; Immenhauser, A.

2011-10-01

Bivalve shells can provide excellent archives of past environmental change but have not been used to interpret ocean acidification events. We investigated carbon, oxygen and trace element records from different shell layers in the mussels Mytilus galloprovincialis (from the Mediterranean) and M. edulis (from the Wadden Sea) combined with detailed investigations of the shell ultrastructure. Mussels from the harbour of Ischia (Mediterranean, Italy) were transplanted and grown in water with mean pHT 7.3 and mean pHT 8.1 near CO2 vents on the east coast of the island of Ischia. The shells of transplanted mussels were compared with M. edulis collected at pH ~8.2 from Sylt (German Wadden Sea). Most prominently, the shells recorded the shock of transplantation, both in their shell ultrastructure, textural and geochemical record. Shell calcite, precipitated subsequently under acidified seawater responded to the pH gradient by an in part disturbed ultrastructure. Geochemical data from all test sites show a strong metabolic effect that exceeds the influence of the low-pH environment. These field experiments showed that care is needed when interpreting potential ocean acidification signals because various parameters affect shell chemistry and ultrastructure. Besides metabolic processes, seawater pH, factors such as salinity, water temperature, food availability and population density all affect the biogenic carbonate shell archive.

Prospects for reconstructing paleoenvironmental conditions from organic compounds in polar snow and ice

USGS Publications Warehouse

Giorio, Chiara; Kehrwald, Natalie; Barbante, Carlo; Kalberer, Markus; King, Amy C.F.; Thomas, Elizabeth R.; Wolff, Eric W.; Zennaro, Piero

2018-01-01

Polar ice cores provide information about past climate and environmental changes over periods ranging from a few years up to 800,000 years. The majority of chemical studies have focused on determining inorganic components, such as major ions and trace elements as well as on their isotopic fingerprint. In this paper, we review the different classes of organic compounds that might yield environmental information, discussing existing research and what is needed to improve knowledge. We also discuss the problems of sampling, analysis and interpretation of organic molecules in ice. This review highlights the great potential for organic compounds to be used as proxies for anthropogenic activities, past fire events from different types of biomass, terrestrial biogenic emissions and marine biological activity, along with the possibility of inferring past temperature fluctuations and even large-scale climate variability. In parallel, comprehensive research needs to be done to assess the atmospheric stability of these compounds, their ability to be transported long distances in the atmosphere, and their stability in the archive in order to better interpret their fluxes in ice cores. In addition, specific decontamination procedures, analytical methods with low detection limits (ng/L or lower), fast analysis time and low sample requests need to be developed in order to ensure a good time resolution in the archive.

The origins of scientific cinematography and early medical applications.

PubMed

Barboi, Alexandru C; Goetz, Christopher G; Musetoiu, Radu

2004-06-08

To examine the neurologic cinematographic contributions of Gheorghe Marinescu. Near the end of the 19th century, cinematography developed and was immediately recognized as a new technique applicable to medical documentation. After studying with several prominent European neurologists and deeply influenced by Jean-Martin Charcot, Marinescu returned to Bucharest in 1897 and applied moving picture techniques to the study of neurologic patients. The Romanian State Archives were researched for original Marinescu films, and related publications were translated from Romanian and French. Between 1899 and 1902, Marinescu perfected the use of cinematography as a research method in neurosciences and published five articles based on cinematographic documents. He focused his studies particularly on organic gait disorders, locomotor ataxia, and hysteria. He adapted Charcot's method of lining up several patients with the same disorder and showing them together to permit appreciation of archetypes and formes frustes. He decomposed the moving pictures into sequential tracings for publication. He documented treatment results with cases filmed before and after therapy. Processed and digitized excerpts of these films accompany this manuscript. Marinescu's cinematographic studies led to several original contributions in clinical neurology. Remaining film archives include examples of many neurologic diseases, his examination techniques, and the working medical environment of the young founder of the Romanian school of neurology.

Prospects for reconstructing paleoenvironmental conditions from organic compounds in polar snow and ice

NASA Astrophysics Data System (ADS)

Giorio, Chiara; Kehrwald, Natalie; Barbante, Carlo; Kalberer, Markus; King, Amy C. F.; Thomas, Elizabeth R.; Wolff, Eric W.; Zennaro, Piero

2018-03-01

Polar ice cores provide information about past climate and environmental changes over periods ranging from a few years up to 800,000 years. The majority of chemical studies have focused on determining inorganic components, such as major ions and trace elements as well as on their isotopic fingerprint. In this paper, we review the different classes of organic compounds that might yield environmental information, discussing existing research and what is needed to improve knowledge. We also discuss the problems of sampling, analysis and interpretation of organic molecules in ice. This review highlights the great potential for organic compounds to be used as proxies for anthropogenic activities, past fire events from different types of biomass, terrestrial biogenic emissions and marine biological activity, along with the possibility of inferring past temperature fluctuations and even large-scale climate variability. In parallel, comprehensive research needs to be done to assess the atmospheric stability of these compounds, their ability to be transported long distances in the atmosphere, and their stability in the archive in order to better interpret their fluxes in ice cores. In addition, specific decontamination procedures, analytical methods with low detection limits (ng/L or lower), fast analysis time and low sample requests need to be developed in order to ensure a good time resolution in the archive.

Archive of ground penetrating radar data collected during USGS field activity 13BIM01—Dauphin Island, Alabama, April 2013

USGS Publications Warehouse

Forde, Arnell S.; Smith, Christopher G.; Reynolds, Billy J.

2016-03-18

From April 13 to 20, 2013, scientists from the U.S. Geological Survey St. Petersburg Coastal and Marine Science Center (USGS-SPCMSC) conducted geophysical and sediment sampling surveys on Dauphin Island, Alabama, as part of Field Activity 13BIM01. The objectives of the study were to quantify inorganic and organic accretion rates in back-barrier and mainland marsh and estuarine environments. Various field and laboratory methods were used to achieve these objectives, including subsurface imaging using Ground Penetrating Radar (GPR), sediment sampling, lithologic and microfossil analyses, and geochronology techniques to produce barrier island stratigraphic cross sections to help interpret the recent (last 2000 years) geologic evolution of the island.This data series report is an archive of GPR and associated Global Positioning System (GPS) data collected in April 2013 from Dauphin Island and adjacent barrier-island environments. In addition to GPR data, marsh core and vibracore data were also collected collected but are not reported (or included) in the current report. Data products, including elevation-corrected subsurface profile images of the processed GPR data, unprocessed digital GPR trace data, post-processed GPS data, Geographic Information System (GIS) files and accompanying Federal Geographic Data Committee (FGDC) metadata, can be downloaded from the Data Downloads page.

Biological nanopore MspA for DNA sequencing

NASA Astrophysics Data System (ADS)

Manrao, Elizabeth A.

Unlocking the information hidden in the human genome provides insight into the inner workings of complex biological systems and can be used to greatly improve health-care. In order to allow for widespread sequencing, new technologies are required that provide fast and inexpensive readings of DNA. Nanopore sequencing is a third generation DNA sequencing technology that is currently being developed to fulfill this need. In nanopore sequencing, a voltage is applied across a small pore in an electrolyte solution and the resulting ionic current is recorded. When DNA passes through the channel, the ionic current is partially blocked. If the DNA bases uniquely modulate the ionic current flowing through the channel, the time trace of the current can be related to the sequence of DNA passing through the pore. There are two main challenges to realizing nanopore sequencing: identifying a pore with sensitivity to single nucleotides and controlling the translocation of DNA through the pore so that the small single nucleotide current signatures are distinguishable from background noise. In this dissertation, I explore the use of Mycobacterium smegmatis porin A (MspA) for nanopore sequencing. In order to determine MspA's sensitivity to single nucleotides, DNA strands of various compositions are held in the pore as the resulting ionic current is measured. DNA is immobilized in MspA by attaching it to a large molecule which acts as an anchor. This technique confirms the single nucleotide resolution of the pore and additionally shows that MspA is sensitive to epigenetic modifications and single nucleotide polymorphisms. The forces from the electric field within MspA, the effective charge of nucleotides, and elasticity of DNA are estimated using a Freely Jointed Chain model of single stranded DNA. These results offer insight into the interactions of DNA within the pore. With the nucleotide sensitivity of MspA confirmed, a method is introduced to controllably pass DNA through the pore. Using a DNA polymerase, DNA strands are stepped through MspA one nucleotide at a time. The steps are observable as distinct levels on the ionic-current time-trace and are related to the DNA sequence. These experiments overcome the two fundamental challenges to realizing MspA nanopore sequencing and pave the way to the development of a commercial technology.

IMNGS: A comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies.

PubMed

Lagkouvardos, Ilias; Joseph, Divya; Kapfhammer, Martin; Giritli, Sabahattin; Horn, Matthias; Haller, Dirk; Clavel, Thomas

2016-09-23

The SRA (Sequence Read Archive) serves as primary depository for massive amounts of Next Generation Sequencing data, and currently host over 100,000 16S rRNA gene amplicon-based microbial profiles from various host habitats and environments. This number is increasing rapidly and there is a dire need for approaches to utilize this pool of knowledge. Here we created IMNGS (Integrated Microbial Next Generation Sequencing), an innovative platform that uniformly and systematically screens for and processes all prokaryotic 16S rRNA gene amplicon datasets available in SRA and uses them to build sample-specific sequence databases and OTU-based profiles. Via a web interface, this integrative sequence resource can easily be queried by users. We show examples of how the approach allows testing the ecological importance of specific microorganisms in different hosts or ecosystems, and performing targeted diversity studies for selected taxonomic groups. The platform also offers a complete workflow for de novo analysis of users' own raw 16S rRNA gene amplicon datasets for the sake of comparison with existing data. IMNGS can be accessed at www.imngs.org.

Trace fossils in diatomaceous strata of Miocene Monterey Formation: their character and implications

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

Savdra, C.E.; Bottjer, D.J.

Younger parts of the Miocene Monterey Formation are commonly characterized by relatively unaltered diatomaceous strata. A common characteristic of these deposits is the preservation of varvelike lamination, indicative of deposition under anoxic or nearly anoxic conditions. Although laminated rock types are volumetrically dominant, bioturbated intervals are by no means rare, but little attention has been paid to the trace fossils themselves. Our study of trace fossils in the Monterey Formation demonstrated the significance of these biogenic structures in paleoenvironmental and paleoecologic analyses. In particular, trace fossils provide a means for detailed reconstruction of paleo-oxygenation conditions during Monterey deposition. Trace fossilsmore » in several Monterey sections exposed in central and southern California were examined in detail. At all localities, three major ichnofossil assemblages or ichnofacies were recognized: (1) Chondrites, (2) Planolites, and (3) Thalassinoides. The size and diversity of the three major ichnofacies and their lithologic associations suggest that the distribution of these facies is controlled primarily by the level of paleo-bottom water oxygenation. The Chondrites ichnofacies represents very low paleo-oxygen levels just above the anoxic threshold. The Planolites ichnofacies, with greater variety of larger burrow types, is indicative of slightly higher levels of oxygenation. Moderately to well-oxygenated conditions are suggested by the Thalassinoides ichnofacies. More detailed information on paleoenvironmental conditions can be gleaned by applying a refined trace-fossil tiering model. When used in detailed (centimeter-scale) vertical sequence analyses, this tiering model permits the translation of data on the composition, size parameters, and cross-cutting relationships of trace-fossil assemblages into relative paleo-oxygenation curves.« less

The New world of ';Big Data' Analytics and High Performance Data: A Paradigm shift in the way we interact with very large Earth Observation datasets (Invited)

NASA Astrophysics Data System (ADS)

Purss, M. B.; Lewis, A.; Ip, A.; Evans, B.

2013-12-01

The next decade promises an exponential increase in volumes of open data from Earth observing satellites. The ESA Sentinels, the Japan Meteorological Agency's Himawari 8/9 geostationary satellites, various NASA missions, and of course the many EO satellites planned from China, will produce petabyte scale datasets of national and global significance. It is vital that we develop new ways of managing, accessing and using this ';big-data' from satellites, to produce value added information within realistic timeframes. A paradigm shift is required away from traditional ';scene based' (and labour intensive) approaches with data storage and delivery for processing at local sites, to emerging High Performance Data (HPD) models where the data are organised and co-located with High Performance Computational (HPC) infrastructures in a way that enables users to bring themselves, their algorithms and the HPC processing power to the data. Automated workflows, that allow the entire archive of data to be rapidly reprocessed from raw data to fully calibrated products, are a crucial requirement for the effective stewardship of these datasets. New concepts such as arranging and viewing data as ';data objects' which underpin the delivery of ';information as a service' are also integral to realising the transition into HPD analytics. As Australia's national remote sensing and geoscience agency, Geoscience Australia faces a pressing need to solve the problems of ';big-data', in particular around the 25-year archive of calibrated Landsat data. The challenge is to ensure standardised information can be extracted from the entire archive and applied to nationally significant problems in hazards, water management, land management, resource development and the environment. Ultimately, these uses justify government investment in these unique systems. A key challenge was how best to organise the archive of calibrated Landsat data (estimated to grow to almost 1 PB by the end of 2014) in a way that supports HPD applications yet with the ability to trace each observation (pixel) back to its original satellite acquisition. The approach taken was to develop a multi-dimensional array (a data cube) underpinned by the partitioning the data into tiles, without any temporal aggregation. This allows for flexible spatio-temporal queries of the archive whilst minimising the need to perform geospatial processing just to locate the pixels of interest. Equally important is the development and implementation of international data interoperability standards (such as OGC web services and ISO metadata standards) that will provide advanced access for users to interact with and query the data cube without needing to download any data or to go through specialised data portals. This new approach will vastly improve access to, and the impact of, Australia's Landsat archive holdings.

Tracing the microbial biosphere into the Messinian Salinity Crisis

NASA Astrophysics Data System (ADS)

Natalicchio, Marcello; Dela Pierre, Francesco; Birgel, Daniel; Lozar, Francesca; Peckmann, Jörn

2016-04-01

The Messinian salinity crisis (MSC), one of the largest environmental crises in Earth history, occurred in the Mediterranean Basin about 6 Ma ago. The isolation of the Mediterranean from the Atlantic Ocean caused the transformation of the Mediterranean sea into a giant salina. The establishment of harsh conditions (hypersalinity and anoxia) in the water mass had a strong impact on the aquatic biosphere, resulting in the apparent disappearance of many marine biota. This aspect is however controversial, mostly because of the finding of fossils of biota that actually survived the onset of the MSC. To trace the response of life to this catastrophic event, we studied the microbial biosphere (both body fossils and molecular fossils) archived in the sediments straddling the MSC onset (shales, carbonates and sulphates) from marginal subbasins (Piedmont Basin, northern Italy, and Nijar Basin, southern Spain). Despite the significant reduction of calcareous plankton, the progressive rise of other microorganisms (prokaryotes and eukaryotes) is documented in the studied sediments at the MSC onset. These microorganisms include remains of euryhaline and stenohaline diatoms and filamentous microfossils interpreted as vacuolated sulphide-oxidizing bacteria. This fossil assemblage, which typifies both marginal (gypsum) and more distal (carbonates and shale) deposits, indicates conditions of high primary productivity in the surface waters, favoured by increased nutrient influx in the course of high riverine runoff. Molecular fossils allow tracing of the microbial biosphere into the geological past. The rise of algal compounds (e.g. dinosterol) in the basal MSC deposits (gypsum, carbonate and shales), accompanied by the simultaneous increase of terrigenous organic material (n-alkanes), agree with the eutrophication of the basin. In addition, the MSC deposits show an instant and significant increase of archaeal biomarkers, including the archaeal membrane lipids archaeol and extended archaeol, mostly produced by halophilic archaea, documenting a change toward harsh conditions. The co-occurrence of crenarchaeol, a compound mostly sourced by marine planktic Thaumarchaeota, above the MSC onset indicates that normal marine conditions were still present, probably in the upper water column, which was apparently underlain by a lower hypersaline layer. The local presence of tetrahymanol, a biomarker of ciliates or anoxygenic phototrophic bacteria, confirms water mass stratification, since this compound is predominantly found in stratified water bodies. In conclusion, the comprehensive study of body fossils and molecular fossils from different peripheral Mediterranean subbasins reveals that the onset of the MSC was typified by an expansion of microorganisms. The microbial biosphere archived in the basal MSC sediments agrees with a stratified basin characterized by locally persistent marine conditions.

Intramolecular stable isotope distributions detect plant metabolic responses on century time scales

NASA Astrophysics Data System (ADS)

Schleucher, Jürgen; Ehlers, Ina; Augusti, Angela; Betson, Tatiana

2014-05-01

Plants respond to environmental changes on a vast range of time scales, and plant gas exchanges constitute important feedback mechanisms in the global C cycle. Responses on time scales of decades to centuries are most important for climate models, for prediction of crop productivity, and for adaptation to climate change. Unfortunately, responses on these timescale are least understood. We argue that the knowledge gap on intermediate time scales is due to a lack of adequate methods that can bridge between short-term manipulative experiments (e.g. FACE) and paleo research. Manipulative experiments in plant ecophysiology give information on metabolism on time scales up to years. However, this information cannot be linked to results from retrospective studies in paleo research, because little metabolic information can be derived from paleo archives. Stable isotopes are prominent tools in plant ecophysiology, biogeochemistry and in paleo research, but in all applications to date, isotope ratios of whole molecules are measured. However, it is well established that stable isotope abundance varies among intramolecular groups of biochemical metabolites, that is each so-called "isotopomer" has a distinct abundance. This intramolecular variation carries information on metabolic regulation, which can even be traced to individual enzymes (Schleucher et al., Plant, Cell Environ 1999). Here, we apply intramolecular isotope distributions to study the metabolic response of plants to increasing atmospheric [CO2] during the past century. Greenhouse experiments show that the deuterium abundance among the two positions in the C6H2 group of photosynthetic glucose depends on [CO2] during growth. This is observed for all plants using C3 photosynthesis, and reflects the metabolic flux ratio between photorespiration and photosynthesis. Photorespiration is a major C flux that limits assimilation in C3 plants, which encompass the overwhelming fraction of terrestrial photosynthesis and the vast majority of crop species. To access century time scales, we traced this metabolic signal in historic material of two crop species during the past 100 years and find the same response as predicted from the greenhouse experiments. This allows estimating how much photorespiration has been reduced due to the anthropogenic CO2 emission during the 20th century, and shows that plants have not acclimated to increasing [CO2] during more than 100 generations. In summary, we demonstrate that metabolic responses of plants to environmental changes create intramolecular isotope signals. These signals can be identified in manipulation experiments and can be retrieved from plant archives. The isotope abundance of each intramolecular position is set by specific isotope fractionations, such as enzyme isotope effects or hydrogen exchange with xylem water (Augusti et al., Chem. Geol. 2008). Therefore it may be possible to simultaneously reconstruct several physiologic or climate signals from an archive of a single molecule. The principles governing intramolecular isotope distributions are general for all metabolites and isotopes (D, 13C), therefore intramolecular isotope distributions can multiply the information content of paleo archives. In particular, they allow extraction of metabolic information on long time scales, thereby connecting plant physiology with paleo research.

Functional PMS2 Hybrid Alleles Containing a Pseudogene-Specific Missense Variant Trace Back to a Single Ancient Intrachromosomal Recombination Event

PubMed Central

Ganster, Christina; Wernstedt, Annekatrin; Kehrer-Sawatzki, Hildegard; Messiaen, Ludwine; Schmidt, Konrad; Rahner, Nils; Heinimann, Karl; Fonatsch, Christa; Zschocke, Johannes; Wimmer, Katharina

2012-01-01

Sequence exchange between PMS2 and its pseudogene PMS2CL, embedded in an inverted duplication on chromosome 7p22, has been reported to be an ongoing process that leads to functional PMS2 hybrid alleles containing PMS2- and PMS2CL-specific sequence variants at the 5′-and the 3′-end, respectively. The frequency of PMS2 hybrid alleles, their biological significance, and the mechanisms underlying their formation are largely unknown. Here we show that overall hybrid alleles account for one-third of 384 PMS2 alleles analyzed in individuals of different ethnic backgrounds. Depending on the population, 14–60% of hybrid alleles carry PMS2CL-specific sequences in exons 13–15, the remainder only in exon 15. We show that exons 13–15 hybrid alleles, named H1 hybrid alleles, constitute different haplotypes but trace back to a single ancient intrachromosomal recombination event with crossover. Taking advantage of an ancestral sequence variant specific for all H1 alleles we developed a simple gDNA-based polymerase chain reaction (PCR) assay that can be used to identify H1-allele carriers with high sensitivity and specificity (100 and 99%, respectively). Because H1 hybrid alleles harbor missense variant p.N775S of so far unknown functional significance, we assessed the H1-carrier frequency in 164 colorectal cancer patients. So far, we found no indication that the variant plays a major role with regard to cancer susceptibility. PMID:20186689

Functional PMS2 hybrid alleles containing a pseudogene-specific missense variant trace back to a single ancient intrachromosomal recombination event.

PubMed

Ganster, Christina; Wernstedt, Annekatrin; Kehrer-Sawatzki, Hildegard; Messiaen, Ludwine; Schmidt, Konrad; Rahner, Nils; Heinimann, Karl; Fonatsch, Christa; Zschocke, Johannes; Wimmer, Katharina

2010-05-01

Sequence exchange between PMS2 and its pseudogene PMS2CL, embedded in an inverted duplication on chromosome 7p22, has been reported to be an ongoing process that leads to functional PMS2 hybrid alleles containing PMS2- and PMS2CL-specific sequence variants at the 5'-and the 3'-end, respectively. The frequency of PMS2 hybrid alleles, their biological significance, and the mechanisms underlying their formation are largely unknown. Here we show that overall hybrid alleles account for one-third of 384 PMS2 alleles analyzed in individuals of different ethnic backgrounds. Depending on the population, 14-60% of hybrid alleles carry PMS2CL-specific sequences in exons 13-15, the remainder only in exon 15. We show that exons 13-15 hybrid alleles, named H1 hybrid alleles, constitute different haplotypes but trace back to a single ancient intrachromosomal recombination event with crossover. Taking advantage of an ancestral sequence variant specific for all H1 alleles we developed a simple gDNA-based polymerase chain reaction (PCR) assay that can be used to identify H1-allele carriers with high sensitivity and specificity (100 and 99%, respectively). Because H1 hybrid alleles harbor missense variant p.N775S of so far unknown functional significance, we assessed the H1-carrier frequency in 164 colorectal cancer patients. So far, we found no indication that the variant plays a major role with regard to cancer susceptibility. (c) 2010 Wiley-Liss, Inc.

Very low luminosity stars with very large amplitude flares

NASA Technical Reports Server (NTRS)

Schaefer, Bradley E.

1990-01-01

CCD frames of CZ Cnc, KY Cep, the gamma-ray burster optical transient, and NSV 12006 are analyzed. Also studied are 549 archival photographic plates of the CZ Cnc field. These observations are compared with the data of Lovas (1976). Flare events on CZ Cnc are examined. Based on the data it is noted that CZ Cnc is a main-sequence star, has a magnitude of 16.1, a distance of 100 pc, occasional large-amplitude flares, and frequent flares with amplitudes greater than 4 mag.

Top dogs: wolf domestication and wealth.

PubMed

Driscoll, Carlos A; Macdonald, David W

2010-01-01

A phylogeographic analysis of gene sequences important in determining body size in dogs, recently published in BMC Biology, traces the appearance of small body size to the Neolithic Middle East. This finding strengthens the association of this event with the development of sedentary societies, and perhaps even has implications for the inception of human social inequality.

Draft Genome Sequences of 37 Salmonella enterica Strains Isolated from Poultry Sources in Nigeria

PubMed Central

Useh, Nicodemus M.; Ngbede, Emmanuel O.; Akange, Nguavese; Thomas, Milton; Foley, Andrew; Keena, Mitchel Chan; Nelson, Eric; Christopher-Hennings, Jane; Tomita, Masaru

2016-01-01

Here, we report the availability of draft genomes of several Salmonella serotypes, isolated from poultry sources from Nigeria. These genomes will help to further understand the biological diversity of S. enterica and will serve as references in microbial trace-back studies to improve food safety. PMID:27151793

Multi-locus sequence subtypes of Campylobacter detected on the surface and from internal tissue of retail chicken livers

USDA-ARS?s Scientific Manuscript database

Foodborne campylobacteriosis has been traced to undercooked chicken liver. The objectives of this study were to measure prevalence of Campylobacter associated with chicken livers at retail and determine which subtypes are detected on the surface and inner tissue of livers. Fifteen packages of fres...

Catastrophic valley fills record large Himalayan earthquakes, Pokhara, Nepal

NASA Astrophysics Data System (ADS)

Stolle, Amelie; Bernhardt, Anne; Schwanghart, Wolfgang; Hoelzmann, Philipp; Adhikari, Basanta R.; Fort, Monique; Korup, Oliver

2017-12-01

Uncertain timing and magnitudes of past mega-earthquakes continue to confound seismic risk appraisals in the Himalayas. Telltale traces of surface ruptures are rare, while fault trenches document several events at best, so that additional proxies of strong ground motion are needed to complement the paleoseismological record. We study Nepal's Pokhara basin, which has the largest and most extensively dated archive of earthquake-triggered valley fills in the Himalayas. These sediments form a 148-km2 fan that issues from the steep Seti Khola gorge in the Annapurna Massif, invading and plugging 15 tributary valleys with tens of meters of debris, and impounding several lakes. Nearly a dozen new radiocarbon ages corroborate at least three episodes of catastrophic sedimentation on the fan between ∼700 and ∼1700 AD, coinciding with great earthquakes in ∼1100, 1255, and 1344 AD, and emplacing roughly >5 km3 of debris that forms the Pokhara Formation. We offer a first systematic sedimentological study of this formation, revealing four lithofacies characterized by thick sequences of mid-fan fluvial conglomerates, debris-flow beds, and fan-marginal slackwater deposits. New geochemical provenance analyses reveal that these upstream dipping deposits of Higher Himalayan origin contain lenses of locally derived river clasts that mark time gaps between at least three major sediment pulses that buried different parts of the fan. The spatial pattern of 14C dates across the fan and the provenance data are key to distinguishing these individual sediment pulses, as these are not evident from their sedimentology alone. Our study demonstrates how geomorphic and sedimentary evidence of catastrophic valley infill can help to independently verify and augment paleoseismological fault-trench records of great Himalayan earthquakes, while offering unparalleled insights into their long-term geomorphic impacts on major drainage basins.

The volcanic double event at the dawn of the Dark Ages

NASA Astrophysics Data System (ADS)

Toohey, Matthew; Sigl, Michael; Krüger, Kirstin; Stordal, Frode; Svensen, Henrik

2016-04-01

Documentary records report dimming of the sun by a mysterious dust cloud covering Europe for 12-18 months in 536-537 CE, which was followed by a general climatic downturn and global societal decline. Tree rings and other climate proxies have corroborated the occurrence of this event as well as characterized its extent and duration, but failed to trace its origin. New volcanic timeseries, based on a multi-disciplinary approach that integrates novel, global-scale time markers with state-of-the-art continuous ice core aerosol measurements, automated objective ice-core layer counting, tephra analyses, and detailed examination of historical archives, show unequivocally that the 536-540 climate anomaly was concurrent with two or more major volcanic eruptions, with the largest eruptions likely occurring in the years 536 and 540 CE. Using a coupled aerosol-climate model, with eruption parameters constrained by ice core records and historical observations of the aerosol cloud, we reconstruct the radiative forcing resulting from the 536/540 CE eruption sequence. Comparing with existing reconstructions of the volcanic forcing over the past 1200 years, we estimate that the decadal-scale Northern Hemisphere (NH) extra-tropical radiative forcing from this volcanic "double event" was larger than that of any known period. Earth system model simulations including the volcanic forcing are used to explore the temperature and precipitation anomalies associated with the eruptions, and compared to available proxy records, including maximum latewood density (MXD) temperature reconstructions. Special attention is placed on the decadal persistence of the cooling signal in tree rings, and whether the climate model simulations reproduce such long-term climate anomalies. Finally, the climate model results are used to explore the probability of socioeconomic crisis resulting directly from the volcanic radiative forcing in different regions of the world.

Extreme flood event reconstruction spanning the last century in the El Bibane Lagoon (southeastern Tunisia): a multi-proxy approach

NASA Astrophysics Data System (ADS)

Affouri, Aida; Dezileau, Laurent; Kallel, Nejib

2017-06-01

Climate models project that rising atmospheric carbon dioxide concentrations will increase the frequency and the severity of some extreme weather events. The flood events represent a major risk for populations and infrastructures settled on coastal lowlands. Recent studies of lagoon sediments have enhanced our knowledge on extreme hydrological events such as palaeo-storms and on their relation with climate change over the last millennium. However, few studies have been undertaken to reconstruct past flood events from lagoon sediments. Here, the past flood activity was investigated using a multi-proxy approach combining sedimentological and geochemical analysis of surfaces sediments from a southeastern Tunisian catchment in order to trace the origin of sediment deposits in the El Bibane Lagoon. Three sediment sources were identified: marine, fluvial and aeolian. When applying this multi-proxy approach on core BL12-10, recovered from the El Bibane Lagoon, we can see that finer material, a high content of the clay and silt, and a high content of the elemental ratios (Fe / Ca and Ti / Ca) characterise the sedimentological signature of the palaeo-flood levels identified in the lagoonal sequence. For the last century, which is the period covered by the BL12-10 short core, three palaeo-flood events were identified. The age of these flood events have been determined by 210Pb and 137Cs chronology and give ages of AD 1995 ± 6, 1970 ± 9 and 1945 ± 9. These results show a good temporal correlation with historical flood events recorded in southern Tunisia in the last century (AD 1932, 1969, 1979 and 1995). Our finding suggests that reconstruction of the history of the hydrological extreme events during the upper Holocene is possible in this location through the use of the sedimentary archives.

Speleothem records of acid sulphate deposition and organic carbon mobilisation

NASA Astrophysics Data System (ADS)

Wynn, Peter; Fairchild, Ian; Bourdin, Clement; Baldini, James; Muller, Wolfgang; Hartland, Adam; Bartlett, Rebecca

2017-04-01

Dramatic increases in measured surface water DOC in recent decades have been variously attributed to either temperature rise, or destabilisation of long-term soil carbon pools following sulphur peak emissions status. However, whilst both drivers of DOC dynamics are plausible, they remain difficult to test due to the restricted nature of the available records of riverine DOC flux (1978 to present), and the limited availability of SO2 emissions inventory data at the regional scale. Speleothems offer long term records of both sulphur and carbon. New techniques to extract sulphur concentrations and isotopes from speleothem calcite have enabled archives of pollution history and environmental acidification to be reconstructed. Due to the large dynamic range in sulphur isotopic values from end member sources (marine aerosol +21 ‰ to continental biogenic emissions -30 ‰) and limited environmental fractionation under oxidising conditions, sulphur isotopes form an ideal tracer of industrial pollution and environmental acidification in the palaeo-record. We couple this acidification history to the carbon record, using organic matter fluorescence and trace metals. Trace metal ratios and abundance can be used to infer the type and size of organic ligand and are therefore sensitive to changes in temperature as a driver of organic carbon processing and biodegradation. This allows fluorescent properties and ratios of trace metals in speleothem carbonate to be used to represent both the flux of organic carbon into the cave as well as the degradation pathway. Here we present some of the first results of this work, exploring sulphur acidification as a mechanistic control on carbon solubility and export throughout the twentieth century.

A fast ultrasound-assisted extraction procedure for trace elements determination in hair samples by ICP-MS for forensic analysis.

PubMed

Batista, Bruno Lemos; Rodrigues, Jairo Lisboa; Souza, Vanessa Cristina de Oliveira; Barbosa, Fernando

2009-11-20

An ultrasound-assisted extraction method is proposed for the determination of trace elements in hair samples by inductively coupled plasma-mass spectrometry (ICP-MS) for forensic investigation. Prior to analysis, 25mg of hair samples were accurately weighed into (15 mL) conical tubes. Then, 2 mL of 20% HNO(3) is added to the samples, sonicated at 2 min (50W, 100% amplitude), and then further diluted to 10 mL with Milli-Q water. Resulted diluted slurries are centrifuged and the analytes are directly determined in the supernatant. Calibrations against aqueous solutions were carried out with rhodium as internal standard. The method was successfully applied for the extraction of Al, As, Ba, Be, Cd, Co, Cr, Cu, Mn, Pb, Tl, U, V and Zn with a method detection limit (3s, n=20) of 0.1, 0.4, 0.2, 0.09, 0.08, 0.04, 0.1, 2.9, 1.0, 0.9, 0.04, 0.05, 0.1 and 4.2 ng/g, respectively. Method accuracy is traceable to Certified Reference Materials (CRMs) 85 and 86 human hair from the International Atomic Energy Agency (IAEA). Additional validation data are provided based on the analysis of hair samples from the trace elements intercomparison program operated by the Institut National de Sante' Publique du Quebec, Canada. The proposed method is very simple and can be applied for forensic purposes with the elimination of sample digestion step prior to analysis. Then, a considerable improvement in the sample throughput is archived with the use of the proposed method.

Topside Ionogram Scaler With True Height Algorithm (TOPIST): Automated processing of ISIS topside ionograms

NASA Astrophysics Data System (ADS)

Bilitza, Dieter; Huang, Xueqin; Reinisch, Bodo W.; Benson, Robert F.; Hills, H. Kent; Schar, William B.

2004-02-01

The United States/Canadian ISIS-1 and ISIS-2 satellites collected several million topside ionograms in the 1960s and 1970s with a multinational network of ground stations that provided good global coverage. However, processing of these ionograms into electron density profiles required time-consuming manual scaling of the traces from the analog ionograms, and as a result, only a few percent of the ionograms had been processed into electron density profiles. In recent years an effort began to digitize the analog recordings to prepare the ionograms for computerized analysis. As of November 2002, approximately 390,000 ISIS-1 and ISIS-2 digital topside-sounder ionograms have been produced. The Topside Ionogram Scaler With True Height Algorithm (TOPIST) program was developed for the automated scaling of the echo traces and for the inversion of these traces into topside electron density profiles. The program is based on the techniques that have been successfully applied in the analysis of ground-based Digisonde ionograms. The TOPIST software also includes an "editing option" for manual scaling of the more difficult ionograms, which could not be scaled during the automated TOPIST run. TOPIST is now successfully scaling ˜60% of the ISIS ionograms, and the electron density profiles are available through the online archive of the National Space Science Data Center at ftp://nssdcftp.gsfc.nasa.gov/spacecraft_data/isis/topside_sounder. This data restoration effort is producing a unique global database of topside electron densities over more than one solar cycle, which will be of particular importance for improvements of topside ionosphere models, especially the International Reference Ionosphere.

Status of the ISS Trace Contaminant Control System

NASA Technical Reports Server (NTRS)

Macatangay, Ariel V.; Perry, Jay L.; Johnson, Sharon A.; Belcher, Paul A.

2009-01-01

A habitable atmosphere is a fundamental requirement for human spaceflight. To meet such a requirement, the cabin atmosphere must be constantly scrubbed to maintain human life and system functionality. The primary system for atmospheric scrubbing of the US on-orbit segment (USOS) of the International Space Station (ISS) is the Trace Contaminant Control System (TCCS). As part of the Environmental Control and Life Support Systems (ECLSS) atmosphere revitalization rack in the US Lab, the TCCS operates continuously, scrubbing trace contaminants generated primarily by two sources: the metabolic offgassing of crew members and the offgassing of equipment in the ISS. It has been online for approximately 95% since activated in February 2001. The TCCS is comprised of a charcoal bed, a catalytic oxidizer, and a lithium hydroxide post-sorbent bed, all of which are designed to be replaced onorbit when necessary. In 2006, all three beds were replaced following an observed increase in the system resistance that occurred over a period several months. The beds were returned to ground and subjected to a test, teardown and evaluation to investigate the root cause(s) of the decrease in flow rate through the system. In addition, various chemical and physical analyses of the bed materials were performed to determine contaminant loading and any changes in performance. This paper will mainly focus on the results of these analyses and how this correlates with what has been observed from archival sampling and onorbit events. This may provide insight into the future performance of the TCCS and rate of change for orbital replacement units in the TCCS.

Facies analysis and sequence stratigraphic framework of upper Campanian strata (Neslen and Mount Garfield formations, Bluecastle Tongue of the Castlegate sandstone, and Mancos shale), Eastern Book cliffs, Colorado and Utah

USGS Publications Warehouse

Kirschbaum, Mark A.; Hettinger, Robert D.

2004-01-01

Facies and sequence-stratigraphic analysis identifies six high-resolution sequences within upper Campanian strata across about 120 miles of the Book Cliffs in western Colorado and eastern Utah. The six sequences are named after prominent sandstone units and include, in ascending order, upper Sego sequence, Neslen sequence, Corcoran sequence, Buck Canyon/lower Cozzette sequence, upper Cozzette sequence, and Cozzette/Rollins sequence. A seventh sequence, the Bluecastle sequence, is present in the extreme western part of the study area. Facies analysis documents deepening- and shallowing- upward successions, parasequence stacking patterns, downlap in subsurface cross sections, facies dislocations, basinward shifts in facies, and truncation of strata.All six sequences display major incision into shoreface deposits of the Sego Sandstone and sandstones of the Corcoran and Cozzette Members of the Mount Garfield Formation. The incised surfaces represent sequence-boundary unconformities that allowed bypass of sediment to lowstand shorelines that are either attached to the older highstand shorelines or are detached from the older highstand shorelines and located southeast of the main study area. The sequence boundary unconformities represent valley incisions that were cut during successive lowstands of relative sea level. The overlying valley-fill deposits generally consist of tidally influenced strata deposited during an overall base level rise. Transgressive surfaces can be traced or projected over, or locally into, estuarine deposits above and landward of their associated shoreface deposits. Maximum flooding surfaces can be traced or projected landward from offshore strata into, or above, coastal-plain deposits. With the exception of the Cozzette/Rollins sequence, the majority of coal-bearing coastal-plain strata was deposited before maximum flooding and is therefore within the transgressive systems tracts. Maximum flooding was followed by strong progradation of parasequences and low preservation potential of coastal-plain strata within the highstand systems tract. The large incised valleys, lack of transgressive retrogradational parasequences, strong progradational nature of highstand parasequences, and low preservation of coastal-plain strata in the highstand systems tracts argue for relatively low accommodation space during deposition of the Sego, Corcoran, and Cozzette sequences. The Buck Canyon/Cozzette and Cozzette/Rollins sequences contrast with other sequences in that the preservation of retrogradational parasequences and the development of large estuaries coincident with maximum flooding indicate a relative increase in accommodation space during deposition of these strata. Following maximum flooding, the Buck Canyon/Cozzette sequence follows the pattern of the other sequences, but the Cozzette/Rollins sequence exhibits a contrasting offlapping pattern with development of offshore clinoforms that downlap and eventually parallel its maximum flooding surface. This highstand systems tract preserves a thick coal-bearing section where the Rollins Sandstone Member of the Mount Garfield Formation parasequences prograde out of the study area, stepping up as much as 800 ft stratigraphically over a distance of about 90 miles. This progradational stacking pattern indicates a higher accommodation space and increased sedimentation rate compared to the previous sequences.

Anthropogenic accumulation of metals and metalloids in carbonate-rich sediments: Insights from the ancient harbor setting of Tyre (Lebanon)

NASA Astrophysics Data System (ADS)

Elmaleh, A.; Galy, A.; Allard, T.; Dairon, R.; Day, J. A.; Michel, F.; Marriner, N.; Morhange, C.; Couffignal, F.

2012-04-01

The Antique and Byzantine sediments of the northern harbor of Tyre (Lebanon) store high amounts of metals and metalloids as the result of a millennial anthropogenic contamination as well as of efficient trapping and immobilization processes. Geochemical and mineralogical analyses reveal the contrasted patterns for the accumulation of trace metal(loid)s in the sedimentary sequence recovered by coring the inner part, now emerged, of the ancient harbor. Lead, Sn, Cu and Ag concentrations can be as high as 3000, 150, 1000, and 1.2 μg/g, respectively. Enrichment factors were calculated with respect to (1) Th and (2) the chemistry of the substratum and appear to be driven by anthropogenic inputs. Indeed, a drastic change in both excess concentrations and concentration ratios is observed through Roman and Byzantine times, pointing to major intensification of the trade and use of metals in Tyre, coherent with historical data. Good preservation of the archeological signal, despite (1) sediment disturbances that have caused age depth inversions, and (2) the large time lapse since the time of deposition of anthropogenic trace metal(loid)s is probably due to the reducing character of the sediments. Tyre's sedimentary sequence provides an interesting analog for modern carbonate-rich harbor environments, in which a millenary accumulation of trace metal(loid)s has been overall well preserved and suggests a restricted mobility of anthropogenic contamination for a period of time in excess of 1500 years.

An Easy Phylogenetically Informative Method to Trace the Globally Invasive Potamopyrgus Mud Snail from River's eDNA.

PubMed

Clusa, Laura; Ardura, Alba; Gower, Fiona; Miralles, Laura; Tsartsianidou, Valentina; Zaiko, Anastasija; Garcia-Vazquez, Eva

2016-01-01

Potamopyrgus antipodarum (New Zealand mud snail) is a prosobranch mollusk native to New Zealand with a wide invasive distribution range. Its non-indigenous populations are reported from Australia, Asia, Europe and North America. Being an extremely tolerant species, Potamopyrgus is capable to survive in a great range of salinity and temperature conditions, which explains its high invasiveness and successful spread outside the native range. Here we report the first finding of Potamopyrgus antipodarum in a basin of the Cantabrian corridor in North Iberia (Bay of Biscay, Spain). Two haplotypes already described in Europe were found in different sectors of River Nora (Nalon basin), suggesting the secondary introductions from earlier established invasive populations. To enhance the surveillance of the species and tracking its further spread in the region, we developed a specific set of primers for the genus Potamopyrgus that amplify a fragment of 16S rDNA. The sequences obtained from PCR on DNA extracted from tissue and water samples (environmental DNA, eDNA) were identical in each location, suggesting clonal reproduction of the introduced individuals. Multiple introduction events from different source populations were inferred from our sequence data. The eDNA tool developed here can serve for tracing New Zealand mud snail populations outside its native range, and for inventorying mud snail population assemblages in the native settings if high throughput sequencing methodologies are employed.

An Easy Phylogenetically Informative Method to Trace the Globally Invasive Potamopyrgus Mud Snail from River’s eDNA

PubMed Central

Clusa, Laura; Ardura, Alba; Gower, Fiona; Miralles, Laura; Tsartsianidou, Valentina; Zaiko, Anastasija; Garcia-Vazquez, Eva

2016-01-01

Potamopyrgus antipodarum (New Zealand mud snail) is a prosobranch mollusk native to New Zealand with a wide invasive distribution range. Its non-indigenous populations are reported from Australia, Asia, Europe and North America. Being an extremely tolerant species, Potamopyrgus is capable to survive in a great range of salinity and temperature conditions, which explains its high invasiveness and successful spread outside the native range. Here we report the first finding of Potamopyrgus antipodarum in a basin of the Cantabrian corridor in North Iberia (Bay of Biscay, Spain). Two haplotypes already described in Europe were found in different sectors of River Nora (Nalon basin), suggesting the secondary introductions from earlier established invasive populations. To enhance the surveillance of the species and tracking its further spread in the region, we developed a specific set of primers for the genus Potamopyrgus that amplify a fragment of 16S rDNA. The sequences obtained from PCR on DNA extracted from tissue and water samples (environmental DNA, eDNA) were identical in each location, suggesting clonal reproduction of the introduced individuals. Multiple introduction events from different source populations were inferred from our sequence data. The eDNA tool developed here can serve for tracing New Zealand mud snail populations outside its native range, and for inventorying mud snail population assemblages in the native settings if high throughput sequencing methodologies are employed. PMID:27706172

Forensic botany: species identification of botanical trace evidence using a multigene barcoding approach.

PubMed

Ferri, Gianmarco; Alù, Milena; Corradini, Beatrice; Beduschi, Giovanni

2009-09-01

Forensic botany can provide significant supporting evidence during criminal investigations. However, it is still an underutilized field of investigation with its most common application limited to identifying specific as well as suspected illegal plants. The ubiquitous presence of plant species can be useful in forensics, but the absence of an accurate identification system remains the major obstacle to the present inability to routinely and correctly identify trace botanical evidence. Many plant materials cannot be identified and differentiated to the species level by traditional morphological characteristics when botanical specimens are degraded and lack physical features. By taking advantage of a universal barcode system, DNA sequencing, and other biomolecular techniques used routinely in forensic investigations, two chloroplast DNA regions were evaluated for their use as "barcoding" markers for plant identification in the field of forensics. We therefore investigated the forensic use of two non-coding plastid regions, psbA-trnH and trnL-trnF, to create a multimarker system for species identification that could be useful throughout the plant kingdom. The sequences from 63 plants belonging to our local flora were submitted and registered on the GenBank database. Sequence comparison to set up the level of identification (species, genus, or family) through Blast algorithms allowed us to assess the suitability of this method. The results confirmed the effectiveness of our botanic universal multimarker assay in forensic investigations.

Cryptotephra from the 74 ka BP Toba super-eruption in the Billa Surgam caves, southern India

NASA Astrophysics Data System (ADS)

Lane, Christine; Haslam, Michael; Petraglia, Michael; Ditchfield, Peter; Smith, Victoria; Korisettar, Ravi

2011-07-01

The ˜74 ka BP Youngest Toba Tuff (YTT), from the largest known Quaternary volcanic eruption, has been found for the first time as a non-visible ( crypto-) tephra layer within the Billa Surgam caves, southern India. The occurrence of the YTT layer in Charnel House Cave provides the first calendrical age estimate for this much debated Pleistocene faunal sequence and demonstrates the first successful application of cryptotephrochronology within a cave sequence. The YTT layer lies ˜50 cm below a major sedimentological change, which is related to global cooling around the MIS 5 to MIS 4 transition. Using this isochronous event layer the Billa Surgam Cave record can be directly correlated with other archaeological sites in peninsular India and palaeoenvironmental archives across southern Asia.

Short genome report of cellulose-producing commensal Escherichia coli 1094.

PubMed

Bernal-Bayard, Joaquin; Gomez-Valero, Laura; Wessel, Aimee; Khanna, Varun; Bouchier, Christiane; Ghigo, Jean-Marc

2018-01-01

Bacterial surface colonization and biofilm formation often rely on the production of an extracellular polymeric matrix that mediates cell-cell and cell-surface contacts. In Escherichia coli and many Betaproteobacteria and Gammaproteobacteria cellulose is often the main component of the extracellular matrix. Here we report the complete genome sequence of the cellulose producing strain E. coli 1094 and compare it with five other closely related genomes within E. coli phylogenetic group A. We present a comparative analysis of the regions encoding genes responsible for cellulose biosynthesis and discuss the changes that could have led to the loss of this important adaptive advantage in several E. coli strains. Data deposition: The annotated genome sequence has been deposited at the European Nucleotide Archive under the accession number PRJEB21000.

Animation control of surface motion capture.

PubMed

Tejera, Margara; Casas, Dan; Hilton, Adrian

2013-12-01

Surface motion capture (SurfCap) of actor performance from multiple view video provides reconstruction of the natural nonrigid deformation of skin and clothing. This paper introduces techniques for interactive animation control of SurfCap sequences which allow the flexibility in editing and interactive manipulation associated with existing tools for animation from skeletal motion capture (MoCap). Laplacian mesh editing is extended using a basis model learned from SurfCap sequences to constrain the surface shape to reproduce natural deformation. Three novel approaches for animation control of SurfCap sequences, which exploit the constrained Laplacian mesh editing, are introduced: 1) space–time editing for interactive sequence manipulation; 2) skeleton-driven animation to achieve natural nonrigid surface deformation; and 3) hybrid combination of skeletal MoCap driven and SurfCap sequence to extend the range of movement. These approaches are combined with high-level parametric control of SurfCap sequences in a hybrid surface and skeleton-driven animation control framework to achieve natural surface deformation with an extended range of movement by exploiting existing MoCap archives. Evaluation of each approach and the integrated animation framework are presented on real SurfCap sequences for actors performing multiple motions with a variety of clothing styles. Results demonstrate that these techniques enable flexible control for interactive animation with the natural nonrigid surface dynamics of the captured performance and provide a powerful tool to extend current SurfCap databases by incorporating new motions from MoCap sequences.

Inception and Early Evolution of the Aleutian Arc

NASA Astrophysics Data System (ADS)

Bezard, R.; Hoernle, K.; Hauff, F.; Portnyagin, M.; Werner, R.; Yogodzinski, G.; Jicha, B.; Garbe-Schönberg, D.; Turner, S.; Schaefer, B. F.

2017-12-01

Constraining the timing and style of subduction initiation in the Aleutian system is critical to model the Cenozoic geodynamic evolution of the Pacific. Until now, the oldest ages for the Aleutian arc suggest a subduction inception at c.a. 46-47 Ma. However, the compositions of these samples (arc tholeiites and calc-alkaline rocks) are different from those of typical early-arc sequences found at extensively studied subduction systems (Izu-Bonin-Mariana), dominated by FABs and boninites. Thus, if the FAB/boninite model applies to the Aleutian, the oldest units might not have been recovered yet and the arc inception could have occurred earlier than 47 Ma. To test this hypothesis, we have sampled the lowermost submarine Aleutian sequences at ten forearc and rear-arc localities during the R/V SONNE Cruise 249. We present preliminary whole-rock major and trace element concentrations, Sr-Nd-Hf-Pb isotopes as well as U-Pb zircon dating on the recovered igneous rocks. The sample compositions range from tholeiitic to calc-alkaline. No boninites were found. Most of the samples show strong subduction signatures. However, the remaining rocks present no or minor arc-type trace element features. These samples are either depleted tholeiites with similar trace element characteristics to FABs or enriched calc-alkaline rocks. Preliminary zircon dating suggests an age of 47.2 ± 1.2 Ma for one of the samples with strong arc signatures, consistent with the oldest published ages for the Aleutian so far. However, based on their compositional similarities to FABs, the depleted tholeiites should be older than the arc-type rocks, suggesting that subduction initiation could have occurred earlier than the above-mentioned age. The absence of boninite could either reflect an incomplete sampling of the early-arc sequences or a different initiation style compared to other Pacific subduction zones. Further ages and radiogenic isotope data should refine these interpretations.

Post-mortem testing; germline BRCA1/2 variant detection using archival FFPE non-tumor tissue. A new paradigm in genetic counseling.

PubMed

Petersen, Annabeth Høgh; Aagaard, Mads Malik; Nielsen, Henriette Roed; Steffensen, Karina Dahl; Waldstrøm, Marianne; Bojesen, Anders

2016-08-01

Accurate estimation of cancer risk in HBOC families often requires BRCA1/2 testing, but this may be impossible in deceased family members. Previous, testing archival formalin-fixed, paraffin-embedded (FFPE) tissue for germline BRCA1/2 variants was unsuccessful, except for the Jewish founder mutations. A high-throughput method to systematically test for variants in all coding regions of BRCA1/2 in archival FFPE samples of non-tumor tissue is described, using HaloPlex target enrichment and next-generation sequencing. In a validation study, correct identification of variants or wild-type was possible in 25 out of 30 (83%) FFPE samples (age range 1-14 years), with a known variant status in BRCA1/2. No false positive was found. Unsuccessful identification was due to highly degraded DNA or presence of large intragenic deletions. In clinical use, a total of 201 FFPE samples (aged 0-43 years) were processed. Thirty-six samples were rejected because of highly degraded DNA or failed library preparation. Fifteen samples were investigated to search for a known variant. In the remaining 150 samples (aged 0-38 years), three variants known to affect function and one variant likely to affect function in BRCA1, six variants known to affect function and one variant likely to affect function in BRCA2, as well as four variants of unknown significance (VUS) in BRCA1 and three VUS in BRCA2 were discovered. It is now possible to test for germline BRCA1/2 variants in deceased persons, using archival FFPE samples from non-tumor tissue. Accurate genetic counseling is achievable in families where variant testing would otherwise be impossible.

RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education.

PubMed

Burley, Stephen K; Berman, Helen M; Christie, Cole; Duarte, Jose M; Feng, Zukang; Westbrook, John; Young, Jasmine; Zardecki, Christine

2018-01-01

The Protein Data Bank (PDB) is one of two archival resources for experimental data central to biomedical research and education worldwide (the other key Primary Data Archive in biology being the International Nucleotide Sequence Database Collaboration). The PDB currently houses >134,000 atomic level biomolecular structures determined by crystallography, NMR spectroscopy, and 3D electron microscopy. It was established in 1971 as the first open-access, digital-data resource in biology, and is managed by the Worldwide Protein Data Bank partnership (wwPDB; wwpdb.org). US PDB operations are conducted by the RCSB Protein Data Bank (RCSB PDB; RCSB.org; Rutgers University and UC San Diego) and funded by NSF, NIH, and DoE. The RCSB PDB serves as the global Archive Keeper for the wwPDB. During calendar 2016, >591 million structure data files were downloaded from the PDB by Data Consumers working in every sovereign nation recognized by the United Nations. During this same period, the RCSB PDB processed >5300 new atomic level biomolecular structures plus experimental data and metadata coming into the archive from Data Depositors working in the Americas and Oceania. In addition, RCSB PDB served >1 million RCSB.org users worldwide with PDB data integrated with ∼40 external data resources providing rich structural views of fundamental biology, biomedicine, and energy sciences, and >600,000 PDB101.rcsb.org educational website users around the globe. RCSB PDB resources are described in detail together with metrics documenting the impact of access to PDB data on basic and applied research, clinical medicine, education, and the economy. © 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

Post-mortem testing; germline BRCA1/2 variant detection using archival FFPE non-tumor tissue. A new paradigm in genetic counseling

PubMed Central

Petersen, Annabeth Høgh; Aagaard, Mads Malik; Nielsen, Henriette Roed; Steffensen, Karina Dahl; Waldstrøm, Marianne; Bojesen, Anders

2016-01-01

Accurate estimation of cancer risk in HBOC families often requires BRCA1/2 testing, but this may be impossible in deceased family members. Previous, testing archival formalin-fixed, paraffin-embedded (FFPE) tissue for germline BRCA1/2 variants was unsuccessful, except for the Jewish founder mutations. A high-throughput method to systematically test for variants in all coding regions of BRCA1/2 in archival FFPE samples of non-tumor tissue is described, using HaloPlex target enrichment and next-generation sequencing. In a validation study, correct identification of variants or wild-type was possible in 25 out of 30 (83%) FFPE samples (age range 1–14 years), with a known variant status in BRCA1/2. No false positive was found. Unsuccessful identification was due to highly degraded DNA or presence of large intragenic deletions. In clinical use, a total of 201 FFPE samples (aged 0–43 years) were processed. Thirty-six samples were rejected because of highly degraded DNA or failed library preparation. Fifteen samples were investigated to search for a known variant. In the remaining 150 samples (aged 0–38 years), three variants known to affect function and one variant likely to affect function in BRCA1, six variants known to affect function and one variant likely to affect function in BRCA2, as well as four variants of unknown significance (VUS) in BRCA1 and three VUS in BRCA2 were discovered. It is now possible to test for germline BRCA1/2 variants in deceased persons, using archival FFPE samples from non-tumor tissue. Accurate genetic counseling is achievable in families where variant testing would otherwise be impossible. PMID:26733283

RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education

PubMed Central

Berman, Helen M.; Christie, Cole; Duarte, Jose M.; Feng, Zukang; Westbrook, John; Young, Jasmine; Zardecki, Christine

2017-01-01

Abstract The Protein Data Bank (PDB) is one of two archival resources for experimental data central to biomedical research and education worldwide (the other key Primary Data Archive in biology being the International Nucleotide Sequence Database Collaboration). The PDB currently houses >134,000 atomic level biomolecular structures determined by crystallography, NMR spectroscopy, and 3D electron microscopy. It was established in 1971 as the first open‐access, digital‐data resource in biology, and is managed by the Worldwide Protein Data Bank partnership (wwPDB; wwpdb.org). US PDB operations are conducted by the RCSB Protein Data Bank (RCSB PDB; RCSB.org; Rutgers University and UC San Diego) and funded by NSF, NIH, and DoE. The RCSB PDB serves as the global Archive Keeper for the wwPDB. During calendar 2016, >591 million structure data files were downloaded from the PDB by Data Consumers working in every sovereign nation recognized by the United Nations. During this same period, the RCSB PDB processed >5300 new atomic level biomolecular structures plus experimental data and metadata coming into the archive from Data Depositors working in the Americas and Oceania. In addition, RCSB PDB served >1 million RCSB.org users worldwide with PDB data integrated with ∼40 external data resources providing rich structural views of fundamental biology, biomedicine, and energy sciences, and >600,000 PDB101.rcsb.org educational website users around the globe. RCSB PDB resources are described in detail together with metrics documenting the impact of access to PDB data on basic and applied research, clinical medicine, education, and the economy. PMID:29067736

Evaluation of the Cepheid Xpert Flu Assay for rapid identification and differentiation of influenza A, influenza A 2009 H1N1, and influenza B viruses.

PubMed

Novak-Weekley, S M; Marlowe, E M; Poulter, M; Dwyer, D; Speers, D; Rawlinson, W; Baleriola, C; Robinson, C C

2012-05-01

The Xpert Flu Assay cartridge is a next-generation nucleic acid amplification system that provides multiplexed PCR detection of the influenza A, influenza A 2009 H1N1, and influenza B viruses in approximately 70 min with minimal hands-on time. Six laboratories participated in a clinical trial comparing the results of the new Cepheid Xpert Flu Assay to those of culture or real-time PCR with archived and prospectively collected nasal aspirate-wash (NA-W) specimens and nasopharyngeal (NP) swabs from children and adults. Discrepant results were resolved by DNA sequence analysis. After discrepant-result analysis, the sensitivities of the Xpert Flu Assay for prospective NA-W specimens containing the influenza A, influenza A 2009 H1N1, and influenza B viruses compared to those of culture were 90.0%, 100%, and 100%, respectively, while the sensitivities of the assay for prospective NP swabs compared to those of culture were 100%, 100%, and 100%, respectively. The sensitivities of the Xpert Flu Assay for archived NA-W specimens compared to those of Gen-Probe ProFlu+ PCR for the influenza A, influenza A 2009 H1N1, and influenza B viruses were 99.4%, 98.4%, and 100%, respectively, while the sensitivities of the Xpert Flu Assay for archived NP swabs compared to those of ProFlu+ were 98.1%, 100%, and 93.8%, respectively. The sensitivities of the Xpert Flu Assay with archived NP specimens compared to those of culture for the three targets were 97.5%, 100%, and 93.8%, respectively. We conclude that the Cepheid Xpert Flu Assay is an accurate and rapid method that is suitable for on-demand testing for influenza viral infection.

Arkas: Rapid reproducible RNAseq analysis

PubMed Central

Colombo, Anthony R.; J. Triche Jr, Timothy; Ramsingh, Giridharan

2017-01-01

The recently introduced Kallisto pseudoaligner has radically simplified the quantification of transcripts in RNA-sequencing experiments.  We offer cloud-scale RNAseq pipelines Arkas-Quantification, and Arkas-Analysis available within Illumina’s BaseSpace cloud application platform which expedites Kallisto preparatory routines, reliably calculates differential expression, and performs gene-set enrichment of REACTOME pathways .  Due to inherit inefficiencies of scale, Illumina's BaseSpace computing platform offers a massively parallel distributive environment improving data management services and data importing.   Arkas-Quantification deploys Kallisto for parallel cloud computations and is conveniently integrated downstream from the BaseSpace Sequence Read Archive (SRA) import/conversion application titled SRA Import.  Arkas-Analysis annotates the Kallisto results by extracting structured information directly from source FASTA files with per-contig metadata, calculates the differential expression and gene-set enrichment analysis on both coding genes and transcripts. The Arkas cloud pipeline supports ENSEMBL transcriptomes and can be used downstream from the SRA Import facilitating raw sequencing importing, SRA FASTQ conversion, RNA quantification and analysis steps. PMID:28868134

Geochemical record of methane seepage in authigenic carbonates and surrounding host sediments: A case study from the South China Sea

NASA Astrophysics Data System (ADS)

Hu, Yu; Chen, Linying; Feng, Dong; Liang, Qianyong; Xia, Zhen; Chen, Duofu

2017-05-01

Sediments at marine methane seep sites provide potential archives of past fluid flow that serve to explore seepage activities over time. Three gravity cores (D-8, D-F, and D-7) were collected from seep sites on the northern slope of the South China Sea where gas hydrates were drilled in the subsurface. Various carbon and sulfur contents, δ13C values of total inorganic carbon (δ13CTIC), δ34S values of chromium reducible sulfur (δ34SCRS), trace element contents, grain size, and AMS 14C dating of planktonic Foraminifera in the sediments were determined to explore the availability of related proxies at seeps and to trace past methane seepage activities. Evidence for the presence of methane seepage and consequently anaerobic oxidation of methane comes from the occurrence of 13C-depleted authigenic carbonate nodules (δ13C values as low as -49‰) discovered at an interval of 150-200 cm in core D-7. This finding is supported by high S/C ratios and molybdenum enrichment in the same interval. However, low contents of CRS and negative δ34SCRS values are present. It is suggested to reflect a transient methane seepage event, which continued for about 1 ka based on the 14C ages. Cores D-8 and D-F have δ13CTIC values close to zero, low S/C ratios and CRS contents, negative δ34SCRS values, and no trace element enrichment, suggesting a negligible impact of methane-seepage on the sediments. The negative δ34SCRS values of the studied seep-impacted and background sediments suggest that the application of δ34SCRS alone as a proxy to identify AOM-related process may be insufficient. Sediment carbon-sulfur-trace element systematics and 14C ages used here have the potential to be a promising tool to recognize transient methane seepages and constrain their timescales.

The Biomolecular Interaction Network Database and related tools 2005 update

PubMed Central

Alfarano, C.; Andrade, C. E.; Anthony, K.; Bahroos, N.; Bajec, M.; Bantoft, K.; Betel, D.; Bobechko, B.; Boutilier, K.; Burgess, E.; Buzadzija, K.; Cavero, R.; D'Abreo, C.; Donaldson, I.; Dorairajoo, D.; Dumontier, M. J.; Dumontier, M. R.; Earles, V.; Farrall, R.; Feldman, H.; Garderman, E.; Gong, Y.; Gonzaga, R.; Grytsan, V.; Gryz, E.; Gu, V.; Haldorsen, E.; Halupa, A.; Haw, R.; Hrvojic, A.; Hurrell, L.; Isserlin, R.; Jack, F.; Juma, F.; Khan, A.; Kon, T.; Konopinsky, S.; Le, V.; Lee, E.; Ling, S.; Magidin, M.; Moniakis, J.; Montojo, J.; Moore, S.; Muskat, B.; Ng, I.; Paraiso, J. P.; Parker, B.; Pintilie, G.; Pirone, R.; Salama, J. J.; Sgro, S.; Shan, T.; Shu, Y.; Siew, J.; Skinner, D.; Snyder, K.; Stasiuk, R.; Strumpf, D.; Tuekam, B.; Tao, S.; Wang, Z.; White, M.; Willis, R.; Wolting, C.; Wong, S.; Wrong, A.; Xin, C.; Yao, R.; Yates, B.; Zhang, S.; Zheng, K.; Pawson, T.; Ouellette, B. F. F.; Hogue, C. W. V.

2005-01-01

The Biomolecular Interaction Network Database (BIND) (http://bind.ca) archives biomolecular interaction, reaction, complex and pathway information. Our aim is to curate the details about molecular interactions that arise from published experimental research and to provide this information, as well as tools to enable data analysis, freely to researchers worldwide. BIND data are curated into a comprehensive machine-readable archive of computable information and provides users with methods to discover interactions and molecular mechanisms. BIND has worked to develop new methods for visualization that amplify the underlying annotation of genes and proteins to facilitate the study of molecular interaction networks. BIND has maintained an open database policy since its inception in 1999. Data growth has proceeded at a tremendous rate, approaching over 100 000 records. New services provided include a new BIND Query and Submission interface, a Standard Object Access Protocol service and the Small Molecule Interaction Database (http://smid.blueprint.org) that allows users to determine probable small molecule binding sites of new sequences and examine conserved binding residues. PMID:15608229

VizieR Online Data Catalog: XCS-DR1 Cluster Catalogue (Mehrtens+, 2012)

NASA Astrophysics Data System (ADS)

Mehrtens, N.; Romer, A. K.; Hilton, M.; Lloyd-Davies, E. J.; Miller, C. J.; Stanford, S. A.; Hosmer, M.; Hoyle, B.; Collins, C. A.; Liddle, A. R.; Viana, P. T. P.; Nichol, R. C.; Stott, J. P.; Dubois, E. N.; Kay, S. T.; Sahlen, M.; Young, O.; Short, C. J.; Christodoulou, L.; Watson, W. A.; Davidson, M.; Harrison, C. D.; Baruah, L.; Smith, M.; Burke, C.; Mayers, J. A.; Deadman, P.-J.; Rooney, P. J.; Edmondson, E. M.; West, M.; Campbell, H. C.; Edge, A. C.; Mann, R. G.; Sabirli, K.; Wake, D.; Benoist, C.; da Costa, L.; Maia, M. A. G.; Ogando, R.

2013-04-01

The XMM Cluster Survey (XCS) is a serendipitous search for galaxy clusters using all publicly available data in the XMM-Newton Science Archive. Its main aims are to measure cosmological parameters and trace the evolution of X-ray scaling relations. In this paper we present the first data release from the XMM Cluster Survey (XCS-DR1). This consists of 503 optically confirmed, serendipitously detected, X-ray clusters. Of these clusters, 256 are new to the literature and 357 are new X-ray discoveries. We present 463 clusters with a redshift estimate (0.06

Alcoholic dogs and glory for all: the Anti-Saloon League and public relations, 1913.

PubMed

Lamme, Margot Opdycke

2007-01-01

In 1913, the Anti-Saloon League of America declared its intention to pursue national prohibition. While it continued to adhere to its core principles of agitation, it expanded its communication efforts and entered a partnership with the Scientific Temperance Federation, a spin-off of the education arm of the Woman's Christian Temperance Union. The League's tactics were not necessarily new to the temperance movement -- or even to other reform movements of the time. What did set it apart was its single-minded focus on stopping the liquor traffic. Tracing through archival artifacts the League's communication strategies and tactics during 1913, then, this study contributes to a larger body of work that seeks to expand on the traditional model of public relations history.

A Fly-Inspired Mushroom Bodies Model for Sensory-Motor Control Through Sequence and Subsequence Learning.

PubMed

Arena, Paolo; Calí, Marco; Patané, Luca; Portera, Agnese; Strauss, Roland

2016-09-01

Classification and sequence learning are relevant capabilities used by living beings to extract complex information from the environment for behavioral control. The insect world is full of examples where the presentation time of specific stimuli shapes the behavioral response. On the basis of previously developed neural models, inspired by Drosophila melanogaster, a new architecture for classification and sequence learning is here presented under the perspective of the Neural Reuse theory. Classification of relevant input stimuli is performed through resonant neurons, activated by the complex dynamics generated in a lattice of recurrent spiking neurons modeling the insect Mushroom Bodies neuropile. The network devoted to context formation is able to reconstruct the learned sequence and also to trace the subsequences present in the provided input. A sensitivity analysis to parameter variation and noise is reported. Experiments on a roving robot are reported to show the capabilities of the architecture used as a neural controller.

Accuracy of maxillary positioning after standard and inverted orthognathic sequencing.

PubMed

Ritto, Fabio G; Ritto, Thiago G; Ribeiro, Danilo Passeado; Medeiros, Paulo José; de Moraes, Márcio

2014-05-01

This study aimed to compare the accuracy of maxillary positioning after bimaxillary orthognathic surgery, using 2 sequences. A total of 80 cephalograms (40 preoperative and 40 postoperative) from 40 patients were analyzed. Group 1 included radiographs of patients submitted to conventional sequence, whereas group 2 patients were submitted to inverted sequence. The final position of the maxillary central incisor was obtained after vertical and horizontal measurements of the tracings, and it was compared with what had been planned. The null hypothesis, which stated that there would be no difference between the groups, was tested. After applying the Welch t test for comparison of mean differences between maxillary desired and achieved position, considering a statistical significance of 5% and a 2-tailed test, the null hypothesis was not rejected (P > .05). Thus, there was no difference in the accuracy of maxillary positioning between groups. Conventional and inverted sequencing proved to be reliable in positioning the maxilla after LeFort I osteotomy in bimaxillary orthognathic surgeries. Copyright © 2014 Elsevier Inc. All rights reserved.

Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data.

PubMed

Cole, Charles; Krampis, Konstantinos; Karagiannis, Konstantinos; Almeida, Jonas S; Faison, William J; Motwani, Mona; Wan, Quan; Golikov, Anton; Pan, Yang; Simonyan, Vahan; Mazumder, Raja

2014-01-27

Next-generation sequencing (NGS) technologies have resulted in petabytes of scattered data, decentralized in archives, databases and sometimes in isolated hard-disks which are inaccessible for browsing and analysis. It is expected that curated secondary databases will help organize some of this Big Data thereby allowing users better navigate, search and compute on it. To address the above challenge, we have implemented a NGS biocuration workflow and are analyzing short read sequences and associated metadata from cancer patients to better understand the human variome. Curation of variation and other related information from control (normal tissue) and case (tumor) samples will provide comprehensive background information that can be used in genomic medicine research and application studies. Our approach includes a CloudBioLinux Virtual Machine which is used upstream of an integrated High-performance Integrated Virtual Environment (HIVE) that encapsulates Curated Short Read archive (CSR) and a proteome-wide variation effect analysis tool (SNVDis). As a proof-of-concept, we have curated and analyzed control and case breast cancer datasets from the NCI cancer genomics program - The Cancer Genome Atlas (TCGA). Our efforts include reviewing and recording in CSR available clinical information on patients, mapping of the reads to the reference followed by identification of non-synonymous Single Nucleotide Variations (nsSNVs) and integrating the data with tools that allow analysis of effect nsSNVs on the human proteome. Furthermore, we have also developed a novel phylogenetic analysis algorithm that uses SNV positions and can be used to classify the patient population. The workflow described here lays the foundation for analysis of short read sequence data to identify rare and novel SNVs that are not present in dbSNP and therefore provides a more comprehensive understanding of the human variome. Variation results for single genes as well as the entire study are available from the CSR website (http://hive.biochemistry.gwu.edu/dna.cgi?cmd=csr). Availability of thousands of sequenced samples from patients provides a rich repository of sequence information that can be utilized to identify individual level SNVs and their effect on the human proteome beyond what the dbSNP database provides.

High-throughput detection of RNA processing in bacteria.

PubMed

Gill, Erin E; Chan, Luisa S; Winsor, Geoffrey L; Dobson, Neil; Lo, Raymond; Ho Sui, Shannan J; Dhillon, Bhavjinder K; Taylor, Patrick K; Shrestha, Raunak; Spencer, Cory; Hancock, Robert E W; Unrau, Peter J; Brinkman, Fiona S L

2018-03-27

Understanding the RNA processing of an organism's transcriptome is an essential but challenging step in understanding its biology. Here we investigate with unprecedented detail the transcriptome of Pseudomonas aeruginosa PAO1, a medically important and innately multi-drug resistant bacterium. We systematically mapped RNA cleavage and dephosphorylation sites that result in 5'-monophosphate terminated RNA (pRNA) using monophosphate RNA-Seq (pRNA-Seq). Transcriptional start sites (TSS) were also mapped using differential RNA-Seq (dRNA-Seq) and both datasets were compared to conventional RNA-Seq performed in a variety of growth conditions. The pRNA-Seq library revealed known tRNA, rRNA and transfer-messenger RNA (tmRNA) processing sites, together with previously uncharacterized RNA cleavage events that were found disproportionately near the 5' ends of transcripts associated with basic bacterial functions such as oxidative phosphorylation and purine metabolism. The majority (97%) of the processed mRNAs were cleaved at precise codon positions within defined sequence motifs indicative of distinct endonucleolytic activities. The most abundant of these motifs corresponded closely to an E. coli RNase E site previously established in vitro. Using the dRNA-Seq library, we performed an operon analysis and predicted 3159 potential TSS. A correlation analysis uncovered 105 antiparallel pairs of TSS that were separated by 18 bp from each other and were centered on single palindromic TAT(A/T)ATA motifs (likely - 10 promoter elements), suggesting that, consistent with previous in vitro experimentation, these sites can initiate transcription bi-directionally and may thus provide a novel form of transcriptional regulation. TSS and RNA-Seq analysis allowed us to confirm expression of small non-coding RNAs (ncRNAs), many of which are differentially expressed in swarming and biofilm formation conditions. This study uses pRNA-Seq, a method that provides a genome-wide survey of RNA processing, to study the bacterium Pseudomonas aeruginosa and discover extensive transcript processing not previously appreciated. We have also gained novel insight into RNA maturation and turnover as well as a potential novel form of transcription regulation. NOTE: All sequence data has been submitted to the NCBI sequence read archive. Accession numbers are as follows: [NCBI sequence read archive: SRX156386, SRX157659, SRX157660, SRX157661, SRX157683 and SRX158075]. The sequence data is viewable using Jbrowse on www.pseudomonas.com .

Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data

PubMed Central

2014-01-01

Background Next-generation sequencing (NGS) technologies have resulted in petabytes of scattered data, decentralized in archives, databases and sometimes in isolated hard-disks which are inaccessible for browsing and analysis. It is expected that curated secondary databases will help organize some of this Big Data thereby allowing users better navigate, search and compute on it. Results To address the above challenge, we have implemented a NGS biocuration workflow and are analyzing short read sequences and associated metadata from cancer patients to better understand the human variome. Curation of variation and other related information from control (normal tissue) and case (tumor) samples will provide comprehensive background information that can be used in genomic medicine research and application studies. Our approach includes a CloudBioLinux Virtual Machine which is used upstream of an integrated High-performance Integrated Virtual Environment (HIVE) that encapsulates Curated Short Read archive (CSR) and a proteome-wide variation effect analysis tool (SNVDis). As a proof-of-concept, we have curated and analyzed control and case breast cancer datasets from the NCI cancer genomics program - The Cancer Genome Atlas (TCGA). Our efforts include reviewing and recording in CSR available clinical information on patients, mapping of the reads to the reference followed by identification of non-synonymous Single Nucleotide Variations (nsSNVs) and integrating the data with tools that allow analysis of effect nsSNVs on the human proteome. Furthermore, we have also developed a novel phylogenetic analysis algorithm that uses SNV positions and can be used to classify the patient population. The workflow described here lays the foundation for analysis of short read sequence data to identify rare and novel SNVs that are not present in dbSNP and therefore provides a more comprehensive understanding of the human variome. Variation results for single genes as well as the entire study are available from the CSR website (http://hive.biochemistry.gwu.edu/dna.cgi?cmd=csr). Conclusions Availability of thousands of sequenced samples from patients provides a rich repository of sequence information that can be utilized to identify individual level SNVs and their effect on the human proteome beyond what the dbSNP database provides. PMID:24467687

High-risk human papilloma virus in archival tissues of oral pathosis and normal oral mucosa.

PubMed

Dhanapal, Raghu; Ranganathan, K; Kondaiah, Paturu; Devi, R Uma; Joshua, Elizabeth; Saraswathi, T R

2015-01-01

Oral cancer ranks third among all cancers in the Indian population. Human papilloma virus (HPV) plays a significant role in oral carcinogenesis. Population-based subtype variations are present in the HPV prevalence. This study gives an emphasis on the parameters to be considered in formalin fixed paraffin embedded tissues for polymerase chain reaction (PCR)-based research work. Cross-sectional study on archival paraffin-embedded tissue samples of oral squamous cell carcinoma (OSCC), epithelial dysplasia, and normal oral mucosa surrounding impacted tooth was amplified by PCR for the E6 gene of HPV type 16 and E1 gene of HPV type 18. HPV 18 was positive in three OSCC cases. There was no statistically significant association of the positivity of HPV with the age, gender or habit. The HPV positive patients had a tobacco habit and were of a younger age group. The presence of HPV in carcinomatous tissue highlights the possible role of HPV in carcinogenesis and archival paraffin embedded tissue specimen can be used for this analysis. Recent studies on genomic analyses have highlighted that the HPV positive tumors are a separate subgroup based on genomic sequencing. The results of a larger retrospective study will help further in our understanding of the role of HPV in carcinogenesis, this study could form the baseline for such follow-up studies.

Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples.

PubMed

Kresse, Stine H; Namløs, Heidi M; Lorenz, Susanne; Berner, Jeanne-Marie; Myklebost, Ola; Bjerkehagen, Bodil; Meza-Zepeda, Leonardo A

2018-01-01

Nucleic acid material of adequate quality is crucial for successful high-throughput sequencing (HTS) analysis. DNA and RNA isolated from archival FFPE material are frequently degraded and not readily amplifiable due to chemical damage introduced during fixation. To identify optimal nucleic acid extraction kits, DNA and RNA quantity, quality and performance in HTS applications were evaluated. DNA and RNA were isolated from five sarcoma archival FFPE blocks, using eight extraction protocols from seven kits from three different commercial vendors. For DNA extraction, the truXTRAC FFPE DNA kit from Covaris gave higher yields and better amplifiable DNA, but all protocols gave comparable HTS library yields using Agilent SureSelect XT and performed well in downstream variant calling. For RNA extraction, all protocols gave comparable yields and amplifiable RNA. However, for fusion gene detection using the Archer FusionPlex Sarcoma Assay, the truXTRAC FFPE RNA kit from Covaris and Agencourt FormaPure kit from Beckman Coulter showed the highest percentage of unique read-pairs, providing higher complexity of HTS data and more frequent detection of recurrent fusion genes. truXTRAC simultaneous DNA and RNA extraction gave similar outputs as individual protocols. These findings show that although successful HTS libraries could be generated in most cases, the different protocols gave variable quantity and quality for FFPE nucleic acid extraction. Selecting the optimal procedure is highly valuable and may generate results in borderline quality specimens.

A novel presenilin 1 mutation (Ala275Val) as cause of early-onset familial Alzheimer disease.

PubMed

Luedecke, Daniel; Becktepe, Jos S; Lehmbeck, Jan T; Finckh, Ulrich; Yamamoto, Raina; Jahn, Holger; Boelmans, Kai

2014-04-30

Mutations in the presenilin 1 (PS1) gene (PSEN1) are associated with familial Alzheimer disease (FAD). Here, we report on a 50-year-old patient presenting with progressive deterioration of his short-term memory and a family history of early-onset dementia. Diagnostic workup included a neuropsychological examination, structural magnetic resonance (MR) imaging, cerebrospinal fluid (CSF) biomarkers including total tau, phosphorylated tau, and Aβ42 levels, as well as sequencing relevant fragments of the genes PSEN1, PSEN2, and APP. Additionally, we were able to obtain archival paraffin-embedded cerebellar tissue from the patient's father for cosegregation analysis. Clinical, neuropsychological and MR imaging data were indicative of early-onset Alzheimer disease. Furthermore, CSF biomarkers showed a typical pattern for Alzheimer disease. DNA sequencing revealed a heterozygous nucleotide transition (c.824C>T) in exon 8 of PSEN1, leading to an amino acid change from alanine to valine at codon 275 (Ala275Val). The same mutation was found in an archival brain specimen of the patient's demented father, but not in a blood sample of the non-demented mother. This mutation alters a conserved residue in the large hydrophilic loop of PS1, suggesting pathogenic relevance. Cosegregegation analysis and the structural as well as the presumed functional role of the mutated and highly conserved residue suggest FAD causing characteristics of the novel PSEN1 mutation Ala275Val. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

A Detailed Far-ultraviolet Spectral Atlas of O-type Stars

NASA Astrophysics Data System (ADS)

Smith, Myron A.

2012-10-01

In this paper, we present a spectral atlas covering the wavelength interval 930-1188 Å for O2-O9.5 stars using Far-Ultraviolet Spectroscopic Explorer archival data. The stars selected for the atlas were drawn from three populations: Galactic main-sequence (classes III-V) stars, supergiants, and main-sequence stars in the Magellanic Clouds, which have low metallicities. For several of these stars, we have prepared FITS files comprised of pairs of merged spectra for user access via the Multimission Archive at Space Telescope (MAST). We chose spectra from the first population with spectral types O4, O5, O6, O7, O8, and O9.5 and used them to compile tables and figures with identifications of all possible atmospheric and interstellar medium lines in the region 949-1188 Å. Our identified line totals for these six representative spectra are 821 (500), 992 (663), 1077 (749), 1178 (847), 1359 (1001), and 1798 (1392) lines, respectively, where the numbers in parentheses are the totals of lines formed in the atmospheres, according to spectral synthesis models. The total number of unique atmospheric identifications for the six main-sequence O-star template spectra is 1792, whereas the number of atmospheric lines in common to these spectra is 300. The number of identified lines decreases toward earlier types (increasing effective temperature), while the percentages of "missed" features (unknown lines not predicted from our spectral syntheses) drop from a high of 8% at type B0.2, from our recently published B-star far-UV atlas, to 1%-3% for type O spectra. The percentages of overpredicted lines are similar, despite their being much higher for B-star spectra. We discuss the statistics of line populations among the various elemental ionization states. Also, as an aid to users we list those isolated lines that can be used to determine stellar temperatures and the presence of possible chemical anomalies. Finally, we have prepared FITS files that give pairs of merged spectra for stars in our population sequences, for access via MAST.

Investigating the Microscopic Location of Trace Elements in High-Alpine Glacier Ice

NASA Astrophysics Data System (ADS)

Avak, Sven Erik; Birrer, Mario; Laurent, Oscar; Guillong, Marcel; Wälle, Markus; Jenk, Theo Manuel; Bartels-Rausch, Thorsten; Schwikowski, Margit; Eichler, Anja

2017-04-01

Past changes in atmospheric pollution can be reconstructed from high-alpine ice core trace element records (Schwikowski et al., 2004). Percolation of meltwater alters the information originally stored in these environmental archives. Eichler et al. (2001) suggested that the preservation of major ions with respect to meltwater percolation depends on their location in the crystal ice lattice, i.e. grain boundaries versus grain interiors. Other studies have also focused on the effect of meltwater on organic pollutant concentrations as well as on stable isotope profiles in ice cores, whereas no information exists about trace elements. Here, we investigate for the first time the effect of the microscopic location of anthropogenic, dust and volcanic related trace elements on the behavior during meltwater percolation by using two different approaches. On the one hand we assess the microscopic location of trace elements indirectly by analyzing trace element concentrations in a high-alpine ice core, which has been shown to be affected by an inflow of meltwater, using discrete inductively coupled plasma mass spectrometry (ICP-MS). Impurities located at grain boundaries are prone to be removed by meltwater and tend to be depleted in the affected section of the record whereas those incorporated into the ice interior are preserved and not disturbed in the record. In the second approach we work towards a direct quantification of differences in concentrations of trace elements between ice grain boundaries and grain interiors in samples both from unaffected and affected sections of this ice core. Therefore we use cryocell laser ablation (LA) ICP-MS, which is the method of choice for the direct in situ chemical analysis of trace elements at a sub-millimeter resolution in glacier ice (Reinhardt et al., 2001, Della Lunga et al., 2014, Sneed et al., 2015). We will present first results of both approaches with regard to the evaluation of the potential of trace elements as environmental proxies in glaciers partially affected by melting. References Della Lunga, D., Müller, W., Rasmussen, S. O. & Svensson, A. 2014: Location of cation impurities in NGRIP deep ice revealed by cryo-cell UV-laser-ablation ICPMS, Journal of Glaciology, 60, 970-988. Eichler, A., Schwikowski, M., Gäggeler, H. W. 2001: Meltwater-induced relocation of chemical species in Alpine firn, Tellus B, 53, 192-203. Reinhardt, H., Kriews, M., Miller, H., Schrems, O., Lüdke, C., Hoffmann, E. & Skole, J. 2001: Laser ablation inductively coupled plasma mass spectrometry: a new tool for trace element analysis in ice cores, Fresenius' Journal of Analytical Chemistry, 370, 629-636. Schwikowski, M., Barbante, C., Doering, T., Gäggeler, H. W., Boutron, C., Schotterer, U., Tobler, L., van de Velde, K., Ferrari, C., Cozzi, G., Rosman, K., Cescon, P. 2004: Post-17th-Century Changes of European Lead Emissions Recorded in High-Altitude Alpine Snow and Ice, Environmental Science & Technology, 38, 957-964. Sneed, S. B., Mayewski, P. A., Sayre, W. G., Handley, M. J., Kurbatov, A. V., Taylor, K. C., Bohleber, P., Wagenbach, D., Erhardt, T. & Spaulding, N. E. 2015: New LA-ICP-MS cryocell and calibration technique for sub-millimeter analysis of ice cores, Journal of Glaciology, 61, 233-242.

Deep learning and shapes similarity for joint segmentation and tracing single neurons in SEM images

NASA Astrophysics Data System (ADS)

Rao, Qiang; Xiao, Chi; Han, Hua; Chen, Xi; Shen, Lijun; Xie, Qiwei

2017-02-01

Extracting the structure of single neurons is critical for understanding how they function within the neural circuits. Recent developments in microscopy techniques, and the widely recognized need for openness and standardization provide a community resource for automated reconstruction of dendritic and axonal morphology of single neurons. In order to look into the fine structure of neurons, we use the Automated Tape-collecting Ultra Microtome Scanning Electron Microscopy (ATUM-SEM) to get images sequence of serial sections of animal brain tissue that densely packed with neurons. Different from other neuron reconstruction method, we propose a method that enhances the SEM images by detecting the neuronal membranes with deep convolutional neural network (DCNN) and segments single neurons by active contour with group shape similarity. We joint the segmentation and tracing together and they interact with each other by alternate iteration that tracing aids the selection of candidate region patch for active contour segmentation while the segmentation provides the neuron geometrical features which improve the robustness of tracing. The tracing model mainly relies on the neuron geometrical features and is updated after neuron being segmented on the every next section. Our method enables the reconstruction of neurons of the drosophila mushroom body which is cut to serial sections and imaged under SEM. Our method provides an elementary step for the whole reconstruction of neuronal networks.

IJS procedure for RELAP5 to TRACE input model conversion using SNAP

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

Prosek, A.; Berar, O. A.

2012-07-01

The TRAC/RELAP Advanced Computational Engine (TRACE) advanced, best-estimate reactor systems code developed by the U.S. Nuclear Regulatory Commission comes with a graphical user interface called Symbolic Nuclear Analysis Package (SNAP). Much of efforts have been done in the past to develop the RELAP5 input decks. The purpose of this study is to demonstrate the Institut 'Josef Stefan' (IJS) conversion procedure from RELAP5 to TRACE input model of BETHSY facility. The IJS conversion procedure consists of eleven steps and is based on the use of SNAP. For calculations of the selected BETHSY 6.2TC test the RELAP5/MOD3.3 Patch 4 and TRACE V5.0more » Patch 1 were used. The selected BETHSY 6.2TC test was 15.24 cm equivalent diameter horizontal cold leg break in the reference pressurized water reactor without high pressure and low pressure safety injection. The application of the IJS procedure for conversion of BETHSY input model showed that it is important to perform the steps in proper sequence. The overall calculated results obtained with TRACE using the converted RELAP5 model were close to experimental data and comparable to RELAP5/MOD3.3 calculations. Therefore it can be concluded, that proposed IJS conversion procedure was successfully demonstrated on the BETHSY integral test facility input model. (authors)« less

Visualization of Concurrent Program Executions

NASA Technical Reports Server (NTRS)

Artho, Cyrille; Havelund, Klaus; Honiden, Shinichi

2007-01-01

Various program analysis techniques are efficient at discovering failures and properties. However, it is often difficult to evaluate results, such as program traces. This calls for abstraction and visualization tools. We propose an approach based on UML sequence diagrams, addressing shortcomings of such diagrams for concurrency. The resulting visualization is expressive and provides all the necessary information at a glance.

Draft Genome Sequences of 37 Salmonella enterica Strains Isolated from Poultry Sources in Nigeria.

PubMed

Useh, Nicodemus M; Ngbede, Emmanuel O; Akange, Nguavese; Thomas, Milton; Foley, Andrew; Keena, Mitchel Chan; Nelson, Eric; Christopher-Hennings, Jane; Tomita, Masaru; Suzuki, Haruo; Scaria, Joy

2016-05-05

Here, we report the availability of draft genomes of several Salmonella serotypes, isolated from poultry sources from Nigeria. These genomes will help to further understand the biological diversity of S. enterica and will serve as references in microbial trace-back studies to improve food safety. Copyright © 2016 Useh et al.

Prospective Teachers' Learning to Provide Instructional Explanations: How Does It Look and What Might It Take?

ERIC Educational Resources Information Center

Charalambous, Charalambos Y.; Hill, Heather C.; Ball, Deborah L.

2011-01-01

Several studies have documented prospective teachers' (PSTs) difficulties in offering instructional explanations. However, less is known about PSTs' learning to provide explanations. To address this gap, we trace changes in the explanations offered by a purposeful sample of PSTs before and after a mathematics content/methods course sequence.…

Permafrost as palaeo-environmental archive - potentials and limitations

NASA Astrophysics Data System (ADS)

Schirrmeister, L.; Wetterich, S.; Meyer, H.; Grosse, G.; Schwamborn, G.; Siegert, C.

2009-04-01

Since 1994, the Periglacial Research Group of the Alfred Wegener Institute is studying permafrost sequences of the Beringian landmass. The study sites in Siberia cover lake banks on Taymyr Peninsula, coastal sites at the Laptev and the East Siberian Seas, locations in the Lena Delta, at the lower Kolyma river, the middle Lena and the lower Aldan rivers, and the catchment area of the El'gygytgyn crater lake in Chukotka. In Alaska, permafrost tunnels near Fairbanks and Barrow, and coastal sites on the Seward Peninsula coast were studied. In addition, Canadian sites on Herschel Island in the Beaufort Sea and at the adjacent coast of the Yukon plain were studied. Subsurface exposures like tunnels and cellars provided the opportunity for three-dimensional studies of sedimentary and ground ice features, relatively ‘clean' field conditions for in-situ experiments, monitoring procedures, and detailed and repeatable sampling. Permafrost cores were drilled in order to study inaccessible sequences below the terrain surface and shelf sea floor. Cores were transported and stored frozen for further high-resolution analysis. Reference core sections were preserved for subsequent later studies. Terrestrial sediment cores are highly localized records, sometimes problematic in extrapolating horizons in inhomogeneous sediments like ground ice-deformed permafrost deposits, and drill campaigns are usually cost intensive and logistical challenging. Coastal permafrost cliffs often naturally expose large cross sections trough modern and ancient landscapes. Contrary to cores, they provide an opportunity to study the wider context of depositional environments and ground ice features. Due to the relative easy access to coasts and the recurring natural exposure of cliffs by thermo-abrasive wave action they are very convenient study objects for regional comparisons and correlation of past environmental conditions. Finally, palaeogeographical reconstructions are also guided by remote sensing-based analyses of geomorphological surface patterns, like Yedoma hills, thermokarst depressions, pingos or thermoerosional valleys. We generally relied on a multidisciplinary approach to study permafrost sequences in order to use the rich palaeo-environmental information stored in these frozen records. Cryofacies analysis describes both sediment and ice structures that allow interpretation of freezing conditions, thaw events, temperature regimes, and the local accumulation conditions. Ground ice bodies were sampled by ice screw and chain saw for analysis of hydrochemical and stable isotope composition. Several ground ice types were classified. The interaction between ice, sediment, and cryosoil were determined. The isotope signatures of sub-vertically layered ice wedges contain information about temperature variations, evaporation conditions and precipitation sources during different periods of ice wedge formation. The stratigraphy of the permafrost sequences was determined by lithostratigraphical classifications and geochronological results. Numerous sediment parameters were measured for differentiation between horizons in individual exposures, for local and regional stratigraphic correlation of permafrost sequences as well as for reconstruction of accumulation and transport conditions. Age determinations were carried out by radiocarbon analyses on organic remains, isochron uranium-thorium disequilibria technique on peats, optical stimulated luminescence on clastic sediments, and 36Cl/Cl stable isotope ratios measurements in ground ice. For palaeo-ecological reconstructions various fossil bioindicators were studied including pollen, plant macro-remains, insects, ostracods, testate amoebae, diatoms, chironomids, and mammal bones of the so-called mammoth fauna. By combining these data sets, we assembled a complex picture of the climate, landscape and vegetation dynamics of the studied regions during the Quaternary past. Derived palaeo-information includes mean annual air temperatures, mean winter temperatures, mean Juli temperatures, precipitation, humidity, soil climate and chemistry, hydrology and hydrochemistry of waters). The general potential of permafrost archives includes spatial (circumarctic, high arctic to boreal zones) and temporal (Mid Pleistocene to modern) environmental gradients. Lateral cross sections contain information about permafrost degradation during interglacial periods, the aggradation of ice-rich sequences during stadial and interstadial periods, and extreme changes in periglacial hydrology during the late Quaternary. The spatial reconstruction of ancient landscapes is possible by detailed study of kilometer-long coastal exposures. Temporally relative high resolution (about 50 years) isotope data from ice wedges reflect the Late Pleistocene to Holocene climate transition. Using transfer functions for pollen, plant macro remains or chironomids, the numerical estimation of palaeo-climate data (temperature and precipitation) is possible. The limitations of permafrost archives are the frequent lack of continuous sequences due to thermokarst or thermo-erosion events. Local stratigraphies are sometimes difficult to correlate on a regional scale because of permafrost degradation and neotectonic influence on the accumulative/erosive environment in some regions. Until now there are still uncertainties for comparing different geochronological methods, some of them related to unknown influences of permafrost processes on chemical and physical parameters important to the age determination technique. Due to strong cryoturbation patterns and sometimes challenging sampling situations on near-vertical frozen exposures the geochronological resolution in permafrost sequences is usually lower than in lacustrine sequences or glacial ice cores. Eventually, as for any other archive, we need to consider the effect of local versus regional signals derived from the palaeo-ecological interpretation of fossil records.

Masking as an effective quality control method for next-generation sequencing data analysis.

PubMed

Yun, Sajung; Yun, Sijung

2014-12-13

Next generation sequencing produces base calls with low quality scores that can affect the accuracy of identifying simple nucleotide variation calls, including single nucleotide polymorphisms and small insertions and deletions. Here we compare the effectiveness of two data preprocessing methods, masking and trimming, and the accuracy of simple nucleotide variation calls on whole-genome sequence data from Caenorhabditis elegans. Masking substitutes low quality base calls with 'N's (undetermined bases), whereas trimming removes low quality bases that results in a shorter read lengths. We demonstrate that masking is more effective than trimming in reducing the false-positive rate in single nucleotide polymorphism (SNP) calling. However, both of the preprocessing methods did not affect the false-negative rate in SNP calling with statistical significance compared to the data analysis without preprocessing. False-positive rate and false-negative rate for small insertions and deletions did not show differences between masking and trimming. We recommend masking over trimming as a more effective preprocessing method for next generation sequencing data analysis since masking reduces the false-positive rate in SNP calling without sacrificing the false-negative rate although trimming is more commonly used currently in the field. The perl script for masking is available at http://code.google.com/p/subn/. The sequencing data used in the study were deposited in the Sequence Read Archive (SRX450968 and SRX451773).

Quark enables semi-reference-based compression of RNA-seq data.

PubMed

Sarkar, Hirak; Patro, Rob

2017-11-01

The past decade has seen an exponential increase in biological sequencing capacity, and there has been a simultaneous effort to help organize and archive some of the vast quantities of sequencing data that are being generated. Although these developments are tremendous from the perspective of maximizing the scientific utility of available data, they come with heavy costs. The storage and transmission of such vast amounts of sequencing data is expensive. We present Quark, a semi-reference-based compression tool designed for RNA-seq data. Quark makes use of a reference sequence when encoding reads, but produces a representation that can be decoded independently, without the need for a reference. This allows Quark to achieve markedly better compression rates than existing reference-free schemes, while still relieving the burden of assuming a specific, shared reference sequence between the encoder and decoder. We demonstrate that Quark achieves state-of-the-art compression rates, and that, typically, only a small fraction of the reference sequence must be encoded along with the reads to allow reference-free decompression. Quark is implemented in C ++11, and is available under a GPLv3 license at www.github.com/COMBINE-lab/quark. rob.patro@cs.stonybrook.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

IMGD: an integrated platform supporting comparative genomics and phylogenetics of insect mitochondrial genomes

PubMed Central

Lee, Wonhoon; Park, Jongsun; Choi, Jaeyoung; Jung, Kyongyong; Park, Bongsoo; Kim, Donghan; Lee, Jaeyoung; Ahn, Kyohun; Song, Wonho; Kang, Seogchan; Lee, Yong-Hwan; Lee, Seunghwan

2009-01-01

Background Sequences and organization of the mitochondrial genome have been used as markers to investigate evolutionary history and relationships in many taxonomic groups. The rapidly increasing mitochondrial genome sequences from diverse insects provide ample opportunities to explore various global evolutionary questions in the superclass Hexapoda. To adequately support such questions, it is imperative to establish an informatics platform that facilitates the retrieval and utilization of available mitochondrial genome sequence data. Results The Insect Mitochondrial Genome Database (IMGD) is a new integrated platform that archives the mitochondrial genome sequences from 25,747 hexapod species, including 112 completely sequenced and 20 nearly completed genomes and 113,985 partially sequenced mitochondrial genomes. The Species-driven User Interface (SUI) of IMGD supports data retrieval and diverse analyses at multi-taxon levels. The Phyloviewer implemented in IMGD provides three methods for drawing phylogenetic trees and displays the resulting trees on the web. The SNP database incorporated to IMGD presents the distribution of SNPs and INDELs in the mitochondrial genomes of multiple isolates within eight species. A newly developed comparative SNU Genome Browser supports the graphical presentation and interactive interface for the identified SNPs/INDELs. Conclusion The IMGD provides a solid foundation for the comparative mitochondrial genomics and phylogenetics of insects. All data and functions described here are available at the web site . PMID:19351385

A transcriptome-wide, organ-specific regulatory map of Dendrobium officinale, an important traditional Chinese orchid herb

PubMed Central

Meng, Yijun; Yu, Dongliang; Xue, Jie; Lu, Jiangjie; Feng, Shangguo; Shen, Chenjia; Wang, Huizhong

2016-01-01

Dendrobium officinale is an important traditional Chinese herb. Here, we did a transcriptome-wide, organ-specific study on this valuable plant by combining RNA, small RNA (sRNA) and degradome sequencing. RNA sequencing of four organs (flower, root, leaf and stem) of Dendrobium officinale enabled us to obtain 536,558 assembled transcripts, from which 2,645, 256, 42 and 54 were identified to be highly expressed in the four organs respectively. Based on sRNA sequencing, 2,038, 2, 21 and 24 sRNAs were identified to be specifically accumulated in the four organs respectively. A total of 1,047 mature microRNA (miRNA) candidates were detected. Based on secondary structure predictions and sequencing, tens of potential miRNA precursors were identified from the assembled transcripts. Interestingly, phase-distributed sRNAs with degradome-based processing evidences were discovered on the long-stem structures of two precursors. Target identification was performed for the 1,047 miRNA candidates, resulting in the discovery of 1,257 miRNA--target pairs. Finally, some biological meaningful subnetworks involving hormone signaling, development, secondary metabolism and Argonaute 1-related regulation were established. All of the sequencing data sets are available at NCBI Sequence Read Archive (http://www.ncbi.nlm.nih.gov/sra/). Summarily, our study provides a valuable resource for the in-depth molecular and functional studies on this important Chinese orchid herb. PMID:26732614

The Universal Protein Resource (UniProt): an expanding universe of protein information.

PubMed

Wu, Cathy H; Apweiler, Rolf; Bairoch, Amos; Natale, Darren A; Barker, Winona C; Boeckmann, Brigitte; Ferro, Serenella; Gasteiger, Elisabeth; Huang, Hongzhan; Lopez, Rodrigo; Magrane, Michele; Martin, Maria J; Mazumder, Raja; O'Donovan, Claire; Redaschi, Nicole; Suzek, Baris

2006-01-01

The Universal Protein Resource (UniProt) provides a central resource on protein sequences and functional annotation with three database components, each addressing a key need in protein bioinformatics. The UniProt Knowledgebase (UniProtKB), comprising the manually annotated UniProtKB/Swiss-Prot section and the automatically annotated UniProtKB/TrEMBL section, is the preeminent storehouse of protein annotation. The extensive cross-references, functional and feature annotations and literature-based evidence attribution enable scientists to analyse proteins and query across databases. The UniProt Reference Clusters (UniRef) speed similarity searches via sequence space compression by merging sequences that are 100% (UniRef100), 90% (UniRef90) or 50% (UniRef50) identical. Finally, the UniProt Archive (UniParc) stores all publicly available protein sequences, containing the history of sequence data with links to the source databases. UniProt databases continue to grow in size and in availability of information. Recent and upcoming changes to database contents, formats, controlled vocabularies and services are described. New download availability includes all major releases of UniProtKB, sequence collections by taxonomic division and complete proteomes. A bibliography mapping service has been added, and an ID mapping service will be available soon. UniProt databases can be accessed online at http://www.uniprot.org or downloaded at ftp://ftp.uniprot.org/pub/databases/.

Isotope Tracing of Long-Term Cadmium Fluxes in an Agricultural Soil.

PubMed

Salmanzadeh, Mahdiyeh; Hartland, Adam; Stirling, Claudine H; Balks, Megan R; Schipper, Louis A; Joshi, Chaitanya; George, Ejin

2017-07-05

Globally widespread phosphate fertilizer applications have resulted in long-term increases in the concentration of cadmium (Cd) in soils. The accumulation of this biotoxic, and bioaccumulative metal presents problems for the management of soil-plant-animal systems, because the magnitude and direction of removal fluxes (e.g., crop uptake, leaching) have been difficult to estimate. Here, Cd isotopic compositions (δ 114/110 Cd) of archived fertilizer and soil samples from a 66 year-long agricultural field trial in Winchmore, New Zealand, were used to constrain the Cd soil mass balance between 1959 and 2015 AD, informing future soil Cd accumulation trajectories. The isotopic partitioning of soil Cd sources in this system was aided by a change in phosphate source rocks in 1998 AD, and a corresponding shift in fertilizer isotope composition. The dominant influence of mixing between isotopically distinct Cd end-members was confirmed by a Bayesian modeling approach. Furthermore, isotope mass balance modeling revealed that Cd removal processes most likely increased in magnitude substantially between 2000 and 2015 AD, implying an increase in Cd bioaccumulation and/or leaching over that interval. Natural-abundance stable isotopes are introduced here as a powerful tool for tracing the fate of Cd in agricultural soils, and potentially the wider environment.

OBSERVATIONAL EVIDENCE AGAINST LONG-LIVED SPIRAL ARMS IN GALAXIES

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

Foyle, K.; Rix, H.-W.; Walter, F.

2011-07-10

We test whether the spiral patterns apparent in many large disk galaxies should be thought of as dynamical features that are stationary in a corotating frame for {approx}> t{sub dyn}, as implied by the density wave approach for explaining spiral arms. If such spiral arms have enhanced star formation (SF), observational tracers for different stages of the SF sequence should show a spatial ordering, from upstream to downstream in the corotating frame: dense H I, CO, tracing molecular hydrogen gas, 24 {mu}m emission tracing enshrouded SF, and UV emission tracing unobscured young stars. We argue that such a spatial orderingmore » should be reflected in the angular cross-correlation (CC, in polar coordinates) using all azimuthal positions among pairs of these tracers; the peak of the CC should be offset from zero, in different directions inside and outside the corotation radius. Recent spiral SF simulations by Dobbs and Pringle show explicitly that for the case of a stationary spiral arm potential such angular offsets between gas and young stars of differing ages should be observable as cross-correlation offsets. We calculate the angular cross-correlations for different observational SF sequence tracers in 12 nearby spiral galaxies, drawing on a data set with high-quality maps of the neutral gas (H I, THINGS) and molecular gas (CO, HERACLES), along with 24 {mu}m emission (Spitzer, SINGS); we include FUV images (GALEX) and 3.6 {mu}m emission (Spitzer, IRAC) for some galaxies, tracing aging stars and longer timescales. In none of the resulting tracer cross-correlations for this sample do we find systematic angular offsets, which would be expected for a stationary dynamical spiral pattern of well-defined pattern speed. This result indicates that spiral density waves in their simplest form are not an important aspect of explaining spirals in large disk galaxies.« less

Lu-Hf, in-situ Sr and Pb isotope and trace element systematics for mantle eclogites from the Diavik diamond mine: Evidence for Paleoproterozoic subduction beneath the Slave craton, Canada

NASA Astrophysics Data System (ADS)

Schmidberger, Stefanie S.; Simonetti, Antonio; Heaman, Larry M.; Creaser, Robert A.; Whiteford, Sean

2007-02-01

Lu-Hf, Sm-Nd and in-situ clinopyroxene Sr and Pb isotope systematics, and mineral major and in-situ trace element compositions were obtained for a suite of non-diamond and diamond-bearing eclogites from the Diavik kimberlites (A154; 55 Ma old), Slave craton (Canada). Temperature estimates of last equilibration in the lithosphere for the non-diamond-bearing Diavik eclogites define two groups; low-temperature (800-1050 °C) and high-temperature eclogites (1100-1300 °C). Most diamond-eclogites indicate temperatures similar to those of the high-temperature eclogites. Isotopic and major and trace element systematics for the non-diamond- and diamond-bearing eclogites indicate overlapping chemical compositions suggesting similar rock formational histories. Calculated whole rock major and trace element abundances using chemical and modal abundances for constituent minerals exhibit broad similarities with mafic cumulates from ophiolite sequences. Most importantly the calculated whole rock eclogite compositions display positive Sr and Eu anomalies, typically interpreted as the result of plagioclase accumulation in cumulate rocks of oceanic crust sequences. Initial whole rock Hf isotopic values and in-situ Sr isotope data from clinopyroxene grains provide evidence that the eclogites were derived from precursor rocks with depleted mantle isotope characteristics. These combined results support the interpretation that the eclogites from Diavik represent remnants of subducted oceanic crust. Lu-Hf isotope systematics indicate that the oceanic protolith for the eclogites formed in the Paleoproterozoic at ˜ 2.1 Ga, which is in agreement with the in-situ Pb isotope data from clinopyroxene. This result also corroborates the ˜ 2.1 Ga Lu-Hf model ages recorded by mantle zircons from eclogite found within the Jericho kimberlite in the northern Slave Province (˜ 200 km northwest of Diavik). The results from both studies indicate a link between eclogite formation and Paleoproterozoic subduction of oceanic lithosphere along the present-day western margin of the Archean Slave craton.

Quantitative Tracking of Combinatorially Engineered Populations with Multiplexed Binary Assemblies.

PubMed

Zeitoun, Ramsey I; Pines, Gur; Grau, Willliam C; Gill, Ryan T

2017-04-21

Advances in synthetic biology and genomics have enabled full-scale genome engineering efforts on laboratory time scales. However, the absence of sufficient approaches for mapping engineered genomes at system-wide scales onto performance has limited the adoption of more sophisticated algorithms for engineering complex biological systems. Here we report on the development and application of a robust approach to quantitatively map combinatorially engineered populations at scales up to several dozen target sites. This approach works by assembling genome engineered sites with cell-specific barcodes into a format compatible with high-throughput sequencing technologies. This approach, called barcoded-TRACE (bTRACE) was applied to assess E. coli populations engineered by recursive multiplex recombineering across both 6-target sites and 31-target sites. The 31-target library was then tracked throughout growth selections in the presence and absence of isopentenol (a potential next-generation biofuel). We also use the resolution of bTRACE to compare the influence of technical and biological noise on genome engineering efforts.

Network-wide reorganization of procedural memory during NREM sleep revealed by fMRI

PubMed Central

Vahdat, Shahabeddin; Fogel, Stuart; Benali, Habib; Doyon, Julien

2017-01-01

Sleep is necessary for the optimal consolidation of newly acquired procedural memories. However, the mechanisms by which motor memory traces develop during sleep remain controversial in humans, as this process has been mainly investigated indirectly by comparing pre- and post-sleep conditions. Here, we used functional magnetic resonance imaging and electroencephalography during sleep following motor sequence learning to investigate how newly-formed memory traces evolve dynamically over time. We provide direct evidence for transient reactivation followed by downscaling of functional connectivity in a cortically-dominant pattern formed during learning, as well as gradual reorganization of this representation toward a subcortically-dominant consolidated trace during non-rapid eye movement (NREM) sleep. Importantly, the putamen functional connectivity within the consolidated network during NREM sleep was related to overnight behavioral gains. Our results demonstrate that NREM sleep is necessary for two complementary processes: the restoration and reorganization of newly-learned information during sleep, which underlie human motor memory consolidation. DOI: http://dx.doi.org/10.7554/eLife.24987.001 PMID:28892464

Petroleum formation during serpentinization: the evidence of trace elements

NASA Astrophysics Data System (ADS)

Szatmari, P.; Fonseca, T. C.; Miekeley, N. F.

2002-05-01

An organic source of petroleum formation is well attested by many biomarkers. This need not, however, exclude contribution from inorganic sources. During serpentinization, in the absence of free oxygen, oxidation of bivalent Fe to magnetite breaks up the water molecule, generating hydrogen and creating one of the most reducing environments near the Earth's surface (Janecky & Seyfried, 1986). Szatmari (1989) proposed that some petroleum forms at plate boundaries by Fischer-Tropsch-type synthesis over serpentinizing peridotites and suggested that Ni, an element rare in the continental crust but important in both petroleum and the mantle, may be indicative of such a source. Recently, Holm and Charlou (2001) observed hydrocarbon formation by Fischer-Tropsch-type synthesis over serpentinizing peridotites of the Mid-Atlantic Ridge. To test whether the relative amounts of other trace elements in petroleum are in agreement with a serpentinizing source, we analyzed by internally coupled plasma-mass spectroscopy (ICP-MS) 22 trace elements in 68 oils sampled in seven sedimentary basins throughout Brazil. We found that trace elements in the oils correlate well with mantle peridotites and reflects the process of hydrothermal serpentinization during continental breakup. Four groups may be distinguished. In serpentinites, trace elements of the first group, Ti, Cr, Mn, and Fe, are largely retained in low-solubility magnetite and other spinels formed during serpentinization or inherited from the original peridotites. In the oils, when normalized to mantle peridotites, these elements are at relatively low levels, about 10,000 times less than their abundances in mantle peridotites, reflecting their low availability from stable minerals. In contrast, trace elements of the second group, which includes V, Co, Ni, Cu, Zn, Ga, Rb, Sr, Y, Ba, La, Ce, and Nd, pass during serpentinization mostly into serpentine minerals or solution. In the oils, when normalized to mantle peridotites, these elements are at higher levels than those of the first group, about 300 times less than their abundances in mantle peridotites, reflecting their higher availability during serpentinization. Within both groups, trace metal ratios and A/(A+B) type proportionalities in the oils are close to mantle peridotites. V behaves somewhat differently: in lacustrine sequences V contents in the oils are low and the ratios of V to other elements of the second group are mantle-like, whereas in marine sequences V and its ratios to other trace elements rise by orders of magnitude. Trace elements commonly enriched in formation fluids and hydrothermal brines (Rb, Sr, Ba, Cu, Zn), when normalized to mantle peridotites, are enriched in the oils by about 0.5 order of magnitude relative to other elements of the second group. The third group of elements includes S, Mo, and As. These elements occur in the oils at abundances similar to sea water and are, when normalized to mantle peridotites and Ni, enriched in the oils by several orders of magnitude, indicating sea water reacting with peridotites during sepentinization as their possible source. Finally trace elements of the fourth group, such as Pb and Ag, are enriched in the oils by several orders of magnitude relative to both mantle peridotites and sea water and were presumably mobilized from shales by hydrothermal fluids. References:Holm, N.G. and Charlou, J.L., 2001, EPSL 191, 1-8. Janecky, D.R. and Seyfried, W.E., 1986, Geochim. Cosmochim. Acta 50, 1357-1378. Szatmari, P., 1989, AAPG Bull. 73, 989-998.

[Assessment of an algorithm to identify paediatric-onset celiac disease cases through administrative healthcare databases].

PubMed

Pitter, Gisella; Gnavi, Roberto; Romor, Pierantonio; Zanotti, Renzo; Simonato, Lorenzo; Canova, Cristina

2017-01-01

to assess the role of four administrative healthcare databases (pathology reports, copayment exemptions, hospital discharge records, gluten-free food prescriptions) for the identification of possible paediatric cases of celiac disease. population-based observational study with record linkage of administrative healthcare databases. SETTING AND PARTICIPANT S: children born alive in the Friuli Venezia Giulia Region (Northern Italy) to resident mothers in the years 1989-2012, identified using the regional Medical Birth Register. we defined possible celiac disease as having at least one of the following, from 2002 onward: 1. a pathology report of intestinal villous atrophy; 2. a copayment exemption for celiac disease; 3. a hospital discharge record with ICD-9-CM code of celiac disease; 4. a gluten-free food prescription. We evaluated the proportion of subjects identified by each archive and by combinations of archives, and examined the temporal relationship of the different sources in cases identified by more than one source. RESULT S: out of 962 possible cases of celiac disease, 660 (68.6%) had a pathology report, 714 (74.2%) a copayment exemption, 667 (69.3%) a hospital discharge record, and 636 (66.1%) a gluten-free food prescription. The four sources coexisted in 42.2% of subjects, whereas 30.2% were identified by two or three sources and 27.6% by a single source (16.9% by pathology reports, 4.2% by hospital discharge records, 3.9% by copayment exemptions, and 2.6% by gluten-free food prescriptions). Excluding pathology reports, 70.6% of cases were identified by at least two sources. A definition based on copayment exemptions and discharge records traced 80.5% of the 962 possible cases of celiac disease; whereas a definition based on copayment exemptions, discharge records, and gluten-free food prescriptions traced 83.1% of those cases. The temporal relationship of the different sources was compatible with the typical diagnostic pathway of subjects with celiac disease. the four sources were only partially consistent. A relevant proportion of all possible cases of paediatric celiac disease were identified exclusively by pathology reports.

Influences of different dietary contents of macrominerals on the availability of trace elements in horses.

PubMed

Neustädter, L-T; Kamphues, J; Ratert, C

2018-04-01

In this study, influences of a reduced macromineral intake on the trace element metabolism in horses at maintenance were investigated. Background of this study is the revised recommendation on the macromineral supply for horses (GfE ). Balance studies on three adult pony geldings with body weights of 405 / 348 / 384 kg were performed to obtain data on apparent digestibility (aD), retention and serum concentrations of different trace elements (Cu, Zn, Se) at different dietary macromineral levels. A mineral supplement or a complementary feed-with a reduced macromineral content-was added to a hay-based diet (daily 5.5 kg hay per animal, split in three servings a day), beside distilled water was offered. The diets were offered one after the other in a way that all ponies had the same sequence of treatments. The native macromineral contents of the daily offered amount of hay already surpassed the new recommendations whereas dietary trace elements needed to be supplemented. There were no statistically significant differences (p ≤ .05) concerning the aD of copper, zinc and selenium comparing the diets with and without macromineral supplementation. Serum levels of these three trace elements were not affected by the different macromineral content of the diet. Results of this study, based on a 22-day feeding period for each treatment, indicate that a macromineral supplementation of a hay-based diet for adult horses at maintenance was not necessary. However, no negative effects of added macrominerals on the trace element metabolism occurred in this study. © 2017 Blackwell Verlag GmbH.

Preserving a Unique Archive for Long-Term Solar Variability Studies

NASA Astrophysics Data System (ADS)

Webb, David F.; Hewins, Ian; McFadden, Robert; Emery, Barbara; Gibson, Sarah; Denig, William

2016-05-01

In 1964 (solar cycle 20) Patrick McIntosh began creating hand-drawn synoptic maps of solar activity, based on Hydrogen alpha (Hα) imaging measurements. These synoptic maps were unique because they traced the polarity inversion lines (PILs), connecting widely separated filaments, fibril patterns and plage corridors to reveal the large-scale organization of the solar magnetic field. He and his assistants later included coronal hole (CH) boundaries to the maps, usually from ground-based He-I 10830 images. They continued making these maps until 2010 (the start of solar cycle 24), yielding more than 40 years (~ 540 Carrington rotations) or nearly four complete solar cycles (SCs) of synoptic maps. The McIntosh collection of maps forms a unique and consistent set of global solar magnetic field data, and are unique tools for studying the structure and evolution of the large-scale solar fields and polarity boundaries, because: 1) they have excellent spatial resolution for defining polarity boundaries, 2) the organization of the fields into long-lived, coherent features is clear, and 3) the data are relatively homogeneous over four solar cycles. After digitization and archiving, these maps -- along with computer codes permitting efficient searches of the map arrays -- will be made publicly available at NOAA’s National Centers for Environmental Information (NCEI) in their final, searchable form. This poster is a progress report of the project so far and some suggested scientific applications.

Exome capture sequencing reveals new insights into hepatitis B virus-induced hepatocellular carcinoma at the early stage of tumorigenesis.

PubMed

Chen, Yong; Wang, Lijuan; Xu, Hexiang; Liu, Xingxiang; Zhao, Yingren

2013-10-01

Hepatocellular carcinoma (HCC), the most common type of liver cancer, is the third primary cause of cancer-related mortality worldwide. The molecular mechanisms underlying the initiation and formation of HCC remain obscure. In the present study, we performed exome sequencing using tumor and normal tissues from 3 hepatitis B virus (HBV)-positive BCLC stage A HCC patients. Bioinformatic analysis was performed to find candidate protein-altering somatic mutations. Eighty damaging mutations were validated and 59 genes were reported to be mutated in HBV-related HCCs for the first time here. Further analysis using whole genome sequencing (WGS) data of 88 HBV-related HCC patients from the European Genome-phenome Archive database showed that mutations in 33 of the 59 genes were also detected in other samples. Variants of two newly found genes, ZNF717 and PARP4, were detected in more than 10% of the WGS samples. Several other genes, such as FLNA and CNTN2, are also noteworthy. Thus, the exome sequencing analysis of three BCLC stage A patients provides new insights into the molecular events governing the early steps of HBV-induced HCC tumorigenesis.

X-rays across the galaxy population - I. Tracing the main sequence of star formation

NASA Astrophysics Data System (ADS)

Aird, J.; Coil, A. L.; Georgakakis, A.

2017-03-01

We use deep Chandra imaging to measure the distribution of X-ray luminosities (LX) for samples of star-forming galaxies as a function of stellar mass and redshift, using a Bayesian method to push below the nominal X-ray detection limits. Our luminosity distributions all show narrow peaks at LX ≲ 1042 erg s-1 that we associate with star formation, as opposed to AGN that are traced by a broad tail to higher LX. Tracking the luminosity of these peaks as a function of stellar mass reveals an 'X-ray main sequence' with a constant slope ≈0.63 ± 0.03 over 8.5 ≲ log {M}_{ast }/M_{⊙} ≲ 11.5 and 0.1 ≲ z ≲ 4, with a normalization that increases with redshift as (1 + z)3.79 ± 0.12. We also compare the peak X-ray luminosities with UV-to-IR tracers of star formation rates (SFRs) to calibrate the scaling between LX and SFR. We find that LX ∝ SFR0.83 × (1 + z)1.3, where the redshift evolution and non-linearity likely reflect changes in high-mass X-ray binary populations of star-forming galaxies. Using galaxies with a broader range of SFR, we also constrain a stellar-mass-dependent contribution to LX, likely related to low-mass X-ray binaries. Using this calibration, we convert our X-ray main sequence to SFRs and measure a star-forming main sequence with a constant slope ≈0.76 ± 0.06 and a normalization that evolves with redshift as (1 + z)2.95 ± 0.33. Based on the X-ray emission, there is no evidence for a break in the main sequence at high stellar masses, although we cannot rule out a turnover given the uncertainties in the scaling of LX to SFR.

Tracing the phylogeographic history of Southeast Asian long-tailed macaques through mitogenomes of museum specimens.

PubMed

Yao, Lu; Li, Hongjie; Martin, Robert D; Moreau, Corrie S; Malhi, Ripan S

2017-11-01

The biogeographical history of Southeast Asia is complicated due to the continuous emergences and disappearances of land bridges throughout the Pleistocene. Here, we use long-tailed macaques (Macaca fascicularis), which are widely distributed throughout the mainland and islands of Southeast Asia, asa model for better understanding the biogeographical patterns of diversification in this geographically complex region. A reliable intraspecific phylogeny including individuals from localities on oceanic islands, continental islands, and the mainland is needed to trace relatedness along with the pattern and timing of colonization in this region. We used high-throughput sequencing techniques to sequence mitochondrial genomes (mitogenomes) from 95 Southeast Asian M. fascicularis specimens housed at natural history museums around the world. To achieve a comprehensive picture, we more than tripled the mitogenome sample size for M. fascicularis from previous studies, and for the first time included documented samples from the Philippines and several small Indonesian islands. Confirming the result from a previous, recent intraspecific phylogeny for M. fascicularis, the newly reconstructed phylogeny of 135 specimens divides the samples into two major clades: Clade A includes haplotypes from the mainland and some from northern Sumatra, while Clade B includes all insular haplotypes along with lineages from southern Sumatra. This study resolves a previous disparity by revealing a disjunction in the origin of Sumatran macaques, with separate lineages originating within the two major clades, suggesting that at least two major migrations to Sumatra occurred. However, our dated phylogeny reveals that the two major clades split ∼1.88Ma, which is earlier than in previously published phylogenies. Our new data reveal that most Philippine macaque lineages diverged from the Borneo stock within the last ∼0.06-0.43Ma. Finally, our study provides insight into successful sequencing of DNA across museums and shotgun sequencing of DNA specimens asa method to sequence the mitogenome. Copyright © 2017 Elsevier Inc. All rights reserved.

Decrease in gamma-band activity tracks sequence learning

PubMed Central

Madhavan, Radhika; Millman, Daniel; Tang, Hanlin; Crone, Nathan E.; Lenz, Fredrick A.; Tierney, Travis S.; Madsen, Joseph R.; Kreiman, Gabriel; Anderson, William S.

2015-01-01

Learning novel sequences constitutes an example of declarative memory formation, involving conscious recall of temporal events. Performance in sequence learning tasks improves with repetition and involves forming temporal associations over scales of seconds to minutes. To further understand the neural circuits underlying declarative sequence learning over trials, we tracked changes in intracranial field potentials (IFPs) recorded from 1142 electrodes implanted throughout temporal and frontal cortical areas in 14 human subjects, while they learned the temporal-order of multiple sequences of images over trials through repeated recall. We observed an increase in power in the gamma frequency band (30–100 Hz) in the recall phase, particularly in areas within the temporal lobe including the parahippocampal gyrus. The degree of this gamma power enhancement decreased over trials with improved sequence recall. Modulation of gamma power was directly correlated with the improvement in recall performance. When presenting new sequences, gamma power was reset to high values and decreased again after learning. These observations suggest that signals in the gamma frequency band may play a more prominent role during the early steps of the learning process rather than during the maintenance of memory traces. PMID:25653598

Automated quantitative assessment of proteins' biological function in protein knowledge bases.

PubMed

Mayr, Gabriele; Lepperdinger, Günter; Lackner, Peter

2008-01-01

Primary protein sequence data are archived in databases together with information regarding corresponding biological functions. In this respect, UniProt/Swiss-Prot is currently the most comprehensive collection and it is routinely cross-examined when trying to unravel the biological role of hypothetical proteins. Bioscientists frequently extract single entries and further evaluate those on a subjective basis. In lieu of a standardized procedure for scoring the existing knowledge regarding individual proteins, we here report about a computer-assisted method, which we applied to score the present knowledge about any given Swiss-Prot entry. Applying this quantitative score allows the comparison of proteins with respect to their sequence yet highlights the comprehension of functional data. pfs analysis may be also applied for quality control of individual entries or for database management in order to rank entry listings.

Integrated segmentation and recognition of connected Ottoman script

NASA Astrophysics Data System (ADS)

Yalniz, Ismet Zeki; Altingovde, Ismail Sengor; Güdükbay, Uğur; Ulusoy, Özgür

2009-11-01

We propose a novel context-sensitive segmentation and recognition method for connected letters in Ottoman script. This method first extracts a set of segments from a connected script and determines the candidate letters to which extracted segments are most similar. Next, a function is defined for scoring each different syntactically correct sequence of these candidate letters. To find the candidate letter sequence that maximizes the score function, a directed acyclic graph is constructed. The letters are finally recognized by computing the longest path in this graph. Experiments using a collection of printed Ottoman documents reveal that the proposed method provides >90% precision and recall figures in terms of character recognition. In a further set of experiments, we also demonstrate that the framework can be used as a building block for an information retrieval system for digital Ottoman archives.

Chronicles from the End of the Word: the Holocene climate variability in Tierra del Fuego

NASA Astrophysics Data System (ADS)

Waldmann, N.; Ariztegui, D.; Anselmetti, F.; Austin, J.; Moy, C.; Borromei, A.; Coronato, A.; Recasens, C.; Dunbar, R.; Martinez, M.; Olivera, D.

2008-12-01

Latest advances in the chronology and environmental importance of Antarctic paleoclimate records point towards a larger heterogeneity than previously thought. Thus, realistic inter-hemispheric correlations rely in the development of a tight array of well constrained records with a dense latitudinal coverage. Climatic records from southernmost Patagonia are hence critical corner-stones to link these Antarctic paleoclimatic archives with their South American counterparts. At 55° S on the Island of Tierra del Fuego, Lago Fagnano is located in one of the most substantially and extensively glaciated regions of southernmost South America during the Late Pleistocene. This elongated lake is the largest (~110 km long) and southernmost non-ice covered water body in the world. Existing on-shore geomorphological reconstructions combined with new lacustrine subsurface data, allowed us to better constrain the magnitude and chronology of the Fagnano glacier fluctuations since the LGM. The former Fagnano glacier flowed eastwards from the Darwin Cordillera fed by more than 50 tributary glaciers. The glacier spread over the low ranges and lowlands through three different lobes and was drained by four main outwash basins directly into the Atlantic Ocean. During the maximum ice-expansion, the ice-covered area was ca. 4000 km2 with a maximum length of ca. 132 km. A set of submerged frontal moraines covered by lacustrine infilling identified in the seismic survey suggests occasional eastward re-advances of the paleo-glacier within the overall westward deglaciation pattern. These re-advances may correspond to cold events such as the Antarctic Cold Reversal (ACR), the Huelmo- Mascardi Cold Event (HMCE) and/or the Younger Dryas Chronozone (YDC). The ongoing development of a robust age model blended with a multi-proxy dataset will potentially clarify remaining controversial issues dealing with the geographical extension and chronology of these cold episodes during the last deglaciation. A multi-proxy study of selected cores retrieved from the deepest part of the lacustrine basin allows characterizing the Holocene sedimentary record. Detailed petrophysical, sedimentological and geochemical studies of a complete laminated sequence reveal fluctuations in major and trace elements, as well as total organic matter content and palynological data suggesting an apparent cyclicity. These results provide a unique dataset that can be compared with other marine and continental archives to improve our understanding of the forcing mechanisms behind climate change and to validate the outcome of existing ocean and atmospheric climatic models for the Southern Hemisphere.

A tale of phenocrysts: trace element contents of boninites and forearc basalts from IODP Expedition 352

NASA Astrophysics Data System (ADS)

Chapman, T.; Clarke, G. L.; Reagan, M. K.; Sakuyama, T.; Godard, M.; Shervais, J. W.; Prytulak, J.; Shimizu, K.; Nelson, W. R.; Heaton, D. E.; Whattam, S. A.; Li, H.; Pearce, J. A.

2016-12-01

The Izu-Bonin Mariana (IBM) forearc represents an ideal location to study the dynamics of subduction initiation and to reveal the volcanic sequences appropriate to assess ophiolite origins. The volcanic stratigraphy recovered on Expedition 352 illustrates an abrupt shift from forearc basalt (FAB) to boninite magmatism, with limited transitional rock types, as observed from submersible and previous drill work in the Izu-Bonin and Mariana sections. The transition represents a change from decompression melting to fluxed melting of the mantle wedge. The volcanic stratigraphy has several distinct boninite chemical evolution trends (basaltic boninite, low- and high-silica boninite). Mineral assemblages and phenocryst trace element compositions vary throughout the volcanic sequence providing an opportunity to explore more completely boninite and FAB transitions and petrogenesis. FABs are characterised by early plagioclase crystallization and HREE enriched clinopyroxene with high Ti contents. Basaltic boninite and some low-silica boninite lavas have overlapping REE concentrations consistent with early plagioclase growth preceded by clinopyroxene. In contrast, textures and HREE depleted concentrations of clinopyroxene in high-silica boninite imply late plagioclase growth relative to olivine and orthopyroxene. Variations in mineral compositions and paragenesis in boninites reflect changes in magma compositions and a progressive depletion of mantle sources over time. This is illustrated via key incompatible and compatible trace element ratios and concentrations (e.g. Zr/Ti & V or Cr). The transition from FAB to low-Si boninite was subtle in terms of mineral modes, but was more evident in terms of the phase and lava compositions.

Searching for filaments and large-scale structure around DAFT/FADA clusters

NASA Astrophysics Data System (ADS)

Durret, F.; Márquez, I.; Acebrón, A.; Adami, C.; Cabrera-Lavers, A.; Capelato, H.; Martinet, N.; Sarron, F.; Ulmer, M. P.

2016-04-01

Context. Clusters of galaxies are located at the intersection of cosmic filaments and are still accreting galaxies and groups along these preferential directions. However, because of their relatively low contrast on the sky, filaments are difficult to detect (unless a large amount of spectroscopic data are available), and unambiguous detections have been limited until now to relatively low redshifts (z< ~ 0.3). Aims: This project is aimed at searching for extensions and filaments around clusters, traced by galaxies selected to be at the cluster redshift based on the red sequence. In the 0.4

The AMBRE project: Parameterisation of FGK-type stars from the ESO:HARPS archived spectra

NASA Astrophysics Data System (ADS)

De Pascale, M.; Worley, C. C.; de Laverny, P.; Recio-Blanco, A.; Hill, V.; Bijaoui, A.

2014-10-01

Context. The AMBRE project is a collaboration between the European Southern Observatory (ESO) and the Observatoire de la Côte d'Azur (OCA). It has been established to determine the stellar atmospheric parameters of the archived spectra of four ESO spectrographs. Aims: The analysis of the ESO:HARPS archived spectra for the determination of their atmospheric parameters (effective temperature, surface gravity, global metallicities, and abundance of α-elements over iron) is presented. The sample being analysed (AMBRE:HARPS) covers the period from 2003 to 2010 and is comprised of 126 688 scientific spectra corresponding to ~17 218 different stars. Methods: For the analysis of the AMBRE:HARPS spectral sample, the automated pipeline developed for the analysis of the AMBRE:FEROS archived spectra has been adapted to the characteristics of the HARPS spectra. Within the pipeline, the stellar parameters are determined by the MATISSE algorithm, which has been developed at OCA for the analysis of large samples of stellar spectra in the framework of galactic archaeology. In the present application, MATISSE uses the AMBRE grid of synthetic spectra, which covers FGKM-type stars for a range of gravities and metallicities. Results: We first determined the radial velocity and its associated error for the ~15% of the AMBRE:HARPS spectra, for which this velocity had not been derived by the ESO:HARPS reduction pipeline. The stellar atmospheric parameters and the associated chemical index [α/Fe] with their associated errors have then been estimated for all the spectra of the AMBRE:HARPS archived sample. Based on key quality criteria, we accepted and delivered the parameterisation of 93 116 (74% of the total sample) spectra to ESO. These spectra correspond to ~10 706 stars; each are observed between one and several hundred times. This automatic parameterisation of the AMBRE:HARPS spectra shows that the large majority of these stars are cool main-sequence dwarfs with metallicities greater than -0.5 dex (as expected, given that HARPS has been extensively used for planet searches around GK-stars).

Databases for Microbiologists

DOE PAGES

Zhulin, Igor B.

2015-05-26

Databases play an increasingly important role in biology. They archive, store, maintain, and share information on genes, genomes, expression data, protein sequences and structures, metabolites and reactions, interactions, and pathways. All these data are critically important to microbiologists. Furthermore, microbiology has its own databases that deal with model microorganisms, microbial diversity, physiology, and pathogenesis. Thousands of biological databases are currently available, and it becomes increasingly difficult to keep up with their development. Finally, the purpose of this minireview is to provide a brief survey of current databases that are of interest to microbiologists.

Databases for Microbiologists

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

Zhulin, Igor B.

Databases play an increasingly important role in biology. They archive, store, maintain, and share information on genes, genomes, expression data, protein sequences and structures, metabolites and reactions, interactions, and pathways. All these data are critically important to microbiologists. Furthermore, microbiology has its own databases that deal with model microorganisms, microbial diversity, physiology, and pathogenesis. Thousands of biological databases are currently available, and it becomes increasingly difficult to keep up with their development. Finally, the purpose of this minireview is to provide a brief survey of current databases that are of interest to microbiologists.

Databases for Microbiologists

PubMed Central

2015-01-01

Databases play an increasingly important role in biology. They archive, store, maintain, and share information on genes, genomes, expression data, protein sequences and structures, metabolites and reactions, interactions, and pathways. All these data are critically important to microbiologists. Furthermore, microbiology has its own databases that deal with model microorganisms, microbial diversity, physiology, and pathogenesis. Thousands of biological databases are currently available, and it becomes increasingly difficult to keep up with their development. The purpose of this minireview is to provide a brief survey of current databases that are of interest to microbiologists. PMID:26013493