11 results on '"Charles Troup"'
Search Results
2. Evaluation of a rapid DNA process with the RapidHIT® ID system using a specialized cartridge for extracted and quantified human DNA
- Author
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Dean Tsou, Phong Thanh Nguyen, Arnaldo Barican, Robert A. Schueren, Mattias Vangbo, Frank Lin, Bruce Goldman, Susana Salceda, Jim Klevenberg, David J. King, Corey Smith, Jacklyn Buscaino, Melissa Kuhn, Charles Troup, and Leto Farrales
- Subjects
0301 basic medicine ,Chromatography ,Computer science ,Sample (material) ,Buccal swab ,DNA extraction ,Pathology and Forensic Medicine ,law.invention ,03 medical and health sciences ,chemistry.chemical_compound ,Cartridge ,030104 developmental biology ,0302 clinical medicine ,chemistry ,law ,Genetics ,Crime scene ,A-DNA ,030216 legal & forensic medicine ,DNA ,Polymerase chain reaction - Abstract
The turn-around time of urgent crime scene DNA samples is often far longer than desired by law enforcement. Crime scene DNA sample processing involves both complex and routine processing steps. Simplification and integration of the routine steps would dramatically improve turn-around time and reduce the risk of operator contamination. Routine DNA extraction and quantitation is readily available. However, PCR amplification and electrophoretic analysis remain largely manual. Rapid DNA Analysis is a hands-free “swab in – profile out” process which consists of automated DNA extraction, amplification, separation, detection, and allele calling without human intervention. RapidHIT® 200 and RapidHIT ID are rapid DNA systems developed by IntegenX (Pleasanton, CA) and validated for the use of buccal swabs. A new generation of the RapidHIT sample cartridge for RapidHIT ID has been designed and tested which allows the loading of extracted and quantified DNA. RapidHIT EXT sample cartridge allows a user to generate a forensic DNA profile from less than 250 pg of extracted and quantified DNA in less than 90 min with less than one-minute hands-on time. Once the sample is loaded in the RapidHIT EXT sample cartridge, a DNA profile is produced after amplification, detection and automated data analysis. We report on sensitivity, reproducibility, concordance, DNA mixtures and carryover for EXT sample cartridges pre-loaded with GlobalFiler® Express and AmpFLSTR® NGM SElect™ Express, (Thermo Fisher Scientific, Waltham, MA) STR chemistries. Purified and quantified DNA from mock crime scene samples were used to demonstrate the utility of these cartridges in an established forensic laboratory.
- Published
- 2018
3. Validation of a rapid DNA process with the RapidHIT® ID system using GlobalFiler® Express chemistry, a platform optimized for decentralized testing environments
- Author
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Frank Lin, Mattias Vangbo, Charles Park, Dean Tsou, Susana Salceda, Francesca Pearson, Phong Thanh Nguyen, Jacklyn Buscaino, Robert A. Schueren, Corey Smith, Sayali Salodkar, Melissa Kuhn, Charles Troup, Bruce Goldman, Dennis Lehto, David A King, Jim Klevenberg, Rick Pittaro, Arnaldo Barican, and Justus Wunderle
- Subjects
0301 basic medicine ,Combined DNA Index System ,business.industry ,Process (computing) ,Computer security ,computer.software_genre ,Pathology and Forensic Medicine ,03 medical and health sciences ,Identification (information) ,030104 developmental biology ,0302 clinical medicine ,Software ,DNA profiling ,Software deployment ,Rapid dna ,Embedded system ,Genetics ,Microsatellite ,030216 legal & forensic medicine ,business ,computer - Abstract
The RapidHIT® ID is a fully automated sample-to-answer system for short tandem repeat (STR)-based human identification. The RapidHIT ID has been optimized for use in decentralized environments and processes presumed single source DNA samples, generating Combined DNA Index System (CODIS)-compatible DNA profiles in less than 90min. The system is easy to use, requiring less than one minute of hands-on time. Profiles are reviewed using centralized linking software, RapidLINK™ (IntegenX, Pleasanton, CA), a software tool designed to collate DNA profiles from single or multiple RapidHIT ID systems at different geographic locations. The RapidHIT ID has been designed to employ GlobalFiler® Express and AmpFLSTR® NGMSElect™, Thermo Fisher Scientific (Waltham, MA) STR chemistries. The Developmental Validation studies were performed using GlobalFiler® Express with single source reference samples according to Scientific Working Group for DNA Analysis Methods guidelines. These results show that multiple RapidHIT ID systems networked with RapidLINK software form a highly reliable system for wide-scale deployment in locations such as police booking stations and border crossings enabling real-time testing of arrestees, potential human trafficking victims, and other instances where rapid turnaround is essential.
- Published
- 2017
- Full Text
- View/download PDF
4. Developmental validation of a fully integrated sample-to-profile rapid human identification system for processing single-source reference buccal samples
- Author
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Richard Joseph Belcinski, Dennis W. Harris, David Wesley Wyrick, Neelima Mehendale, Stefanie Gangano, Brian Ciopyk, Yuan Li, Mattias Vangbo, Peter M. Vallone, Erica L.R. Butts, Alex Kindwall, Stevan B. Jovanovich, Helen Franklin, Stephen Williams, Charles Park, Timothy Woudenberg, Jim Klevenberg, David J. King, Bill Nielsen, Greg Bogdan, Robert A. Schueren, Omar El-Sissi, Kaiwan Chear, Charles Troup, Francesca Pearson, Nancy Stainton, Dean Burgi, Roger McIntosh, Lori K. Hennessy, Jennifer Gass, Jacklyn Buscaino, and David Eberhart
- Subjects
Sample (material) ,Buccal swab ,system ,Biology ,Polymerase Chain Reaction ,Pathology and Forensic Medicine ,Capillary electrophoresis ,Genetics ,Humans ,CODIS ,Integrated sample-to-profile ,Genotyping ,Forensics ,Rapid DNA ,Chromatography ,Mouth Mucosa ,Reproducibility of Results ,Buccal swabs ,Buccal administration ,DNA profiling ,DNA extraction ,PCR ,Short tandem repeats (STR) ,Forensic Anthropology ,Microsatellite ,Human identification ,Microsatellite Repeats - Abstract
Short tandem repeat (STR) DNA typing is a global standard for human identification. Current practice involves highly trained forensic analysts, operating in a laboratory setting, using multiple instruments to process samples and analyze the data. Here, we report the developmental validation of a fully integrated and automated DNA profiling system, the RapidHIT ® System, capable of producing up to five high quality STR profiles with full controls in approximately 90min using PowerPlex ® 16 HS RapidHIT chemistry. The system integrates all sample handling steps: starting from lysis of cells on buccal swabs or other buccal sample types through DNA extraction, normalization, amplification,capillary array electrophoresis, detection, and integrated software analysis. The results describe the developmental validation of the RapidHIT™ System for buccal samples processed with the DNA IQ™ extraction chemistry using a guandinium chaotropic agent and paramagnetic beads followed by amplification using a modified version of PowerPlex 16 HS chemistry (PowerPlex 16 HS RapidHIT chemistry), and capillary electrophoresis with manual review of genotyping data following interpretation guidelines. All processing from the buccal swab to generation and processing of the profile occurs on the RapidHIT platform. Result are concordant with traditional methods, with 88% first pass success rates for both the CODIS and PowerPlex 16 loci. Average peak height ratios were 0.89 for buccal swabs. The system produces full profiles from swabs with at least 176 ng of saliva DNA. Rapid DNA identification systems will significantly enhance capabilities for forensic labs, intelligence, defense, law enforcement, refugee and immigration applications, and kinship analysis.
- Published
- 2015
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5. Opportunity observation of an Algerian Eddy to the south of Cape Palos (southwestern Mediterranean Sea)
- Author
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Manuel Vargas-Yáñez, Ricardo F. Sánchez-Leal, Aida Alvera-Azcárate, Charles Troupin, Francina Moya, Enrique Ballesteros, Mariano Serra, Rosa Balbín, Vicenç Moltó, and Mª Carmen García-Martínez
- Subjects
Algerian Eddy ,Algerian Current ,western Mediterranean ,mesoscale structures ,Aquaculture. Fisheries. Angling ,SH1-691 - Abstract
Large anticyclonic eddies can detach from the Algerian Current, forming open-sea Algerian Eddies. These mesoscale structures have been intensively studied by means of sea surface temperature and altimetry data, and using numerical models. However, few studies describe an in situ sampling of their whole vertical structure. Furthermore, the area extending from Cape La Nao (western edge of the Balearic Channels) to the Almería-Orán Front has received very little attention, and it could be considered that there is a gap in our present oceanographic knowledge of this part of the western Mediterranean. An Algerian Eddy lasting for several months was detected in December 2021 to the south of Cape Palos. In order to analyse this eddy, an opportunity sampling was designed taking advantage of the periodic monitoring campaign RADMED 0222. This sampling revealed that the eddy had a baroclinic character, affecting the whole water column. These results suggest that this eddy was generated at the Algerian Current, finally affecting an area close to the eastern Spanish coast. The presence of these structures in this region of the western Mediterranean could alter the southward progression of the Northern Current and even the presence and structure of the Almería-Orán Front.
- Published
- 2023
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6. Evaluation of a rapid DNA process with the RapidHIT
- Author
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Jacklyn, Buscaino, Arnaldo, Barican, Leto, Farrales, Bruce, Goldman, Jim, Klevenberg, Melissa, Kuhn, Frank, Lin, Phong, Nguyen, Susana, Salceda, Robert, Schueren, Corey, Smith, Charles, Troup, Dean, Tsou, Mattias, Vangbo, and David, King
- Subjects
Male ,Time Factors ,Electrophoresis, Capillary ,Humans ,Reproducibility of Results ,Female ,DNA ,DNA Fingerprinting ,Polymerase Chain Reaction ,Microsatellite Repeats - Abstract
The turn-around time of urgent crime scene DNA samples is often far longer than desired by law enforcement. Crime scene DNA sample processing involves both complex and routine processing steps. Simplification and integration of the routine steps would dramatically improve turn-around time and reduce the risk of operator contamination. Routine DNA extraction and quantitation is readily available. However, PCR amplification and electrophoretic analysis remain largely manual. Rapid DNA Analysis is a hands-free "swab in - profile out" process which consists of automated DNA extraction, amplification, separation, detection, and allele calling without human intervention. RapidHIT
- Published
- 2017
7. Validation of a rapid DNA process with the RapidHIT
- Author
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Susana, Salceda, Arnaldo, Barican, Jacklyn, Buscaino, Bruce, Goldman, Jim, Klevenberg, Melissa, Kuhn, Dennis, Lehto, Frank, Lin, Phong, Nguyen, Charles, Park, Francesca, Pearson, Rick, Pittaro, Sayali, Salodkar, Robert, Schueren, Corey, Smith, Charles, Troup, Dean, Tsou, Mattias, Vangbo, Justus, Wunderle, and David, King
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Species Specificity ,Animals ,High-Throughput Nucleotide Sequencing ,Humans ,Reproducibility of Results ,DNA ,DNA Fingerprinting ,Software ,Microsatellite Repeats - Abstract
The RapidHIT
- Published
- 2016
8. Normalization of Array CGH Data
- Author
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Bo Curry, Jayati Ghosh, and Charles Troup
- Subjects
Normalization (statistics) ,business.industry ,Pattern recognition ,Artificial intelligence ,Biology ,business - Published
- 2008
9. Analysis of 23 Years of Daily Cloud-Free Chlorophyll and Suspended Particulate Matter in the Greater North Sea
- Author
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Aida Alvera-Azcárate, Dimitry Van der Zande, Alexander Barth, Charles Troupin, Samuel Martin, and Jean-Marie Beckers
- Subjects
spring bloom phenology ,remote sensing ,ocean color ,chlorophyll ,suspended particle matter ,North Sea ,Science ,General. Including nature conservation, geographical distribution ,QH1-199.5 - Abstract
Satellite-derived estimates of ocean color variables are available for several decades now and allow performing studies of the long-term changes occurred in an ecosystem. A daily, gap-free analysis of chlorophyll (CHL) and suspended particulate matter (SPM, indicative of light availability in the subsurface) at 1 km resolution over the Greater North Sea during the period 1998–2020 is presented. Interannual changes are described, with maximum average CHL values increasing during the period 1998–2008, a slightly decreasing trend in 2009–2017 and an stagnation in recent years. The typical spring bloom is observed to happen earlier each year, with about 1 month difference between 1998 and 2020. The duration of the bloom (time between onset and offset) appears also to be increasing with time, but the average CHL value during the spring bloom does not show a clear trend. The causes for earlier spring blooms are still unclear, although a rising water temperature can partially explain them through enhanced phytoplankton cell division rates or through increased water column stratification. SPM values during winter months (prior to the development of the spring bloom) do not exhibit a clear trend over the same period, although slightly higher SPM values are observed in recent years. The influence of sea surface temperature in the spring bloom timing appears to be dominant over the influence of SPM concentration, according to our results. The number of satellites available over the years for producing CHL and SPM in this work has an influence in the total amount of available data before interpolation. The amount of missing data has an influence in the total variability that is retained in the final dataset, and our results suggest that at least three satellites would be needed for a good representation of ocean color variability.
- Published
- 2021
- Full Text
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10. A New Global Ocean Climatology
- Author
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Kanwal Shahzadi, Nadia Pinardi, Alexander Barth, Charles Troupin, Vladyslav Lyubartsev, and Simona Simoncelli
- Subjects
global ocean climatologies ,temperature analysis ,salinity analysis ,data interpolating variational analysis ,quality control ,multi-model ensemble ,Environmental sciences ,GE1-350 - Abstract
A new global ocean temperature and salinity climatology is proposed for two time periods: a long time mean using multiple sensor data for the 1900–2017 period and a shorter time mean using only profiling float data for the 2003–2017 period. We use the historical database of World Ocean Database 2018. The estimation approach is novel as an additional quality control procedure is implemented, along with a new mapping algorithm based on Data Interpolating Variational Analysis. The new procedure, in addition to the traditional quality control approach, resulted in low sensitivity in terms of the first guess field choice. The roughness index and the root mean square of residuals are new indices applied to the selection of the free mapping parameters along with sensitivity experiments. Overall, the new estimates were consistent with previous climatologies, but several differences were found. The cause of these discrepancies is difficult to identify due to several differences in the procedures. To minimise these uncertainties, a multi-model ensemble mean is proposed as the least uncertain estimate of the global ocean temperature and salinity climatology.
- Published
- 2021
- Full Text
- View/download PDF
11. Design and implementation of microarray gene expression markup language (MAGE-ML)
- Author
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Ugis Sarkans, Robert Hubley, Bruce J. Aronow, Doug Bassett, Alan J. Robinson, Scott Markel, Jason E. Stewart, Alvis Brazma, Steve Chervitz, Christian J. Stoeckert, Derek Bernhart, Martin Senger, Daniel Iordan, WL Marks, Angel Pizarro, Marcin Swiatek, Joseph White, Jason Goncalves, Paul T. Spellman, Charles Troup, Marc Lepage, Gavin Sherlock, Catherine A. Ball, Eric W. Deutsch, Michael W. Miller, and Mohammadreza Shojatalab
- Subjects
Markup language ,Microarray ,business.industry ,Minimum information about a microarray experiment ,Microarray analysis techniques ,Research ,Gene Expression Profiling ,Database schema ,Computational biology ,Sequence Analysis, DNA ,Biology ,computer.software_genre ,Models, Biological ,Gene expression profiling ,Microarray gene expression ,Microarray databases ,Computer Simulation ,Programming Languages ,Artificial intelligence ,business ,computer ,Natural language processing ,Oligonucleotide Array Sequence Analysis - Abstract
Meaningful exchange of microarray data is currently difficult because it is rare that published data provide sufficient information depth or are even in the same format from one publication to another. MAGE will help microarray data producers and users to exchange information by providing a common platform for data exchange, and MAGE-STK will make the adoption of MAGE easier., Background Meaningful exchange of microarray data is currently difficult because it is rare that published data provide sufficient information depth or are even in the same format from one publication to another. Only when data can be easily exchanged will the entire biological community be able to derive the full benefit from such microarray studies. Results To this end we have developed three key ingredients towards standardizing the storage and exchange of microarray data. First, we have created a minimal information for the annotation of a microarray experiment (MIAME)-compliant conceptualization of microarray experiments modeled using the unified modeling language (UML) named MAGE-OM (microarray gene expression object model). Second, we have translated MAGE-OM into an XML-based data format, MAGE-ML, to facilitate the exchange of data. Third, some of us are now using MAGE (or its progenitors) in data production settings. Finally, we have developed a freely available software tool kit (MAGE-STK) that eases the integration of MAGE-ML into end users' systems. Conclusions MAGE will help microarray data producers and users to exchange information by providing a common platform for data exchange, and MAGE-STK will make the adoption of MAGE easier.
- Published
- 2002
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