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Engineering a peer-to-peer collaboratory for tissue microarray research

C. Schmidt, M. Parashar, Wenjin Chen, D.J. Foran
Proceedings of the Second International Workshop on Challenges of Large Applications in Distributed Environments, 2004. CLADE 2004.  
This paper presents the design of a prototype peer-topeer collaboratory for imaging, analyzing, and seamlessly sharing tissue microarrays (TMA), correlated clinical data, and experimental results across  ...  of digitized TMAs and a peer-to-peer infrastruture for indexing and discovery of TMA data and metadata, and a novel, optimized decentralized search engine that supports flexible querying with search guarantees  ...  This paper presents the design of a prototype peer-topeer collaboratory for imaging, analyzing, and seamlessly sharing tissue microarrays (TMA), correlated clinical data, and experimental results across  ... 
doi:10.1109/clade.2004.1309093 dblp:conf/clade/SchmidtPCF04 fatcat:fi7gnrl2yfh7lf7t6jenfd4zdy

Decentralized Data Sharing of Tissue Microarrays for Investigative Research in Oncology

Wenjin Chen, Cristina Schmidt, Manish Parashar, Michael Reiss, David J. Foran
2006 Cancer Informatics  
Specifi cally, we present a self-organizing, peer-to-peer indexing and discovery infrastructure for quantitatively assessing digitized TMA's.  ...  Tissue microarray technology holds great potential for reducing the time and cost associated with conducting research in tissue banking, proteomics, and outcome studies.  ...  The authors are extremely grateful to The Cancer Institute of New Jersey and the Hospital of the University of Pennsylvania for the specimens and support that they have provided for this research.  ... 
doi:10.1177/117693510600200014 fatcat:vtocq7owpndxdltzjbs4edmexy

Decentralized data sharing of tissue microarrays for investigative research in oncology

Wenjin Chen, Cristina Schmidt, Manish Parashar, Michael Reiss, David J Foran
2007 Cancer Informatics  
Specifically, we present a self-organizing, peer-to-peer indexing and discovery infrastructure for quantitatively assessing digitized TMA's.  ...  Tissue microarray technology holds great potential for reducing the time and cost associated with conducting research in tissue banking, proteomics, and outcome studies.  ...  The authors are extremely grateful to The Cancer Institute of New Jersey and the Hospital of the University of Pennsylvania for the specimens and support that they have provided for this research.  ... 
pmid:19081778 pmcid:PMC2600512 fatcat:uo25ys2thzgdbg2bt52rs6n7lq

Nanoinformatics: a new area of research in nanomedicine

Victor Maojo, Fritts, Diana de la Iglesia, Cachau, Garcia-Remesal, Mitchell, Kulikowski
2012 International Journal of Nanomedicine  
Over a decade ago, nanotechnologists began research on applications of nanomaterials for medicine. This research has revealed a wide range of different challenges, as well as many opportunities.  ...  research to clinical problems and findings.  ...  Research Resources/National Center for Advancing Translational Sciences (Public Health Services research grants UL1-RR025764 and UL1RR025764-02S2).  ... 
doi:10.2147/ijn.s24582 pmid:22866003 pmcid:PMC3410693 fatcat:5im7a34ogbffpcwpg6ycoylor4

Horse gluteus is a null-sarcolipin muscle with enhanced sarcoplasmic reticulum calcium transport [article]

Joseph M. Autry, Bengt Svensson, Samuel F. Carlson, Zhenhui Chen, L. Michel Espinoza-Fonseca, David D. Thomas
2019 bioRxiv   pre-print
Horses are bred for peak athletic performance but exhibit a high incidence of exertional rhabdomyolysis, suggesting Ca2+ as a correlative linkage.  ...  Thus, the SLN gene is not translated to a stable protein in horse gluteus, yet the supra-high level of SLN RNA suggests a non-coding role.  ...  Acknowledgments We thank Seth Robia, Howard Young, and Naresh Bal for insightful discussions. We thank Samantha Yuen, Morgan Zander, Ty Gaedtke, and Keri Gardner for technical support.  ... 
doi:10.1101/688531 fatcat:qmf76mcb3jfi3axwhcgujx3yv4

What's that gene (or protein)? Online resources for exploring functions of genes, transcripts, and proteins

James R. A. Hutchins, Doug Kellogg
2014 Molecular Biology of the Cell  
The genomic era has enabled research projects that use approaches including genome-scale screens, microarray analysis, next-generation sequencing, and mass spectrometry-based proteomics to discover genes  ...  Recent years have seen a profusion of Internet-based resources to aid this process.  ...  The definitive resource for protein 3D structures is the Protein Data Bank (PDB), for which records can be readily retrieved from the Research Collaboratory for Structural Bioinformatics (RCSB) website  ... 
doi:10.1091/mbc.e13-10-0602 pmid:24723265 pmcid:PMC3982986 fatcat:53kmvwius5dm5lekojvblip7ga

When do researchers collaborate? Toward a model of collaboration propensity

Jeremy P. Birnholtz
2007 Journal of the American Society for Information Science and Technology  
He was never too busy for a quick chat about a logistical issue or to provide thorough and thoughtful feedback on a draft.  ...  Moreover, despite a packed trans-Atlantic commuting schedule, Homer is always available for a quick meeting about how my research is going and his thoughtful, pragmatic questions about collaboration helped  ...  Although I have space to  ... 
doi:10.1002/asi.20684 fatcat:ehw2p3dod5h43ki7ubtaxnco4q

A Guide to Bioinformatics for Immunologists

Fiona J. Whelan, Nicholas V. L. Yap, Michael G. Surette, G. Brian Golding, Dawn M. E. Bowdish
2013 Frontiers in Immunology  
Herein, we review a representative set of publicly available, easy-to-use bioinformatic tools using our own research on an under-annotated human gene, SCARA3, as an example.  ...  We argue that these tools are largely applicable to many facets of immunology research.  ...  The Protein Data Bank (PDB) is a worldwide collection of macromolecular structures governed by the Research Collaboratory for Structural Bioinformatics (RCSB).  ... 
doi:10.3389/fimmu.2013.00416 pmid:24363654 pmcid:PMC3849744 fatcat:g4xphza7g5cwjeaowfyfnghauq

Use of Bioinformatics Tools in Different Spheres of Life Sciences

Muhammad Aamer Mehmood
2014 Journal of Data Mining in Genomics & Proteomics  
Acknowledgment Authors thank Higher Education Commission (HEC), Pakistan, for funding their research work and apologise to all those colleagues whose work could not be discussed here due to space constraints  ...  Similarly, wwPDB (worldwide PDB) is a composite of 3D structures in the RCSB (Research Collaboratory for Structural Bioinformatics), PDB, MSD, and PDBj [46] .  ...  [129] PIR An integrated public resource to support genomic and proteomic research [34] Miscellaneous Databases Medherb Resource database for medicinally important herbs [130] Reactome A peer-reviewed  ... 
doi:10.4172/2153-0602.1000158 fatcat:m5ziueg3ifaobfnovyguaqlixa

Searching the Biological Literature [chapter]

2014 Using the Biological Literature  
2008 2 Acknowledgements I am very grateful to my colleague, Amanda Izenstark whose dedication and most remarkable technological expertise proved essential for completion of this work.  ...  It is based on a credit course whose purpose is to help graduate students and upper level undergraduate students find the information they need.  ...  They also respond to health related emergencies. This web site has a search engine and many links to very useful sites especially for the general public.  ... 
doi:10.1201/b16753-3 fatcat:buv3dqlndrg6vjlbdxjjg4pn6y

An approach for pipelining nested collections in scientific workflows

Timothy M. McPhillips, Shawn Bowers
2005 SIGMOD record  
These 18 people are providing a truly valuable service to readers, to authors, and to reviewers.  ...  Moreover, he thanks Gianluigi Greco for his recent contribution to the weighted extension, and Alfredo Mazzitelli for his valuable work in designing and implementing the tools for experiments.  ...  tissue structure within the placenta in cancer research.  ... 
doi:10.1145/1084805.1084809 fatcat:sgtpcat7vzc3veb4dx2jgskpte

2501

Magda Shaheen, Senait Teklehaimanot
2017 Journal of Clinical and Translational Science  
OBJECTIVES/SPECIFIC AIMS: Examine mental health service use and its correlates among depressed group in a national sample of population≥20 years old.  ...  For the use of antidepressant drug among the depressed group, AA, Hispanics, uninsured and foreign born were less likely to use antidepressant drug relative to other groups [OR=0.26 (95% CI=0.20–0.33),  ...  We used the Community-Engaged Research Navigation model to establish a multisite deidentified database extracted from EHRs of female adolescents aged 12-21 years (January 2011-December 2012) and their  ... 
doi:10.1017/cts.2017.287 fatcat:yp5uxjopfzhuzovziwsbbhl2au

Thermophilic lignocellulose deconstruction

Sara E. Blumer-Schuette, Steven D. Brown, Kyle B. Sander, Edward A. Bayer, Irina Kataeva, Jeffrey V. Zurawski, Jonathan M. Conway, Michael W. W. Adams, Robert M. Kelly
2014 FEMS Microbiology Reviews  
Meeting those targets requires either metabolically engineering solventogenic thermophiles with additional biomass-deconstruction enzymes or engineering plant biomass degraders to produce a liquid biofuel  ...  Plant-biomass-deconstructing thermophilic bacteria from the genera Clostridium (cellulosomal) and Caldicellulosiruptor (noncellulosomal), which have potential as metabolic engineering platforms for producing  ...  Acknowledgements The BioEnergy Science Center is a U.S. Department of Energy Bioenergy Research Center supported by the Office of Biological and Environmental Research in the DOE Office of Science.  ... 
doi:10.1111/1574-6976.12044 pmid:24118059 fatcat:yypbaplfi5dwnjsx4v5v54zbpm

86th SIBS National Congress | Palermo, Italy, 24-25 October 2013

The Editors
2015 Journal of Biological Research  
Acknowledgements: this research was supported by GACR P502/12/P163.  ...  The individuals who regularly eat pasta are characterized by a lower Body Mass Index than those who do not consume habitually; the same is for those who regularly take breakfast, according as noted by  ...  Stem cells have a key role in regenerative medicine and tissue engineering.  ... 
doi:10.4081/jbr.2015.5161 fatcat:ursnvtpxazbonnqu745joie4xm

Cytokine Gene Expression in the Tunica Albuginea of Patients with Peyronie's Disease. Pilot Study with a Control Group

Carlo Pavone, Giovanni Caruana, Daniela Abbadessa, Giovanna Scaduto, Giuseppa Gambino, Vincenzo Serretta, Riccardo Alessandro, Paolo Colomba
2012 Urologia Journal  
Stem cells have a key role in regenerative medicine and tissue engineering.  ...  Controlling the P2Y14 receptor signaling might improve future bone tissue engineering approaches in regenerative dentistry.  ...  The resulting homogenate, with a dry matter content of 14% (w/w), was diluted with water to a 9% dry matter in a working volume of 1.5 L, and immediately treated at 100°C for 10 min under continuous mixing  ... 
doi:10.5301/ru.2012.9686 pmid:23032634 fatcat:5nqz7i2mubc23kzbzohtfmyd7i
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