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Search Results: 1 - 10 of 302858 matches for " Ian J Jacobs "
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A Perl toolkit for LIMS development
James A Morris, Simon A Gayther, Ian J Jacobs, Christopher Jones
Source Code for Biology and Medicine , 2008, DOI: 10.1186/1751-0473-3-4
Abstract: We have developed ArrayPipeline, a Perl toolkit providing object oriented methods that facilitate the rapid development of bespoke LIMS applications. The toolkit includes Perl objects that encapsulate key components of a LIMS, providing methods for creating interactive web pages, interacting with databases, error tracking and reporting, and user and session management. The MT_Plate object provides methods for manipulation and management of microtitre plates, while a given LIMS can be encapsulated by extension of the core modules, providing system specific methods for database interaction and web page management.This important addition to the Perl developer's library will make the development of in house LIMS applications quicker and easier encouraging laboratories to create bespoke LIMS applications to meet their specific data management requirements.High throughput investigation techniques such as microarrays are now well established in scientific research. As the costs of these techniques fall, greater numbers of laboratories are adopting these approaches. High throughput techniques and the equipment associated with them provide researchers with a number of new challenges, one of which is the management and storage of the vast quantities of data they generate. Laboratory notebooks and computer spreadsheets still form the data management strategy for many research scientists, and this simple approach has advantages in the ease of storage and viewing of the data for low throughput approaches however this approach is inadequate for the amounts of data generated using the latest laboratory techniques.The solution to this data management challenge is the implementation of a Laboratory Information Management System (LIMS), a computer application designed to track samples, store data generated by laboratory equipment and experiments and report these data. There are numerous commercial LIMS applications available however these can be very costly and sometimes overly compl
OSPACS: Ultrasound image management system
Will Stott, Andy Ryan, Ian J Jacobs, Usha Menon, Conrad Bessant, Christopher Jones
Source Code for Biology and Medicine , 2008, DOI: 10.1186/1751-0473-3-11
Abstract: We have developed a system enabling the accurate archiving and management of ultrasound images gathered during a clinical screening trial. It is based upon a Windows application utilizing an open-source DICOM image viewer and a relational database. The system automates the bulk import of DICOM files from removable media by cross-validating the patient information against an external database, anonymizing the data as well as the image, and then storing the contents of the file as a field in a database record. These image records may then be retrieved from the database and presented in a tree-view control so that the user can select particular images for display in a DICOM viewer or export them to external media.This system provides error-free automation of ultrasound image archiving and management, suitable for use in a clinical trial. An open-source project has been established to promote continued development of the system.Medical sonography (ultrasonography) uses ultrasound to provide real-time images of soft tissues, internal organs and the fetus in utero. Because medical sonography is non-invasive and generally considered to have no harmful side effects, it has seen increasing use for a variety of diagnostic purposes in recent years. One of the most common applications of ultrasound imaging is in routine obstetric care, assessing the stage and status of pregnancy and the health and development of the fetus. Other applications include the imaging of most of the internal organs, muscles, ligaments and tendons.DICOM 3.0 (Digital Imaging and Communications in Medicine) is a standard describing the handling, transfer and storage of medical imaging data, including ultrasound scans [1]. A DICOM data object (or data set) combines a medical image in one of several standards (either still, or video) with patient information and other scan data. The linked storage of these data is an important feature of the standard, ensuring that the descriptive patient data are always a
Crises and Opportunities: A Manifesto for Change
Ian Johnson,Garry Jacobs
Cadmus , 2012,
Abstract: Piecemeal fragmented strategies cannot address the pressing challenges facing humanity today. Economic theory has to be radically reinvented to squarely face the reality of rising unemployment, widening inequalities, growing ecological threats, frustrated social aspirations and unmet human needs. Monetary and fiscal policies are too crude and insufficient to steer the essential change of course required to address multidimensional demographic, ecological, economic, political and social crises. New values are needed to guide policy formulation and new institutions are needed to support peaceful social evolution and inclusive, equitable development in an increasingly globalized and interconnected world.
Mitochondrial Transcription Terminator Family Members mTTF and mTerf5 Have Opposing Roles in Coordination of mtDNA Synthesis
Priit J?ers,Samantha C. Lewis,Atsushi Fukuoh,Mikael Parhiala,Simo Ellil?,Ian J. Holt,Howard T. Jacobs
PLOS Genetics , 2013, DOI: 10.1371/journal.pgen.1003800
Abstract: All genomes require a system for avoidance or handling of collisions between the machineries of DNA replication and transcription. We have investigated the roles in this process of the mTERF (mitochondrial transcription termination factor) family members mTTF and mTerf5 in Drosophila melanogaster. The two mTTF binding sites in Drosophila mtDNA, which also bind mTerf5, were found to coincide with major sites of replication pausing. RNAi-mediated knockdown of either factor resulted in mtDNA depletion and developmental arrest. mTTF knockdown decreased site-specific replication pausing, but led to an increase in replication stalling and fork regression in broad zones around each mTTF binding site. Lagging-strand DNA synthesis was impaired, with extended RNA/DNA hybrid segments seen in replication intermediates. This was accompanied by the accumulation of recombination intermediates and nicked/broken mtDNA species. Conversely, mTerf5 knockdown led to enhanced replication pausing at mTTF binding sites, a decrease in fragile replication intermediates containing single-stranded segments, and the disappearance of species containing segments of RNA/DNA hybrid. These findings indicate an essential and previously undescribed role for proteins of the mTERF family in the integration of transcription and DNA replication, preventing unregulated collisions and facilitating productive interactions between the two machineries that are inferred to be essential for completion of lagging-strand DNA synthesis.
Epigenotyping in Peripheral Blood Cell DNA and Breast Cancer Risk: A Proof of Principle Study
Martin Widschwendter, Sophia Apostolidou, Elke Raum, Dietrich Rothenbacher, Heidi Fiegl, Usha Menon, Christa Stegmaier, Ian J. Jacobs, Hermann Brenner
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0002656
Abstract: Background Epigenetic changes are emerging as one of the most important events in carcinogenesis. Two alterations in the pattern of DNA methylation in breast cancer (BC) have been previously reported; active estrogen receptor-α (ER-α) is associated with decreased methylation of ER-α target (ERT) genes, and polycomb group target (PCGT) genes are more likely than other genes to have promoter DNA hypermethylation in cancer. However, whether DNA methylation in normal unrelated cells is associated with BC risk and whether these imprints can be related to factors which can be modified by the environment, is unclear. Methodology/Principal Findings Using quantitative methylation analysis in a case-control study (n = 1,083) we found that DNA methylation of peripheral blood cell DNA provides good prediction of BC risk. We also report that invasive ductal and invasive lobular BC is characterized by two different sets of genes, the latter particular by genes involved in the differentiation of the mesenchyme (PITX2, TITF1, GDNF and MYOD1). Finally we demonstrate that only ERT genes predict ER positive BC; lack of peripheral blood cell DNA methylation of ZNF217 predicted BC independent of age and family history (odds ratio 1.49; 95% confidence interval 1.12–1.97; P = 0.006) and was associated with ER-α bioactivity in the corresponding serum. Conclusion/Significance This first large-scale epigenotyping study demonstrates that DNA methylation may serve as a link between the environment and the genome. Factors that can be modulated by the environment (like estrogens) leave an imprint in the DNA of cells that are unrelated to the target organ and indicate the predisposition to develop a cancer. Further research will need to demonstrate whether DNA methylation profiles will be able to serve as a new tool to predict the risk of developing chronic diseases with sufficient accuracy to guide preventive measures.
Clear Cell Papillary Renal Cell Carcinoma: A Rare Subtype  [PDF]
Armin Kamyab, Michael J. Jacobs
Journal of Cancer Therapy (JCT) , 2011, DOI: 10.4236/jct.2011.25091
Abstract: Introduction: Renal cell carcinoma (RCC) is generally divided into clear cell, papillary, and chromophobe subtypes. Clear cell papillary RCC is a recently described subtype. Case report: We report the case of a 42 year old female who was found on computed tomography scan of the abdomen to have a cyst which appeared to involve the right kidney. Pathology of the cyst wall revealed features consistent with a RCC, clear cell papillary type. Discussion: Clear cell papillary RCC are a recently described entity with less than 100 cases reported in the literature. Most cases in the literature have been associated with end-stage renal disease, however more case are being reported in patients without renal disease. Conclusion: Clear cell papillary RCC is a rare distinct entity in the spectrum of renal cell carcinoma. Based on the literature they appear to be clinically indolent tumors; however, more research is required to further characterize and prognosticate these rare tumors.
Illustrating the levels of war – Operation Zitadelle (Kursk), 5-14 July 1943, a case study
J Jacobs
Scientia Militaria: South African Journal of Military Studies , 2005,
An Epigenetic Signature in Peripheral Blood Predicts Active Ovarian Cancer
Andrew E. Teschendorff,Usha Menon,Aleksandra Gentry-Maharaj,Susan J. Ramus,Simon A. Gayther,Sophia Apostolidou,Allison Jones,Matthias Lechner,Stephan Beck,Ian J. Jacobs,Martin Widschwendter
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0008274
Abstract: Recent studies have shown that DNA methylation (DNAm) markers in peripheral blood may hold promise as diagnostic or early detection/risk markers for epithelial cancers. However, to date no study has evaluated the diagnostic and predictive potential of such markers in a large case control cohort and on a genome-wide basis.
Pilot randomized trial of therapeutic hypothermia with serial cranial ultrasound and 18-22 month follow-up for neonatal encephalopathy in a low resource hospital setting in uganda: study protocol
Nicola J Robertson, Cornelia F Hagmann, Dominique Acolet, Elizabeth Allen, Natasha Nyombi, Diana Elbourne, Anthony Costello, Ian Jacobs, Margaret Nakakeeto, Frances Cowan
Trials , 2011, DOI: 10.1186/1745-6215-12-138
Abstract: Under the UCL Uganda Women's Health Initiative, a pilot randomized controlled trial in infants with perinatal asphyxia was set up in the special care baby unit in Mulago Hospital, a large public hospital with ~20,000 births in Kampala, Uganda to determine:(i) The feasibility of achieving consent, neurological assessment, randomization and whole body cooling to a core temperature 33-34°C using water bottles(ii) The temperature profile of encephalopathic infants with standard care(iii) The pattern, severity and evolution of brain tissue injury as seen on cranial ultrasound and relation with outcome(iv) The feasibility of neurodevelopmental follow-up at 18-22 months of ageEthical approval was obtained from Makerere University and Mulago Hospital. All infants were in-born. Parental consent for entry into the trial was obtained. Thirty-six infants were randomized either to standard care plus cooling (target rectal temperature of 33-34°C for 72 hrs, started within 3 h of birth) or standard care alone. All other aspects of management were the same. Cooling was performed using water bottles filled with tepid tap water (25°C). Rectal, axillary, ambient and surface water bottle temperatures were monitored continuously for the first 80 h. Encephalopathy scoring was performed on days 1-4, a structured, scorable neurological examination and head circumference were performed on days 7 and 17. Cranial ultrasound was performed on days 1, 3 and 7 and scored. Griffiths developmental quotient, head circumference, neurological examination and assessment of gross motor function were obtained at 18-22 months.We will highlight differences in neonatal care and infrastructure that need to be taken into account when considering a large safety and efficacy RCT of therapeutic hypothermia in low and mid resource settings in the future.Current controlled trials ISRCTN92213707In the UK and other developed world settings, moderate-severe encephalopathy following perinatal asphyxia occurs in 1-2/10
Photon number resolving detection using time-multiplexing
Daryl Achilles,Christine Silberhorn,Cezary Sliwa,Konrad Banaszek,Ian A. Walmsley,Michael J. Fitch,Bryan C. Jacobs,Todd B. Pittman,James D. Franson
Physics , 2003, DOI: 10.1080/09500340408235288
Abstract: Detectors that can resolve photon number are needed in many quantum information technologies. In order to be useful in quantum information processing, such detectors should be simple, easy to use, and be scalable to resolve any number of photons, as the application may require great portability such as in quantum cryptography. Here we describe the construction of a time-multiplexed detector, which uses a pair of standard avalanche photodiodes operated in Geiger mode. The detection technique is analysed theoretically and tested experimentally using a pulsed source of weak coherent light.
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