PCCR: Pancreatic Cancer Collaborative Registry

The Pancreatic Cancer Collaborative Registry (PCCR) is a multi-institutional web-based system aimed to collect a variety of data on pancreatic cancer patients and high-risk subjects in a standard and efficient way. The PCCR was initiated by a group of experts in medical oncology, gastroenterology, genetics, pathology, epidemiology, nutrition, and computer science with the goal of facilitating rapid and uniform collection of critical information and biological samples to be used in developing diagnostic, prevention and treatment strategies against pancreatic cancer. The PCCR is a multi-tier web application that utilizes Java/JSP technology and has Oracle 10 g database as a back-end. The PCCR uses a “confederation model” that encourages participation of any interested center, irrespective of its size or location. The PCCR utilizes a standardized approach to data collection and reporting, and uses extensive validation procedures to prevent entering erroneous data. The PCCR controlled vocabulary is harmonized with the NCI Thesaurus (NCIt) or Systematized Nomenclature of Medicine-Clinical Terms (SNOMED-CT). The PCCR questionnaire has accommodated standards accepted in cancer research and healthcare. Currently, seven cancer centers in the USA, as well as one center in Italy are participating in the PCCR. At present, the PCCR database contains data on more than 2,700 subjects (PC patients and individuals at high risk of getting this disease). The PCCR has been certified by the NCI Center for Biomedical Informatics and Information Technology as a cancer Biomedical Informatics Grid (caBIG®) Bronze Compatible product. The PCCR provides a foundation for collaborative PC research. It has all the necessary prerequisites for subsequent evolution of the developed infrastructure from simply gathering PC-related data into a biomedical computing platform vital for successful PC studies, care and treatment. Studies utilizing data collected in the PCCR may engender new approaches to disease prognosis, risk factor assessment, and therapeutic interventions

Statistics for Fission-Track Thermochronology

This chapter introduces statistical tools to extract geologically meaningful information from fission-track (FT) data using both the external detector and LA-ICP-MS methods. The spontaneous fission of 238U is a Poisson process resulting in large single-grain age uncertainties. To overcome this imprecision, it is nearly always necessary to analyse multiple grains per sample. The degree to which the analytical uncertainties can explain the observed scatter of the single-grain data can be visually assessed on a radial plot and objectively quantified by a chi-square test. For sufficiently low values of the chi-square statistic (or sufficiently high p values), the pooled age of all the grains gives a suitable description of the underlying ‘true’ age population. Samples may fail the chi-square test for several reasons. A first possibility is that the true age population does not consist of a single discrete age component, but is characterised by a continuous range of ages. In this case, a ‘random effects’ model can constrain the true age distribution using two parameters: the ‘central age’ and the ‘(over)dispersion’. A second reason why FT data sets might fail the chi-square test is if they are underlain by multimodal age distributions. Such distributions may consist of discrete age components, continuous age distributions, or a combination of the two. Formalised statistical tests such as chi-square can be useful in preventing overfitting of relatively small data sets. However, they should be used with caution when applied to large data sets (including length measurements) which generate sufficient statistical ‘power’ to reject any simple yet geologically plausible hypothesis

Timing of uplift and evolution of the Lüliang Mountains, North China Craton

This study analyses evidence for reformed basin development and basin-mountain coupling associated with development of the Ordos Basin and the Lüliang Mountains, China. Gaining an improved understanding of the timing and nature of uplift and evolution of the Lüliang Mountains is important for the reconstruction of the eastern sedimentary boundary of the Ordos Basin (a major petroliferous basin) as well as for providing insight into the evolution and breakup of the North China Craton (NCC). Based on systematic sampling for fission track analysis, it is suggested that the main phase of uplift of the Lüliang Mountains occurred since later part of the Early Cretaceous. Three evolutionary stages of uplift and development are identified: slow initial uplift (120–65 Ma), accelerated uplift (65–23 Ma), and intensive uplift (23 Ma to present), with the majority of the uplift activity having occurred during the Cenozoic. The history of uplift is non-equilibrium and exhibits complexity in temporal and spatial aspects. The middle and northern parts of the Lüliang Mountains were uplifted earlier than the southern part. The most intensive episode of uplift activity commenced in the Miocene and was associated with a genetic coupling relationship with the eastern neighboring Cenozoic Shanxi Grabens. The uplifting and evolutionary processes of the Lüliang Mountains area since later part of the Early Cretaceous share a unified regional geodynamic setting, which was accompanied by uplift of the Mesozoic Ordos Basin and development of the neighboring Cenozoic Shanxi Grabens. Collectively, this regional orogenic activity is related principally to the far-field effects of both the compression sourced from the southwestern Tibet Plateau and westward subduction of the Pacific Plate in Cenozoic

Impact Factor: outdated artefact or stepping-stone to journal certification?

A review of Garfield's journal impact factor and its specific implementation as the Thomson Reuters Impact Factor reveals several weaknesses in this commonly-used indicator of journal standing. Key limitations include the mismatch between citing and cited documents, the deceptive display of three decimals that belies the real precision, and the absence of confidence intervals. These are minor issues that are easily amended and should be corrected, but more substantive improvements are needed. There are indications that the scientific community seeks and needs better certification of journal procedures to improve the quality of published science. Comprehensive certification of editorial and review procedures could help ensure adequate procedures to detect duplicate and fraudulent submissions.Comment: 25 pages, 12 figures, 6 table

Detection of antibodies directed at M. hyorhinis p37 in the serum of men with newly diagnosed prostate cancer

<p>Abstract</p> <p>Background</p> <p>Recent epidemiologic, genetic, and molecular studies suggest infection and inflammation initiate certain cancers, including cancers of the prostate. Over the past several years, our group has been studying how mycoplasmas could possibly initiate and propagate cancers of the prostate. Specifically, <it>Mycoplasma hyorhinis </it>encoded protein p37 was found to promote invasion of prostate cancer cells and cause changes in growth, morphology and gene expression of these cells to a more aggressive phenotype. Moreover, we found that chronic exposure of benign human prostate cells to <it>M. hyorhinis </it>resulted in significant phenotypic and karyotypic changes that ultimately resulted in the malignant transformation of the benign cells. In this study, we set out to investigate another potential link between mycoplasma and human prostate cancer.</p> <p>Methods</p> <p>We report the incidence of men with prostate cancer and benign prostatic hyperplasia (BPH) being seropositive for <it>M. hyorhinis</it>. Antibodies to <it>M. hyorhinis </it>were surveyed by a novel indirect enzyme-linked immunosorbent assay (ELISA) in serum samples collected from men presenting to an outpatient Urology clinic for BPH (N = 105) or prostate cancer (N = 114) from 2006-2009.</p> <p>Results</p> <p>A seropositive rate of 36% in men with BPH and 52% in men with prostate cancer was reported, thus leading us to speculate a possible connection between <it>M. hyorhinis </it>exposure with prostate cancer.</p> <p>Conclusions</p> <p>These results further support a potential exacerbating role for mycoplasma in the development of prostate cancer.</p

Decrypting magnetic fabrics (AMS, AARM, AIRM) through the analysis of mineral shape fabrics and distribution anisotropy

The fieldwork was supported by the DIPS project (grant no. 240467) and the MIMES project (grant no. 244155) funded by the Norwegian Research Council awarded to O.G. O.P.'s position was funded from Y-TEC.Anisotropy of magnetic susceptibility (AMS) and anisotropy of magnetic remanence (AARM and AIRM) are efficient and versatile techniques to indirectly determine rock fabrics. Yet, deciphering the source of a magnetic fabric remains a crucial and challenging step, notably in the presence of ferrimagnetic phases. Here we use X-ray micro-computed tomography to directly compare mineral shape-preferred orientation and spatial distribution fabrics to AMS, AARM and AIRM fabrics from five hypabyssal trachyandesite samples. Magnetite grains in the trachyandesite are euhedral with a mean aspect ratio of 1.44 (0.24 s.d., long/short axis), and > 50% of the magnetite grains occur in clusters, and they are therefore prone to interact magnetically. Amphibole grains are prolate with magnetite in breakdown rims. We identified three components of the petrofabric that influence the AMS of the analyzed samples: the magnetite and the amphibole shape fabrics and the magnetite spatial distribution. Depending on their relative strength, orientation and shape, these three components interfere either constructively or destructively to produce the AMS fabric. If the three components are coaxial, the result is a relatively strongly anisotropic AMS fabric (P’ = 1.079). If shape fabrics and/or magnetite distribution are non-coaxial, the resulting AMS is weakly anisotropic (P’ = 1.012). This study thus reports quantitative petrofabric data that show the effect of magnetite distribution anisotropy on magnetic fabrics in igneous rocks, which has so far only been predicted by experimental and theoretical models. Our results have first-order implications for the interpretation of petrofabrics using magnetic methods.Publisher PDFPeer reviewe

Persistent Exposure to Mycoplasma Induces Malignant Transformation of Human Prostate Cells

Recent epidemiologic, genetic, and molecular studies suggest infection and inflammation initiate certain cancers, including those of the prostate. The American Cancer Society, estimates that approximately 20% of all worldwide cancers are caused by infection. Mycoplasma, a genus of bacteria that lack a cell wall, are among the few prokaryotes that can grow in close relationship with mammalian cells, often without any apparent pathology, for extended periods of time. In this study, the capacity of Mycoplasma genitalium, a prevalent sexually transmitted infection, and Mycoplasma hyorhinis, a mycoplasma found at unusually high frequency among patients with AIDS, to induce a malignant phenotype in benign human prostate cells (BPH-1) was evaluated using a series of in vitro and in vivo assays. After 19 weeks of culture, infected BPH-1 cells achieved anchorage-independent growth and increased migration and invasion. Malignant transformation of infected BPH-1 cells was confirmed by the formation of xenograft tumors in athymic mice. Associated with these changes was an increase in karyotypic entropy, evident by the accumulation of chromosomal aberrations and polysomy. This is the first report describing the capacity of M. genitalium or M. hyorhinis infection to lead to the malignant transformation of benign human epithelial cells and may serve as a model to further study the relationship between prostatitis and prostatic carcinogenesis

Quantifying fracture geometry with X-ray tomography: Technique of Iterative Local Thresholding (TILT) for 3D image segmentation

This paper presents a new method—the Technique of Iterative Local Thresholding (TILT)—for processing 3D X-ray computed tomography (xCT) images for visualization and quantification of rock fractures. The TILT method includes the following advancements. First, custom masks are generated by a fracture-dilation procedure, which significantly amplifies the fracture signal on the intensity histogram used for local thresholding. Second, TILT is particularly well suited for fracture characterization in granular rocks because the multi-scale Hessian fracture (MHF) filter has been incorporated to distinguish fractures from pores in the rock matrix. Third, TILT wraps the thresholding and fracture isolation steps in an optimized iterative routine for binary segmentation, minimizing human intervention and enabling automated processing of large 3D datasets. As an illustrative example, we applied TILT to 3D xCT images of reacted and unreacted fractured limestone cores. Other segmentation methods were also applied to provide insights regarding variability in image processing. The results show that TILT significantly enhanced separability of grayscale intensities, outperformed the other methods in automation, and was successful in isolating fractures from the porous rock matrix. Because the other methods are more likely to misclassify fracture edges as void and/or have limited capacity in distinguishing fractures from pores, those methods estimated larger fracture volumes (up to 80 %), surface areas (up to 60 %), and roughness (up to a factor of 2). These differences in fracture geometry would lead to significant disparities in hydraulic permeability predictions, as determined by 2D flow simulations

Long-lived magnetism on chondrite parent bodies

publisher: Elsevier articletitle: Long-lived magnetism on chondrite parent bodies journaltitle: Earth and Planetary Science Letters articlelink: http://dx.doi.org/10.1016/j.epsl.2017.07.035 content_type: article copyright: © 2017 The Authors. Published by Elsevier B.V.© 2017 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). The attached file is the published version of the article