A robust genomic signature for the detection of colorectal cancer patients with microsatellite instability phenotype and high mutation frequency.

Microsatellite instability (MSI) occurs in 10-20% of colorectal tumours and is associated with good prognosis. Here we describe the development and validation of a genomic signature that identifies colorectal cancer patients with MSI caused by DNA mismatch repair deficiency with high accuracy. Microsatellite status for 276 stage II and III colorectal tumours has been determined. Full-genome expression data was used to identify genes that correlate with MSI status. A subset of these samples (n = 73) had sequencing data for 615 genes available. An MSI gene signature of 64 genes was developed and validated in two independent validation sets: the first consisting of frozen samples from 132 stage II patients; and the second consisting of FFPE samples from the PETACC-3 trial (n = 625). The 64-gene MSI signature identified MSI patients in the first validation set with a sensitivity of 90.3% and an overall accuracy of 84.8%, with an AUC of 0.942 (95% CI, 0.888-0.975). In the second validation, the signature also showed excellent performance, with a sensitivity 94.3% and an overall accuracy of 90.6%, with an AUC of 0.965 (95% CI, 0.943-0.988). Besides correct identification of MSI patients, the gene signature identified a group of MSI-like patients that were MSS by standard assessment but MSI by signature assessment. The MSI-signature could be linked to a deficient MMR phenotype, as both MSI and MSI-like patients showed a high mutation frequency (8.2% and 6.4% of 615 genes assayed, respectively) as compared to patients classified as MSS (1.6% mutation frequency). The MSI signature showed prognostic power in stage II patients (n = 215) with a hazard ratio of 0.252 (p = 0.0145). Patients with an MSI-like phenotype had also an improved survival when compared to MSS patients. The MSI signature was translated to a diagnostic microarray and technically and clinically validated in FFPE and frozen samples.

Estudi GPGPU dedicat al processament de neuroimatges

La tecnologia GPGPU permet paral∙lelitzar càlculs executant operacions aritmètiques en els múltiples processadors de que disposen els xips gràfics. S'ha fet servir l'entorn de desenvolupament CUDA de la companyia NVIDIA, que actualment és la solució GPGPU més avançada del mercat. L'algorisme de neuroimatge implementat pertany a un estudi VBM desenvolupat amb l'eina SPM. Es tracta concretament del procés de segmentació d'imatges de ressonància magnètica cerebrals, en els diferents teixits dels quals es composa el cervell: matèria blanca, matèria grisa i líquid cefaloraquidi. S'han implementat models en els llenguatges Matlab, C i CUDA, i s'ha fet un estudi comparatiu per plataformes hardware diferents.

Mejorando la robustez de aplicaciones frente a fallos transitorios

Computer chips implementation technologies evolving to obtain more performance are increasing the probability of transient faults. As this probability grows and on-chip solutions are expensive or tend to degrade processor performance, the efforts to deal with these transient faults in higher levels (such as the operating system or even at the application level) are increasing. Mostly, these efforts are trying to avoid silent data corruptions using hardware, software and hybrid based techniques to add redundancy to detect the errors generated by the transient faults. This work presents our proposal to improve the robustness of applications with source code based transformation adding redundancy. Also, our proposal takes account of the tradeoff between the improved robustness and the overhead generated by the added redundancy.

Serum-Mediane von Placentaprotein-Markern: Relevanz der Unterschiede zwischen spontanen und nach-in-vitro-Fertilisation eingetretenen Schwangerschaften für das fetale Trisomie-Screening.

Trisomy-21 (Down syndrome) is the most frequent chromosomal abnorm- ality but only one third of cases would be detected by amniocentesis based on maternal age alone. Serum screening tests in the early second trimester increase the detec- tion rate to 60-65%, and more recently it was found that such screening was also possible in the first trimester by quantifying a diffe- rent panel of markers. The concen- trations of these placental proteins are strongly dependent on gestatio- nal age; thus control medians must be established and precise dating is essential. Serum chorionic gonado- trophin (HCG) levels were recently found to be increased in IVF preg- nancies compared to spontaneous gestations, leading to a falsely ele- vated trisomy screening risk. The aim of this preliminary study was to find out whether, in the first-trime- ster screening, the markers similarly differed between IVF and spontane- ous pregnancies which would call for the establishment of separate normal medians for IVF patients. We compared 24 pregnancies ob- tained after ovarian stimulation and IVF with six women after thawed embryo transfer (unstimulated cycle) and 63 gestation- and maternal-age matched spontaneously pregnant controls. A single serum was ob- tained between 6 and 16 weeks of gestation and various placental protein levels determined by im- munometric assays. Serum levels of pregnancy-associated plasma protein A (PAPP-A), which is the major marker in the first-trimes- ter screening test, were reduced in IVF pregnancies: after 9 weeks of gestation, multiples of median (MoMs) ranged between 0.23 and 3.58 (logarithmic mean 0.743). For the frozen/thawed transfers, this value was 1.08. In the 9-12 week group containing 6 cases of IVF, three thawed transfers and 25 con- trols, PAPP-A was significantly redu- ced in the stimulated compared to the nonstimulated cycles. In the late first and early second trimester the difference was not significant in our small group but the trend persisted. Pregnancies after IVF will thus show an increased incidence of false positive results in fetal trisomy-21 screening, and special medians should be established for these pati- ents.

Polarity of endogenous and exogenous glycosyl-phosphatidylinositol-anchored membrane proteins in Madin-Darby canine kidney cells.

Madin-Darby canine kidney cells (MDCK) were transfected with a cDNA encoding the glycosyl-phosphatidylinositol (GPI)-anchored protein mouse Thy-1 in order to study the steady-state surface distribution of exogenous and endogenous GPI-linked proteins. Immunofluorescence of transfected cells grown on collagen-coated coverslips showed that expression of Thy-1 was variable throughout the epithelium, with some cells expressing large amounts of Thy-1 adjacent to very faintly staining cells. Selective surface iodination of cells grown on collagen-coated or uncoated transwell filters followed by immunoprecipitation of Thy-1 demonstrated that all the Thy-1 was present exclusively in the apical plasma membrane. Although cells grown on uncoated filters had much smaller amounts of Thy-1, it was consistently localized on the apical surfaces. Immunofluorescent localization of Thy-1 on 1 micron frozen sections of filter-grown cells demonstrated that all the Thy-1 was on the apical surface and there was no detectable intracellular pool. Phosphatidylinositol-specific phospholipase C digestion of intact iodinated monolayers released Thy-1 only into the apical medium, indicating that Thy-1 was processed normally in transfected cells and was anchored by a GPI-tail. In agreement with previous findings, endogenous GPI-linked proteins were found only on the apical plasma membrane. These results suggest that there is a common mechanism for sorting and targeting of GPI-linked proteins in polarized epithelial cells.

Solubility of cytoskeletal proteins in immunohistochemistry and the influence of fixation.

For accurate and quantitative immunohistochemical localization of antigens it is crucial to know the solubility of tissue proteins and their degree of loss during processing. In this study we focused on the solubility of several cytoskeletal proteins in cat brain tissue at various ages and their loss during immunohistochemical procedures. We further examined whether fixation affected either solubility or immunocytochemical detectability of several cytoskeletal proteins. An assay was designed to measure the solubility of cytoskeletal proteins in cryostat sections. Quantity and quality of proteins lost or remaining in tissue were measured and analyzed by electrophoresis and immunoblots. Most microtubule proteins were found to be soluble in unfixed and alcohol fixed tissues. Furthermore, the microtubule proteins remaining in the tissue had a changed cellular distribution. In contrast, brain spectrin and all three neurofilament subunits were insoluble and remained in the tissue, allowing their immunocytochemical localization in alcohol-fixed tissue. Synapsin I, a protein associated with the spectrin cytoskeleton, was soluble, and aldehyde fixation is advised for its immunohistochemical localization. With aldehyde fixation, the immunoreactivity of some antibodies against neurofilament proteins was reduced in axons unveiling novel immunogenic sites in nuclei that may represent artifacts of fixation. In conclusion, protein solubility and the effects of fixation are influential factors in cytoskeletal immunohistochemistry, and should be considered before assessments for a quantitative distribution are made.

Uncovering hidden duplicated content in public transcriptomics data.

As part of the development of the database Bgee (a dataBase for Gene Expression Evolution), we annotate and analyse expression data from different types and different sources, notably Affymetrix data from GEO and ArrayExpress, and RNA-Seq data from SRA. During our quality control procedure, we have identified duplicated content in GEO and ArrayExpress, affecting ∼14% of our data: fully or partially duplicated experiments from independent data submissions, Affymetrix chips reused in several experiments, or reused within an experiment. We present here the procedure that we have established to filter such duplicates from Affymetrix data, and our procedure to identify future potential duplicates in RNA-Seq data. Database URL: http://bgee.unil.ch/

MIMAS 3.0 is a Multiomics Information Management and Annotation System.

BACKGROUND: DNA sequence integrity, mRNA concentrations and protein-DNA interactions have been subject to genome-wide analyses based on microarrays with ever increasing efficiency and reliability over the past fifteen years. However, very recently novel technologies for Ultra High-Throughput DNA Sequencing (UHTS) have been harnessed to study these phenomena with unprecedented precision. As a consequence, the extensive bioinformatics environment available for array data management, analysis, interpretation and publication must be extended to include these novel sequencing data types. DESCRIPTION: MIMAS was originally conceived as a simple, convenient and local Microarray Information Management and Annotation System focused on GeneChips for expression profiling studies. MIMAS 3.0 enables users to manage data from high-density oligonucleotide SNP Chips, expression arrays (both 3'UTR and tiling) and promoter arrays, BeadArrays as well as UHTS data using MIAME-compliant standardized vocabulary. Importantly, researchers can export data in MAGE-TAB format and upload them to the EBI's ArrayExpress certified data repository using a one-step procedure. CONCLUSION: We have vastly extended the capability of the system such that it processes the data output of six types of GeneChips (Affymetrix), two different BeadArrays for mRNA and miRNA (Illumina) and the Genome Analyzer (a popular Ultra-High Throughput DNA Sequencer, Illumina), without compromising on its flexibility and user-friendliness. MIMAS, appropriately renamed into Multiomics Information Management and Annotation System, is currently used by scientists working in approximately 50 academic laboratories and genomics platforms in Switzerland and France. MIMAS 3.0 is freely available via http://multiomics.sourceforge.net/.

Comparison between precipitin and ELISA tests in the bloodmeal detection of Aedes aegypti (Linnaeus) and Aedes fluviatilis (Lutz) mosquitoes experimentally fed on feline, canine and human hosts

The identification of arthropod bloodmeals is important in many epidemiological studies, as, the understanding of the life cycle of vectors and the patogens they transmit, as well as helping to define arthropods' control strategies. The precipitin test has been used for decades, but ELISA is slowly becoming more popular. To compare the two tests for sensitivity, specificity and accuracy to detect small insect bloodmeals, Aedes aegypti or Ae. fluviatilis mosquitoes were fed either on feline, canine or human hosts. Mosquitoes were frozen at 6, 12, 24, 48 or 72 h after feeding. Precipitin test showed better specificity and accuracy and ELISA test showed higher sensitivity. Better results with both tests were achieved when mosquitoes were frozen within 48 h from feeding.

Cryo-negative staining reveals conformational flexibility within yeast RNA polymerase I.

The structure of the yeast DNA-dependent RNA polymerase I (RNA Pol I), prepared by cryo-negative staining, was studied by electron microscopy. A structural model of the enzyme at a resolution of 1.8 nm was determined from the analysis of isolated molecules and showed an excellent fit with the atomic structure of the RNA Pol II Delta4/7. The high signal-to-noise ratio (SNR) of the stained molecular images revealed a conformational flexibility within the image data set that could be recovered in three-dimensions after implementation of a novel strategy to sort the "open" and "closed" conformations in our heterogeneous data set. This conformational change mapped in the "wall/flap" domain of the second largest subunit (beta-like) and allows a better accessibility of the DNA-binding groove. This displacement of the wall/flap domain could play an important role in the transition between initiation and elongation state of the enzyme. Moreover, a protrusion was apparent in the cryo-negatively stained model, which was absent in the atomic structure and was not detected in previous 3D models of RNA Pol I. This structure could, however, be detected in unstained views of the enzyme obtained from frozen hydrated 2D crystals, indicating that this novel feature is not induced by the staining process. Unexpectedly, negatively charged molybdenum compounds were found to accumulate within the DNA-binding groove, which is best explained by the highly positive electrostatic potential of this region of the molecule, thus, suggesting that the stain distribution reflects the overall surface charge of the molecule.

The category 'natural' in the discourse of couples who used medically assisted procreation

As a constantly evolving set of complex biotechnologies, medically assisted procreation (MAP) jeopardises a category that seems to be taken for granted: that of 'natural'. What is 'natural' or not when MAP is used to procreate? What are the boundaries between a 'natural' and a 'non-natural' fertilisation? Drawing upon a dialogical approach to language and cognition, our study examined the semantic field of the category 'natural' as expressed in interviews between a psychiatrist and seven couples who resorted to MAP and had to decide whether to keep their frozen pre-embryonic cells (zygotes) for further procreation or to allow them be destroyed. We examined how these couples evoked the category 'natural' and showed that in their argumentation, the category 'natural' encompassed a wide variety of phenomena, which shifted the boundaries between the 'natural' and 'non-natural'. In so doing, the couples 'renaturalised' MAP, normalized it, moved the boundaries between what is legitimate or not, and showed their accountability. Hence, reference to the category 'natural' seemed to act both as an argumentative and a psychological resource in the elaboration of the person's experience in resorting to MAP.

A Happy and a Healthy 2012

Many of us start the New Year with the best of intentions to lose weight, get fitter and eat well. It's that sense of new possibilities and fresh beginnings that can also help motivate changes in lifestyle. The Public Health Agency advises that making small changes to your own and your family's lifestyle can have a significant impact on improving overall health. Taking time to reflect, and making a plan, can all help. Choosing healthier food and increasing your physical activity will help maintain a healthy weight and prevent unwanted weight gain, which can have serious implications for a person's physical and mental health as it is associated with an increased risk of heart disease, stroke, type 2 diabetes, some cancers, respiratory problems, joint pain and depression.What can I do to improve my health?Make 1 or 2 small changes at a time - don't try to change your lifestyle radically or all at once as you're more likely to fail. Small changes in what you eat, or how active you are, are easier to make and more likely to be maintained.Mary Black, Assistant Director of Health and Wellbeing Improvement, PHA, said: "The New Year brings a time when many people reflect on their lives and very often eating more healthily is one of things they identify for change. I recommend setting a couple of small, achievable targets that can then be continued in the long term, for example:Eat breakfast everyday;Eat an extra portion of vegetables every day;Swap deep fried chips for oven chips;Choose fruit for between-meal snacks instead of a biscuit or bun;Begin to enjoy a hot drink on its own without feeling the need to have something sweet at the same time.Be active. Any sort of activity will be good for you. Think about how you can be more active each day. This doesn't have to involve running a marathon or joining a gym. Some suggestions include:· Go for walks with the children/family or friends. It's free! Walk on your lunch break;· Take the stairs instead of the elevator or escalator;· Park further away and walk to work/school;· Get off the bus a stop earlier and walk the rest;· Minimise the amount of time you are sitting down - take breaks from the computer at work or watching TV at home and walk around;· Children and adults can build up to the recommended daily activity levels in 10 minute sessions rather than doing it all in one session.Adults need at least 30 minutes, five days a week of moderate physical activity and children need 60 minutes of physical activity every day.Mary continued "It's easy for people to get into the habit of spending their spare time sitting down - watching TV, playing computer games, listening to their MP3 players - but being active will help you maintain a healthy weight and generally make you feel better. It can also improve your mood, reduce anxiety and protect against depression."It is what you do most of the time that really matters, so if you eat too much or don't exercise on any one day, don't worry too much - just accept it and get back to your new way of eating and being more active as soon as possible.

Consumer Focused Review of the Pork Supply Chain

Pig meat production was valued at €290 (£198) million at farm gate in Republic of Ireland (ROI) in 2007. In Northern Ireland (NI) in 2006, pig meat was estimated to account for almost seven percent of gross turnover in the food and drinks processing sector at £190 (€280) million. Whilst researching for this report it emerged that comparable figures for the value of the pig meat industry on ROI and NI are not available. This report showed that pig production on the IOI has changed from a small-scale enterprise carried out by a large number of mixed farmers to a modern industry comprised of a small number of specialist producers operating large-scale units. Most products for retailers are prepared and packed in specialised cutting and processing units which may or may not be integrated in the slaughter plant. For some pork products, various additives such as salt, herbs and flavour enhancers are added. Pork products are then stored and transported, frozen or chilled to wholesale, retail and catering facilities for ultimate sale to consumers.

Growing up in Ireland. Key findings: infant cohort (at 3 years).

 The latest results from the study paint a picture of how these families are faring across a range of areas in their lives including their health, family life and financial and economic circumstances. In general the findings show that three-year-olds in Ireland are in good health with a few notable public health and related issues (including overweight and obesity), there is overall stability in family structures over the short term and that the recession has had a substantial effect on families with young children over the last number of years. These are the first longitudinal findings from the study. The first wave of fieldwork with the families of the Infant Cohort included approximately 11,100 nine-month-olds, their parents and carers. Interviews began in September 2008 and were completed in March 2009. Interviews for the second round of interviews with this cohort took place between January and August 2011. A total of 90% of the original sample of nine-month-olds were successfully re-interviewed. (A full download of the results released today, presented in three briefing documents can be found by clicking here. Key findings include: Health â?¢ Most of the children were described as being in good health; 75% were rated as very healthy and a further 23% were rated as healthy, but a few minor problems. Girls were more likely to be reported as very healthy (78%) compared with boys (72%). â?¢ One in four or almost one quarter of three-year-old children were overweight (19%) or obese (6%). â?¢ Childrenâ?Ts weight was related to household social class. 5% of children in families in the professional/managerial group were classified as obese at three years of age compared with 9% of those in the most disadvantaged social class group. However, at least one-fifth of children in every social class were overweight. â?¢ Childrens consumption of energy-dense foods such as crisps, sweets, chips, and non-diet fizzy drinks increased as parental education fell. 63% of children whose mother had a lower secondary education or less ate at least one portion of crisps compared with 36% of those from degree-level backgrounds, although consumption of biscuits/chocolates was over 70% for both groups of children. â?¢ Two-thirds (66%) of three-year-olds had received at least one course of antibiotics in the 12 months preceding the interview. Children with a full medical card (35% of the sample) or a GP-only medical card (5% of the sample) were more likely to have received a course of antibiotics than â?¢ Children with a full medical card received a higher number of antibiotic courses on average (2.6) compared with those without a medical card (2.1). â?¢ Just under 16% of three-year-old children were reported as having at least one longstanding illness, condition or disability. The most commonly reported illness types included Asthma (5.8%), Eczema/Skin allergies (3.9%) and Food/digestive allergies (1.2%) Family Life and Childcare â?¢ While the overall distribution of family structure was stable, there have been transitions from one-parent families to two-parent families and vice-versa over the 27 months between interview â?" approximately 2 to 3 percent in each direction. â?¢ 50% of three year olds were in some form of non-parental childcare for eight or more hours a week. The most common form used was centre-based childcare which almost tripled between nine months and three years, from 11% to 30%. â?¢ A similar percentage of grandparents were caring for children at both nine months and three years, 12% and 11% respectively. A total of 10% of three-year-olds were being minded by a childminder, an increase of 3 percentage points from when the children were nine months of age. â?¢ Children who were in some form of non-parental childcare were spending an average of 23 hours a week in their main type of childcare. â?¢ At time of interview the vast majority of mothers reported that they had regular contact with the Study Childâ?Ts grandparents (91%). In offering support to parents, grandparents were most likely to babysit (50%), and buy clothes (40%) at least on a monthly basis. One-parent families were more likely than two-parent families to receive financial support from grandparents with just under one-third (66%) of one-parent families receiving financial support from grandparents at least once every three months. â?¢ The most frequently used discipline technique was â?~discussing or explaining why the behaviour was wrongâ?T, with 63% of mothers saying they always did this. â?¢ 12% of mothers said they used â?~smackingâ?T as a form of discipline now and again and less than 1% used â?~smackingâ?T as a form of discipline more frequently. Over half reported that they never smacked the Study Child. Financial and Economic Circumstances â?¢ Just over half (53%) of mothers of three-year-olds worked outside the home, 38% said they were on home duties and 6% said they were unemployed. â?¢ The biggest change in terms of the work status of three-year-oldsâ?T parents was an increase in the percentage of unemployed fathers â?" 6% when the child was nine months rising to almost 14% when s/he was three years of age. â?¢ 61% of families of three-year-olds reported experiencing difficulties in making â?~ends meetâ?T. This was a substantial increase from 44% in the first round of interviews when the children were nine-months-old. â?¢ Almost two thirds (63%) of all families with three-year-olds reported that the recession had had a very significant or significant effect on them. â?¢ The most frequently recorded effects were: a reduction in wages (63%); canâ?Tt afford luxuries (54%), social welfare reduction (53%) and canâ?Tt afford/cut back on basics (32%). Growing Up in Ireland is a Government funded study tracking the development of two nationally representative cohorts of children: an Infant Cohort which was interviewed initially at nine months and subsequently at three years of age; and a Child Cohort which was interviewed initially at nine years and subsequently at 13 years of age. The study is being conducted by a consortium of researchers led by the Economic and Social Research Institute (ESRI) and Trinity College Dublin. For Further Information Please Contact: Jillian Heffernan Communications Officer, Growing Up in Ireland Tel: 01 896 3378 Mobile: 087 9016880This resource was contributed to our repository by the National Documentation Centre on Drug Use.

On the presence of hepatic stellate cells in portal spaces

Previous studies in mice with hypervitaminosis A have demonstrated that fat-storing cells (hepatic stellate cells-HSCs) participate in schistosomal granuloma fibrogenesis. The origin of such cells in portal areas, away from the Disse spaces, was herein investigated. HSCs were identified in frozen sections of the liver by means of Sudan III staining. They appeared as red-stained cells disposed along the sinusoids of normal mice, but were never found within portal spaces. However, in the chronically inflamed portal spaces of Capillaria hepatica-infected mice, Sudan III-positive cells were frequently present among leukocytes and fibroblast-like cells. Thus, there are no resident HSCs in portal spaces, but their presence there in chronic inflammatory processes indicates that they are able to migrate from peri-sinusoidal areas in order to reach the portal areas.