The influence of ocean variations on the climate of Ireland

The influence of the ocean circulation on the climate of Ireland is more subtle than it first appears. Temperatures in Ireland are warmer than similar Pacific maritime climates. It is heat - carried primarily in the Atlantic overturning circulation - released over the Atlantic that provides this additional warmth. We investigate variations in Irish climate using long-term station-based time series. The Atlantic multidecadal oscillation (AMO) explains over 90% of the pronounced decadal temperature and summer precipitation variation. Understanding the impact of these ocean variations when interpreting long climate records, particularly in the context of a changing climate, is crucial

SDRF2GRAPH – a visualization tool of a spreadsheet-based description of experimental processes

<p>Abstract</p> <p>Background</p> <p>As larger datasets are produced with the development of genome-scale experimental techniques, it has become essential to explicitly describe the meta-data (information describing the data) generated by an experiment. The experimental process is a part of the meta-data required to interpret the produced data, and SDRF (Sample and Data Relationship Format) supports its description in a spreadsheet or tab-delimited file. This format was primarily developed to describe microarray studies in MAGE-tab, and it is being applied in a broader context in ISA-tab. While the format provides an explicit framework to describe experiments, increase of experimental steps makes it less obvious to understand the content of the SDRF files.</p> <p>Results</p> <p>Here, we describe a new tool, SDRF2GRAPH, for displaying experimental steps described in an SDRF file as an investigation design graph, a directed acyclic graph representing experimental steps. A spreadsheet, in Microsoft Excel for example, which is used to edit and inspect the descriptions, can be directly input via a web-based interface without converting to tab-delimited text. This makes it much easier to organize large contents of SDRF described in multiple spreadsheets.</p> <p>Conclusion</p> <p>SDRF2GRAPH is applicable for a wide range of SDRF files for not only microarray-based analysis but also other genome-scale technologies, such as next generation sequencers. Visualization of the Investigation Design Graph (IDG) structure leads to an easy understanding of the experimental process described in the SDRF files even if the experiment is complicated, and such visualization also encourages the creation of SDRF files by providing prompt visual feedback.</p

Answering biological questions: querying a systems biology database for nutrigenomics

The requirement of systems biology for connecting different levels of biological research leads directly to a need for integrating vast amounts of diverse information in general and of omics data in particular. The nutritional phenotype database addresses this challenge for nutrigenomics. A particularly urgent objective in coping with the data avalanche is making biologically meaningful information accessible to the researcher. This contribution describes how we intend to meet this objective with the nutritional phenotype database. We outline relevant parts of the system architecture, describe the kinds of data managed by it, and show how the system can support retrieval of biologically meaningful information by means of ontologies, full-text queries, and structured queries. Our contribution points out critical points, describes several technical hurdles. It demonstrates how pathway analysis can improve queries and comparisons for nutrition studies. Finally, three directions for future research are given

Networking expertise: Discursive coalitions and collaborative networks of experts in a public creationism controversy in the UK

Experts do play a particular role in public socio-scientific debates, even more so if they form heterogeneous coalition with other actors and experts. A case study about a public science education controversy surrounding the teaching of evolution/creationism in the UK press is used to investigate in detail how connections and coalitions between experts and other actors involved in the controversy emerged and played out. The research focuses on the question of what role collaborative and other networks of experts played in terms of influence, visibility, credibility, consensus and weight of argument. Issues that are considered in the research are the status of the members of the coalitions forming during the debate and how it is displayed in media representations and letters and petitions, and also how these networks and coalitions of experts perform in relation to each other

Aging increases cell-to-cell transcriptional variability upon immune stimulation

Aging is characterized by progressive loss of physiological and cellular functions, but the molecular basis of this decline remains unclear. We explored how aging affects transcriptional dynamics using single-cell RNA sequencing of unstimulated and stimulated naïve and effector memory CD4(+) T cells from young and old mice from two divergent species. In young animals, immunological activation drives a conserved transcriptomic switch, resulting in tightly controlled gene expression characterized by a strong up-regulation of a core activation program, coupled with a decrease in cell-to-cell variability. Aging perturbed the activation of this core program and increased expression heterogeneity across populations of cells in both species. These discoveries suggest that increased cell-to-cell transcriptional variability will be a hallmark feature of aging across most, if not all, mammalian tissues.Funded by the European Research Council (F.C., T.F.R., D.T.O., S.A.T., and M.J.T.S.), EMBO Young Investigators Programme (D.T.O.), Cancer Research UK (H.-C.C., M.d.l.R., D.T.O., and J.C.M.), Janet Thornton Fellowship (WT098051 to C.P.M.-J.), Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (107609/Z/15/Z to M.d.l.R.), European Molecular Biology Laboratory (N.E., A.A.K., M.J.T.S., S.A.T., and J.C.M.), Medical Research Council Biostatistics Unit (MRC_MC_UP_0801/1 to C.A.V.), WTSI (C.P.M.-J., S.A.T., J.C.M., and D.T.O.), and Biotechnology and Biological Sciences Research Council–Collaborative Awards in Science and Engineering Studentship with Abcam plc (A.A.K.)

Transposed-letter priming effects in reading aloud words and nonwords

A masked nonword prime generated by transposing adjacent inner letters in a word (e.g., jugde) facilitates the recognition of the target word (JUDGE) more than a prime in which the relevant letters are replaced by different letters (e.g., junpe). This transposed-letter (TL) priming effect has been widely interpreted as evidence that the coding of letter position is flexible, rather than precise. Although the TL priming effect has been extensively investigated in the domain of visual word recognition using the lexical decision task, very few studies have investigated this empirical phenomenon in reading aloud. In the present study, we investigated TL priming effects in reading aloud words and nonwords and found that these effects are of equal magnitude for the two types of items. We take this result as support for the view that the TL priming effect arises from noisy perception of letter order within the prime prior to the mapping of orthography to phonology.6 page(s

Hyperpolarized¹³C-Pyruvate Metabolism as a Surrogate for Tumor Grade and Poor Outcome in Renal Cell Carcinoma—A Proof of Principle Study

Differentiating aggressive clear cell renal cell carcinoma (ccRCC) from indolent lesions is challenging using conventional imaging. This work prospectively compared the metabolic imaging phenotype of renal tumors using carbon-13 MRI following injection of hyperpolarized [1-13C]pyruvate (HP-13C-MRI) and validated these findings with histopathology. Nine patients with treatment-naïve renal tumors (6 ccRCCs, 1 liposarcoma, 1 pheochromocytoma, 1 oncocytoma) underwent pre-operative HP-13C-MRI and conventional proton (1H) MRI. Multi-regional tissue samples were collected using patient-specific 3D-printed tumor molds for spatial registration between imaging and molecular analysis. The apparent exchange rate constant (kPL) between 13C-pyruvate and 13C-lactate was calculated. Immunohistochemistry for the pyruvate transporter (MCT1) from 44 multi-regional samples, as well as associations between MCT1 expression and outcome in the TCGA-KIRC dataset, were investigated. Increasing kPL in ccRCC was correlated with increasing overall tumor grade (ρ = 0.92, p = 0.009) and MCT1 expression (r = 0.89, p = 0.016), with similar results acquired from the multi-regional analysis. Conventional 1H-MRI parameters did not discriminate tumor grades. The correlation between MCT1 and ccRCC grade was confirmed within a TCGA dataset (p &lt; 0.001), where MCT1 expression was a predictor of overall and disease-free survival. In conclusion, metabolic imaging using HP-13C-MRI differentiates tumor aggressiveness in ccRCC and correlates with the expression of MCT1, a predictor of survival. HP-13C-MRI may non-invasively characterize metabolic phenotypes within renal cancer.</jats:p

Sensitivity of Calcification to Thermal Stress Varies among Genera of Massive Reef-Building Corals

Reductions in calcification in reef-building corals occur when thermal conditions are suboptimal, but it is unclear how they vary between genera in response to the same thermal stress event. Using densitometry techniques, we investigate reductions in the calcification rate of massive Porites spp. from the Great Barrier Reef (GBR), and P. astreoides, Montastraea faveolata, and M. franksi from the Mesoamerican Barrier Reef (MBR), and correlate them to thermal stress associated with ocean warming. Results show that Porites spp. are more sensitive to increasing temperature than Montastraea, with calcification rates decreasing by 0.40 g cm−2 year−1 in Porites spp. and 0.12 g cm−2 year−1 in Montastraea spp. for each 1°C increase. Under similar warming trends, the predicted calcification rates at 2100 are close to zero in Porites spp. and reduced by 40% in Montastraea spp. However, these predictions do not account for ocean acidification. Although yearly mean aragonite saturation (Ωar) at MBR sites has recently decreased, only P. astreoides at Chinchorro showed a reduction in calcification. In corals at the other sites calcification did not change, indicating there was no widespread effect of Ωar changes on coral calcification rate in the MBR. Even in the absence of ocean acidification, differential reductions in calcification between Porites spp. and Montastraea spp. associated with warming might be expected to have significant ecological repercussions. For instance, Porites spp. invest increased calcification in extension, and under warming scenarios it may reduce their ability to compete for space. As a consequence, shifts in taxonomic composition would be expected in Indo-Pacific reefs with uncertain repercussions for biodiversity. By contrast, Montastraea spp. use their increased calcification resources to construct denser skeletons. Reductions in calcification would therefore make them more susceptible to both physical and biological breakdown, seriously affecting ecosystem function in Atlantic reefs

MGEx-Udb: A Mammalian Uterus Database for Expression-Based Cataloguing of Genes across Conditions, Including Endometriosis and Cervical Cancer

Gene expression profiling of uterus tissue has been performed in various contexts, but a significant amount of the data remains underutilized as it is not covered by the existing general resources.). The database can be queried with gene names/IDs, sub-tissue locations, as well as various conditions such as the cervical cancer, endometrial cycles and disorders, and experimental treatments. Accordingly, the output would be a) transcribed and dormant genes listed for the queried condition/location, or b) expression profile of the gene of interest in various uterine conditions. The results also include the reliability score for the expression status of each gene. MGEx-Udb also provides information related to Gene Ontology annotations, protein-protein interactions, transcripts, promoters, and expression status by other sequencing techniques, and facilitates various other types of analysis of the individual genes or co-expressed gene clusters.In brief, MGEx-Udb enables easy cataloguing of co-expressed genes and also facilitates bio-marker discovery for various uterine conditions

PathEx: a novel multi factors based datasets selector web tool

<p>Abstract</p> <p>Background</p> <p>Microarray experiments have become very popular in life science research. However, if such experiments are only considered independently, the possibilities for analysis and interpretation of many life science phenomena are reduced. The accumulation of publicly available data provides biomedical researchers with a valuable opportunity to either discover new phenomena or improve the interpretation and validation of other phenomena that partially understood or well known. This can only be achieved by intelligently exploiting this rich mine of information.</p> <p>Description</p> <p>Considering that technologies like microarrays remain prohibitively expensive for researchers with limited means to order their own experimental chips, it would be beneficial to re-use previously published microarray data. For certain researchers interested in finding gene groups (requiring many replicates), there is a great need for tools to help them to select appropriate datasets for analysis. These tools may be effective, if and only if, they are able to re-use previously deposited experiments or to create new experiments not initially envisioned by the depositors. However, the generation of new experiments requires that all published microarray data be completely annotated, which is not currently the case. Thus, we propose the PathEx approach.</p> <p>Conclusion</p> <p>This paper presents PathEx, a human-focused web solution built around a two-component system: one database component, enriched with relevant biological information (expression array, omics data, literature) from different sources, and another component comprising sophisticated web interfaces that allow users to perform complex dataset building queries on the contents integrated into the PathEx database.</p