Metal silicide/poly-Si Schottky diodes for uncooled microbolometers

Nickel silicide Schottky diodes formed on polycrystalline Si films are proposed as temperature sensors of monolithic uncooled microbolometer IR focal plane arrays. Structure and composition of nickel silicide/polycrystalline silicon films synthesized in a low-temperature process are examined by means of transmission electron microscopy. The Ni silicide is identified as multi-phase compound composed by 20 to 40% of Ni3Si, 30 to 60% of Ni2Si and 10 to 30% of NiSi with probable minor content of NiSi2 at the silicide/poly-Si interface. Rectification ratios of the Schottky diodes vary from ~100 to ~20 for the temperature increasing from 22 to 70C; they exceed 1000 at 80K. A barrier of ~0.95 eV is found to control the photovoltage spectra at room temperature. A set of barriers is observed in photo-emf spectra at 80K and attributed to the Ni-silicide/poly-Si interface. Absolute values of temperature coefficients of voltage and current are found to vary from 0.3 to 0.6%/K for forward biasing and around 2.5%/K for reverse biasing of the diodes.Comment: 18 pages, 7 figure

GOSim – an R-package for computation of information theoretic GO similarities between terms and gene products

<p>Abstract</p> <p>Background</p> <p>With the increased availability of high throughput data, such as DNA microarray data, researchers are capable of producing large amounts of biological data. During the analysis of such data often there is the need to further explore the similarity of genes not only with respect to their expression, but also with respect to their functional annotation which can be obtained from Gene Ontology (GO).</p> <p>Results</p> <p>We present the freely available software package <it>GOSim</it>, which allows to calculate the functional similarity of genes based on various information theoretic similarity concepts for GO terms. <it>GOSim </it>extends existing tools by providing additional lately developed functional similarity measures for genes. These can e.g. be used to cluster genes according to their biological function. Vice versa, they can also be used to evaluate the homogeneity of a given grouping of genes with respect to their GO annotation. <it>GOSim </it>hence provides the researcher with a flexible and powerful tool to combine knowledge stored in GO with experimental data. It can be seen as complementary to other tools that, for instance, search for significantly overrepresented GO terms within a given group of genes.</p> <p>Conclusion</p> <p><it>GOSim </it>is implemented as a package for the statistical computing environment <it>R </it>and is distributed under GPL within the CRAN project.</p

Ethical Issues in Environmental Health Research Related to Public Health Emergencies: Reflections on the GuLF STUDY

Health research in the context of an environmental disaster with implications for public health raises challenging ethical issues. This article explores ethical issues that arose in the Gulf Long-term Follow-up Study (GuLF STUDY) and provides guidance for future research. Ethical issues encountered by GuLF STUDY investigators included a) minimizing risks and promoting benefits to participants, b) obtaining valid informed consent, c) providing financial compensation to participants, d) working with vulnerable participants, e) protecting participant confidentiality, f) addressing conflicts of interest, g) dealing with legal implications of research, and h) obtaining expeditious review from the institutional review board (IRB), community groups, and other committees. To ensure that ethical issues are handled properly, it is important for investigators to work closely with IRBs during the development and implementation of research and to consult with groups representing the community. Researchers should consider developing protocols, consent forms, survey instruments, and other documents prior to the advent of a public health emergency to allow for adequate and timely review by constituents. When an emergency arises, these materials can be quickly modified to take into account unique circumstances and implementation details

Exact score distribution computation for ontological similarity searches

<p>Abstract</p> <p>Background</p> <p>Semantic similarity searches in ontologies are an important component of many bioinformatic algorithms, e.g., finding functionally related proteins with the Gene Ontology or phenotypically similar diseases with the Human Phenotype Ontology (HPO). We have recently shown that the performance of semantic similarity searches can be improved by ranking results according to the probability of obtaining a given score at random rather than by the scores themselves. However, to date, there are no algorithms for computing the exact distribution of semantic similarity scores, which is necessary for computing the exact <it>P</it>-value of a given score.</p> <p>Results</p> <p>In this paper we consider the exact computation of score distributions for similarity searches in ontologies, and introduce a simple null hypothesis which can be used to compute a <it>P</it>-value for the statistical significance of similarity scores. We concentrate on measures based on Resnik's definition of ontological similarity. A new algorithm is proposed that collapses subgraphs of the ontology graph and thereby allows fast score distribution computation. The new algorithm is several orders of magnitude faster than the naive approach, as we demonstrate by computing score distributions for similarity searches in the HPO. It is shown that exact <it>P</it>-value calculation improves clinical diagnosis using the HPO compared to approaches based on sampling.</p> <p>Conclusions</p> <p>The new algorithm enables for the first time exact <it>P</it>-value calculation via exact score distribution computation for ontology similarity searches. The approach is applicable to any ontology for which the annotation-propagation rule holds and can improve any bioinformatic method that makes only use of the raw similarity scores. The algorithm was implemented in Java, supports any ontology in OBO format, and is available for non-commercial and academic usage under: <url>https://compbio.charite.de/svn/hpo/trunk/src/tools/significance/</url></p

Revisiting Date and Party Hubs: Novel Approaches to Role Assignment in Protein Interaction Networks

The idea of 'date' and 'party' hubs has been influential in the study of protein-protein interaction networks. Date hubs display low co-expression with their partners, whilst party hubs have high co-expression. It was proposed that party hubs are local coordinators whereas date hubs are global connectors. Here we show that the reported importance of date hubs to network connectivity can in fact be attributed to a tiny subset of them. Crucially, these few, extremely central, hubs do not display particularly low expression correlation, undermining the idea of a link between this quantity and hub function. The date/party distinction was originally motivated by an approximately bimodal distribution of hub co-expression; we show that this feature is not always robust to methodological changes. Additionally, topological properties of hubs do not in general correlate with co-expression. Thus, we suggest that a date/party dichotomy is not meaningful and it might be more useful to conceive of roles for protein-protein interactions rather than individual proteins. We find significant correlations between interaction centrality and the functional similarity of the interacting proteins.Comment: 27 pages, 5 main figures, 4 supplementary figure

“Excellence R Us”: university research and the fetishisation of excellence

The rhetoric of “excellence” is pervasive across the academy. It is used to refer to research outputs as well as researchers, theory and education, individuals and organisations, from art history to zoology. But does “excellence” actually mean anything? Does this pervasive narrative of “excellence” do any good? Drawing on a range of sources we interrogate “excellence” as a concept and find that it has no intrinsic meaning in academia. Rather it functions as a linguistic interchange mechanism. To investigate whether this linguistic function is useful we examine how the rhetoric of excellence combines with narratives of scarcity and competition to show that the hypercompetition that arises from the performance of “excellence” is completely at odds with the qualities of good research. We trace the roots of issues in reproducibility, fraud, and homophily to this rhetoric. But we also show that this rhetoric is an internal, and not primarily an external, imposition. We conclude by proposing an alternative rhetoric based on soundness and capacity-building. In the final analysis, it turns out that that “excellence” is not excellent. Used in its current unqualified form it is a pernicious and dangerous rhetoric that undermines the very foundations of good research and scholarship

Predicting functional associations from metabolism using bi-partite network algorithms

<p>Abstract</p> <p>Background</p> <p>Metabolic reconstructions contain detailed information about metabolic enzymes and their reactants and products. These networks can be used to infer functional associations between metabolic enzymes. Many methods are based on the number of metabolites shared by two enzymes, or the shortest path between two enzymes. Metabolite sharing can miss associations between non-consecutive enzymes in a serial pathway, and shortest-path algorithms are sensitive to high-degree metabolites such as water and ATP that create connections between enzymes with little functional similarity.</p> <p>Results</p> <p>We present new, fast methods to infer functional associations in metabolic networks. A local method, the degree-corrected Poisson score, is based only on the metabolites shared by two enzymes, but uses the known metabolite degree distribution. A global method, based on graph diffusion kernels, predicts associations between enzymes that do not share metabolites. Both methods are robust to high-degree metabolites. They out-perform previous methods in predicting shared Gene Ontology (GO) annotations and in predicting experimentally observed synthetic lethal genetic interactions. Including cellular compartment information improves GO annotation predictions but degrades synthetic lethal interaction prediction. These new methods perform nearly as well as computationally demanding methods based on flux balance analysis.</p> <p>Conclusions</p> <p>We present fast, accurate methods to predict functional associations from metabolic networks. Biological significance is demonstrated by identifying enzymes whose strong metabolic correlations are missed by conventional annotations in GO, most often enzymes involved in transport vs. synthesis of the same metabolite or other enzyme pairs that share a metabolite but are separated by conventional pathway boundaries. More generally, the methods described here may be valuable for analyzing other types of networks with long-tailed degree distributions and high-degree hubs.</p

Gravitational Geometric Phase in the Presence of Torsion

We investigate the relativistic and non-relativistic quantum dynamics of a neutral spin-1/2 particle submitted an external electromagnetic field in the presence of a cosmic dislocation. We analyze the explicit contribution of the torsion in the geometric phase acquired in the dynamic of this neutral spinorial particle. We discuss the influence of the torsion in the relativistic geometric phase. Using the Foldy-Wouthuysen approximation, the non-relativistic quantum dynamics are studied and the influence of the torsion in the Aharonov-Casher and He-McKellar-Wilkens effects are discussed.Comment: 14 pages, no figur

Trapping dust particles in the outer regions of protoplanetary disks

In order to explain grain growth to mm sized particles and their retention in outer regions of protoplanetary disks, as it is observed at sub-mm and mm wavelengths, we investigate if strong inhomogeneities in the gas density profiles can slow down excessive radial drift and can help dust particles to grow. We use coagulation/fragmentation and disk-structure models, to simulate the evolution of dust in a bumpy surface density profile which we mimic with a sinusoidal disturbance. For different values of the amplitude and length scale of the bumps, we investigate the ability of this model to produce and retain large particles on million years time scales. In addition, we introduced a comparison between the pressure inhomogeneities considered in this work and the pressure profiles that come from magnetorotational instability. Using the Common Astronomy Software Applications ALMA simulator, we study if there are observational signatures of these pressure inhomogeneities that can be seen with ALMA. We present the favorable conditions to trap dust particles and the corresponding calculations predicting the spectral slope in the mm-wavelength range, to compare with current observations. Finally we present simulated images using different antenna configurations of ALMA at different frequencies, to show that the ring structures will be detectable at the distances of the Taurus Auriga or Ophiucus star forming regions.Comment: Pages 15, Figures 14. Accepted for publication in Astronomy and Astrophysic

Conflict of Interest Policies at Canadian Universities: Clarity and Content

[À l'origine dans / Was originally part of : ESPUM - Dép. médecine sociale et préventive - Travaux et publications]Abstract Discussions of conflict of interest (COI) in the university have tended to focus on financial interests in the context of medical research; much less attention has been given to COI in general or to the policies that seek to manage COI. Are university COI policies accessible and understandable? To whom are these policies addressed (faculty, staff, students)? Is COI clearly defined in these policies and are procedures laid out for avoiding or remedying such situations? To begin tackling these important ethical and governance questions, our study examines the COI policies at the Group of Thirteen (G13) leading Canadian research universities. Using automated readability analysis tools and an ethical content analysis, we begin the task of comparing the strengths and weaknesses of these documents, paying particular attention to their clarity, readability, and utility in explaining and managing COI.This study was supported by a grant from the Institute of Genetics of the Canadian Institutes of Health Researc