Gene Expressio Array Exploration Using K-Formal Concept Analysis

Proceeding of: 9th International Conference, ICFCA 2011, Nicosia, Cyprus, May 2-6, 2011.DNA micro-arrays are a mechanism for eliciting gene expression values, the concentration of the transcription products of a set of genes, under different chemical conditions. The phenomena of interest—up-regulation, down-regulation and co-regulation—are hypothesized to stem from the functional relationships among transcription products. In [1,2,3] a generalisation of Formal Concept Analysis was developed with data mining applications in mind, K-Formal Concept Analysis, where incidences take values in certain kinds of semirings, instead of the usual Boolean carrier set. In this paper, we use (Rmin+)- and (Rmax+) to analyse gene expression data for Arabidopsis thaliana. We introduce the mechanism to render the data in the appropriate algebra and profit by the wealth of different Galois Connections available in Generalized Formal Concept Analysis to carry different analysis for up- and down-regulated genes.Spanish Government-Comision Interministerial de Ciencia y Tecnología projects 2008-06382/TEC and 2008-02473/TEC and the regional projects S-505/TIC/0223 (DGUI-CM) and CCG08-UC3M/TIC- 4457 (Comunidad Aut onoma de Madrid - UC3M)

The role of perceived benefits and costs in patients’ medical decisions

Background  Many decisions can be understood in terms of actors’ valuations of benefits and costs. The article investigates whether this is also true of patient medical decision making. It aims to investigate (i) the importance patients attach to various reasons for and against nine medical decisions; (ii) how well the importance attached to benefits and costs predicts action or inaction; and (iii) how such valuations are related to decision confidence. Methods  In a national random digit dial telephone survey of U.S. adults, patients rated the importance of various reasons for and against medical decisions they had made or talked to a health‐care provider about during the past 2 years. Participants were 2575 English‐speaking adults age 40 and older. Data were analysed by means of logistic regressions predicting action/inaction and linear regressions predicting confidence. Results  Aggregating individual reasons into those that may be regarded as benefits and those that may be regarded as costs, and weighting them by their importance to the patient, shows the expected relationship to action. Perceived benefits and costs are also significantly related to the confidence patients report about their decision. Conclusion  The factors patients say are important in their medical decisions reflect a subjective weighing of benefits and costs and predict action/inaction although they do not necessarily indicate that patients are well informed. The greater the difference between the importance attached to benefits and costs, the greater patients’ confidence in their decision.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/102701/1/hex739.pd

Decision-making processes for breast, colorectal, and prostate cancer screening: results from the DECISIONS study

Patients should understand the risks and benefits of cancer screening in order to make informed screening decisions

Chloroplast HCF101 is a scaffold protein for [4Fe-4S] cluster assembly

Oxygen-evolving chloroplasts possess their own iron-sulfur cluster assembly proteins including members of the SUF (sulfur mobilization) and the NFU family. Recently, the chloroplast protein HCF101 (high chlorophyll fluorescence 101) has been shown to be essential for the accumulation of the membrane complex Photosystem I and the soluble ferredoxin-thioredoxin reductases, both containing [4Fe-4S] clusters. The protein belongs to the FSC-NTPase ([4Fe-4S]-cluster-containing P-loop NTPase) superfamily, several members of which play a crucial role in Fe/S cluster biosynthesis. Although the C-terminal ISC-binding site, conserved in other members of the FSC-NTPase family, is not present in chloroplast HCF101 homologues using Mössbauer and EPR spectroscopy, we provide evidence that HCF101 binds a [4Fe-4S] cluster. 55Fe incorporation studies of mitochondrially targeted HCF101 in Saccharomyces cerevisiae confirmed the assembly of an Fe/S cluster in HCF101 in an Nfs1-dependent manner. Site-directed mutagenesis identified three HCF101-specific cysteine residues required for assembly and/or stability of the cluster. We further demonstrate that the reconstituted cluster is transiently bound and can be transferred from HCF101 to a [4Fe-4S] apoprotein. Together, our findings suggest that HCF101 may serve as a chloroplast scaffold protein that specifically assembles [4Fe-4S] clusters and transfers them to the chloroplast membrane and soluble target proteins

De Novo Transcriptome Assembly and Comparative Analysis Elucidate Complicated Mechanism Regulating Astragalus chrysochlorus Response to Selenium Stimuli

Astragalus species are medicinal plants that are used in the world for years. Some Astragalus species are known for selenium accumulation and tolerance and one of them is Astragalus chrysochlorus, a secondary selenium accumulator. In this study, we employed Illumina deep sequencing technology for the first time to de novo assemble A. chrysochlorus transcriptome and identify the differentially expressed genes after selenate treatment. Totally, 59,656 unigenes were annotated with different databases and 53,960 unigenes were detected in NR database. Transcriptome in A. chrysochlorus is closer to Glycine max than other plant species with 43,1 percentage of similarity. Annotated unigenes were also used for gene ontology enrichment and pathway enrichment analysis. The most significant genes and pathways were ABC transporters, plant pathogen interaction, biosynthesis of secondary metabolites and carbohydrate metabolism. Our results will help to enlighten the selenium accumulation and tolerance mechanisms, respectively in plants

The Effect of Question Framing and Response Options on the Relationship between Racial Attitudes and Beliefs about Genes as Causes of Behavior

Prior research suggests that the attribution of individual and group differences to genetic causes is correlated with prejudiced attitudes toward minority groups. Our study suggests that these findings may be due to the wording of the questions and to the choice of response options. Using a series of vignettes in an online survey, we find a relationship between racial attitudes and genetic attributions when respondents are asked to make causal attributions of differences between racial groups. However, when they are asked to make causal attributions for characteristics shown by individuals, no such relationship is found. The response scale used appears to make less, if any, difference in the results. These findings indicate that the way questions about genetic causation of behavior are framed makes a significant contribution to the answers obtained because it significantly changes the meaning of the questions. We argue that such framing needs to be carefully attended to, not only in posing research questions but also in discourse about genetics more generally