Comparing reverse complementary genomic words based on their distance distributions and frequencies

In this work we study reverse complementary genomic word pairs in the human DNA, by comparing both the distance distribution and the frequency of a word to those of its reverse complement. Several measures of dissimilarity between distance distributions are considered, and it is found that the peak dissimilarity works best in this setting. We report the existence of reverse complementary word pairs with very dissimilar distance distributions, as well as word pairs with very similar distance distributions even when both distributions are irregular and contain strong peaks. The association between distribution dissimilarity and frequency discrepancy is explored also, and it is speculated that symmetric pairs combining low and high values of each measure may uncover features of interest. Taken together, our results suggest that some asymmetries in the human genome go far beyond Chargaff's rules. This study uses both the complete human genome and its repeat-masked version.Comment: Post-print of a paper accepted to publication in "Interdisciplinary Sciences: Computational Life Sciences" (ISSN: 1913-2751, ESSN: 1867-1462

Dissimilar Symmetric Word Pairs in the Human Genome

In this work we explore the dissimilarity between symmetric word pairs, by comparing the inter-word distance distribution of a word to that of its reversed complement. We propose a new measure of dissimilarity between such distributions. Since symmetric pairs with different patterns could point to evolutionary features, we search for the pairs with the most dissimilar behaviour. We focus our study on the complete human genome and its repeat-masked version.Comment: Submitted 13-Feb-2017; accepted, after a minor revision, 17-Mar-2017; 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, PACBB 2017, Porto, Portugal, 21-23 June, 201

Comparison of reproducibility, accuracy, sensitivity, and specificity of miRNA quantification platforms

Given the increasing interest in their use as disease biomarkers, the establishment of reproducible, accurate, sensitive, and specific platforms for microRNA (miRNA) quantification in biofluids is of high priority. We compare four platforms for these characteristics: small RNA sequencing (RNA-seq), FirePlex, EdgeSeq, and nCounter. For a pool of synthetic miRNAs, coefficients of variation for technical replicates are lower for EdgeSeq (6.9%) and RNA-seq (8.2%) than for FirePlex (22.4%); nCounter replicates are not performed. Receiver operating characteristic analysis for distinguishing present versus absent miRNAs shows small RNA-seq (area under curve 0.99) is superior to EdgeSeq (0.97), nCounter (0.94), and FirePlex (0.81). Expected differences in expression of placenta-associated miRNAs in plasma from pregnant and non-pregnant women are observed with RNA-seq and EdgeSeq, but not FirePlex or nCounter. These results indicate that differences in performance among miRNA profiling platforms impact ability to detect biological differences among samples and thus their relative utility for research and clinical use

Student Understanding of Control of Variables: Deciding Whether or Not a Variable Influences the Behavior of a System

The ability of adult students to reason on the basis of the control of variables was the subject of an extended investigation. This paper describes the part of the study that focused on the reasoning required to decide whether or not a given variable influences the behavior of a system. The participants were undergraduates taking introductory Physics and K-8 teachers studying physics and physical science in inservice institutes and workshops. Although most of the students recognized the need to control variables, many had significant difficulty with the underlying reasoning. The results indicate serious shortcomings in the preparation of future scientists and in the education of a scientifically literate citizenry. There are also strong implications for the professional development of teachers, many of whom are expected to teach control of variables to young students

MF Calculator: A Web-Based Application for Analyzing Similarity

This paper presents the metric-frequency calculator (MF Calculator), an online application to analyze similarity. The MF Calculator implements a metric-frequency similarity algorithm for the quantitative assessment of similarity in ill-structured data sets. It is widely applicable as it can be used with nominal, ordinal, or interval data when there is little prior control over the variables to be observed regarding number or content. The MF Calculator generates a proximity matrix in CSV, XML or DOC format that can be used as input to traditional statistical techniques such as hierarchical clustering, additive trees, or multidimensional scaling. The MF Calculator also displays a graphical representation of outputs using additive similarity trees. A simulated example illustrates the implementation of the MF calculator. An additional example with real data is presented, in order to illustrate the potential of combining the MF Calculator with cluster analysis. The MF Calculator is a user-friendly tool available free of charge. It can be accessed from http : //mfcalculator.celiasales.org/Calculator.aspx, and it can be used by non-experts from a wide range of social sciences.info:eu-repo/semantics/publishedVersio

Spectroscopic characterization of reaction centers of the (M)Y210W mutant of the photosynthetic bacterium Rhodobacter sphaeroides

The tyrosine-(M)210 of the reaction center of Rhodobacter sphaeroides 2.4.1 has been changed to a tryptophan using site-directed mutagenesis. The reaction center of this mutant has been characterized by low-temperature absorption and fluorescence spectroscopy, time-resolved sub-picosecond spectroscopy, and magnetic resonance spectroscopy. The charge separation process showed bi-exponential kinetics at room temperature, with a main time constant of 36 ps and an additional fast time constant of 5.1 ps. Temperature dependent fluorescence measurements predict that the lifetime of P* becomes 4–5 times slower at cryogenic temperatures. From EPR and absorbance-detected magnetic resonance (ADMR, LD-ADMR) we conclude that the dimeric structure of P is not significantly changed upon mutation. In contrast, the interaction of the accessory bacteriochlorophyll BA with its environment appears to be altered, possibly because of a change in its position

Relación entre el bienestar y el rendimiento académico en alumnos de primer año de medicina

Background: Stress may affect the sense of wellbeing and academic achievement of university students. Aim: To assess the relationship of academic engagement and burnout with academic achievement among first year medical students. Material and Methods: The Utrecht Work Engagement Scale-Student and Maslach Burnout Inventory Student Survey (MBI-SS) were applied to 277 first year medical students of four universities. Their results were correlated with the grades obtained in the different courses. Results: Moderately high engagement and low burnout levels were detected. There was a high level of satisfaction with studies and a moderate exhaustion level. Academic achievement was associated with the degree of engagement with studies but not with burnout. Conglomerate analysis detected a group of students with high levels of wellbeing, characterized by high levels of academic engagement and low burnout. Other group had moderate levels of engagement and lack of personal fulfilment. Other group, identified as extenuated, had high levels of personal exhaustion and depersonalization. Finally the disassociated group had a low academic engagement, low emotional exhaustion, high levels of depersonalization and lack of personal fulfillment. Conclusions: Academic achievement is associated with the level of engagement with studies but not with burnout

In situ methods to localize transgenes and transcripts in interphase nuclei: a tool for transgenic plant research

Genetic engineering of commercially important crops has become routine in many laboratories. However, the inability to predict where a transgene will integrate and to efficiently select plants with stable levels of transgenic expression remains a limitation of this technology. Fluorescence in situ hybridization (FISH) is a powerful technique that can be used to visualize transgene integration sites and provide a better understanding of transgene behavior. Studies using FISH to characterize transgene integration have focused primarily on metaphase chromosomes, because the number and position of integration sites on the chromosomes are more easily determined at this stage. However gene (and transgene) expression occurs mainly during interphase. In order to accurately predict the activity of a transgene, it is critical to understand its location and dynamics in the three-dimensional interphase nucleus. We and others have developed in situ methods to visualize transgenes (including single copy genes) and their transcripts during interphase from different tissues and plant species. These techniques reduce the time necessary for characterization of transgene integration by eliminating the need for time-consuming segregation analysis, and extend characterization to the interphase nucleus, thus increasing the likelihood of accurate prediction of transgene activity. Furthermore, this approach is useful for studying nuclear organization and the dynamics of genes and chromatin

Creativity and the computer nerd: an exploration of attitudes

This study arises from our concern that many of our best art and design students are failing to make the most of the opportunities provided by IT because of their fear or dislike of computers. This not only deprives them of useful skills, but, even more importantly, deprives many IT based developments of their input. In this paper we investigate the relationship between attitudes to creativity and to computers among students. We quickly discard an approach based on theories of personality types as philosophically and educationally problematic. An approach based on the self-concept of artists and designers, in relation to their own creativity and to their feelings about computers, offers more hope of progress. This means that we do not try to define the attributes of "creative people". Rather, we ask what creativity means to students of art and design and relate these responses to their attitudes to computers. Self-concept depends on how the subjects see themselves within society and culture, and is liable to change as culture changes. One major instrument of cultural change at the present time is the growth of IT itself. We then describe a first attempt at using a psychological method - Kelly's Repertory Grids - to investigate the self-concept of artists and designers. It is hoped to continue with this approach in further studies over the next few years