RNA analysis by ion-pair reversed-phase high performance liquid chromatography

Ion-pair reversed-phase high performance liquid chromatography (IP RP HPLC) is presented as a new, superior method for the analysis of RNA. IP RP HPLC provides a fast and reliable alternative to classical methods of RNA analysis, including separation of different RNA species, quantification and purification. RNA is stable under the analysis conditions used; degradation of RNA during the analyses was not observed. The versatility of IP RP HPLC for RNA analysis is demonstrated. Components of an RNA ladder, ranging in size from 155 to 1770 nt, were resolved. RNA transcripts of up to 5219 nt were analyzed, their integrity determined and they were quantified and purified. Purification of mRNA from total RNA is described, separating mouse rRNA from poly(A)+ mRNA. IP RP HPLC is also suitable for the separation and purification of DIG-labeled from unlabeled RNA. RNA purified by IP RP HPLC exhibits improved stability.

Quantitative analysis of mRNA amplification by in vitro transcription

Effective transcript profiling in animal systems requires isolation of homogenous tissue or cells followed by faithful mRNA amplification. Linear amplification based on cDNA synthesis and in vitro transcription is reported to maintain representation of mRNA levels, however, quantitative data demonstrating this as well as a description of inherent limitations is lacking. We show that published protocols produce a template-independent product in addition to amplifying real target mRNA thus reducing the specific activity of the final product. We describe a modified amplification protocol that minimizes the generation of template-independent product and can therefore generate the desired microgram quantities of message-derived material from 100 ng of total RNA. Application of a second, nested round of cDNA synthesis and in vitro transcription reduces the required starting material to 2 ng of total RNA. Quantitative analysis of these products on Caenorhabditis elegans Affymetrix GeneChips shows that this amplification does not reduce overall sensitivity and has only minor effects on fidelity.

Comparative analysis of the gene-dense ACHE/TFR2 region on human chromosome 7q22 with the orthologous region on mouse chromosome 5

Chromosome 7q22 has been the focus of many cytogenetic and molecular studies aimed at delineating regions commonly deleted in myeloid leukemias and myelodysplastic syndromes. We have compared a gene-dense, GC-rich sub-region of 7q22 with the orthologous region on mouse chromosome 5. A physical map of 640 kb of genomic DNA from mouse chromosome 5 was derived from a series of overlapping bacterial artificial chromosomes. A 296 kb segment from the physical map, spanning Ache to Tfr2, was compared with 267 kb of human sequence. We identified a conserved linkage of 12 genes including an open reading frame flanked by Ache and Asr2, a novel cation-chloride cotransporter interacting protein Cip1, Ephb4, Zan and Perq1. While some of these genes have been previously described, in each case we present new data derived from our comparative sequence analysis. Adjacent unfinished sequence data from the mouse contains an orthologous block of 10 additional genes including three novel cDNA sequences that we subsequently mapped to human 7q22. Methods for displaying comparative genomic information, including unfinished sequence data, are becoming increasingly important. We supplement our printed comparative analysis with a new, Web-based program called Laj (local alignments with java). Laj provides interactive access to archived pairwise sequence alignments via the WWW. It displays synchronized views of a dot-plot, a percent identity plot, a nucleotide-level local alignment and a variety of relevant annotations. Our mouse–human comparison can be viewed at http://web.uvic.ca/~bioweb/laj.html. Laj is available at http://bio.cse.psu.edu/, along with online documentation and additional examples of annotated genomic regions.

Genomes OnLine Database (GOLD): a monitor of genome projects world-wide

GOLD is a comprehensive resource for accessing information related to completed and ongoing genome projects world-wide. The database currently provides information on 350 genome projects, of which 48 have been completely sequenced and their analysis published. GOLD was created in 1997 and since April 2000 it has been licensed to Integrated Genomics. The database is freely available through the URL: http://igweb.integratedgenomics.com/GOLD/.

Customer response to media in marketing promotion: print versus online

Il lavoro di tesi, che si compone di tre articoli di ricerca, analizza, nel contesto della marketing promotion, la risposta del consumatore ai media in termini di ricordo, intenzione di acquisto, comportamento di acquisto e preferenza per il medium. Il lavoro, in particolare, mette a confronto due tipologie di media, carta e online, nell’ambito della price e loyalty promotion, utilizzando due disegni di ricerca sperimentali ed uno correlazionale. I risultati del lavoro mostrano che la risposta del consumatore alla comunicazione promozionale e ai media è eterogenea: segmenti di clienti diversi rispondono in maniera differente sia alla comunicazione promozionale che a carta e digitale. Online e carta hanno in media la stessa efficacia sui comportamenti di acquisto dei clienti, ma differiscono rispetto all’effetto su ricordo e atteggiamento e rispetto alla preferenza per il medium espressa dalla clientela. Lo spostamento delle risorse di marketing dalla carta al digitale permetterebbe quindi di ridurre i costi mantenendo lo stesso livello di efficacia. Inoltre, il presente lavoro mostra come sia possibile aumentare la risposta dei consumatori ai media attraverso un approccio di segmentazione della clientela.

Investigating and Understanding Student Learning Outcomes in an Online and Face-to-Face Graduate Level Legal Administration Course: An Embedded Mixed Methods Design

Online education is a new teaching and learning medium with few current guidelines for faculty, administrators or students. Its rapid growth over the last decade has challenged academic institutions to keep up with the demand, while also providing a quality education. Our understanding of the factors that determine quality and effective online learning experiences that lead to student learning outcomes is still evolving. There is a lack of consensus on the effectiveness of online versus face-to-face education in the current research. The U.S. Department of Education conducted a meta-analysis in 2009 and concluded that student-learning outcomes in online courses were equal to and, often times, better than face-to-face traditional courses. Subsequent research has found contradictory findings, and further inquiry is necessary. The purpose of this embedded mixed methods design research study is to further our understanding of the factors that create quality and successful educational outcomes in an online course. To achieve this, the first phase of this study measured and compared learning outcomes in an online and in class graduate-level legal administration course. The second phase of the study entailed interviews with those students in both the online and face-to-face sections to understand their perspectives on the factors contributing to learning outcomes. Six themes emerged from the qualitative findings: convenience, higher order thinking, discussions, professor engagement, professor and student interaction, and face-to-face interaction. Findings from this study indicate the factors students perceive as contributing to learning outcomes in an online course are consistent among all students and are supported in the existing literature. Higher order thinking, however, emerged as a stronger theme than indicated in the current research, and the face-to-face nature of the traditional classroom may be more an issue of familiarity than a factor contributing to learning outcomes. As education continues to reach new heights and developments in technology advance, the factors found to contribute to student learning outcomes will be refined and enhanced. These developments will continue to transform the ways in which we deliver and receive knowledge in both traditional and online classrooms. While there is a growing body of research on online education, the field’s evolution has unsettled earlier findings and posed new areas to investigate.

Analysis of the colorimetric properties of goniochromatic colors using the MacAdam limits under different light sources

Technological innovation in all areas has led to the appearance in recent years of new metallic and pearlescent materials, yet no exhaustive studies have been conducted to assess their colorimetric capabilities. The chromatic variability of these special-effect pigments may largely be due to the three-dimensional effect of their curved shapes and orientations when they are directionally or diffusely illuminated. Our study examines goniochromatic colors using the optimal colors (MacAdam limits) associated with normal colors (photometric scale of relative spectral reflectance from 0 to 1) under certain conventional illuminants and other light sources. From a database of 91 metallic and interference samples and using a multi-gonio-spectrophotometer, we analyzed samples with lightness values of more than 100 and others with lightness values of less than 100, but with higher chromaticities than optimal colors, which places them beyond the MacAdam limits. Our study thus demonstrates the existence of chromatic perceptions beyond the normal solid color associated with these materials and independent of the light source. The challenge for future research, therefore, is to replicate and render these color appearances in current and future color reproduction technologies for computer graphics.

Forensic analysis of buildings affected by mining subsidence based on Differential Interferometry (Part III)

This work presents a forensic analysis of buildings affected by mining subsidence, which is based on deformation data obtained by Differential Interferometry (DInSAR). The proposed test site is La Union village (Murcia, SE Spain) where subsidence was triggered in an industrial area due to the collapse of abandoned underground mining labours occurred in 1998. In the first part of this work the study area was introduced, describing the spatial and temporal evolution of ground subsidence, through the elaboration of a cracks map on the buildings located within the affected area. In the second part, the evolution of the most significant cracks found in the most damaged buildings was monitored using biaxial extensometric units and inclinometers. This article describes the work performed in the third part, where DInSAR processing of satellite radar data, available between 1998 and 2008, has permitted to determine the spatial and temporal evolution of the deformation of all the buildings of the study area in a period when no continuous in situ instrumental data is available. Additionally, the comparison of these results with the forensic data gathered in the 2005–2008 period, reveal that there is a coincidence between damaged buildings, buildings where extensometers register significant movements of cracks, and buildings deformation estimated from radar data. As a result, it has been demonstrated that the integration of DInSAR data into forensic analysis methodologies contributes to improve significantly the assessment of the damages of buildings affected by mining subsidence.

Evaluating EmotiBlog robustness for sentiment analysis tasks

EmotiBlog is a corpus labelled with the homonymous annotation schema designed for detecting subjectivity in the new textual genres. Preliminary research demonstrated its relevance as a Machine Learning resource to detect opinionated data. In this paper we compare EmotiBlog with the JRC corpus in order to check the EmotiBlog robustness of annotation. For this research we concentrate on its coarse-grained labels. We carry out a deep ML experimentation also with the inclusion of lexical resources. The results obtained show a similarity with the ones obtained with the JRC demonstrating the EmotiBlog validity as a resource for the SA task.

Deformable templates for tracking and analysis of intravascular ultrasound sequences

Deformable Template models are first applied to track the inner wall of coronary arteries in intravascular ultrasound sequences, mainly in the assistance to angioplasty surgery. A circular template is used for initializing an elliptical deformable model to track wall deformation when inflating a balloon placed at the tip of the catheter. We define a new energy function for driving the behavior of the template and we test its robustness both in real and synthetic images. Finally we introduce a framework for learning and recognizing spatio-temporal geometric constraints based on Principal Component Analysis (eigenconstraints).

Analysis of the Kondo effect in ferromagnetic atomic-sized contacts

Atomic contacts made of ferromagnetic metals present zero-bias anomalies in the differential conductance due to the Kondo effect. These systems provide a unique opportunity to perform a statistical analysis of the Kondo parameters in nanostructures since a large number of contacts can be easily fabricated using break-junction techniques. The details of the atomic structure differ from one contact to another so a large number of different configurations can be statistically analyzed. Here we present such a statistical analysis of the Kondo effect in atomic contacts made from the ferromagnetic transition metals Ni, Co, and Fe. Our analysis shows clear differences between materials that can be understood by fundamental theoretical considerations. This combination of experiments and theory allows us to extract information about the origin and nature of the Kondo effect in these systems and to explore the influence of geometry and valence in the Kondo screening of atomic-sized nanostructures.

A new algorithm to accelerate harmonic analysis of time series

The Lomb periodogram has been traditionally a tool that allows us to elucidate if a frequency turns out to be important for explaining the behaviour of a given time series. Many linear and nonlinear reiterative harmonic processes that are used for studying the spectral content of a time series take into account this periodogram in order to avoid including spurious frequencies in their models due to the leakage problem of energy from one frequency to others. However, the estimation of the periodogram requires long computation time that makes the harmonic analysis slower when we deal with certain time series. Here we propose an algorithm that accelerates the extraction of the most remarkable frequencies from the periodogram, avoiding its whole estimation of the harmonic process at each iteration. This algorithm allows the user to perform a specific analysis of a given scalar time series. As a result, we obtain a functional model made of (1) a trend component, (2) a linear combination of Fourier terms, and (3) the so-called mixed secular terms by reducing the computation time of the estimation of the periodogram.

Gender analysis of moxifloxacin clinical trials

Purpose: To determine the inclusion of women and the sex-stratification of results in moxifloxacin Clinical Trials (CTs), and to establish whether these CTs considered issues that specifically affect women, such as pregnancy and use of hormonal therapies. Previous publications about women’s inclusion in CTs have not specifically studied therapeutic drugs. Although this type of drug is taken by men and women at a similar rate, adverse effects occur more frequently in the latter. Methods: We reviewed 158 published moxifloxacin trials on humans, retrieved from MedLine and the Cochrane Library (1998–2010), to determine whether they complied with the gender recommendations published by U.S. Food and Drug Administration Guideline. Results: Of a total of 80,417 subjects included in the moxifloxacin CTs, only 33.7% were women in phase I, in contrast to phase II, where women accounted for 45%, phase III, where they represented 38.3% and phase IV, where 51.3% were women. About 40.9% (n = 52) of trials were stratified by sex and 15.3% (n = 13) and 9% (n = 7) provided data by sex on efficacy and adverse effects, respectively. We found little information about the influence of issues that specifically affect women. Only 3 of the 59 journals that published the moxifloxacin CTs stated that authors should stratify their results by sex. Conclusions: Women are under-represented in the published moxifloxacin trials, and this trend is more marked in phase I, as they comprise a higher proportion in the other phases. Data by sex on efficacy and adverse effects are scarce in moxifloxacin trials. These facts, together with the lack of data on women-specific issues, suggest that the therapeutic drug moxifloxacin is only a partially evidence-based medicine.

Partial collapse of a ventilated stone façade: Diagnosis and analysis of the anchorage system

The mechanical behaviour of transventilated façades performed by natural stone is necessarily based on the correct execution of both anchoring elements on the stone cladding as in the ones corresponding to the enclosure support, either with brick masonry walls or reinforced concrete walls. In the case studied in the present work, the origin of the damages suffered on the façade of a building located in Alcoy has been analyzed, where the detachment of part of the outer enclosure occurred. This enclosure is a transventilated façade formed by Bateig Blue stone tiles. To this end, “in situ” tests of the anchoring systems employed have been performed, as well as laboratory tests of mechanical characterization of the material and of different types of anchor, comparing these results with those obtained in both the simplified analytical models of continuum mechanics as developed by the Finite Element Method (FEM).

Sequencing and functional analysis of the genome of a nematode egg-parasitic fungus, Pochonia chlamydosporia

Pochonia chlamydosporia is a worldwide-distributed soil fungus with a great capacity to infect and destroy the eggs and kill females of plant-parasitic nematodes. Additionally, it has the ability to colonize endophytically roots of economically-important crop plants, thereby promoting their growth and eliciting plant defenses. This multitrophic behavior makes P. chlamydosporia a potentially useful tool for sustainable agriculture approaches. We sequenced and assembled ∼41 Mb of P. chlamydosporia genomic DNA and predicted 12,122 gene models, of which many were homologous to genes of fungal pathogens of invertebrates and fungal plant pathogens. Predicted genes (65%) were functionally annotated according to Gene Ontology, and 16% of them found to share homology with genes in the Pathogen Host Interactions (PHI) database. The genome of this fungus is highly enriched in genes encoding hydrolytic enzymes, such as proteases, glycoside hydrolases and carbohydrate esterases. We used RNA-Seq technology in order to identify the genes expressed during endophytic behavior of P. chlamydosporia when colonizing barley roots. Functional annotation of these genes showed that hydrolytic enzymes and transporters are expressed during endophytism. This structural and functional analysis of the P. chlamydosporia genome provides a starting point for understanding the molecular mechanisms involved in the multitrophic lifestyle of this fungus. The genomic information provided here should also prove useful for enhancing the capabilities of this fungus as a biocontrol agent of plant-parasitic nematodes and as a plant growth-promoting organism.