Lessons Learned from Development of a Software Tool to Support Academic Advising

We detail some lessons learned while designing and testing a decision-theoretic advising support tool for undergraduates at a large state university. Between 2009 and 2011 we conducted two surveys of over 500 students in multiple majors and colleges. These surveys asked students detailed questions about their preferences concerning course selection, advising, and career paths. We present data from this study which may be helpful for faculty and staff who advise undergraduate students. We find that advising support software tools can augment the student-advisor relationship, particularly in terms of course planning, but cannot and should not replace in-person advising.Comment: 5 Figures, revised version including more figures and cross-referencin

A Robust Filter for the BeppoSAX Gamma Ray Burst Monitor Triggers

The BeppoSAX Gamma Ray Burst Monitor (GRBM) is triggered any time a statistically significant counting excess is simultaneously revealed by at least two of its four independent detectors. Several spurious effects, including highly ionizing particles crossing two detectors, are recorded as onboard triggers. In fact, a large number of false triggers is detected, in the order of 10/day. A software code, based on an heuristic algorithm, was written to discriminate between real and false triggers. We present the results of the analysis on an homogeneous sample of GRBM triggers, thus providing an estimate of the efficiency of the GRB detection system consisting of the GRBM and the software.Comment: Proc. 5th Huntsville GRB Symposiu

Rapid detection of copy number variations and point mutations in BRCA1/2 genes using a single workflow by ion semiconductor sequencing pipeline

Molecular analysis of BRCA1 (MIM# 604370) and BRCA2 (MIM #600185) genes is essential for familial breast and ovarian cancer prevention and treatment. An efficient, rapid, cost-effective accurate strategy for the detection of pathogenic variants is crucial. Mutations detection of BRCA1/2 genes includes screening for single nucleotide variants (SNVs), small insertions or deletions (indels), and Copy Number Variations (CNVs). Sanger sequencing is unable to identify CNVs and therefore Multiplex Ligation Probe amplification (MLPA) or Multiplex Amplicon Quantification (MAQ) is used to complete the BRCA1/2 genes analysis. The rapid evolution of Next Generation Sequencing (NGS) technologies allows the search for point mutations and CNVs with a single platform and workflow. In this study we test the possibilities of NGS technology to simultaneously detect point mutations and CNVs in BRCA1/2 genes, using the OncomineTM BRCA Research Assay on Personal Genome Machine (PGM) Platform with Ion Reporter Software for sequencing data analysis (Thermo Fisher Scientific). Comparison between the NGS-CNVs, MLPA and MAQ results shows how the NGS approach is the most complete and fast method for the simultaneous detection of all BRCA mutations, avoiding the usual time consuming multistep approach in the routine diagnostic testing of hereditary breast and ovarian cancers

Chloroquine supplementation increases the cytotoxic effect of curcumin against Her2/neu overexpressing breast cancer cells in vitro and in vivo in nude mice while counteracts it in immune competent mice

Autophagy is usually a pro-survival mechanism in cancer cells, especially in the course of chemotherapy, thus autophagy inhibition may enhance the chemotherapy-mediated anti-cancer effect. However, since autophagy is strongly involved in the immunogenicity of cell death by promoting ATP release, its inhibition may reduce the immune response against tumors, negatively influencing the overall outcome of chemotherapy. In this study, we evaluated the in vitro and in vivo anti-cancer effect of curcumin (CUR) against Her2/neu overexpressing breast cancer cells (TUBO) in the presence or in the absence of the autophagy inhibitor chloroquine (CQ). We found that TUBO cell death induced by CUR was increased in vitro by CQ and slightly in vivo in nude mice. Conversely, CQ counteracted the Cur cytotoxic effect in immune competent mice, as demonstrated by the lack of in vivo tumor regression and the reduction of overall mice survival as compared with CUR-treated mice. Immunohistochemistry analysis revealed the presence of a remarkable FoxP3 T cell infiltrate within the tumors in CUR/CQ treated mice and a reduction of T cytotoxic cells, as compared with single CUR treatment. These findings suggest that autophagy is important to elicit anti-tumor immune response and that autophagy inhibition by CQ reduces such response also by recruiting T regulatory (Treg) cells in the tumor microenvironment that may be pro-tumorigenic and might counteract CUR-mediated anti-cancer effects

A novel approach to represent and compare RNA secondary structures

Structural information is crucial in ribonucleic acid (RNA) analysis and functional annotation; nevertheless, how to include such structural data is still a debated problem. Dot-bracket notation is the most common and simple representation for RNA secondary structures but its simplicity leads also to ambiguity requiring further processing steps to dissolve. Here we present BEAR (Brand nEw Alphabet for RNA), a new context-aware structural encoding represented by a string of characters. Each character in BEAR encodes for a specific secondary structure element (loop, stem, bulge and internal loop) with specific length. Furthermore, exploiting this informative and yet simple encoding in multiple alignments of related RNAs, we captured how much structural variation is tolerated in RNA families and convert it into transition rates among secondary structure elements. This allowed us to compute a substitution matrix for secondary structure elements called MBR (Matrix of BEAR-encoded RNA secondary structures), of which we tested the ability in aligning RNA secondary structures. We propose BEAR and the MBR as powerful resources for the RNA secondary structure analysis, comparison and classification, motif finding and phylogeny

Differential effects on membrane permeability and viability of human keratinocyte cells undergoing very low intensity megasonic fields

Among different therapeutic applications of Ultrasound (US), transient membrane sonoporation (SP) - a temporary, non-lethal porosity, mechanically induced in cell membranes through US exposure - represents a compelling opportunity towards an efficient and safe drug delivery. Nevertheless, progresses in this field have been limited by an insufficient understanding of the potential cytotoxic effects of US related to the failure of the cellular repair and to the possible activation of inflammatory pathway. In this framework we studied the in vitro effects of very low-intensity US on a human keratinocyte cell line, which represents an ideal model system of skin protective barrier cells which are the first to be involved during medical US treatments. Bioeffects linked to US application at 1 MHz varying the exposure parameters were investigated by fluorescence microscopy and fluorescence activated cell sorting. Our results indicate that keratinocytes undergoing low US doses can uptake drug model molecules with size and efficiency which depend on exposure parameters. According to sub-cavitation SP models, we have identified the range of doses triggering transient membrane SP, actually with negligible biological damage. By increasing US doses we observed a reduced cells viability and an inflammatory gene overexpression enlightening novel healthy relevant strategies

O programa nacional de fortalecimento da agricultura familiar no Brasil: uma análise sobre a distribuição regional e setorial dos recursos.

No Brasil, as políticas públicas para o espaço rural sempre tenderam a priorizar a agricultura patronal, em detrimento dos agricultores familiares. Todavia, os estudos realizados pelos órgãos FAO - INCRA deram subsídio para a criação do Programa Nacional de Fortalecimento da Agricultura Familiar (PRONAF), resultando em um novo direcionamento dos investimentos públicos, os quais passaram a contemplar o segmento dos agricultores familiares. Entende-se o PRONAF como uma política não-compensatória, que, apesar de seus problemas, tem contribuído de fato para mudanças e melhorias no espaço agrário brasileiro. Desde sua criação no final da década de 1990, o PRONAF passou por várias mudanças em sua estrutura administrativa e operacional, a fim de alcançar seus objetivos e adequar-se face a complexa realidade social agrária brasileira. Sendo assim, o presente estudo visa discutir as ações do Estado por meio desse Programa, a partir de suas linhas de atuação, bem como analisar a distribuição de suas concessões de crédito regional e setorialmente. Assim, os procedimentos metodológicos utilizados para a realização deste trabalho compreendem pesquisa bibliográfica e documental, além de pesquisa em fontes secundárias, no intuito de obter dados e informações relevantes para a análise das relações sociais estabelecidas em meio a esse processo de concretização e espacialização desse Programa. Dentre as implicações do PRONAF pode-se notar em âmbito nacional, uma diminuição da disparidade regional brasileira, bem como a preocupação que o Programa tem demonstrado com os aspectos socioculturais locais e regionais, como forma de garantir que seus investimentos perpassem a dimensão econômica, mas valorize outras dimensões, a exemplo dos elementos culturais