REEF: searching REgionally Enriched Features in genomes

BACKGROUND: In Eukaryotic genomes, different features including genes are not uniformly distributed. The integration of annotation information and genomic position of functional DNA elements in the Eukaryotic genomes opened the way to test novel hypotheses of higher order genome organization and regulation of expression. RESULTS: REEF is a new tool, aimed at identifying genomic regions enriched in specific features, such as a class or group of genes homogeneous for expression and/or functional characteristics. The method for the calculation of local feature enrichment uses test statistic based on the Hypergeometric Distribution applied genome-wide by using a sliding window approach and adopting the False Discovery Rate for controlling multiplicity. REEF software, source code and documentation are freely available at . CONCLUSION: REEF can aid to shed light on the role of organization of specific genomic regions in the determination of their functional role

Go East! I mercati adriatici come bacino di collaborazione e opportunit\ue0 di internazionalizzazione per le PMI del Nord Est

e Piccole e Medie Imprese (PMI) che approcciano i mercati internazionali risultano condizionate da almeno due fattori inibitori: la cosiddetta \u201cliability of foreigness\u201d \u2013 con cui si intende la scarsa conoscenza degli usi, costumi, delle leggi e delle istituzioni che caratterizzano un determinato mercato \u2013 e la \u201cliability of smallness\u201d. Quest\u2019ultima \u2013 anche intesa come \u201cvincolo dimensionale\u201d e pertanto riferita alla limitata disponibilit\ue0 di risorse e competenze a supporto dei processi di internazionalizzazione \u2013 rappresenta a detta di molti uno dei principali fattori che limitano il processo di espansione internazionale della piccola impresa

Synthesis of α-alkylidene cyclic carbonatesviaCO2fixation under ambient conditions promoted by an easily available silver carbamate

The simple and cost-effective compound [Ag(O2CNEt2)], in combination with PPh3, works as an effective catalytic precursor in the carboxylation of propargyl alcohols at ambient temperature and atmospheric CO2pressure, and in most cases under solventless conditions. The silver carbamate revealed a better performance than commercial silver oxide, Ag2O, and allowed to obtain a series of α-alkylidene cyclic carbonates in high yields

CircRNAs in hematopoiesis and hematological malignancies

Cell states in hematopoiesis are controlled by master regulators and by complex circuits of a growing family of RNA species impacting cell phenotype maintenance and plasticity. Circular RNAs (circRNAs) are rapidly gaining the status of particularly stable transcriptome members with distinctive qualities. RNA-seq identified thousands of circRNAs with developmental stage-A nd tissue-specific expression corroborating earlier suggestions that circular isoforms are a natural feature of the cell expression program. CircRNAs are abundantly expressed also in the hematopoietic compartment. There are a number of studies on circRNAs in blood cells, a specific overview is however lacking. In this review we first present current insight in circRNA biogenesis discussing the relevance for hematopoiesis of the highly interleaved processes of splicing and circRNA biogenesis. Regarding molecular functions circRNAs modulate host gene expression, but also compete for binding of microRNAs, RNA-binding proteins or translation initiation and participate in regulatory circuits. We examine circRNA expression in the hematopoietic compartment and in hematologic malignancies and review the recent breakthrough study that identified pathogenic circRNAs derived from leukemia fusion genes. CircRNA high and regulated expression in blood cell types indicate that further studies are warranted to inform the position of these regulators in normal and malignant hematopoiesis

Measuring random force noise for LISA aboard the LISA Pathfinder mission

The LTP (LISA Testflight Package), to be flown aboard the ESA / NASA LISA Pathfinder mission, aims to demonstrate drag-free control for LISA test masses with acceleration noise below 30 fm/s^2/Hz^1/2 from 1-30 mHz. This paper describes the LTP measurement of random, position independent forces acting on the test masses. In addition to putting an overall upper limit for all source of random force noise, LTP will measure the conversion of several key disturbances into acceleration noise and thus allow a more detailed characterization of the drag-free performance to be expected for LISA.Comment: 7 pages, 3 figures. To be published in Classical and Quantum Gravity with the proceedings of the 2003 Amaldi Meetin

Impact of probe annotation on the integration of miRNA-mRNA expression profiles for miRNA target detection

MicroRNAs (miRNAs) are small non-coding RNAs that mediate gene expression at the post-transcriptional and translational levels by an imperfect binding to target mRNA 3'UTR regions. While the ab-initio computational prediction of miRNA-mRNA interactions still poses significant challenges, it is possible to overcome some of its limitations by carefully integrating into the analysis the paired expression profiles of miRNAs and mRNAs. In this work, we show how the choice of a proper probe annotation for microarray platforms is an essential requirement to achieve good sensitivity in the identification of miRNA-mRNA interactions. We compare the results obtained from the analysis of the same expression profiles using both gene and transcript based custom CDFs that we have developed for a number of different annotations (ENSEMBL, RefSeq, AceView). In all cases, transcript-based annotations clearly improve the effectiveness of data integration and thus provide a more reliable confirmation of computationally predicted miRNA-mRNA interaction

The high resolution bathymetric map of the exhalative area of Panarea (Aeolian Islands, Italy)

On November 3, 2002 a shallow submarine gas eruption occurred in an area of 2.3 km2 east of Panarea (Aeolian volcanic arc, Southern Thyrrenian Sea, Italy). The exhalative area, surrounded by the islets of Dattilo, Panarelli, Lisca Bianca, Bottaro and Lisca Nera, has been known since historical times for the hydrothermal activity related to the Panarea volcanic complex. Due to the exceptional characteristics of the phenomenon, different geological, geochemical, geophysical and studies were carried out in this still poorly known volcanic area. A particular effort was devoted to producing a high resolution bathymetric map that also aimed to estimate the amount and location of the active exhalative centers and their variations in space and time. Data were obtained by three RTK multibeam surveys performed between December 2002 and December 2003. Here we show and discuss the technical details of the bathymetric surveys, the bathymetric map at 0.5 m resolution, and the accurate location of the 606 main exhalative centres active during the 2002-2003 crisis. The bathymetric data and the maps show two prevailing principal NE-SW and NW-SE alignments that match the spatial distribution of the exhalation centres. The accurate positioning at submeter accuracy of the gas vents is useful in the monitoring activity and to study their temporal and spatial variability

Detecting seeded motifs in DNA sequences

The problem of detecting DNA motifs with functional relevance in real biological sequences is difficult due to a number of biological, statistical and computational issues and also because of the lack of knowledge about the structure of searched patterns. Many algorithms are implemented in fully automated processes, which are often based upon a guess of input parameters from the user at the very first step. In this paper, we present a novel method for the detection of seeded DNA motifs, composed by regions with a different extent of variability. The method is based on a multi-step approach, which was implemented in a motif searching web tool (MOST). Overrepresented exact patterns are extracted from input sequences and clustered to produce motifs core regions, which are then extended and scored to generate seeded motifs. The combination of automated pattern discovery algorithms and different display tools for the evaluation and selection of results at several analysis steps can potentially lead to much more meaningful results than complete automation can produce. Experimental results on different yeast and human real datasets proved the methodology to be a promising solution for finding seeded motifs. MOST web tool is freely available at

Proposta de planejamento estratégico para a Embrapa Trigo.

Orientadora: Denise Michael dos Santos, Coorientador: Alvaro Augusto Dossa

A digital reconstruction of the 1630–1631 large plague outbreak in Venice

The plague, an infectious disease caused by the bacterium Yersinia pestis, is widely considered to be responsible for the most devastating and deadly pandemics in human history. Starting with the infamous Black Death, plague outbreaks are estimated to have killed around 100 million people over multiple centuries, with local mortality rates as high as 60%. However, detailed pictures of the disease dynamics of these outbreaks centuries ago remain scarce, mainly due to the lack of high-quality historical data in digital form. Here, we present an analysis of the 1630–1631 plague outbreak in the city of Venice, using newly collected daily death records. We identify the presence of a two-peak pattern, for which we present two possible explanations based on computational models of disease dynamics. Systematically digitized historical records like the ones presented here promise to enrich our understanding of historical phenomena of enduring importance. This work contributes to the recently renewed interdisciplinary foray into the epidemiological and societal impact of pre-modern epidemics