A multiple-instance scoring method to predict tissue-specific cis-regulatory motifs and regions

Transcription is the central process of gene regulation. In higher eukaryotes, the transcription of a gene is usually regulated by multiple cis-regulatory regions (CRRs). In different tissues, different transcription factors bind to their cis-regulatory motifs in these CRRs to drive tissue-specific expression patterns of their target genes. By combining the genome-wide gene expression data with the genomic sequence data, we proposed multiple-instance scoring (MIS) method to predict the tissue-specific motifs and the corresponding CRRs. The method is mainly based on the assumption that only a subset of CRRs of the expressed gene should function in the studied tissue. By testing on the simulated datasets and the fly muscle dataset, MIS can identify true motifs when noise is high and shows higher specificity for predicting the tissue-specific functions of CRRs

Study of influence of bulk on break-down and trapping phenomena in power AlGaN/GaN MIS-HEMTs grown on Si-substrate

This thesis work is based on the study of trapping phenomena in power HEMTs based on Gallium-Nitride (GaN). In particular, MIS-HEMT devices are studied and characterized. The main features of these devices are: MIS structure at gate contact, double heterostructures, Silicon substrate. Measurements performed: DC characterization, double pulse, stress and recovery transients, back-gating measurements, breakdown in off-state, on-the-fly measurement

An Event-Driven Platform for Agility Management of Crisis Response

International audienceThis article aims at presenting a whole approach of Information System Interoperability management in a crisis management cell: a Mediation Information System (MIS) may be used to help the crisis cell partners to design, run and manage the workflows of the response to a crisis situation. The architecture of the MIS meets the needs of low coupling between the partners' Information System components and the need of agility for such a platform. It is based on Service Oriented Architecture (SOA) and Event-Driven Architecture (EDA) principles that are combined to the Complex Event Processing (CEP) principles. This should leads on the one hand to an easier orchestration, choreography and real-time monitoring of the workflows' activities, on the other hand to assume on-the-fly automated agility of the crisis response (considering agility as the ability of the processes to remain consistent with the response to the crisis)

in vivo analysis of Drosophila deoxyribonucleoside kinase function in cell cycle, cell survival and anti-cancer drugs resistance.

in vitro studies have shown that Drosophila melanogaster has a highly efficient single deoxyribonucleoside kinase (dNK) multisubstrate enzyme. dNK is related to the mammalian Thymidine Kinase 2 (TK2) group involved in the nucleotide synthesis salvage pathway. To study the dNK function in vivo, we constructed transgenic Drosophila strains and impaired the nucleotide de novo synthesis pathway, using antifolates such as aminopterin. Our results show that dNK overexpression rescues both cell death and cell cycle arrest triggered by this anti-cancer drug, and confers global resistance on the fly. Moreover, we show that fly viability and growth depend on the exquisite ratio between dNK expression and its substrate thymidine (dT) in the medium, and that increased dT concentrations trigger apoptosis and a decrease in body mass when dNK is mis-expressed. Finally, dNK expression, unlike that of TK2, is cell cycle dependent and under the control of CyclinE and the dE2F1 transcription factor involved in the G1/S transition. dNK is therefore functionally more closely related to mammalian TK1 than to TK2. This strongly suggest that dNK plays a role in cell proliferation in physiological conditions

An annotated checklist of the Tephritidae (Diptera) of Florida

A total of 73 species of tephritid flies has been recorded from Florida since the early 1800s. Of these, 7 species are considered to represent occasional waifs or accidental introductions from surrounding regions that are not known to have established populations in Florida; 6 are exotic pests which failed to colonize or were extirpated; and 7 species are represented only by early literature records and are considered dubious for the state. Thus, the tephritid fauna of Florida currently comprises a total of 53 species of which 1 species is precinctive to the state and considered to be endangered

Diversity and Abundance of Hymenopterous Parasitoids Associated with Anastrepha fraterculus (Diptera: Tephritidae) in Native and Exotic Host Plants in Misiones, Northeastern Argentina

Some Major host species used by the tephritid fruit flies Anastrepha fraterculus (Wiede-mann) and Ceratitis capitata (Wiedemann), including Acca sellowiana (O. Berg) Burret, Campomanesia xanthocarpa O. Berg, Psidium guajava L., Prunus persica (L.) Batsch, Eriobotrya japonica (Thunb.) Lindl., Citrus reticulata Blanco var. Murcott, C. aurantium L., C. paradisi Macfadyen var. Dalan Dan, and C. paradisi var. Sudashi, were sampled for fruit fly larvae between Feb and Dec 2000 in the northernmost section of the Paranaense forest, in the Province of Misiones, NE Argentina. Both A. fraterculus and C. capitata were obtained from these host plant species, with A. fraterculus accounting for 93% of all tephritid puparia identified. Ten species of larval-pupal parasitoids were recovered from A. fraterculus; Doryctobracon areolatus (Szépligeti), D. brasiliensis (Szépligeti), Utetes anastrephae (Viereck), Opius bellus (Gahan), Diachasmimorpha longicaudata (Ashmead) (Opiinae, raconidae), Odontosema anastrephae Borgmeier, Lopheucoila anastrephae (Rohwer), Aganaspis pelleranoi (Brèthes) (Eucoilinae, Figitidae), Asobara anastrephae (Muessebeck) (Alyssinae, Braconidae), and Aceratoneuromyia indica (Silvestri) (Tetrastichinae, Eulophidae). All these parasitoids, with the exception of D. longicaudata and A. indica, are native to the Neotropical region. No parasitoids were recovered from C. capitata puparia. Asobara anastrephae and O. anastrephae are newly recorded in Argentina, whereas D. brasiliensis, U. anastrephae, and L. anastrephae are newly reported in Misiones. The eucoiline A. pelleranoi wasthe most abundant parasitoid species. Acca sellowiana and P. guajava harbored the highest parasitoid abundance and diversity.Fil: Schliserman, Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro de Investigaciones y Transferencia de Catamarca. Universidad Nacional de Catamarca. Centro de Investigaciones y Transferencia de Catamarca; ArgentinaFil: Ovruski Alderete, Sergio Marcelo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Planta Piloto de Procesos Industriales Microbiológicos; ArgentinaFil: Decoll, Olga. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Misiones; ArgentinaFil: Wharton, Robert. Texas A&M University; Estados Unido

Dishevelled genes mediate a conserved mammalian PCP pathway to regulate convergent extension during neurulation

The planar cell polarity (PCP) pathway is conserved throughout evolution, but it mediates distinct developmental processes. In Drosophila, members of the PCP pathway localize in a polarized fashion to specify the cellular polarity within the plane of the epithelium, perpendicular to the apicobasal axis of the cell. In Xenopus and zebrafish, several homologs of the components of the fly PCP pathway control convergent extension. We have shown previously that mammalian PCP homologs regulate both cell polarity and polarized extension in the cochlea in the mouse. Here we show, using mice with null mutations in two mammalian Dishevelled homologs, Dvl1 and Dvl2, that during neurulation a homologous mammalian PCP pathway regulates concomitant lengthening and narrowing of the neural plate, a morphogenetic process defined as convergent extension. Dvl2 genetically interacts with Loop-tail, a point mutation in the mammalian PCP gene Vangl2, during neurulation. By generating Dvl2 BAC (bacterial artificial chromosome) transgenes and introducing different domain deletions and a point mutation identical to the dsh1 allele in fly, we further demonstrated a high degree of conservation between Dvl function in mammalian convergent extension and the PCP pathway in fly. In the neuroepithelium of neurulating embryos, Dvl2 shows DEP domain-dependent membrane localization, a pre-requisite for its involvement in convergent extension. Intriguing, the Loop-tail mutation that disrupts both convergent extension in the neuroepithelium and PCP in the cochlea does not disrupt Dvl2 membrane distribution in the neuroepithelium, in contrast to its drastic effect on Dvl2 localization in the cochlea. These results are discussed in light of recent models on PCP and convergent extension

PhishDef: URL Names Say It All

Phishing is an increasingly sophisticated method to steal personal user information using sites that pretend to be legitimate. In this paper, we take the following steps to identify phishing URLs. First, we carefully select lexical features of the URLs that are resistant to obfuscation techniques used by attackers. Second, we evaluate the classification accuracy when using only lexical features, both automatically and hand-selected, vs. when using additional features. We show that lexical features are sufficient for all practical purposes. Third, we thoroughly compare several classification algorithms, and we propose to use an online method (AROW) that is able to overcome noisy training data. Based on the insights gained from our analysis, we propose PhishDef, a phishing detection system that uses only URL names and combines the above three elements. PhishDef is a highly accurate method (when compared to state-of-the-art approaches over real datasets), lightweight (thus appropriate for online and client-side deployment), proactive (based on online classification rather than blacklists), and resilient to training data inaccuracies (thus enabling the use of large noisy training data).Comment: 9 pages, submitted to IEEE INFOCOM 201