PT-Scotch: A tool for efficient parallel graph ordering

The parallel ordering of large graphs is a difficult problem, because on the one hand minimum degree algorithms do not parallelize well, and on the other hand the obtainment of high quality orderings with the nested dissection algorithm requires efficient graph bipartitioning heuristics, the best sequential implementations of which are also hard to parallelize. This paper presents a set of algorithms, implemented in the PT-Scotch software package, which allows one to order large graphs in parallel, yielding orderings the quality of which is only slightly worse than the one of state-of-the-art sequential algorithms. Our implementation uses the classical nested dissection approach but relies on several novel features to solve the parallel graph bipartitioning problem. Thanks to these improvements, PT-Scotch produces consistently better orderings than ParMeTiS on large numbers of processors

Effects of Defensiveness on the Reporting of Personality Disorder Symptoms

Personality disorders are not granted the same clinical attention accorded Axis I disorders despite their instrumental role in treatment and outcome. Even when standardized assessments are used, their clinical utility may be limited by an overly favorable self-presentation. The current study focused on defensiveness, the intentional denial of symptomatology, by examining individuals’ ability to minimize their presentation on personality disorder diagnostic measures. Using a within-subjects simulation design, dually diagnosed inpatients were assessed under both honest and defensive conditions. The study used self-report (Structured Clinical Interview for DSM-IV – Axis II – Personality Questionnaire, SCID-II-PQ) and interview-based (Structured Interview for DSM-IV Personality, SIDP-IV) diagnostic measures and a self-report measure of favorable self-presentation (Paulhus Deception Scales, PDS). The inpatients were quite capable of hiding maladaptive personality traits on diagnostic measures, with similarly large effect sizes on both the SCID-II-PQ and SIDP-IV. In addition to the PDS, two new detection strategies for identifying defensiveness showed promise

Shaping 1,2,4-Triazolium Fluorinated Ionic Liquid Crystals

The synthesis and thermotropic behaviour of some di-alkyloxy-phenyl-1,2,4-triazolium trifluoromethane-sulfonate salts bearing a seven-carbon atom perfluoroalkyl chain on the cation is herein described. The fluorinated salts presenting a 1,2,4-triazole as a core and differing in the length of two alkyloxy chains on the phenyl ring demonstrated a typical liquid crystalline behaviour. The mesomorphic properties of this set of salts were studied by differential scanning calorimetry and polarized optical microscopy. The thermotropic properties are discussed on the grounds of the tuneable structures of the salts. The results showed the existence of a monotropic, columnar, liquid crystalline phase for the salts tested. An increase in the temperature mesophase range and the presence of two enantiotropic mesophases for the sixteen-atom alkyloxy chain salt can be observed by increasing the length of the alkyloxy chain on the phenyl ring

Memetic Multilevel Hypergraph Partitioning

Hypergraph partitioning has a wide range of important applications such as VLSI design or scientific computing. With focus on solution quality, we develop the first multilevel memetic algorithm to tackle the problem. Key components of our contribution are new effective multilevel recombination and mutation operations that provide a large amount of diversity. We perform a wide range of experiments on a benchmark set containing instances from application areas such VLSI, SAT solving, social networks, and scientific computing. Compared to the state-of-the-art hypergraph partitioning tools hMetis, PaToH, and KaHyPar, our new algorithm computes the best result on almost all instances

Paraphyletic species no more - genomic data resolve a Pleistocene radiation and validate morphological species of the Melanoplus scudderi complex (Insecta: Orthoptera)

Rapid speciation events, with taxa generated over a short time period, are among the most investigated biological phenomena. However, molecular systematics often reveals contradictory results compared with morphological/phenotypical diagnoses of species under scenarios of recent and rapid diversification. In this study, we used molecular data from an average of over 29- 000 loci per sample from RADseq to reconstruct the diversification history and delimit the species boundary in a short- winged grasshopper species complex (Melanoplus scudderi group), where Pleistocene diversification has been hypothesized to generate more than 20 putative species with distinct male genitalic shapes. We found that, based on a maximum likelihood molecular phylogeny, each morphological species indeed forms a monophyletic group, contrary to the result from a previous mitochondrial DNA sequence study. By dating the diversification events, the species complex is estimated to have diversified during the Late Pleistocene, supporting the recent radiation hypothesis. Furthermore, coalescent- based species delimitation analyses provide quantitative support for independent genetic lineages, which corresponds to the morphologically defined species. Our results also showed that male genitalic shape may not be predicted by evolutionary distance among species, not only indicating that this trait is labile, but also implying that selection may play a role in character divergence. Additionally, our findings suggest that the rapid speciation events in this flightless grasshopper complex might be primarily associated with the fragmentation of their grassland habitats during the Late Pleistocene. Collectively, our study highlights the importance of integrating multiple sources of information to delineate species, especially for a species complex that diversified rapidly, and whose divergence may be linked to ecological processes that create geographic isolation (i.e. fragmented habitats), as well as selection acting on characters with direct consequences for reproductive isolation (i.e. genitalic divergence).Genomic data validate morphological species designations in Melanoplus grasshoppers from the southeastern U.S.A.The difference in male genitalic shape, which is evolutionarily labile, can be a good diagnostic character to distinguish species of recent and rapid diversification origin.Fragmentation of grassland habitats in the Late Pleistocene might have facilitated rapid speciation events in the flightless Melanoplus grasshoppers.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/155980/1/syen12415-sup-0001-SupInfo.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/155980/2/syen12415_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/155980/3/syen12415.pd

I dati Sentinel per un Framework GIS-based per la Gestione Integrata Costiera : una sperimentazione nel settore veneto della fascia costiera alto adriatica.

Il grande valore delle zone costiere e la loro potenzialit\ue0 hanno imposto di trovare soluzione ai problemi che le affliggono, quali la distruzione degli habitat, la contaminazione delle acque, l\u2019erosione costiera e l'impoverimento delle risorse (UE Commission: ICZM a strategy for Europe COM 2000, Agenda 21). L\u2019Integrated Coastal Zone Management (ICZM) sfrutta l\u2019analisi di vulnerabilit\ue0, di pericolosit\ue0 e di rischio, naturale e antropico, quali imprescindibili fondamenta conoscitive, specialmente per quelle risorse che hanno il carattere di beni comuni. Gli ambienti costieri sono sottoposti alla continua pressione esercitata da grandi masse d'acqua in continuo movimento e apporti sedimentari dei fiumi alla foce. Questi fattori, soprattutto nell\u2019alta fascia adriatica costiera, insieme ad eustatismo e subsidenza, determinano la notevole dinamicit\ue0 che pu\uf2 manifestarsi in differenti forme e in significativa rapidit\ue0 di cambiamento. Gli approcci tradizionali, nel ricorrere a delimitazioni cartografiche che non sono capaci di restituire i veloci cambiamenti che intervengono, evidenziano forti incongruenze con la realt\ue0 osservata. Quindi KPI, indici ed indicatori per le predette analisi \u2013 implementate mediante tecniche e strumenti di analisi geospaziale - necessitano di dati ad aggiornamento frequente che possono essere ottenuti dal telerilevamento satellitare impiegato come piattaforma informativa generalizzata. Nel paper viene presentata una sperimentazione che sfrutta i dati delle costellazioni Sentinel 1 e 2 del programma Copernicus dell\u2019ESA nel settore veneto della fascia costiera adriatica. Tale sperimentazione \u2013 mirata alla produzione di carte delle serie di vegetazione e all\u2019aggiornamento rapido della perimetrazione delle aree ambientali protette - costituisce un primo stato di avanzamento per la definizione di un framework ICZM generalizzabile per applicazioni sulle coste europee ed africane

Sparse approaches for the exact distribution of patterns in long state sequences generated by a Markov source

We present two novel approaches for the computation of the exact distribution of a pattern in a long sequence. Both approaches take into account the sparse structure of the problem and are two-part algorithms. The first approach relies on a partial recursion after a fast computation of the second largest eigenvalue of the transition matrix of a Markov chain embedding. The second approach uses fast Taylor expansions of an exact bivariate rational reconstruction of the distribution. We illustrate the interest of both approaches on a simple toy-example and two biological applications: the transcription factors of the Human Chromosome 5 and the PROSITE signatures of functional motifs in proteins. On these example our methods demonstrate their complementarity and their hability to extend the domain of feasibility for exact computations in pattern problems to a new level

Investigating the inhibition of FTSJ1 a tryptophan tRNA-specific 2’-O-methyltransferase by NV TRIDs, as a mechanism of readthrough in nonsense mutated CFTR

Abstract: Cystic Fibrosis (CF) is an autosomal recessive genetic disease caused by mutations in the CFTR gene, coding for the CFTR chloride channel. About 10% of the CFTR gene mutations are "stop" mutations, which generate a Premature Termination Codon (PTC), thus synthesizing a truncated CFTR protein. A way to bypass PTC relies on ribosome readthrough, which is the ri-bosome’s capacity to skip a PTC, thus generating a full-length protein. “TRIDs” are molecules exerting ribosome readthrough; for some, the mechanism of action is still under debate. We in-vestigate a possible mechanism of action (MOA) by which our recently synthesized TRIDs, namely NV848, NV914, and NV930, could exert their readthrough activity by in silico analysis and in vitro studies. Our results suggest a likely inhibition of FTSJ1, a tryptophan tRNA-specific 2’-O-methyltransferase

Readthrough Approach Using NV Translational Readthrough-Inducing Drugs (TRIDs): A Study of the Possible Off-Target Effects on Natural Termination Codons (NTCs) on TP53 and Housekeeping Gene Expression

Nonsense mutations cause several genetic diseases such as cystic fibrosis, Duchenne muscular dystrophy, β-thalassemia, and Shwachman–Diamond syndrome. These mutations induce the formation of a premature termination codon (PTC) inside the mRNA sequence, resulting in the synthesis of truncated polypeptides. Nonsense suppression therapy mediated by translational readthrough-inducing drugs (TRIDs) is a promising approach to correct these genetic defects. TRIDs generate a ribosome miscoding of the PTC named “translational readthrough” and restore the synthesis of full-length and potentially functional proteins. The new oxadiazole-core TRIDs NV848, NV914, and NV930 (NV) showed translational readthrough activity in nonsense-related in vitro systems. In this work, the possible off-target effect of NV molecules on natural termination codons (NTCs) was investigated. Two different in vitro approaches were used to assess if the NV molecule treatment induces NTC readthrough: (1) a study of the translational-induced p53 molecular weight and functionality; (2) the evaluation of two housekeeping proteins’ (Cys-C and β2M) molecular weights. Our results showed that the treatment with NV848, NV914, or NV930 did not induce any translation alterations in both experimental systems. The data suggested that NV molecules have a specific action for the PTCs and an undetectable effect on the NTCs