The fine-scale architecture of structural variants in 17 mouse genomes.

BACKGROUND: Accurate catalogs of structural variants (SVs) in mammalian genomes are necessary to elucidate the potential mechanisms that drive SV formation and to assess their functional impact. Next generation sequencing methods for SV detection are an advance on array-based methods, but are almost exclusively limited to four basic types: deletions, insertions, inversions and copy number gains. RESULTS: By visual inspection of 100 Mbp of genome to which next generation sequence data from 17 inbred mouse strains had been aligned, we identify and interpret 21 paired-end mapping patterns, which we validate by PCR. These paired-end mapping patterns reveal a greater diversity and complexity in SVs than previously recognized. In addition, Sanger-based sequence analysis of 4,176 breakpoints at 261 SV sites reveal additional complexity at approximately a quarter of structural variants analyzed. We find micro-deletions and micro-insertions at SV breakpoints, ranging from 1 to 107 bp, and SNPs that extend breakpoint micro-homology and may catalyze SV formation. CONCLUSIONS: An integrative approach using experimental analyses to train computational SV calling is essential for the accurate resolution of the architecture of SVs. We find considerable complexity in SV formation; about a quarter of SVs in the mouse are composed of a complex mixture of deletion, insertion, inversion and copy number gain. Computational methods can be adapted to identify most paired-end mapping patterns.

Anàlisi i Disseny d'una aplicación pel Vot Digital

El treball consisteix en un sistema de votació basat en l'anàlisi i disseny basat en les noves tecnologies. L'aplicació es digués VotoDigital, l'esmentat sistema dugués a terme i gestionés el procés de votació.

Aplicación web para la gestión de un catálogo de productos.

El present TFC es basa en l'anàlisi, disseny i implementació d'una aplicació web per a una petita empresa que desitja mostrar per Internet un catàleg de productes audiovisuals i d'entreteniment, amb la finalitat de poder incrementar el nombre de vendes.

Anàlisis, disseny i implementació d'una aplicació de gestió d'històries mèdiques per un sistema multi centres mitjançant tecnologia J2EE, i tecnologia de xarxes de bases de dades

El treball final de carrera 'HISMED', es basa en l'anàlisi, disseny, investigació e implementació d'una aplicació dins l'àmbit assistencial sanitari amb la premissa de voler ser un sistema per oferir un servei sanitari de millor qualitat, i crear un entorn en el qual investigadors, laboratoris, metges i personal docent comparteixen dades amb una rellevància cabdal per les seves professions. Oferint-los una eina de consulta molt potent en quant a l'obtenció de dades clíniques, que els permet explotar la informació segons convingui el cas.

Solució global per la gestió de dades d'empleat mitjançant J2ME/J2EE.

Aquest treball final de carrera es basa en l'anàlisi, disseny i implementació d'una solució per comunicar un empleat i la seva empresa per tal de gestionar informació i dades de l'empleat com poden ser: la nòmina, el full d'hores, el full de despeses i la consulta i sol·licitud de vacances.

Gestiona't : aplicació en J2EE per a la gestió personal del treball

Aquest treball final de carrera es basa en l'anàlisi, disseny i implementació d'una solució per a la autogestió dels recursos humans de l'empresa; és a dir, per tal que tots els treballadors de la mateixa puguin gestionar tot el relacionat amb el seu entorn de treball (les seves dades personals, el seu temps de treball, les tasques relacionades amb el seu càrrec, la sol·licitud de vacances...). Paral·lelament, aquest treball estudia la viabilitat d'emprar com a eina de treball professional diària l'IDE Eclipse amb la integració del plug-in d'Exadel Studio per a l'ús del framework Struts.

Mapping the proteome of Leishmania Viannia parasites using two-dimensional polyacrylamide gel electrophoresis and associated technologies.

In this study we have demonstrated the potential of two-dimensional electrophoresis (2DE)-based technologies as tools for characterization of the Leishmania proteome (the expressed protein complement of the genome). Standardized neutral range (pH 5-7) proteome maps of Leishmania (Viannia) guyanensis and Leishmania (Viannia) panamensis promastigotes were reproducibly generated by 2DE of soluble parasite extracts, which were prepared using lysis buffer containing urea and nonidet P-40 detergent. The Coomassie blue and silver nitrate staining systems both yielded good resolution and representation of protein spots, enabling the detection of approximately 800 and 1,500 distinct proteins, respectively. Several reference protein spots common to the proteomes of all parasite species/strains studied were isolated and identified by peptide mass spectrometry (LC-ES-MS/MS), and bioinformatics approaches as members of the heat shock protein family, ribosomal protein S12, kinetoplast membrane protein 11 and a hypothetical Leishmania-specific 13 kDa protein of unknown function. Immunoblotting of Leishmania protein maps using a monoclonal antibody resulted in the specific detection of the 81.4 kDa and 77.5 kDa subunits of paraflagellar rod proteins 1 and 2, respectively. Moreover, differences in protein expression profiles between distinct parasite clones were reproducibly detected through comparative proteome analyses of paired maps using image analysis software. These data illustrate the resolving power of 2DE-based proteome analysis. The production and basic characterization of good quality Leishmania proteome maps provides an essential first step towards comparative protein expression studies aimed at identifying the molecular determinants of parasite drug resistance and virulence, as well as discovering new drug and vaccine targets.

ZNRD1 (zinc ribbon domain-containing 1) is a host cellular factor that influences HIV-1 replication and disease progression.

BACKGROUND: Human immunodeficiency virus (HIV) takes advantage of multiple host proteins to support its own replication. The gene ZNRD1 (zinc ribbon domain-containing 1) has been identified as encoding a potential host factor that influenced disease progression in HIV-positive individuals in a genomewide association study and also significantly affected HIV replication in a large-scale in vitro short interfering RNA (siRNA) screen. Genes and polymorphisms identified by large-scale analysis need to be followed up by means of functional assays and resequencing efforts to more precisely map causal genes. METHODS: Genotyping and ZNRD1 gene resequencing for 208 HIV-positive subjects (119 who experienced long-term nonprogression [LTNP] and 89 who experienced normal disease progression) was done by either TaqMan genotyping assays or direct sequencing. Genetic association analysis was performed with the SNPassoc package and Haploview software. siRNA and short hairpin RNA (shRNA) specifically targeting ZNRD1 were used to transiently or stably down-regulate ZNRD1 expression in both lymphoid and nonlymphoid cells. Cells were infected with X4 and R5 HIV strains, and efficiency of infection was assessed by reporter gene assay or p24 assay. RESULTS: Genetic association analysis found a strong statistically significant correlation with the LTNP phenotype (single-nucleotide polymorphism rs1048412; [Formula: see text]), independently of HLA-A10 influence. siRNA-based functional analysis showed that ZNRD1 down-regulation by siRNA or shRNA impaired HIV-1 replication at the transcription level in both lymphoid and nonlymphoid cells. CONCLUSION: Genetic association analysis unequivocally identified ZNRD1 as an independent marker of LTNP to AIDS. Moreover, in vitro experiments pointed to viral transcription as the inhibited step. Thus, our data strongly suggest that ZNRD1 is a host cellular factor that influences HIV-1 replication and disease progression in HIV-positive individuals.

Estudo do Ruído Sísmico no Arquipélago de Cabo Verde

Traditionally the study of Earth's internal structure has been based on analysis of seismic waves recorded during the occurrence of earthquakes. Recently, some researchers have shown to be possible to use ambient seismic noise (generally generated by ocean storms) to obtain dispersion curves with satisfactory results. Moreover, the use of ambient seismic noise measurement has advantages because they are independent of the earthquake-station geometry. This study aims to determine the dispersion curves of Rayleigh waves from the analysis of ambient seismic noise records, obtained in Cape Verde archipelago, whose origin and structure has attracted interest from several researchers. Analyzing the data collected between November 2007 and September 2008, Green's functions were determined. The analysis of these functions allowed to construct energy diagrams and to measure dispersion curves of group velocities between pairs of stations.

Retirement incentives, individual heterogeneity and labour transitions of employed and unemployed workers

In this paper we analyze the sensitivity of the labour market decisions of workers close toretirement with respect to the incentives created by public regulations. We improve upon the extensiveprior literature on the effect of pension incentives on retirement in two ways. First, bymodeling the transitions between employment, unemployment and retirement in a simultaneousmanner, paying special attention to the transition from unemployment to retirement (which is particularlyimportant in Spain). Second, by considering the influence of unobserved heterogeneity inthe estimation of the effect of our (carefully constructed) incentive variables.Using administrative data, we find that, when properly defined, economic incentives have astrong impact on labour market decisions in Spain. Unemployment regulations are shown to be particularlyinfluential for retirement behaviour, along with the more traditional determinants linked tothe pension system. Pension variables also have a major bearing on both workers reemploymentdecisions and on the strategic actions of employers. The quantitative impact of the incentives, however,is greatly affected by the existence of unobserved heterogeneity among workers. Its omissionleads to sizable biases in the assessment of the sensitivity to economic incentives, a finding thathas clear consequences for the credibility of any model-based policy analysis. We confirm theimportance of this potential problem in one especially interesting instance: the reform of earlyretirement provisions undertaken in Spain in 2002. We use a difference-in-difference approach tomeasure the behavioural reaction to this change, finding a large overestimation when unobservedheterogeneity is not taken into account.

On the taxonomic status of Nephochaetopteryx calida (Wiedemann) (Diptera, Sarcophagidae)

On the taxonomic status of Nephochaetopteryx calida (Wiedemann) (Diptera, Sarcophagidae). Based on analysis of the holotype of Nephochaetopteryx calida (Wiedemann) it was concluded that this species does not belong to Nephochaetopteryx. The holotype is a female partly damaged and it was not possible to place it in one of Sarcophaginae genera, remaining as Sarcophaga calida Wiedemann, 1830, incertae sedis.

Triathlon event distance specialization: training and injury effects.

We conducted a preliminary, questionnaire-based, retrospective analysis of training and injury in British National Squad Olympic distance (OD) and Ironman distance (IR) triathletes. The main outcome measures were training duration and training frequency and injury frequency and severity. The number of overuse injuries sustained over a 5-year period did not differ between OD and IR. However, the proportions of OD and IR athletes who were affected by injury to particular anatomical sites differed (p < 0.05). Also, fewer OD athletes (16.7 vs. 36.8%, p < 0.05) reported that their injury recurred. Although OD sustained fewer running injuries than IR (1.6 +/- 0.5 vs. 1.9 +/- 0.3, p < 0.05), more subsequently stopped running (41.7 vs. 15.8%) and for longer (33.5 +/- 43.0 vs. 16.7 +/- 16.6 days, p < 0.01). In OD, the number of overuse injuries sustained inversely correlated with percentage training time, and number of sessions, doing bike hill repetitions (r = -0.44 and -0.39, respectively, both p < 0.05). The IR overuse injury number correlated with the amount of intensive sessions done (r = 0.67, p < 0.01 and r = 0.56, p < 0.05 for duration of "speed run" and "speed bike" sessions). Coaches should note that training differences between triathletes who specialize in OD or IR competition may lead to their exhibiting differential risk for injury to specific anatomical sites. It is also important to note that cycle and run training may have a "cumulative stress" influence on injury risk. Therefore, the tendency of some triathletes to modify rather than stop training when injured-usually by increasing load in another discipline from that in which the injury first occurred-may increase both their risk of injury recurrence and time to full rehabilitation.

Search for nonstandard Higgs boson in diphoton events at p anti-p collisions

We estimate the attainable limits on the coupling of a nonstandard Higgs boson to two photons taking into account the data collected by the Fermilab collaborations on diphoton events. We based our analysis on a general set of dimension-6 effective operators that give rise to anomalous couplings in the bosonic sector of the standard model. If the coefficients of all blind operators have the same magnitude, indirect bounds on the anomalous triple vector-boson couplings can also be inferred, provided there is no large cancellation in the Higgs-gamma-gamma coupling.

Evaluating Roadway Subsurface Drainage Practices, 2013

The bearing capacity and service life of a pavement is affected adversely by the presence of undrained water in the pavement layers. In cold winter climates like in Iowa, this problem is magnified further by the risk of frost damage when water is present. Therefore, well-performing subsurface drainage systems form an important aspect of pavement design by the Iowa Department of Transportation (DOT). However, controversial findings are also reported in the literature regarding the benefits of subsurface drainage. The goal of this research was not to investigate whether subdrains are needed in Iowa pavements, but to conduct an extensive performance review of primary interstate pavement subdrains in Iowa, determine the cause of the problem if there are drains that are not functioning properly, and investigate the effect of poor subdrain performance due to improper design, construction, and maintenance on pavement surface distresses, if any. An extensive literature review was performed covering national-level and state-level research studies mainly focusing on the effects of subsurface drainage on performance of asphalt and concrete pavements. Several studies concerning the effects of a recycled portland cement concrete (RPCC) subbase on PCC pavement drainage systems were also reviewed. A detailed forensic test plan was developed in consultation with the project technical advisory committee (TAC) for inspecting and evaluating the Iowa pavement subdrains. Field investigations were conducted on 64 selected (jointed plain concrete pavement/JPCP and hot-mix asphalt/HMA) pavement sites during the fall season of 2012 and were mainly focused on the drainage outlet conditions. Statistical analysis was conducted on the compiled data from field investigations to further investigate the effect of drainage on pavement performance. Most Iowa subsurface drainage system outlet blockage is due to tufa, sediment, and soil. Although higher blockage rates reduce the flow rate of water inside outlet pipes, it does not always stop water flowing from inside the outlet pipe to outside the outlet pipe unless the outlet is completely blocked. Few pavement surface distresses were observed near blocked subsurface drainage outlet spots. More shoulder distresses (shoulder drop or cracking) were observed near blocked drainage outlet spots compared to open ones. Both field observations and limited performance analysis indicate that drainage outlet conditions do not have a significant effect on pavement performance. The use of RPCC subbase in PCC pavements results in tufa formation, a primary cause of drainage outlet blockage in JPCP. Several useful recommendations to potentially improve Iowa subdrain performance, which warrant detailed field investigations, were made