Assembly, quantification, and downstream analysis for high trhoughput sequencing data

Next Generation Sequencing is a set of relatively recent but already well-established technologies with a wide range of applications in life sciences. Despite the fact that they are constantly being improved, multiple challenging problems still exist in the analysis of high throughput sequencing data. In particular, genome assembly still suffers from inability of technologies to overcome issues related to such structural properties of genomes as single nucleotide polymorphisms and repeats, not even mentioning the drawbacks of technologies themselves like sequencing errors which also hinder the reconstruction of the true reference genomes. Other types of issues arise in transcriptome quantification and differential gene expression analysis. Processing millions of reads requires sophisticated algorithms which are able to compute gene expression with high precision and in reasonable amount of time. Following downstream analysis, the utmost computational task is to infer the activity of biological pathways (e.g., metabolic). With many overlapping pathways challenge is to infer the role of each gene in activity of a given pathway. Assignment products of a gene to a wrong pathway may result in misleading differential activity analysis, and thus, wrong scientific conclusions. In this dissertation I present several algorithmic solutions to some of the enumerated problems above. In particular, I designed scaffolding algorithm for genome assembly and created new tools for differential gene and biological pathways expression analysis

Sleep and circadian rhythm disruption in shift work

Department of Hygiene, Nicolae Testemitanu State University of Medicine and Pharmacy of the Republic of MoldovaIntroduction. Circadian rhythm is one of the most important mechanisms in human body, which coordinates biological rhythms with the environmental changes in the day-night cycle. People are diurnal species, so we are used to work during the day and to sleep during the night. Sleep and Circadian Rhythm Disruption (SCRD) occurs when natural circadian rhythms are pushed out of synchronization, for example in shift work. Aim of the study. Define the mechanistic links between sleep and circadian rhythm disruption and hyperglycemia. Apply this knowledge for the development of evidence-based clinical interventions. Transfer this knowledge to the broader community, patients and caregivers. Materials and methods. This study was based on physiological, biological and laboratory investigations, that were used to determine respiratory frequency, heartbeat frequency, muscular strength, tremor, blood and liver tests. Results. It was established that shift-workers have increased level of glucose in blood. Conclusions. Sleep and Circadian Rhythm Disruption in shift work leads to hyperglycemia, that can induce diabetes mellitus

La regulación jurídica de los residuos y su gestión

Treball Final de Grau en Dret. Codi: DR1052. Curs acadèmic 2013/2014El tema que se va a tratar en este Trabajo Final de Grado es “la regulación jurídica de los residuos y su gestión”, el cual se encuentra muy relacionado con el medio ambiente. Así, el concepto de medio ambiente lo extraemos de la doctrina del Tribunal Constitucional y de la jurisprudencia del Tribunal Supremo, donde se establece que el medio ambiente es aquel conjunto de circunstancias físicas, culturales, económicas y sociales que rodean a las personas ofreciéndoles un conjunto de posibilidades para hacer su vida. Y, por residuos se entiende cualquier sustancia u objeto que su poseedor deseche o tenga la intención o la obligación de desechar (artículo 3 de la Ley 22/2011). Este tema lo podemos observar en un contexto en que tanto los residuos ordinarios como lo peligrosos son causas de problemas ambientales que provocan efectos negativos en el medio ambiente, aunque no sólo. Últimamente, está aumentando la producción de basuras domésticas lo cual implica la necesidad de mejorar los sistemas de recogida y almacenamiento de dichos residuos puesto que muchas veces éstos se vierten en lugares no propios y ello produce graves impactos sobre el paisaje, la flora y la fauna. La legislación en materia de residuos ha supuesto una gran evolución puesto que en el siglo XIX, las normas estatales se dedicaban a atribuir la competencia en materia de residuos a los Ayuntamientos y, más adelante, en el siglo XX, van apareciendo reglas sustantivas generales sobre esta materia en el marco de las instrucciones de Sanidad Pública e Higiene, con lo que de alguna manera se va observando una aproximación de lo que vendría a ser la protección del medio ambiente. Así, conviene destacar la primera Ley sectorial sobre residuos, la Ley 42/1975, de 19 de noviembre, sobre Recogida y Tratamiento de los desechos y residuos sólidos urbanos, con un contenido principalmente de carácter económico. A continuación, tenemos la precedente ley a la actual, la Ley 10/1998 de residuos que, a pesar de que durante su aplicación tanto las administraciones públicas como los productores y gestores de residuos fueron adquiriendo experiencia y formación en este campo, al igual que los instrumentos y principios en materia de residuos han evaluado, se ha visto la necesidad de elaborar una nueva ley. Esta es la vigente Ley 22/2011, de 28 de julio, de residuos y suelos contaminados, cuyo origen lo encontramos en el aumento de la producción de residuos que ha habido constantemente y en la importancia de la actividad económica vinculada a los mismos. Además, presenta un dato relevante puesto que traspone a nuestro ordenamiento la denominada Directiva Marco de Residuos, es decir l

Universal scaling dimensions for highly irrelevant operators in the Local Potential Approximation

We study $d$-dimensional scalar field theory in the Local Potential Approximation of the functional renormalization group. Sturm-Liouville methods allow the eigenoperator equation to be cast as a Schrodinger-type equation. Combining solutions in the large field limit with the Wentzel-Kramers-Brillouin approximation, we solve analytically for the scaling dimension $d_n$ of high dimension potential-type operators $\mathcal{O}_n(\varphi)$ around a non-trivial fixed point. We find that $d_n = n(d-d_\varphi)$ to leading order in $n$ as $n \to \infty$, where $d_\varphi=\frac{1}{2}(d-2+\eta)$ is the scaling dimension of the field, $\varphi$, and determine the power-law growth of the subleading correction. For $O(N)$ invariant scalar field theory, the scaling dimension is just double this, for all fixed $N\geq0$ and additionally for $N=-2,-4,\ldots \,.$ These results are universal, independent of the choice of cutoff function which we keep general throughout, subject only to some weak constraints.Comment: 23 pages, no figures. Clarifications added. Version published in PR

Off-shell divergences in quantum gravity

We investigate off-shell perturbative renormalisation of pure quantum gravity for both background metric and quantum fluctuations. We show that at each new loop order, the divergences that do not vanish on-shell are constructed from only the total metric, whilst those that vanish on-shell are renormalised by canonical transformations involving the quantum fields. Purely background metric divergences do not separately appear, and the background metric does not get renormalised. We highlight that renormalisation group identities play a crucial role ensuring consistency in the renormalisation of BRST transformations beyond one loop order. We verify these assertions by computing leading off-shell divergences to two loops, exploiting off-shell BRST invariance and the renormalisation group equations. Although some divergences can be absorbed by field redefinitions, we explain why this does not lead to finite beta-functions for the corresponding field.Comment: 45 page

Experimental investigation of an Air Source Heat Pump

An experimental investigation were driven to catch all working parameters of an Air Source Heat Pump such as temperature differences between refrigerant working states and evaporator respectively condenser environment temperatures. Heat Pump compressor were monitored to know inlet and outlet refrigerant temperatures to build working diagram of the heat pump in heating configuration. At condenser, a plate heat exchanger is used to discharge the energy from refrigerant to water, liquid used in secondary circuit. Heat exchanger temperatures of refrigerant and water were monitored to drive the working diagram of the heat exchanger equipment. Current consumption of Heat Pump were registered together with heat exchanger secondary circuit temperature differences and his water flow to estimate Seasonal Performance Factor during experiment

The single-cell eQTLGen consortium

In recent years, functional genomics approaches combining genetic information with bulk RNA-sequencing data have identified the downstream expression effects of disease-associated genetic risk factors through so-called expression quantitative trait locus (eQTL) analysis. Single-cell RNA-sequencing creates enormous opportunities for mapping eQTLs across different cell types and in dynamic processes, many of which are obscured when using bulk methods. Rapid increase in throughput and reduction in cost per cell now allow this technology to be applied to large-scale population genetics studies. To fully leverage these emerging data resources, we have founded the single-cell eQTLGen consortium (sc-eQTLGen), aimed at pinpointing the cellular contexts in which disease-causing genetic variants affect gene expression. Here, we outline the goals, approach and potential utility of the sc-eQTLGen consortium. We also provide a set of study design considerations for future single-cell eQTL studies.</p