Bioinformatic analysis of proteomics data

Most biochemical reactions in a cell are regulated by highly specialized proteins, which are the prime mediators of the cellular phenotype. Therefore the identification, quantitation and characterization of all proteins in a cell are of utmost importance to understand the molecular processes that mediate cellular physiology. With the advent of robust and reliable mass spectrometers that are able to analyze complex protein mixtures within a reasonable timeframe, the systematic analysis of all proteins in a cell becomes feasible. Besides the ongoing improvements of analytical hardware, standardized methods to analyze and study all proteins have to be developed that allow the generation of testable new hypothesis based on the enormous pre-existing amount of biological information. Here we discuss current strategies on how to gather, filter and analyze proteomic data sates using available software packages

Optimisation in Discrete-event simulation models

Discrete-event simulation is a tool used to simulate and analyse complex real-world systems. As a system gets more complex the number of parameter variations can increase, making it difficult for the user to accurately predict an optimal solution. Optimisation methods are mathematical algorithms that are specialised in finding optimal solutions for a given problem. A combination of discrete-event simulation and optimisation methods could result in a more efficient problem-solving process which has the possibility of providing more optimal solutions. This thesis uses a case study methodology that includes a literature study and a qualitative study to assess the possibilities of using optimisation tools in a simulation setting in an organisation. Optimisation tools in discrete-event simulation software exists in several available software and all of the ones studied in this thesis utilise evolutionary algorithms for optimisation calculations. This thesis handles the importance of finding the right use-case for the implementation of simulation optimisation in a project. A decision tree was created to help users navigate questions one could ask themselves when deciding whether optimisation is suitable in their projects or not

First narrow-band search for continuous gravitational waves from known pulsars in advanced detector data

Spinning neutron stars asymmetric with respect to their rotation axis are potential sources of continuous gravitational waves for ground-based interferometric detectors. In the case of known pulsars a fully coherent search, based on matched filtering, which uses the position and rotational parameters obtained from electromagnetic observations, can be carried out. Matched filtering maximizes the signalto- noise (SNR) ratio, but a large sensitivity loss is expected in case of even a very small mismatch between the assumed and the true signal parameters. For this reason, narrow-band analysis methods have been developed, allowing a fully coherent search for gravitational waves from known pulsars over a fraction of a hertz and several spin-down values. In this paper we describe a narrow-band search of 11 pulsars using data from Advanced LIGO’s first observing run. Although we have found several initial outliers, further studies show no significant evidence for the presence of a gravitational wave signal. Finally, we have placed upper limits on the signal strain amplitude lower than the spin-down limit for 5 of the 11 targets over the bands searched; in the case of J1813-1749 the spin-down limit has been beaten for the first time. For an additional 3 targets, the median upper limit across the search bands is below the spin-down limit. This is the most sensitive narrow-band search for continuous gravitational waves carried out so far

A Case Study into the Environmental Context of Walking School Buses and Other Modes of Travel Used for the Journey to School

The journey to school involves a number of different modes of travel. Approximately half of all journeys to school in New Zealand rely on the use of an automobile. This heavy dependence on automobiles involves a number of environmental detractions. Walking School Buses provide an alternative to cars as a mode of travel for the journey to school. This mode of travel compares favourably in a number of respects when compared to other modes of travel and is generating considerable interest. Based on a case study involving in-depth interviews with ten caregivers this paper compares whether and how Walking School Buses emerged from a different social and cultural background when compared to other modes of travel. Four key influences, in particular parenting culture, the work commitments that caregivers have, the risks posed by strangers and traffic, and the social fragmentation of neighbourhoods were found to be significant in shaping the journey to school. Based on finding a number of similarities between different modes of travel to school it is concluded that the journey to school is embedded in a wider system of social and cultural ideas that shape Walking School Buses and other modes of travel alike

Street food in Palermo: Traditions and market perspectives

Street food protects and promotes the history and tradition of a place. The origin of street foods largely relies on the cultural and natural landscapes that surround the environments where they are prepared and sold. Street food illustrates a culinary heritage that is embedded in the ways of life of people, both residents and visitors. Drawing on a qualitative study, the researchers conducted ten interviews with street food vendors in the city of Palermo (Sicily, Italy) in order to understand this growing phenomenon in urban environments of the Mediterranean, where the street food also brings the customers to ancient times. Results show the strategy of the entrepreneurs as street food vendors and sheds light into the practices and perceptions they have in relation to the street food past, present and future in the context of street food values

Application of dictionary learning to denoise LIGO's blip noise transients

Data streams of gravitational-wave detectors are polluted by transient noise features, or "glitches", of instrumental and environmental origin. In this work, we investigate the use of total-variation methods and learned dictionaries to mitigate the effect of those transients in the data. We focus on a specific type of transient, "blip" glitches, as this is the most common type of glitch present in the LIGO detectors and their waveforms are easy to identify. We randomly select 80 blip glitches scattered in the data from advanced LIGO's O1 run, as provided by the citizen-science project Gravity Spy. Our results show that dictionary-learning methods are a valid approach to model and subtract most of the glitch contribution in all cases analyzed, particularly at frequencies below $\sim 1$ kHz. The high-frequency component of the glitch is best removed when a combination of dictionaries with different atom length is employed. As a further example, we apply our approach to the glitch visible in the LIGO-Livingston data around the time of merger of binary neutron star signal GW170817, finding satisfactory results. This paper is the first step in our ongoing program to automatically classify and subtract all families of gravitational-wave glitches employing variational methods

El delito de defraudación tributaria con especial referencia a la responsabilidad penal de las personas jurídicas

Según entiende Reta, el Derecho Penal Tributario es el desarrollo de la tutela penal del derecho del Estado a percibir los tributos que le permiten cumplir con sus fines constitucionales; protegen estas normas penales la Hacienda Pública y de consiguiente el orden económico, por lo que el Derecho Penal Tributario no es más que un capítulo del Derecho Penal Económico. En igual sentido, para Cairoli no es un derecho autónomo, sino una parte especial del Derecho Penal (...)Contenido: El Derecho Penal Tributario. El delito de defraudación tributaria. Antecedentes. El texto actual. Estructura. La responsabilidad penal de las personas jurídicas y ladefraudación tributari

3-D Scene Reconstruction from Multiple Photometric Images

This thesis deals with the problem of three dimensional scene reconstruction from multiple camera images. This is a well established problem in computer vision and has been significantly researched. In recent years some excellent results have been achieved, however existing algorithms often fall short of many biological systems in terms of robustness and generality. The aim of this research was to develop improved algorithms for reconstructing 3D scenes, with a focus on accurate system modelling and correctly dealing with occlusions. With scene reconstruction the objective is to infer scene parameters describing the 3D structure of the scene from the data given by camera images. This is an illposed inverse problem, where an exact solution cannot be guaranteed. The use of a statistical approach to deal with the scene reconstruction problem is introduced and the differences between maximum a priori (MAP) and minimum mean square estimate (MMSE) considered. It is discussed how traditional stereo matching can be performed using a volumetric scene model. An improved model describing the relationship between the camera data and a discrete model of the scene is presented. This highlights some of the common causes of modelling errors, enabling them to be dealt with objectively. The problems posed by occlusions are considered. Using a greedy algorithm the scene is progressively reconstructed to account for visibility interactions between regions and the idea of a complete scene estimate is established. Some simple and improved techniques for reliably assigning opaque voxels are developed, making use of prior information. Problems with variations in the imaging convolution kernel between images motivate the development of a pixel dissimilarity measure. Belief propagation is then applied to better utilise prior information and obtain an improved global optimum. A new volumetric factor graph model is presented which represents the joint probability distribution of the scene and imaging system. By utilising the structure of the local compatibility functions, an efficient procedure for updating the messages is detailed. To help convergence, a novel approach of accentuating beliefs is shown. Results demonstrate the validity of this approach, however the reconstruction error is similar or slightly higher than from the Greedy algorithm. To simplify the volumetric model, a new approach to belief propagation is demonstrated by applying it to a dynamic model. This approach is developed as an alternative to the full volumetric model because it is less memory and computationally intensive. Using a factor graph, a volumetric known visibility model is presented which ensures the scene is complete with respect to all the camera images. Dynamic updating is also applied to a simpler single depth-map model. Results show this approach is unsuitable for the volumetric known visibility model, however, improved results are obtained with the simple depth-map model

Confusing Head-On Collisions with Precessing Intermediate-Mass Binary Black Hole Mergers

We report a degeneracy between the gravitational-wave signals from quasi-circular precessing black-hole mergers and those from extremely eccentric mergers, namely head-on collisions. Performing model selection on numerically simulated signals of head-on collisions using models for quasi-circular binaries we find that, for signal-to-noise ratios of 15 and 25, typical of Advanced LIGO observations, head-on mergers with respective total masses of $M\in (125,300)M_\odot$ and $M\in (200,440)M_\odot$ would be identified as precessing quasi-circular intermediate-mass black hole binaries, located at a much larger distance. Ruling out the head-on scenario would require to perform model selection using currently nonexistent waveform models for head-on collisions, together with the application of astrophysically motivated priors on the (rare) occurrence of those events. We show that in situations where standard parameter inference of compact binaries may report component masses inside (outside) the pair-instability supernova gap, the true object may be a head-on merger with masses outside (inside) this gap. We briefly discuss the potential implications of these findings for the recent gravitational-wave detection GW190521, which we analyse in detail in [Phys. Rev. Lett. 126, 081101]

Degradation of the mycotoxin fusaric acid in burkholderia ambifaria t16: genes and metabolic pathways involved

Fusaric acid (FA, 5-butylpyridine, 2-carboxylic acid) is a secondary metabolite produced by several Fusarium species, which is toxic for bacteria, plants, animals and humans. This mycotoxin contributes to the virulence of phytopathogenic Fusarium in several crops, causing important economic losses. Moreover, FA reduces survival and competition abilities of bacterial species able to antagonize Fusarium spp. due to its negative effects on viability and production of antibiotics effective against these fungi. Burkholderia ambifaria T16 is a bacterial strain isolated from the rhizosphere of barley that showed the interesting ability to degrade FA and detoxify this mycotoxin from barley seedlings. The genes and metabolic pathways involved in FA degradation have not been identified so far in any bacterial species. By screening of a transposon insertion library and proteomic analysis we were able to identify genes and metabolic pathways that would be involved in FA degradation. A functional 2-methylcitrate cycle (2-MCC), a carbon anaplerotic pathway widely distributed among bacteria and fungi where propionyl-CoA is converted to pyruvate and succinate, was shown to be essential for the growth of B. ambifaria T16 in the presence of FA. Propionyl-CoA and its derived catabolites are lethally toxic to cells when accumulate. For that reason, besides providing succinate and pyruvate, the 2-MCC also has a very important role in the detoxification of propionyl-CoA and its catabolites. The comparison of the proteomic profile of B. ambifaria T16 growing with FA or citrate as sole carbon sources showed that more than 50 enzymes were significantly overexpressed during growth with FA, including 2-MCC enzymes and enzymes that convert butyryl-CoA to propanoyl-CoA, suggesting that propanoyl-CoA is produced during FA degradation. Moreover, several proteins, including an AraC-type transcriptional regulator, a FMN-dependent two-component luciferase like monooxygenase (LLM) system, an amidohydrolase, two enoyl-CoA hydratases and a long-chain fatty acid ligase, encoded in the same gene cluster, were highly over-expressed during growth with FA (>10 fold up-regulation). In the last years, two-component LLMs were shown to catalyze the pyridine-ring cleavage of several N-heterocyclic compounds, suggesting that the mentioned gene cluster is a good candidate to be involved in the initial steps of FA degradation in B. ambifaria T16.Fil: Vinacour, Matias Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones en Biociencias Agrícolas y Ambientales. Universidad de Buenos Aires. Facultad de Agronomía. Instituto de Investigaciones en Biociencias Agrícolas y Ambientales; ArgentinaFil: Forne, I.. Ludwig Maximilians Universitat; AlemaniaFil: Jung, K.. Ludwig Maximilians Universitat; AlemaniaFil: Imhof, A.. Ludwig Maximilians Universitat; AlemaniaFil: Ruiz, Jimena. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones en Biociencias Agrícolas y Ambientales. Universidad de Buenos Aires. Facultad de Agronomía. Instituto de Investigaciones en Biociencias Agrícolas y Ambientales; ArgentinaLVII SAIB Meeting; XVI SAMIGE MeetingCiudad Autonoma de Buenos AiresArgentinaSociedad Argentina de Investigación Bioquímica y Biología MolecularSociedad Argentina de Microbiología Genera