From gene to function: using new technologies for solving old problems.

Recent advances in DNA sequencing have changed the field of genomics as well as that of proteomics making it possible to generate gigabases of genome and transcriptome sequence data at substantially lower cost than it was possible just ten years ago. In recent years, many high-throughput technologies have been developed to interrogate various aspects of cellular processes, including sequence and structural variation and the transcriptome, epigenome, proteome and interactome. These Next Generation Sequencing (NGS) experimental technologies are more mature and accessible than the computational tools available for individual researchers to move, store, analyse and present data in a user-friendly and reproducible fashion. My research work is placed in this scenario and focuses on the analysis of data produced by NGS technologies as well as on the development of new tools aimed at solving the different problems that arise during NGS data analysis. In order to achieve this aim, my group and I have dealt with several open biomedical problems in collaboration with different research groups of the Sapienza University. Some of these experiments have already given interesting results but mostly have represented the occasion and starting point for the development of new tools able to improve some crucial steps of the analyses, solve problems derived by the system complexity and make the results easier to understand for the researchers. Some examples are IsomirT, a tool for the small RNA-Seq analysis and isomiR identification, Phagotto, a tool for analysing deep sequencing data derived from phage-displayed libraries and FIDEA, a web server for the functional interpretation of differential expression analysis. Recent reports have demonstrated that individual microRNAs can be heterogeneous in length and/or sequence producing multiple mature variants that have been dubbed isomiRs. IsomirT is a useful tool to improve and simplify the search for isomiRs starting directly from the results of a miRNA-sequencing experiment. By using it, we observed the behaviour of isomiRs in different cell types and in different biological replicates. Our results indicate that the distribution of the microRNA variants is similar among replicates and different among cells/tissues suggesting that the isomiRs have a functional role in the cell. The use of the NGS technologies for the analysis of antibody selected sequences both using phage display libraries and in vitro selection processes is becoming increasingly popular. By using these technologies, the experimental group headed by prof. Felici has introduced a new experimental pipeline, named PROFILER, aimed at significantly empowering the analysis of antigen-specific libraries. A key step to exploit this idea has been to develop a new tool, Phagotto, for processing and analysing the data derived by sequencing. PROFILER, in combination with Phagotto, seems ideally suited to streamline and guide rational antigen design, adjuvant selection, and quality control of newly produced vaccines. The publicly available web server FIDEA allows experimentalists to obtain a functional interpretation of the results derived from differential expression analysis and to test their hypothesis quickly and easily. The tool performs an enrichment analysis i.e. an analysis of specific properties that are distributed in a non random fashion in the up-regulated and down-regulated genes, taken both together and separately. It has been shown to be very useful and is being heavily used from scientists all over the world, more than 1500 requests for analysis have been submitted to the server in six months. Furthermore, during the course of the PhD I implemented pipelines for the speeding up and optimization of protocols for NGS data analysis and applied them to biomedical projects. Of course not all the proteins have a complete functional annotation and consequently the issue of predicting the function of proteins with a partial or no functional annotation arises. This can be done both by exploiting the 3D structure of the protein or by inferring the function directly from the sequence. A real challenge, however, is the assessment of the accuracy of existing methods. In this context the help that critical assessment experiments can give is essential. We have had the possibility to be involved, as assessors, in the world wide experiment CASP (Critical Assessment of protein Structure Prediction). In particular, we are involved in the assessment of the residue-residue contacts in which the participant groups provide a list of predicted contacts between residues that hopefully can be used as constraints to fold the protein. We proposed and implemented new methodologies to understand which method works better and where future efforts should be focused

New encouraging developments in contact prediction: Assessment of the CASP11 results

This article provides a report on the state-of-the-art in the prediction of intra-molecular residue-residue contacts in proteins based on the assessment of the predictions submitted to the CASP11 experiment. The assessment emphasis is placed on the accuracy in predicting long-range contacts. Twenty-nine groups participated in contact prediction in CASP11. At least eight of them used the recently developed evolutionary coupling techniques, with the top group (CONSIP2) reaching precision of 27% on target proteins that could not be modeled by homology. This result indicates a breakthrough in the development of methods based on the correlated mutation approach. Successful prediction of contacts was shown to be practically helpful in modeling three-dimensional structures; in particular target T0806 was modeled exceedingly well with accuracy not yet seen for ab initio targets of this size (>250 residues

Variedades de função empreendedora sob desordens totalitárias: do Ersatz ao ideal

Communist’s collectivistic approach to social order is based upon the premise that private means of production should be abolished, and instead be managed by a centralized power representing the people as a whole. As such, it defies one of the most inherent characteristics of human condition, the innate, creative, subjective, and perennial search for a better condition in life expressed by the entrepreneurial function. Thispaper uses the Austrian School’s praxeology to show how entrepreneurs, as motors of the market system, end up being also the most relevant and widespread challengers to the socialist approach to economics. The real exercise of entrepreneurship defies the unreal socialist economic system in three basic ways: by exercising this latent entrepreneurial function in the most unfavorable conditions creating secondary markets in order to correct an official planned scarcity; by escaping the widespread statist mentality in socialist societies; and by actually exercising economic calculation in spite of the politburo calculus. The paper shows that as much as there are varieties of social order there is a on the kind of entrepreneurial function, which is impossible to eradicate from individuals. Therefore, even when totalitarian regimes take place, entrepreneurship finds ways to exist and emerges albeit of a different lacunar kind, in the shadows, supplying for consumer’s wellbeing under the limits of such societal disorder and, more importantly, bringing to light the intrinsic impossibility of the socialist economic arrangement.El enfoque colectivista comunista del orden social se basa en la premisa de que los medios privados de producción deben ser abolidos, y en su lugar, gestionados por un poder centralizado que represente al pueblo en su conjunto. Como tal, desafía una de las características más inherentes de la condición humana,la búsqueda innata, creativa, subjetiva y perenne de una mejor condición de vida expresada por la función empresarial. Este documento utiliza la praxiología de la Escuela Austriaca para mostrar cómo los empresarios, como motores del sistema de mercado, se convierten en los retadores más relevantes y extendidos del enfoque socialista de la economía. La búsqueda del emprendimiento desafía el ilusorio sistema socialista de economía de tres maneras: ejerciendo esta función empresarial latente, en las condiciones más desfavorables, creando mercados secundarios para abordar la escasez planificada del gobierno central; deshacerse de la mentalidad estatista generalizada en las sociedades socialistas; y poniendo en práctica el verdadero cálculo económico del mercado, en lugar del “cálculo” económico impuesto por el politburó. El artículo muestra que cuanto más hay variedades de orden social, todavía hay una similitud con el tipo de función empresarial, que es imposible de erradicar de los individuos. Por lo tanto, incluso cuando se producen regímenes totalitarios, el espíritu empresarial encuentra formas de existir y se manifiesta a pesar del tipo lacunar diferente, en las sombras, proporcionando bienestar al consumidor bajo los límites del desorden social y, sobre todo, iluminando la imposibilidad intrínseca del acuerdo de económia socialista.A abordagem coletivista comunista de ordem social é baseada na premissa em que meios de produção privados devem ser abolidos, e ao invés disto, serem gerenciados por um poder centralizado representando o povo como um todo. Assim sendo, ele desafia uma das mais inerentes características da condição humana, a busca inata, criativa, subjetiva e perene para uma melhor condição de vida expressa pela função empreendedora. Este trabalho usa a praxiologia da Escola Austríaca para mostrar como empreendedores, enquanto motores do sistema de mercado, acabam sendo os mais relevantes e generalizados desafiadores da abordagem socialista da economia. Exercer o empreendedorismo desafia o ilusório sistema socialista de economia de três maneiras: exercitando esta função empreendedora latente, nas mais desfavoráveis condições, criando mercados secundários para buscar corrigir a escassez planejada pelo poder central; se livrando da difundida mentalidade estatista em sociedades socialistas; e por colocar em prática o verdadeiro cálculo econômico de mercado, ao invés do “cálculo” econômico imposto pelo politburo. O artigo mostra que, quanto mais existam variedades de ordem social, há ainda uma similaridade com o tipo de função empreendedora, que é impossível erradicar dos indivíduos. Assim sendo, mesmo quando ocorrem regimes totalitários, o empreendedorismo encontra maneiras de existir e se manifesta apesar do diferente tipo lacunar, nas sombras, suprindo o bem-estar do consumidor sob os limites de desordem social e, principalmente, iluminando a impossibilidade intrínseca do arranjo econômico socialista

Mudança no modelo de negócio, percepção de valor dos clientes e seus reflexos na apropriação de valor: um estudo no setor de cartões de crédito

Este trabalho tem como objetivo principal a análise do impacto da mudança do modelo de negócio, principalmente da proposta de valor, sobre a percepção de valor dos clientes e, consequentemente, seus reflexos sobre a apropriação de valor por parte da empresa. Tem ainda como objetivos secundários, o entendimento das mudanças ocorridas no modelo de negócio e seus eventuais impactos sobre os outros elementos do modelo de negócio. O estudo foi conduzido no setor de cartões de crédito brasileiro e foi realizado por meio de três técnicas metodológicas distintas: i) entrevistas com empresas e especialistas do setor; ii) surveys on-line com clientes de uma administradora de cartões de crédito (buscando verificar a percepção de valor antes e depois da mudança do modelo de negócio); e iii) análise de dados secundários transacionais da base de clientes da administradora, também em dois momentos, antes e depois da mudança. Os resultados encontrados não só comprovaram as duas hipóteses do trabalho (a mudança do modelo de negócio impacta a percepção de valor e também a apropriação de valor), como deram uma indicação quantitativa do grau da mudança da percepção e da apropriação de valor, antes e depois da mudança do modelo de negócio. Além disso, as entrevistas realizadas trouxeram relevantes achados sobre o processo de mudança do modelo de negócio no setor de cartões de crédito, bem como os principais desafios enfrentados. Tais achados contribuem de forma significativa ao campo dos estudos em modelos de negócio e percepção de valor, como também fornecem aprendizados e implicações práticas às empresas do setor.The main objective of this work is to analyse the impact caused by business model changes, mainly regarding the value proposition, over the clients´ perceived value, and consequently, its effect upon the captured value for the company. In addition, it has the further following objectives: the understanding of business model changes, and their impacts on other business model elements. The study was conducted in the Brazilian credit card sector and was designed and developed using three different methodological techniques: i) interviews with companies and with market experts; ii) on-line surveys with clients of a credit card operator (for measuring the clients´s perceived value before and after the change); and iii) a secondary data analysis also conducted with credit card operator clients, comparing the usage patterns in two periods (before and after the change). The findings not only confirmed the two proposed research hypothesis (a business model change impacts the clients´perceived value and also the value captured by the company), but also gave a quantitative indication of the degree of impact. Apart from this, the interviews revealed relevant findings about the business model change process in the sector, as well as the main challenges faced by companies. These findings provide a significant contribution for the research field of business models and perceived value, and further reveal useful lessons and practical implications for all those involved in these areas.Coordenação de Aperfeiçoamento de Pessoal de Nível Superio

Experimental Study of Multiphase Pump Wear

The goal of this research is to better understand upstream Oil & Gas Electric Submersible Pump (ESP) reliability issues. The objective of this research is to determine how Liquid-Gas-Particulate (LGP) turbine pump wear differs from Liquid-Particulate (LP) turbine pump wear. This objective is novel because little is known about LGP wear, yet such wear is common in ESPs. To accomplish the research objective, an experimental study of a gas handling ESP was conducted. Tests of two Baker Hughes 1025 MVP G400 Severe Duty turbine pumps were conducted with water, air, and sand. One pump was tested with a Gas Volume Fraction (GVF) of 20% while the other was tested with a GVF of 0%. It was found that particulates migrate radially outward through the pump and cause diffuser sidewall wear to increase through the pump. It was also found that various impeller flow path areas experience more LGP wear than LP wear. In general, pump wear progress faster for LGP wear than for LP wear. It is believed that this is caused primarily by the thinning effect that gas can have on a fluid’s viscosity

Aiding compliance governance in service-based business processes

Assessing whether a company's business practices conform to laws and regulations and follow standards and SLAs, i.e., compliance management, is a complex and costly task. Few software tools aiding compliance management exist; yet, they typically do not address the needs of who is actually in charge of assessing and understanding compliance. We advocate the use of a compliance governance dashboard and suitable root cause analysis techniques that are specifically tailored to the needs of compliance experts and auditors. The design and implementation of these instruments are challenging for at least three reasons: (1) it is fundamental to identify the right level of abstraction for the information to be shown; (2) it is not trivial to visualize different analysis perspectives; and (3) it is difficult to manage and analyze the large amount of involved concepts, instruments, and data. This chapter shows how to address these issues, which concepts and models underlie the problem, and, eventually, how IT can effectively support compliance analysis in Service-Oriented Architectures (SOAs). © 2012, IGI Global

Information technology for active ageing: A review of theory and practice

Active Ageing aims to foster a physically, mentally and socially active lifestyle as a person ages. It is a complex, multi-faceted problem that involves a variety of different actors, such as policy makers, doctors, care givers, family members, friends and, of course, older adults. This review aims to understand the role of a new actor, which increasingly plays the role of enabler and facilitator, i.e., that of the technology provider. The review specifically focuses on Information Technology (IT), with a particular emphasis on software applications, and on how IT can prevent decline, compensate for lost capabilities, aid care, and enhance existing capabilities. The analysis confirms the crucial role of IT in Active Ageing, shows that Active Ageing requires a multidisciplinary approach, and identifies the need for better integration of hardware, software, the environment and the involved actors

Cripto promotes A–P axis specification independently of its stimulatory effect on Nodal autoinduction

The EGF-CFC gene cripto governs anterior–posterior (A–P) axis specification in the vertebrate embryo. Existing models suggest that Cripto facilitates binding of Nodal to an ActRII–activin-like kinase (ALK) 4 receptor complex. Cripto also has a crucial function in cellular transformation that is independent of Nodal and ALK4. However, how ALK4-independent Cripto pathways function in vivo has remained unclear. We have generated cripto mutants carrying the amino acid substitution F78A, which blocks the Nodal–ALK4–Smad2 signaling both in embryonic stem cells and cell-based assays. In criptoF78A/F78A mouse embryos, Nodal fails to expand its own expression domain and that of cripto, indicating that F78 is essential in vivo to stimulate Smad-dependent Nodal autoinduction. In sharp contrast to cripto-null mutants, criptoF78A/F78A embryos establish an A–P axis and initiate gastrulation movements. Our findings provide in vivo evidence that Cripto is required in the Nodal–Smad2 pathway to activate an autoinductive feedback loop, whereas it can promote A–P axis formation and initiate gastrulation movements independently of its stimulatory effect on the canonical Nodal–ALK4–Smad2 signaling pathway

A novel approach to simulate gene-environment interactions in complex diseases

Background: Complex diseases are multifactorial traits caused by both genetic and environmental factors. They represent the major part of human diseases and include those with largest prevalence and mortality (cancer, heart disease, obesity, etc.). Despite a large amount of information that has been collected about both genetic and environmental risk factors, there are few examples of studies on their interactions in epidemiological literature. One reason can be the incomplete knowledge of the power of statistical methods designed to search for risk factors and their interactions in these data sets. An improvement in this direction would lead to a better understanding and description of gene-environment interactions. To this aim, a possible strategy is to challenge the different statistical methods against data sets where the underlying phenomenon is completely known and fully controllable, for example simulated ones. Results: We present a mathematical approach that models gene-environment interactions. By this method it is possible to generate simulated populations having gene-environment interactions of any form, involving any number of genetic and environmental factors and also allowing non-linear interactions as epistasis. In particular, we implemented a simple version of this model in a Gene-Environment iNteraction Simulator (GENS), a tool designed to simulate case-control data sets where a one gene-one environment interaction influences the disease risk. The main aim has been to allow the input of population characteristics by using standard epidemiological measures and to implement constraints to make the simulator behaviour biologically meaningful. Conclusions: By the multi-logistic model implemented in GENS it is possible to simulate case-control samples of complex disease where gene-environment interactions influence the disease risk. The user has full control of the main characteristics of the simulated population and a Monte Carlo process allows random variability. A knowledge-based approach reduces the complexity of the mathematical model by using reasonable biological constraints and makes the simulation more understandable in biological terms. Simulated data sets can be used for the assessment of novel statistical methods or for the evaluation of the statistical power when designing a study