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Search Results: 1 - 10 of 21044 matches for " Valerio Costa "
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Understanding gene regulatory mechanisms by integrating ChIP-seq and RNA-seq data: statistical solutions to biological problems
Claudia Angelini,Valerio Costa
Frontiers in Cell and Developmental Biology , 2014, DOI: 10.3389/fcell.2014.00051
Abstract: The availability of omic data produced from international consortia, as well as from worldwide laboratories, is offering the possibility both to answer long-standing questions in biomedicine/molecular biology and to formulate novel hypotheses to test. However, the impact of such data is not fully exploited due to a limited availability of multi-omic data integration tools and methods. In this paper, we discuss the interplay between gene expression and epigenetic markers/transcription factors. We show how integrating ChIP-seq and RNA-seq data can help to elucidate gene regulatory mechanisms. In particular, we discuss the two following questions: i) Can transcription factor occupancies or histone modification data predict gene expression? ii) Can ChIP-seq and RNA-seq data be used to infer gene regulatory networks? We propose potential directions for statistical data integration. We discuss the importance of incorporating underestimated aspects (such as alternative splicing and long-range chromatin interactions). We also highlight the lack of data benchmarks and the need to develop tools for data integration from a statistical viewpoint, designed in the spirit of reproducible research.
Insolvency Regulations and Economic Recession: An Austro-Libertarian Point of View  [PDF]
Valerio Tavormina
Beijing Law Review (BLR) , 2014, DOI: 10.4236/blr.2014.52014
Abstract:

Economic recovery after a crisis requires above all capital to support the most efficient investments. It is therefore counterproductive to delay selling off the assets of insolvent debtors through lengthy insolvency proceedings instead of letting the creditors free to enforce their claims in the speediest way.

Contrasting Wrongs by Privates to Keep the Market Rolling  [PDF]
Valerio Tavormina
Beijing Law Review (BLR) , 2015, DOI: 10.4236/blr.2015.61009
Abstract: The market must be defended (also) against the countrymen’s offenses, minimizing the costs involved and this minimization requires as a precondition the most precise possible predetermination of the offenses. The more effective regulatory device in preventing wrongs seems the threat of sanctions in excess of the redress, entrusting the decision on their application to the injured party, who should at the same time be the only entitled to reap the benefit, without distinctions between crimes and civil wrongs. The credibility of the threat, as well as any actual restauration of the harm and the prevention of reiteration, requires accuracy, speed and effectiveness in the application of sanctions and therefore: 1) the parties should have the duty to tell the truth and the instruments for finding the facts should be strengthened; 2) the judges’ mistakes should be sanctioned as well; 3) the jurisdiction should be drawn so as to favor a rapid application of sanctions against an incontrovertible finding of the facts; 4) any form of penalties’ remission should be subject to the consent of the injured party.
Uncovering the Complexity of Transcriptomes with RNA-Seq
Valerio Costa,Claudia Angelini,Italia De Feis,Alfredo Ciccodicola
Journal of Biomedicine and Biotechnology , 2010, DOI: 10.1155/2010/853916
Abstract: In recent years, the introduction of massively parallel sequencing platforms for Next Generation Sequencing (NGS) protocols, able to simultaneously sequence hundred thousand DNA fragments, dramatically changed the landscape of the genetics studies. RNA-Seq for transcriptome studies, Chip-Seq for DNA-proteins interaction, CNV-Seq for large genome nucleotide variations are only some of the intriguing new applications supported by these innovative platforms. Among them RNA-Seq is perhaps the most complex NGS application. Expression levels of specific genes, differential splicing, allele-specific expression of transcripts can be accurately determined by RNA-Seq experiments to address many biological-related issues. All these attributes are not readily achievable from previously widespread hybridization-based or tag sequence-based approaches. However, the unprecedented level of sensitivity and the large amount of available data produced by NGS platforms provide clear advantages as well as new challenges and issues. This technology brings the great power to make several new biological observations and discoveries, it also requires a considerable effort in the development of new bioinformatics tools to deal with these massive data files. The paper aims to give a survey of the RNA-Seq methodology, particularly focusing on the challenges that this application presents both from a biological and a bioinformatics point of view.
Non-coding RNA and pseudogenes in neurodegenerative diseases: “The (un)Usual Suspects”
Valerio Costa,Roberta Esposito,Marianna Aprile,Alfredo Ciccodicola
Frontiers in Genetics , 2012, DOI: 10.3389/fgene.2012.00231
Abstract: Neurodegenerative disorders and cancer are severe diseases threatening human health. The glaring differences between neurons and cancer cells mask the processes involved in their pathogenesis. Defects in cell cycle, DNA repair, and cell differentiation can determine unlimited proliferation in cancer, or conversely, compromise neuronal plasticity, leading to cell death and neurodegeneration. Alteration in regulatory networks affecting gene expression contribute to human diseases onset, including neurodegenerative disorders, and deregulation of non-coding RNAs – particularly microRNAs (miRNAs) – is supposed to have a significant impact. Recently, competitive endogenous RNAs (ceRNAs) – acting as sponges – have been identified in cancer, indicating a new and intricate regulatory network. Given that neurodegenerative disorders and cancer share altered genes and pathways, and considering the emerging role of miRNAs in neurogenesis, we hypothesize ceRNAs may be implicated in neurodegenerative diseases. Here we propose, and computationally predict, such regulatory mechanism may be shared between the diseases. It is predictable that similar regulation occurs in other complex diseases, and further investigation is needed.
Metabolic Requirements during Six Minutes Walking Tests in Patients Affected by Chronic Obstructive Pulmonary Disease in Different Stages  [PDF]
Giuseppe Valerio, Pierluigi Bracciale, Fabio Valerio
Open Journal of Respiratory Diseases (OJRD) , 2012, DOI: 10.4236/ojrd.2012.24012
Abstract: Backgrounds: In Chronic Obstructive Pulmonary Disease (COPD) a multi factorial effort limitation becomes pro- gressively relevant as the disease progresses in the consecutive stages. It is measured by both six minutes walking test (6MWT) and maximal cardiopulmonary incremental test (CPET). Aim: It is important to assess in each stage of dis-ease the metabolic load during 6MWT referring to the outcome of CPET and to ascertain whether there is a significant rela- tionship between the measures obtained by CPET and 6MWT. Methods: Four group of fifteen patients affected by COPD in stage I to IV underwent 6MWT and maximal CPET in the same day and results were compared to a group of healthy people. Airflow obstruction was measured by whole body plethysmography, blood gases by gas analysis, maxi- mal oxygen consumption and metabolic parameters by ergometer, lactic acid levels by analyzer. Results: Maximal oxygen consumption (V’O2max) and 6MWT are progressively impaired and related (V’O2max = 1.25 ? 0.26, 1.152 ? 0.4, 1.03 ? 0.44, .85 ? 0.2 l/m; 6MWD = 452 ? 84, 446 ? 82, 381 ? 165, 200 ? 100 respectively in GOLD I to IV stage). Oxygen consumption (V’O2) during 6MWT becomes stable after 3 - 4 minutes and reached at the end of the test close to those measured at de-compensated metabolic acidosis anaerobic threshold (TDMA) (85 ± 0.4 l/m vs. 9 ? 0.4 l/m) in stage I to III, while in COPD there is no difference between V’O2max and V’O2 during 6MWT (0.85 ? 0.2 vs. 0.8 ? 0.23 l/m). 6MWT is more suitable to determine oxygen desaturation than CPET (dSaO2 ?4 ± 2% vs. ?2 ± 1%). 6MWD, the workload performed in 6MWT and V’O2max are significantly related. Conclusion: 6MWT looks as a suitable sub maximal test related CPET. Metabolic requirements under 6MWT are close to TDMA and are obtained in a suitable, self paced, usual exercise, close to everyday experience and thus related to activity daily levels. As the disease worsens the differences between V’O2 during 6MWT and V’O2max wane.
Maintenance Task Scheduling, Reaching a Twofold Objective  [PDF]
Valerio Boschian-Campaner
American Journal of Operations Research (AJOR) , 2015, DOI: 10.4236/ajor.2015.53014
Abstract: In this paper, the problem of maintenance task scheduling is tackled with a twofold objective: meeting the performance criteria of a company and taking into account some operators’ requirements. The production manager makes sure that makespan is optimised while developing operators’ flexibility. The use of skill matrixes enables him to make pairs and to develop training in order to make trainees more autonomous. Operators’ requirements are in particular related to periods of unavailability and their wishes relating to their tasks. Given the complexity of the problem, an exact solution isn’t conceivable and our research focuses on a metaheuritic method giving us a solution that is considered satisfactory. A multi-criteria analysis of the results is performed in order to reach a compromise among conflicting goals.
Grassland Height Assessment by Satellite Images  [PDF]
Alessandro Cimbelli, Valerio Vitale
Advances in Remote Sensing (ARS) , 2017, DOI: 10.4236/ars.2017.61003
Abstract:
Images collected by optical and radar satellite sensors represent a most viable solution for the extraction of biophysical parameters of the earth surface. The mid-resolution dataset acquired by Landsat and Sentinel satellites have recently become available free of charge for all users. At the same time, some software for image processing and GIS, like QGIS, R, and ImageJ, have reached a high level of maturity and a large community of users, thanks to their open source license. In this project, free satellite images and open source software have been used for the assessment of the grassland biomass. The overall goal is the enhancement of the statistics of grassland production and dried fodder for the animal breeding. Currently, the National Institute of Statistics collects this kind of dataset at the province level. The project consists in some “in situ” surveys in a specific site in central Italy and in the building of a regression model between the grassland heights and the corresponding radiometric values of the most relevant image bands.
PPARG: Gene Expression Regulation and Next-Generation Sequencing for Unsolved Issues
Valerio Costa,Maria Assunta Gallo,Francesca Letizia,Marianna Aprile,Amelia Casamassimi,Alfredo Ciccodicola
PPAR Research , 2010, DOI: 10.1155/2010/409168
Abstract: Peroxisome proliferator-activated receptor gamma (PPAR ) is one of the most extensively studied ligand-inducible transcription factors (TFs), able to modulate its transcriptional activity through conformational changes. It is of particular interest because of its pleiotropic functions: it plays a crucial role in the expression of key genes involved in adipogenesis, lipid and glucid metabolism, atherosclerosis, inflammation, and cancer. Its protein isoforms, the wide number of PPAR target genes, ligands, and coregulators contribute to determine the complexity of its function. In addition, the presence of genetic variants is likely to affect expression levels of target genes although the impact of PPARG gene variations on the expression of target genes is not fully understood. The introduction of massively parallel sequencing platforms—in the Next Generation Sequencing (NGS) era—has revolutionized the way of investigating the genetic causes of inherited diseases. In this context, DNA-Seq for identifying—within both coding and regulatory regions of PPARG gene—novel nucleotide variations and haplotypes associated to human diseases, ChIP-Seq for defining a PPAR binding map, and RNA-Seq for unraveling the wide and intricate gene pathways regulated by PPARG, represent incredible steps toward the understanding of PPAR in health and disease. 1. Introduction Gene transcription requires an elaborate network of intra- and extracellular signals, such as hormones, xenobiotics, micro- and macronutrients (lipid metabolites, vitamins, ions, etc.) and drugs, that converge to the nucleus following different pathways, resulting in the expression of each gene in each tissue. It is a current assumption that transcription is mostly shaped by environmental factors, acting both via direct and indirect mechanisms. Translating exogenous and endogenous signals which affect gene transcription, into a cellular physiological response requires the coordinated action and the fine tuning of transcription factors (TFs) acting at DNA level, including those belonging to the nuclear receptor (NR) superfamily [1, 2]. The human NR superfamily comprises 48 ligand-inducible transcription factors that respond to a variety of stimuli and are able to modulate their transcriptional activity through conformational changes [3]. The most extensively studied members of this TF superfamily are the Peroxisome proliferator-activated receptors (PPARs, also known as nuclear receptor family 1C, NR1C). Crystallographic studies have shown that all NRs superfamily members, and among them PPARs, share common
How initial and boundary conditions affect protoplanetary migration in a turbulent sub-Keplerian accretion disc: 2D non viscous SPH simulations
Vincenzo Costa,Valerio Pirronello,Gaetano Belvedere,Antonino Del Popolo,Diego Molteni,Giuseppe Lanzafame
Physics , 2009, DOI: 10.1111/j.1365-2966.2009.15815.x
Abstract: Current theories on planetary formation establish that giant planet formation should be contextual to their quick migration towards the central star due to the protoplanets-disc interactions on a timescale of the order of $10^5$ years, for objects of nearly 10 terrestrial masses. Such a timescale should be smaller by an order of magnitude than that of gas accretion onto the protoplanet during the hierarchical growing-up of protoplanets by collisions with other minor objects. These arguments have recently been analysed using N-body and/or fluid-dynamics codes or a mixing of them. In this work, inviscid 2D simulations are performed, using the SPH method, to study the migration of one protoplanet, to evaluate the effectiveness of the accretion disc in the protoplanet dragging towards the central star, as a function of the mass of the planet itself, of disc tangential kinematics. To this purpose, the SPH scheme is considered suitable to study the roles of turbulence, kinematic and boundary conditions, due to its intrinsic advective turbulence, especially in 2D and in 3D codes. Simulations are performed both in disc sub-Keplerian and in Keplerian kinematic conditions as a parameter study of protoplanetary migration if moderate and consistent deviations from Keplerian Kinematics occur. Our results show migration times of a few orbital periods for Earth-like planets in sub-Keplerian conditions, while for Jupiter-like planets estimates give that about $10^4$ orbital periods are needed to half the orbital size. Timescales of planet migration are strongly dependent on the relative position of the planet with respect to the shock region near the centrifugal barrier of the disc flow.
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