The genetic history of Italians: new-insights from uniparentally-inherited markers

Genetic differences among human groups can be ascribed both to the broad-scale extents of pre-historical and historical migrations and to the fine-scale impacts of socio-cultural and geographic heterogeneity. In this thesis, the genetic information provided by uniparental markers were exploited to address different aspects of the Italian population history, by combining macro- and micro-geographic investigations at different spatial and temporal scales. To firstly assess the overall Italian variability, Y-chromosome and mtDNA markers were deeply typed in ~900 individuals from continental Italy, Sicily and Sardinia. Sex-biased patterns and contrasting demographic histories were observed for males and females. Differential European and Mediterranean contributions were invoked to explain the paternal genetic sub-structure observed in peninsular Italy, compared to the homogeneous maternal genetic landscape. If Neolithic showed to be one principal determinant of the detected paternal structure, local insights into specific Italian regional contexts highlighted the importance of Post-Neolithic contributions. Among them, migrations from the Balkans (particularly Greece) during late Metal Ages, played a relevant role in the cultural and genetic transitions occurred in Sicily and Southern Italy. On a finer geographic and temporal perspective, the more recent layers of Italian genetic history and some aspects of the gene-culture interaction were assessed by exploring the genetic variability within two “marginal populations”: Arbereshe of Southern Italy and Partecipanza in Northern Italy. The Arbereshe are Albanian-speaking communities settled in Sicily and Calabria since the end of Middle Ages. Despite sharing common genetic and cultural backgrounds, these groups revealed diverging micro-evolutionary histories, implying different founding events and different patterns of cultural isolation and local admixture. Partecipanza is an idiosyncratic institution of Medieval origin aimed at sharing and devolving collective lands. This case-study exemplified that socio-economic stratification within the same population may induce sex-biased genetic structuring and the maintenance of otherwise hidden historical genetic traces

Point Normal Orientation and Surface Reconstruction by Incorporating Isovalue Constraints to Poisson Equation

Oriented normals are common pre-requisites for many geometric algorithms based on point clouds, such as Poisson surface reconstruction. However, it is not trivial to obtain a consistent orientation. In this work, we bridge orientation and reconstruction in implicit space and propose a novel approach to orient point clouds by incorporating isovalue constraints to the Poisson equation. Feeding a well-oriented point cloud into a reconstruction approach, the indicator function values of the sample points should be close to the isovalue. Based on this observation and the Poisson equation, we propose an optimization formulation that combines isovalue constraints with local consistency requirements for normals. We optimize normals and implicit functions simultaneously and solve for a globally consistent orientation. Owing to the sparsity of the linear system, an average laptop can be used to run our method within reasonable time. Experiments show that our method can achieve high performance in non-uniform and noisy data and manage varying sampling densities, artifacts, multiple connected components, and nested surfaces

Optimal Centers’ Allocation in Smoothing or Interpolating with Radial Basis Functions

This work was supported by FEDER/Junta de Andalucía-Consejería de Transformación Económica, Industria, Conocimiento y Universidades (Research Project A-FQM-76-UGR20, University of Granada) and by the Junta de Andalucía (Research Group FQM191).Function interpolation and approximation are classical problems of vital importance in many science/engineering areas and communities. In this paper, we propose a powerful methodology for the optimal placement of centers, when approximating or interpolating a curve or surface to a data set, using a base of functions of radial type. In fact, we chose a radial basis function under tension (RBFT), depending on a positive parameter, that also provides a convenient way to control the behavior of the corresponding interpolation or approximation method. We, therefore, propose a new technique, based on multi-objective genetic algorithms, to optimize both the number of centers of the base of radial functions and their optimal placement. To achieve this goal, we use a methodology based on an appropriate modification of a non-dominated genetic classification algorithm (of type NSGA-II). In our approach, the additional goal of maintaining the number of centers as small as possible was also taken into consideration. The good behavior and efficiency of the algorithm presented were tested using different experimental results, at least for functions of one independent variable.Junta de Andalucía-Consejería de Transformación Econímica, Industria, Conocimiento y Universidades A-FQM-76-UGR20Universidad de GranadaEuropean Regional Development FundJunta de Andalucía FQM19

A comparison of hole-filling methods in 3D

This paper presents a review of the most relevant current techniques that deal with hole-filling in 3D models. Contrary to earlier reports, which approach mesh repairing in a sparse and global manner, the objective of this review is twofold. First, a specific and comprehensive review of hole-filling techniques (as a relevant part in the field of mesh repairing) is carried out. We present a brief summary of each technique with attention paid to its algorithmic essence, main contributions and limitations. Second, a solid comparison between 34 methods is established. To do this, we define 19 possible meaningful features and properties that can be found in a generic hole-filling process. Then, we use these features to assess the virtues and deficiencies of the method and to build comparative tables. The purpose of this review is to make a comparative hole-filling state-of-the-art available to researchers, showing pros and cons in a common framework.• Ministerio de Economía y Competitividad: Proyecto DPI2013-43344-R (I+D+i) • Gobierno de Castilla-La Mancha: Proyecto PEII-2014-017-PpeerReviewe

3D Mesh Simplification. A survey of algorithms and CAD model simplification tests

Simplification of highly detailed CAD models is an important step when CAD models are visualized or by other means utilized in augmented reality applications. Without simplification, CAD models may cause severe processing and storage is- sues especially in mobile devices. In addition, simplified models may have other advantages like better visual clarity or improved reliability when used for visual pose tracking. The geometry of CAD models is invariably presented in form of a 3D mesh. In this paper, we survey mesh simplification algorithms in general and focus especially to algorithms that can be used to simplify CAD models. We test some commonly known algorithms with real world CAD data and characterize some new CAD related simplification algorithms that have not been surveyed in previous mesh simplification reviews.Siirretty Doriast

Exploitation of Ebola Virus VP35 Protein to identify new drugs counteracting its type I IFN antagonism

Ebolaviruses (EBOVs) are among the most virulent and deadly pathogens ever known, causing fulminant haemorrhagic fevers in humans and non-human primates. The 2014 outbreak of Ebola virus disease (EVD) in West Africa has claimed more lives than all previous EVD outbreaks combined. The EBOV high mortality rates have been related to the virus-induced impairment of the host innate immunity reaction due to two virus-coded proteins, VP24 and VP35. EBOV VP35 is a multifunctional protein, it is essential for viral replication as a component of the viral RNA polymerase and it also participates in nucleocapsid assembly. Early during EBOV infection, alpha-beta interferon (IFN-α/β) production would be triggered upon recognition of viral dsRNA products by cytoplasmic retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs). However, this recognition is efficiently prevented by the double-stranded RNA (dsRNA) binding activity of the EBOV VP35 protein, which hides RLRs binding sites on the dsRNA phosphate backbone as well the 5’-triphosphate (5’-ppp) dsRNA ends to RIG-I recognition. In addition to dsRNA binding and sequestration, EBOV VP35 inhibits IFN-α/β production preventing the activation of the IFN regulatory factor 3 (IRF-3) by direct interaction with cellular proteins. Previous studies demonstrated that single amino acid changes in the VP35 dsRNA binding domain reduce EBOV virulence, indicating that VP35 is an attractive target for antiviral drugs development. Within this context, here we report the establishment of a novel method to characterize the EBOV VP35 inhibitory function of the dsRNA-dependent RIG-I-mediated IFN-β signaling pathway in a BLS2 cell culture setting. In such system, a plasmid containing the promoter region of IFN-β gene linked with a luciferase reporter gene was transfected, together with a EBOV VP35 mammalian expression plasmid, into the IFN-sensitive A549 cell line, and the IFN-induction was stimulated through dsRNA transfection. Through alanine scanning mutational studies with biochemical, cellular and computational methods we highlighted the importance of some VP35 residues involved in dsRNA end-capping binding, such as R312, K282 and R322, that may serve as target for the development of small-molecule inhibitors against EBOV. Furthermore, we identified a synthetic compound that increased IFN-induction only under antiviral response stimulation and subverted VP35 inhibition, proving to be very attractive for the development of an antiviral drug. In conclusion, our results provide the establishment of a new assay as a straightforward tool for the screening of antiviral compounds that target i) dsRNA-VP35 or cellular protein-VP35 interaction and ii) dsRNA-dependent RIG-I-mediated IFN signaling pathway, in order to potentiate the IFN response against VP35 inhibition, setting the bases for further drug development

Sustainable Agriculture for Climate Change Adaptation

© 2020 by the authors. This is an open access work distributed under the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.As we lie firmly entrenched within what many have termed the Anthropocene, the time of humans, human influence on the functioning of the planet has never been greater or in greater need of mitigation. Climate change, the accelerated warming of the planet’s surface attributed to human activities, is now at the forefront of global politics. The 21st United Nations Climate Change Conference of the Parties (COP21) Paris Agreement saw a landmark agreement reached between countries belonging to the United Nations Framework Convention on Climate Change (UNFCCC). The agreement seeks to arrest climate change and maintain the global temperature rise below a 2 ◦C increase compared to pre-industrial levels, and to devise means and ways to adapt to its effects. The agriculture sector not only contributes to climate change but, as a land-based industry, is also greatly affected by climate change. This publication is a collection of carefully selected papers addressing multiple climate related issues from across the five continents, providing a truly global perspective