Molecular Perception for Visualization and Computation: The Proxima Library

Proxima is a molecular perception library designed with a double purpose: To be used with immersive molecular viewers (thus providing any required feature not supported by third party libraries) and to be integrated in workflow managers thus providing the functionalities needed for the first steps of molecular modeling studies. It thus stands at the boundary between visualization and computation. The purpose of the present article is to provide a general introduction to the first release of Proxima, describe its most significant features, and highlight its performance by means of some case studies. The current version of Proxima is available for evaluation purposes at https://bitbucket.org/sns-smartlab/proxima/src/master/

Virtual Reality bridge between Chemistry and Cultural Heritage: the "Sala degli Stemmi" Case Study

In this contribution, we present a multiscale and multidisciplinary VR architecture that aims at creating a common environment where cultural heritage and chemistry meet in order to strengthen the role already played by chemistry in the process of restoration of cultural goods. Our aim is to create a user friendly platform where experts of both fields can share data and ideas in a direct way, in order to achieve deeper insights into cultural goods combining the scientific and historical points of view. As a case study we present the 3D reconstruction of the "Sala degli Stemmi", which is one of the two historical rooms at Palazzo della Carovana in Pisa, presenting a number of artworks that underwent a process of chemical analysis and restoration in 2012. The whole architecture has been developed using the Unity game engine, and it is usable with HTC Vive headsets. The implementation of the VR environment and the potential applications, from both the scientific and educational points of view, are discussed in some detail

Dissipation instability of Couette-like adiabatic flows in a plane channel

The mixed convection flow in a plane channel with adiabatic boundaries is examined. The boundaries have an externally prescribed relative velocity defining a Couette-like setup for the flow. A stationary flow regime is maintained with a constant velocity difference between the boundaries, considered as thermally insulated. The effect of viscous dissipation induces a heat source in the flow domain and, hence, a temperature gradient. The nonuniform temperature distribution causes, in turn, a buoyancy force and a combined forced and free flow regime. Dual mixed convection flows occur for a given velocity difference. Their structure is analysed where, in general, only one branch of the dual flows is compatible with the Oberbeck-Boussinesq approximation, for realistic values of the Gebhart number. A linear stability analysis of the basic stationary flows with viscous dissipation is carried out. The stability eigenvalue problem is solved numerically, leading to the determination of the neutral stability curves and the critical values of the P\'eclet number, for different Gebhart numbers. An analytical asymptotic solution in the special case of perturbations with infinite wavelength is also developed.Comment: 24 pages, 11 figure

Early embryonic development, assisted reproductive technologies, and pluripotent stem cell biology in domestic mammals

Over many decades assisted reproductive technologies, including artificial insemination, embryo transfer, in vitro production (IVP) of embryos, cloning by somatic cell nuclear transfer (SCNT), and stem cell culture, have been developed with the aim of refining breeding strategies for improved production and health in animal husbandry. More recently, biomedical applications of these technologies, in particular, SCNT and stem cell culture, have been pursued in domestic mammals in order to create models for human disease and therapy. The following review focuses on presenting important aspects of pre-implantation development in cattle, pigs, horses, and dogs. Biological aspects and impact of assisted reproductive technologies including IVP, SCNT, and culture of pluripotent stem cells are also addressed. © 2013 Elsevier Ltd

DJ-1: A promising therapeutic candidate for ischemia-reperfusion injury.

DJ-1 is a multifaceted protein with pleiotropic functions that has been implicated in multiple diseases, ranging from neurodegeneration to cancer and ischemia-reperfusion injury. Ischemia is a complex pathological state arising when tissues and organs do not receive adequate levels of oxygen and nutrients. When the blood flow is restored, significant damage occurs over and above that of ischemia alone and is termed ischemia-reperfusion injury. Despite great efforts in the scientific community to ameliorate this pathology, its complex nature has rendered it challenging to obtain satisfactory treatments that translate to the clinic. In this review, we will describe the recent findings on the participation of the protein DJ-1 in the pathophysiology of ischemia-reperfusion injury, firstly introducing the features and functions of DJ-1 and, successively highlighting the therapeutic potential of the protein

Early germline differentiation in bivalves: TDRD7 as a candidate investigational unit for Ruditapes philippinarum germ granule assembly

The germline is a key feature of sexual animals and the ways in which it separates from the soma differ widely across Metazoa. However, at least at some point during germline differentiation, some cytoplasmic supramolecular structures (collectively called germ plasm-related structures) are present and involved in its specification and/or differentiation. The factors involved in the assembly of these granular structures are various and non-ubiquitous among animals, even if some functional patterns and the presence of certain domains appear to be shared among some. For instance, the LOTUS domain is shared by Oskar, the Holometabola germ plasm master regulator, and some Tudor-family proteins assessed as being involved in the proper assembly of germ granules of different animals. Here, we looked for the presence of LOTUS-containing proteins in the transcriptome of Ruditapes philippinarum (Bivalvia). Such species is of particular interest because it displays annual renewal of gonads, sided by the renewal of germline differentiation pathways. Moreover, previous works have identified in its early germ cells cytoplasmic granules containing germline determinants. We selected the orthologue of TDRD7 as a candidate involved in the early steps of germline differentiation through bioinformatic predictions and immunohistological patterning (immunohistochemistry and immunofluorescence). We observed the expression of the protein in putative precursors of germline cells, upstream to the germline marker Vasa. This, added to the fact that orthologues of this protein are involved in the assembly of germ granules in mouse, zebrafish, and fly, makes it a worthy study unit for investigations on the formation of such structures in bivalves