Generalized Fluctuation-Dissipation Relation and Effective Temperature upon Heating a Deeply Supercooled Liquid

We show that a generalized fluctuation-dissipation relation applies upon instantaneously increasing the temperature of a deeply supercooled liquid. This has the same two-step shape of the relation found upon cooling the liquid, but with opposite violation, indicating an effective temperature that is lower than bath temperature. We show that the effective temperature exhibits some sensible time-dependence and that it retains its connection with the partitioned phase space visited in ageing. We underline the potential relevance of our numerical results for experimental studies of the fluctuation-dissipation relation in glassy systems.Comment: 5 pages, 4 figure

Genome-wide identification of coding and non-coding conserved sequence tags in human and mouse genomes

<p>Abstract</p> <p>Background</p> <p>The accurate detection of genes and the identification of functional regions is still an open issue in the annotation of genomic sequences. This problem affects new genomes but also those of very well studied organisms such as human and mouse where, despite the great efforts, the inventory of genes and regulatory regions is far from complete. Comparative genomics is an effective approach to address this problem. Unfortunately it is limited by the computational requirements needed to perform genome-wide comparisons and by the problem of discriminating between conserved coding and non-coding sequences. This discrimination is often based (thus dependent) on the availability of annotated proteins.</p> <p>Results</p> <p>In this paper we present the results of a comprehensive comparison of human and mouse genomes performed with a new high throughput grid-based system which allows the rapid detection of conserved sequences and accurate assessment of their coding potential. By detecting clusters of coding conserved sequences the system is also suitable to accurately identify potential gene loci.</p> <p>Following this analysis we created a collection of human-mouse conserved sequence tags and carefully compared our results to reliable annotations in order to benchmark the reliability of our classifications. Strikingly we were able to detect several potential gene loci supported by EST sequences but not corresponding to as yet annotated genes.</p> <p>Conclusion</p> <p>Here we present a new system which allows comprehensive comparison of genomes to detect conserved coding and non-coding sequences and the identification of potential gene loci. Our system does not require the availability of any annotated sequence thus is suitable for the analysis of new or poorly annotated genomes.</p

Gene analogue finder: a GRID solution for finding functionally analogous gene products

<p>Abstract</p> <p>Background</p> <p>To date more than 2,1 million gene products from more than 100000 different species have been described specifying their function, the processes they are involved in and their cellular localization using a very well defined and structured vocabulary, the gene ontology (GO). Such vast, well defined knowledge opens the possibility of compare gene products at the level of functionality, finding gene products which have a similar function or are involved in similar biological processes without relying on the conventional sequence similarity approach. Comparisons within such a large space of knowledge are highly data and computing intensive. For this reason this project was based upon the use of the computational GRID, a technology offering large computing and storage resources.</p> <p>Results</p> <p>We have developed a tool, G<b>EN</b>e Analo<b>G</b>ue F<b>IN</b>d<b>E</b>r (ENGINE) that parallelizes the search process and distributes the calculation and data over the computational GRID, splitting the process into many sub-processes and joining the calculation and the data on the same machine and therefore completing the whole search in about 3 days instead of occupying one single machine for more than 5 CPU years. The results of the functional comparison contain potential functional analogues for more than 79000 gene products from the most important species. 46% of the analyzed gene products are well enough described for such an analysis to individuate functional analogues, such as well-known members of the same gene family, or gene products with similar functions which would never have been associated by standard methods.</p> <p>Conclusion</p> <p>ENGINE has produced a list of potential functionally analogous relations between gene products within and between species using, in place of the sequence, the gene description of the GO, thus demonstrating the potential of the GO. However, the current limiting factor is the quality of the associations of many gene products from non-model organisms that often have electronic associations, since experimental information is missing. With future improvements of the GO, this limit will be reduced. ENGINE will manifest its power when it is applied to the whole GODB of more than 2,1 million gene products from more than 100000 organisms. The data produced by this search is planed to be available as a supplement to the GO database as soon as we are able to provide regular updates.</p

Loss of Renal Function After Retrograde Ureteral Placement of an Allium Stent for Severe Ureteral Stricture

Background: Ureteral strictures are a recurrent chronic condition that leads to severe side effects and poor quality of life. Management of ureteral stricture is a great challenge for urologists and no specific guidelines exist. Retrograde Allium®ureteral stent (AUS) is a newly developed ureteral stent to treat either bulbar urethral or ureteral stenosis. Case Presentation: We describe a case of a 74-year-old Caucasian adult male presenting with a severe ureteral stricture secondary to an ureteroscopy for stone disease. Treatment with retrograde AUS placement produced a complete loss of renal function after 36 months, probably because of the development of a long achalasic stretch of the ureter. Conclusions: AUS is a new and promising device for the treatment of ureteral stenosis. However, a lack of standardization of the technique recommends a close instrumental follow-up after the procedure to decide the optimal time for stent removal

Enhanced LDL oxidation in uremic patients: An additional mechanism for accelerated atherosclerosis?

Enhanced LDL oxidation in uremic patients: An additional mechanism for accelerated atherosclerosis? Since oxidized low-density lipoprotein (LDL) is more atherogenic than native LDL, LDL oxidation was investigated in uremic patients who often develop accelerated atherogenesis. Three groups of uremic patients were studied (10 on predialysis conservative therapy, 11 on repetitive hemodialysis, 13 on peritoneal dialysis) and compared with seventy matched controls. LDL oxidation was evaluated in all patients as: (i) the susceptibility to in vitro oxidation (by measuring the resistence to Cu++-induced formation of conjugated dienes), (ii) vitamin E concentration in LDL, and (iii) presence of plasma anti-oxidized LDL antibodies, expressed as the ratio anti-oxLDL/anti-nativeLDL antibodies. The lipid profile was studied in all patients. Vitamin E concentration did not differ between the various groups, although LDL from uremic patients appeared more susceptible to in vitro and in vivo oxidation (as demonstrated by an earlier generation of conjugated dienes and by the presence of an higher antibody ratio) compared to control subjects. Subclass analysis of the different patients revealed that peritoneal dialysis treatment ameliorated the oxidation markers. However, a prolonged dialytic treatment caused a decrease in vitamin E concentration in LDL and increased their susceptibility to oxidation

Cross-talk between microRNAs, long non-coding RNAs and p21Cip1 in glioma: diagnostic, prognostic and therapeutic roles

Glioblastoma multiforme is considered one of the most common malignant primary intracranial tumors. Despite treatment with a combination of surgery, chemotherapy and radiotherapy, patients with glioblastoma multiform have poor prognosis. It has been widely accepted that the occurrence, progression, and even recurrence of glioblastoma multiforme strictly depends on the presence of glioma cancer stem cells. The presence of glioma stem cells reduces the efficacy of standard therapies, thus increasing the imperative to identify new targets and therapeutic strategies in glioblastoma patients. In this regard, the p21Cip1 pathway has been found to play an important role in the maintenance of the glioma stem cells. It has been shown that this pathway regulates cancer stem cell pool by preventing hyperproliferation and exhaustion. MicroRNAs, endogenous small non-coding RNAs, and long non-coding RNAs, regulate post-transcription gene expression. These are not only altered in glioma, but also in other cancer types, and are involved in tumor development and progression. Notably, they have also been shown to modulate the expression of proteins in the p21Cip1 signaling pathway. This review highlights the extent and complexity of cross-talk between microRNAs, long non-coding RNAs and the p21Cip1 pathway, and demonstrates how such interplay orchestrates the regulation of protein expression and functions in glioma and glioma stem cells

The GENIUS Grid Portal and robot certificates: a new tool for e-Science

<p>Abstract</p> <p>Background</p> <p>Grid technology is the computing model which allows users to share a wide <it>pletora </it>of distributed computational resources regardless of their geographical location. Up to now, the high security policy requested in order to access distributed computing resources has been a rather big limiting factor when trying to broaden the usage of Grids into a wide community of users. Grid security is indeed based on the Public Key Infrastructure (PKI) of X.509 certificates and the procedure to get and manage those certificates is unfortunately not straightforward. A first step to make Grids more appealing for new users has recently been achieved with the adoption of robot certificates.</p> <p>Methods</p> <p>Robot certificates have recently been introduced to perform automated tasks on Grids on behalf of users. They are extremely useful for instance to automate grid service monitoring, data processing production, distributed data collection systems. Basically these certificates can be used to identify a person responsible for an unattended service or process acting as client and/or server. Robot certificates can be installed on a smart card and used behind a portal by everyone interested in running the related applications in a Grid environment using a user-friendly graphic interface. In this work, the GENIUS Grid Portal, powered by EnginFrame, has been extended in order to support the new authentication based on the adoption of these robot certificates.</p> <p>Results</p> <p>The work carried out and reported in this manuscript is particularly relevant for all users who are not familiar with personal digital certificates and the technical aspects of the Grid Security Infrastructure (GSI). The valuable benefits introduced by robot certificates in e-Science can so be extended to users belonging to several scientific domains, providing an asset in raising Grid awareness to a wide number of potential users.</p> <p>Conclusion</p> <p>The adoption of Grid portals extended with robot certificates, can really contribute to creating transparent access to computational resources of Grid Infrastructures, enhancing the spread of this new paradigm in researchers' working life to address new global scientific challenges. The evaluated solution can of course be extended to other portals, applications and scientific communities.</p

TTV and other anelloviruses: The astonishingly wide spread of a viral infection

The broad family of viruses known as anelloviruses (AV) infects both humans and numerous animal species. They have a tiny, covalently closed single-stranded DNA genome and the astonishing capacity to infect a very high percentage of healthy and ill people with chronic infections that could last a lifetime. AV, and particularly the prototype Torquetenovirus, have established a successful interaction with the host's immune system and the rate at which they replicate is a gauge to measure overall immune function, even though many aspects of their life cycle and pathogenesis are still poorly understood