The Sicilian Grid Infrastructure for High Performance Computing

The conjugation of High Performance Computing (HPC) and Grid paradigm with applications based on commercial software is one among the major challenges of today e-Infrastructures. Several research communities from either industry or academia need to run high parallel applications based on licensed software over hundreds of CPU cores; a satisfactory fulfillment of such requests is one of the keys for the penetration of this computing paradigm into the industry world and sustainability of Grid infrastructures. This problem has been tackled in the context of the PI2S2 project that created a regional e-Infrastructure in Sicily, the first in Italy over a regional area. Present article will describe the features added in order to integrate an HPC facility into the PI2S2 Grid infrastructure, the adoption of the InifiniBand low-latency net connection, the gLite middleware extended to support MPI/MPI2 jobs, the newly developed license server and the specific scheduling policy adopted. Moreover, it will show the results of some relevant use cases belonging to Computer Fluid-Dynamics (Fluent, OpenFOAM), Chemistry (GAMESS), Astro-Physics (Flash) and Bio-Informatics (ClustalW))

The Sicilian Grid Infrastructure for High Performance Computing

The conjugation of High Performance Computing (HPC) and Grid paradigm with applications based on commercial software is one among the major challenges of today e-Infrastructures. Several research communities from either industry or academia need to run high parallel applications based on licensed software over hundreds of CPU cores; a satisfactory fulfillment of such requests is one of the keys for the penetration of this computing paradigm into the industry world and sustainability of Grid infrastructures. This problem has been tackled in the context of the PI2S2 project that created a regional e-Infrastructure in Sicily, the first in Italy over a regional area. Present paper will describe the features added in order to integrate an HPC facility into the PI2S2 Grid infrastructure, the adoption of the InifiniBand low-latency net connection, the gLite middleware extended to support MPI/MPI2 jobs, the newly developed license server and the specific scheduling policy adopted. Moreover, it will show the results of some relevant use cases belonging to Computer Fluid-Dynamics (Fluent, OpenFOAM), Chemistry (GAMESS), Astro-Physics (Flash) and Bio-Informatics (ClustalW))

Che-1 sustains hypoxic response of colorectal cancer cells by affecting Hif-1α stabilization

BACKGROUND: Solid tumours are less oxygenated than normal tissues. Consequently, cancer cells acquire to be adapted to a hypoxic environment. The poor oxygenation of solid tumours is also a major indicator of an adverse cancer prognosis and leads to resistance to conventional anticancer treatments. We previously showed the involvement of Che-1/AATF (Che-1) in cancer cell survival under stress conditions. Herein we hypothesized that Che-1 plays a role in the response of cancer cells to hypoxia. METHODS: The human colon adenocarcinoma HCT116 and HT29 cell lines undepleted or depleted for Che-1 expression by siRNA, were treated under normoxic and hypoxic conditions to perform studies regarding the role of this protein in metabolic adaptation and cell proliferation. Che-1 expression was detected using western blot assays; cell metabolism was assessed by NMR spectroscopy and functional assays. Additional molecular studies were performed by RNA seq, qRT-PCR and ChIP analyses. RESULTS: Here we report that Che-1 expression is required for the adaptation of cells to hypoxia, playing an important role in metabolic modulation. Indeed, Che-1 depletion impacted on HIF-1α stabilization, thus downregulating the expression of several genes involved in the response to hypoxia and affecting glucose metabolism. CONCLUSIONS: We show that Che-1 a novel player in the regulation of HIF-1α in response to hypoxia. Notably, we found that Che-1 is required for SIAH-2 expression, a member of E3 ubiquitin ligase family that is involved in the degradation of the hydroxylase PHD3, the master regulator of HIF-1α stability. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13046-017-0497-1) contains supplementary material, which is available to authorized users

A deep learning approach for automatic video coding of deictic gestures in children with autism

Autism is a heterogeneous neurodevelopmental condition characterized by impairments in social communication, along with restrictive and repetitive patterns of interests and behaviors and sensory atypicalities. Early impairments in gestural communication, especially in deictic gestures, are significantly associated with autism and strong predictors of language development. Despite the implication of deictic gestures in autism has been acknowledged, it has not been sufficiently explored by artificial intelligence. To address this, the paper proposes an automatic digital coding approach based on deep learning models. By using a transformer architecture, a multi-frame modeling strategy has been implemented and applied on 37 video clips of naturalistic mother-child interactions with the aim to recognize four main deictic gestures: pointing, giving, showing and requesting. The system was trained and validated on 31 clips, internally tested on 6 clips and externally tested on 5 extra clips, using Python. Preprocessing phase involves using a 1024 feature extractor based on Densenet pretrained on Imagenet. Preliminary results showed respectively 100% of accuracy for training set, 80% for validation set and 67% for internal testing set. These findings suggest that the proposed system is a very promising approach for the automatic analysis of deictic gestures. In future work, we plan to validate our model on a larger number of samples to achieve higher and more reliable performances

Che-1/AATF-induced transcriptionally active chromatin promotes cell proliferation in multiple myeloma

Multiple myeloma (MM) is a hematologic malignancy produced by a clonal expansion of plasma cells and characterized by abnormal production and secretion of monoclonal antibodies. This pathology exhibits an enormous heterogeneity resulting not only from genetic alterations but also from several epigenetic dysregulations. Here we provide evidence that Che-1/AATF (Che-1), an interactor of RNA polymerase II, promotes MM proliferation by affecting chromatin structure and sustaining global gene expression. We found that Che-1 depletion leads to a reduction of "active chromatin" by inducing a global decrease of histone acetylation. In this context, Che-1 directly interacts with histones and displaces histone deacetylase class I members from them. Strikingly, transgenic mice expressing human Che-1 in plasma cells develop MM with clinical features resembling those observed in the human disease. Finally, Che-1 downregulation decreases BRD4 chromatin accumulation to further sensitize MM cells to bromodomain and external domain inhibitors. These findings identify Che-1 as a promising target for MM therapy, alone or in combination with bromodomain and external domain inhibitors

Additional file 1: Figure S1. of Che-1 sustains hypoxic response of colorectal cancer cells by affecting Hif-1Îą stabilization

Che-1 is involved in the metabolic switch in response to hypoxia. A- and B- HT29 (A) and A549 (B) cells were transiently transfected with stealth siRNA negative control (siControl) or siRNA Che-1 (siChe-1) and exposed to hypoxia for 16 h where indicated and pH was measured. C- and D- Score plots indicating metabolic differences between hypoxic and normoxic samples from HT29 (C) and A549 (D) cells transiently transfected as in A. E- HT29 cells were transfected as in A and the medium lactate content was evaluated. (TIF 5841 kb

Additional file 2: Figure S2. of Che-1 sustains hypoxic response of colorectal cancer cells by affecting Hif-1α stabilization

Che-1 regulates genes transcription in response to hypoxia. A- Quantitative RT–PCR (qRT–PCR) for metabolic genes expression was performed in HT29 cells transiently transfected with Stealth siRNA negative control (siControl) or siRNA Che-1 (siChe-1) and exposed to hypoxia for 4 h. Values were normalized to RPL19 mRNA expression. Error bars represent the standard error of three different experiments. *P = 0,0010, **P ≤ 0,0003, ***P ≤ 0,004, n.s., not significant. (TIF 1835 kb