APENet: LQCD clusters à la APE Ammendola, R.; Guagnelli, M.; Mazza, G. ...
Nuclear physics. B, Proceedings supplement/Nuclear physics. B, Proceedings supplements,
03/2005, Volume:
140
Journal Article
Open access
Developed by the APE group, APENet is a new high speed, low latency, 3-dimensional interconnect architecture optimized for PC clusters running LQCD-like numerical applications. The hardware ...implementation is based on a single PCI-X 133MHz network interface card hosting six independent bi-directional channels with a peak bandwidth of 676 MB/s each direction. We discuss preliminary benchmark results showing exciting performances similar or better than those found in high-end commercial network systems.
We have isolated a rat cDNA, named FE65, hybridizing to an mRNA of about 2,300 nucleotides present in rat brain, undetectable in rat liver and very poorly represented in other tissues. An mRNA of the ...same size is present in human neuroblastoma cells and is absent from other human cell lines. The FE65 cDNA contains an open reading frame (ORF) coding for a polypeptide of 499 amino acids in which 143 residues can be aligned with the DNA binding domain of the integrases encoded by mammalian immunodeficiency viruses. The remaining part of the FE65 ORF is not homologous with the correspondent regions of the integrases; the first 206 residues of the FE65 ORF show numerous negative charges and a short sequence not dispensable for the function of the transactivating acidic domain of the jun family transcriptional factors. A plasmid which expresses FE65 amino acids 1-232 fused to the yeast GAL4 DNA binding domain was co-transfected with a plasmid containing five GAL4 binding sites upstream of a minimal Adenovirus promoter controlling the expression of the CAT gene. This experiment showed that the fused protein GAL4-FE65 is able to obtain a 30-40 fold increase of the CAT gene expression compared to the expression observed in the presence of the GAL4 DNA binding domain alone. Two types of FE65 mRNA are present in rat brain, differing only for six nucleotides. We demonstrate that this is the consequence of a neuron-specific alternative splicing of a six-nucleotide miniexon, which is also present in the human genome, in an intron/exon context very similar to that of the rat FE65 gene.
Intracellular redox conditions influence the activity of several transcription factors leading to a modulation of the expression of the genes controlled by these factors. We examined the changes in ...cell transcription patterns after oxidative stress induced by diethylmaleate (DEM). Using the differential display technique we identified several differentially expressed sequence tags, four of which are identical or highly homologous to sequences contained in the human cDNAs encoding vimentin,
c-fos, cytochrome oxidase IV and ribosomal protein L4; another one corresponds to a transcript of the mitochondrial genome of unknown function. The remaining five cDNAs are not recorded in any sequence data bank. One of these, named Rox3, lights up two mRNA species of ∼3400 and 3600 bp, significantly increased after treatment with DEM or with other oxidizing agents. This increase appears precociously after exposure to DEM and it is completely prevented by pretreatment with
N-acetylcysteine. The Rox3 fragment was used to screen a cDNA library; one fully sequenced clone showed 100% homology with the putative human guanine nucleotide regulatory protein nep1.
Reactive oxygen species (ROS) have been considered for a long time only as molecules for inducing oxidative damage to proteins, lipids, and nucleic acids. However, in the last few years some ...physiological effects of ROS have been hypothesized, consisting of the redox regulation of several biological processes, including the transduction of mitogenic signals. This means that intracellular generation of ROS could be necessary to maintain homeostasis, as well as that their formation/scavenging should be controlled processes. We developed an experimental procedure that causes redox perturbations in intact cells, based on the exposure of living cells to diethylmaleate (DEM), a GSH-depleting agent. By this procedure we demonstrated that ROS generated following DEM treatment induces a G1 arrest, that is accompanied by several redox-dependent changes in cell cycle-related proteins. One of these is the p53-independent accumulation of p21waf1/cip1, which requires the integrity of the ras-MAPK pathway. Accordingly, DEM treatment strongly activates ERK2. On the other hand, redox perturbations provoked by DEM induce several early phenomena, including p21waf1/cip1 and Rb dephosphorylation.
There is no generally accepted treatment for chronic hepatitis B (HB) infection in children.
To evaluate the efficacy of a prolonged course of high dose interferon alone or after prednisone priming ...in children with chronic HB infection.
The outcome of 31 children with HB e antigen (HBeAg)-positive chronic hepatitis who randomly received either no treatment (n = 9) or 10 million units of interferon alpha-2b/m2, alone (n = 13) or after prednisone priming (n = 9), three times weekly for 1 year was studied.
One patient withdrew from treatment. By the end of the first year treatment induced a loss of HB virus DNA and HBeAg from serum in 10 of 21 patients (48%), and a loss of HB surface antigen (HBsAg) in 4 (19%). Alanine aminotransferase values became normal in one patient (4.8%). Response rates in the two groups of treated patients were similar. In controls only one patient lost HBeAg and HBV DNA (11%; P = 0.05), and none lost HBsAg or showed alanine aminotransferase normalization (P = 0.21 and 0.70, respectively). After a posttreatment 2-year follow-up there were still no differences in the response rates of the two treatments; of the 21 pooled treated patients, 61% lost HBeAg and DNA and 67% normalized alanine aminotransferase (vs. 33 and 44% of controls, respectively; P = 0.32 and 0.40). Reversion to HBeAg and HBV DNA negativity in treated patients occurred significantly earlier (P = 0.02 and 0.006, respectively) than in controls. No further patient lost HBsAg, but one reacquired HBsAg. Treated patients had posttreatment histologic scores better than controls (P = 0.03).
Our medium term follow-up results indicate that a prolonged course of high dose interferon in children with chronic HB infection, regardless of prednisone priming, poorly affects response rates but significantly speeds termination of active viral replication.
The integrated low-level trigger and data acquisition (TDAQ) system of the NA62 experiment at CERN is described. The requirements of a large and fast data reduction in a high-rate environment for a ...medium-scale, distributed ensemble of many different sub-detectors led to the concept of a fully digital integrated system with good scaling capabilities. The NA62 TDAQ system is rather unique in allowing full flexibility on this scale, allowing in principle any information available from the detector to be used for triggering. The design concept, implementation and performances from the first years of running are illustrated.
The identification and characterization of a mouse tRNA(Trp) pseudogene is reported. A synthetic oligonucleotide (31 mer), identical with the 3' half of a tRNA(Trp), was used to examine three mouse ...lambda clones that are known to contain clusters of tRNA genes. A fragment of one of these lambda clones strongly hybridizes to the oligonucleotide; the sequence of this region shows the presence of a gene significantly homologous to the chick tRNA(Trp). However two point mutations and a three base deletion prevent the folding of a possible transcript of this gene. The presence of a conserved promoter sequence for RNA polymerase III, that should allow the transcription of this gene, does not ensure the transcription of the gene, at least in our in vitro system.
Precise measurements of the branching ratios for the flavor-changing neutral current decays \(K\to\pi\nu\bar{\nu}\) can provide unique constraints on CKM unitarity and, potentially, evidence for new ...physics. It is important to measure both decay modes, \(K^+\to\pi^+\nu\bar{\nu}\) and \(K_L\to\pi^0\nu\bar{\nu}\), since different new physics models affect the rates for each channel differently. The goal of the NA62 experiment at the CERN SPS is to measure the BR for the charged channel to within 10%. For the neutral channel, the BR has never been measured. We are designing the KLEVER experiment to measure BR(\(K_L\to\pi^0\nu\bar{\nu}\)) to \(\sim\)20% using a high-energy neutral beam at the CERN SPS starting in LHC Run 4. The boost from the high-energy beam facilitates the rejection of background channels such as \(K_L\to\pi^0\pi^0\) by detection of the additional photons in the final state. On the other hand, the layout poses particular challenges for the design of the small-angle vetoes, which must reject photons from \(K_L\) decays escaping through the beam exit amidst an intense background from soft photons and neutrons in the beam. Background from \(\Lambda \to n\pi^0\) decays in the beam must also be kept under control. We present findings from our design studies for the beamline and experiment, with an emphasis on the challenges faced and the potential sensitivity for the measurement of BR(\(K_L\to\pi^0\nu\bar{\nu}\)).
Status of the apeNEXT project Ammendola, R.; Bodin, F.; Boucaud, Ph ...
Nuclear physics. B, Proceedings supplement/Nuclear physics. B, Proceedings supplements,
05/2003, Volume:
119
Journal Article
Open access
We present the current status of the apeNEXT project. Aim of this project is the development of the next generation of APE machines which will provide multi-teraflop computing power. Like previous ...machines, apeNEXT is based on a custom designed processor, which is specifically optimized for simulating QCD. We discuss the machine design, report on benchmarks, and give an overview on the status of the software development.
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