Modeling and Analysis of Bus Contention for Hardware Accelerators in FPGA SoCs (Artifact)

This artifact provides the means for reproducing the experiments presented in the paper "Modeling and Analysis of Bus Contention for Hardware Accelerators in FPGA SoC". In particular, it provides the means and describes how to replicate the experimental study that has been carried out to evaluate the proposed analysis with synthetic workloads

Modeling and Analysis of Bus Contention for Hardware Accelerators in FPGA SoCs

FPGA System-on-Chips (SoCs) are heterogeneous platforms that combine general-purpose processors with a field-programmable gate array (FPGA) fabric. The FPGA fabric is composed of a programmable logic in which hardware accelerators can be deployed to accelerate the execution of specific functionality. The main source of unpredictability when bounding the execution times of hardware accelerators pertains the access to the shared memories via the on-chip bus. This work is focused on bounding the worst-case bus contention experienced by the hardware accelerators deployed in the FPGA fabric. To this end, this work considers the AMBA AXI bus, which is the de-facto standard communication interface used in most the commercial off-the-shelf (COTS) FPGA SoCs, and presents an analysis technique to bound the response times of hardware accelerators implemented on such platforms. A fine-grained modeling of the AXI bus and AXI interconnects is first provided. Then, contention delays are studied under hierarchical bus infrastructures with arbitrary depths. Experimental results are finally presented to validate the proposed model with execution traces on two modern FPGA-based SoC produced by Xilinx (Zynq-7000 and Zynq-Ultrascale+ families) and to assess the performance of the proposed analysis

A Bandwidth Reservation Mechanism for AXI-Based Hardware Accelerators on FPGAs

Hardware platforms for real-time embedded systems are evolving towards heterogeneous architectures comprising different types of processing cores and dedicated hardware accelerators, which can be implemented on silicon or dynamically deployed on FPGA fabric. Such accelerators typically access a shared memory to exchange a significant amount of data with other processing elements. Existing COTS solutions focus on maximizing the overall throughput of the system, rather than guaranteeing the timing constraints of individual hardware accelerators. This paper presents the AXI budgeting unit (ABU), a hardware-based solution to implement a bandwidth reservation mechanism on top of the AMBA AXI standard infrastructure for hardware accelerators deployed on FPGAs. An accurate and tractable model, as well as the corresponding analysis, are also proposed to bound the response time of hardware accelerators in the presence of ABUs, in order to verify whether they can complete before their deadlines. Finally, a set of experiments are reported to evaluate the proposed approach on a state-of-the-art platform, namely the Zynq-7020 by Xilinx. The resource consumption of the ABU has been quantified to be less than 1% of the total FPGA resources of the Zynq-7020

Novel nontoxic mitochondrial probe for confocal fluorescence microscopy.

We propose a 2,5-Bis[1-(4-N-methylpyridinium)ethen-2-yl)]-N-methylpyrrole ditriflate (PEPEP) as a novel nontoxic, nonpotentiometric mitochondrial probe for confocal fluorescence microscopy. PEPEP is a representative chromophore of a large family of heterocyclic fluorescent dyes that show fluorescence emission in aqueous media and great DNA affinity. We check its cytotoxicity and intracellular localization in mammalian and yeast cell cultures. We demonstrate that PEPEP is a very efficient dye for fluorescence confocal microscopy and a valuable alternative to the most frequently used mitochondrial stains. © 2006 Society of Photo-Optical Instrumentation Engineers

Accurate pHEMT nonlinear modeling in the presence of low-frequency dispersive effects

Low-frequency (LF) dispersive phenomena due to device self-heating and/or the presence of "traps" (i.e., surface state densities and bulk spurious energy levels) must be taken into account in the large-signal dynamic modeling of III-V field-effect transistors when accurate performance predictions are pursued, since these effects cause important deviations between direct current (dc) and dynamic drain current characteristics. In this paper, a new model for the accurate characterization of these phenomena above their cutoff frequencies is presented, which is able to fully exploit, in the identification phase, large-signal current-voltage (I-V) measurements carried out under quasi-sinusoidal regime using a recently proposed setup. Detailed experimental results for model validation under LF small- and large-signal operating conditions are provided. Furthermore, the I-V model proposed has been embedded into a microwave large-signal pseudomorphic high electron-mobility transistor (pHEMT) model in order to point out the strong influence of LF modeling on the degree of accuracy achievable under millimeter-wave nonlinear operation. Large-signal experimental validation at microwave frequencies is provided for the model proposed, by showing the excellent intermodulation distortion (IMD) predictions obtained with different loads despite the very low power level of IMD products involved. Details on the millimeter-wave IMD measurement setup are also provided. Finally, IMD measurements and simulations on a Ka-band highly linear power amplifier, designed by Ericsson using the Triquint GaAs 0.25-/spl mu/m pHEMT process, are shown for further model validation

Concepciones, dimensiones y perspectivas del desarrollo

En el presente artículo, se intentará conceptualizar el concepto de desarrollo reflexionando sobre el mismo a partir de su definición y sus características, diferenciándolo del crecimiento, y se abordará la relación entre desarrollo y pobreza.Facultad de Humanidades y Ciencias de la EducaciónFacultad de Ciencias Jurídicas y Sociale

Immunotherapy in Pancreatic Cancer: Why Do We Keep Failing? A Focus on Tumour Immune Microenvironment, Predictive Biomarkers and Treatment Outcomes

The advent of immunotherapy and targeted therapies has dramatically changed the outcomes of patients affected by many malignancies. Pancreatic cancer (PC) remains one the few tumors that is not treated with new generation therapies, as chemotherapy still represents the only effective therapeutic strategy in advanced-stage disease. Agents aiming to reactivate the host immune system against cancer cells, such as those targeting immune checkpoints, failed to demonstrate significant activity, despite the success of these treatments in other tumors. In many cases, the proportion of patients who derived benefits in early-phase trials was too small and unpredictable to justify larger studies. The population of PC patients with high microsatellite instability/mismatch repair deficiency is currently the only population that may benefit from immunotherapy; nevertheless, the prevalence of these alterations is too low to determine a real change in the treatment scenario of this tumor. The reasons for the unsuccess of immunotherapy may lie in the extremely peculiar tumor microenvironment, including distinctive immune composition and cross talk between different cells. These unique features may also explain why the biomarkers commonly used to predict immunotherapy efficacy in other tumors seem to be useless in PC. In the current paper, we provide a comprehensive and up-to-date review of immunotherapy in PC, from the analysis of the tumor immune microenvironment to immune biomarkers and treatment outcomes, with the aim to highlight that simply transferring the knowledge acquired on immunotherapy in other tumors might not be a successful strategy in patients affected by PC

High altitude adaptation in Daghestani populations from the Caucasus

We have surveyed 15 high-altitude adaptation candidate genes for signals of positive selection in North Caucasian highlanders using targeted re-sequencing. A total of 49 unrelated Daghestani from three ethnic groups (Avars, Kubachians, and Laks) living in ancient villages located at around 2,000 m above sea level were chosen as the study population. Caucasian (Adygei living at sea level, N = 20) and CEU (CEPH Utah residents with ancestry from northern and western Europe; N = 20) were used as controls. Candidate genes were compared with 20 putatively neutral control regions resequenced in the same individuals. The regions of interest were amplified by long-PCR, pooled according to individual, indexed by adding an eight-nucleotide tag, and sequenced using the Illumina GAII platform. 1,066 SNPs were called using false discovery and false negative thresholds of ~6%. The neutral regions provided an empirical null distribution to compare with the candidate genes for signals of selection. Two genes stood out. In Laks, a non-synonymous variant within HIF1A already known to be associated with improvement in oxygen metabolism was rediscovered, and in Kubachians a cluster of 13 SNPs located in a conserved intronic region within EGLN1 showing high population differentiation was found. These variants illustrate both the common pathways of adaptation to high altitude in different populations and features specific to the Daghestani populations, showing how even a mildly hypoxic environment can lead to genetic adaptation

Occurrence of extended spectrum \u3b2-lactamases, KPC-Type, and MCR-1.2-producing enterobacteriaceae from wells, river water, and wastewater treatment plants in Oltrep\uf2 Pavese area, Northern Italy

To evaluate the water compartment antibiotic-resistance contamination rates, 11 wells, five streams, and four treatment plants located in the Oltrepo Pavese area were screened for the presence of third generation cephalosporins resistant Gram-negative bacteria. Enterobacteriaceae were also characterized for the Extended-Spectrum-beta-Lactamases (ESBLs), carbapenemases, and mcr-1 genes presence. From December 2014 to November 2015, 246 water samples were filtered, plated on Plate Count Agar, MacConkey Agar, and MacConkey Agar with cefotaxime. Isolates were species identified using AutoSCAN-4-System and ESBLs, carbapenemases, and colistin resistance determinants were characterized by PCR, sequencing, and microarray. Plasmid conjugative transfer experiments, PCR-based Replicon typing, Pulsed-Field Gel Electrophoresis, Multi-Locus-Sequence-Typing, and in-silico plasmid characterization were performed. A total of 132 enterobacteria isolates grew on MacConkey agar with cefotaxime: 82 (62.1%) were obtained from streams, 41 (31.1%) from treatment plants, and 9 (6.8%) from wells. Thirty out of 132 (22.7%) isolates, mainly belonging to Escherichia coli (n = 15) species, showed a synergic effect with piperacillin-tazobactam. A single ESBL gene of bla(CTX-M)-type was identified in 19/30 isolates. In further two E. coli strains, a bla(CTX-M-1) gene co-existed with a bla(SHv)-type ESBL determinant. A bla(SHv-12) gene was detected in two isolates of E. coli (n = 1) and Klebsiella oxytoca (n = 1), while any ESBL determinant was ascertained in seven Yersinia enterocolitica strains, A bla(DHA)-type gene was detected in a cefoxitin resistant Y. enterocolitica from a stream. Interestingly, two Klebsiella pneumoniae strains of ST307 and ST258, collected from a well and a wastewater treatment plant, resulted KPC-2, and KPC-3 producers, respectively. Moreover, we report the first detection of mcr-1.2 ST10 E. coli on a conjugative lncX4 plasmid (33.303 bp in size) from a stream of Oltrepo Pavese (Northern Italy). Both ESBLs E. coli and ESBLs/carbapenemase-producing K. pneumoniae strains showed clonal heterogeneity by Pulsed-Field Gel Electrophoresis and Multi-Locus-Sequence-Typing. During one-year study and taking in account the whole Gram-negative bacterial population, an average percentage of cefotaxime resistance of 69, 32, and 10.3% has been obtained for the wastewater treatment plants, streams, and wells, respectively. These results, of concern for public health, highlight the need to improve hygienic measures to reduce the load of discharged bacteria with emerging resistance mechanisms

Substantial Histone Reduction Modulates Genomewide Nucleosomal Occupancy and Global Transcriptional Output

The basic unit of genome packaging is the nucleosome, and nucleosomes have long been proposed to restrict DNA accessibility both to damage and to transcription. Nucleosome number in cells was considered fixed, but recently aging yeast and mammalian cells were shown to contain fewer nucleosomes. We show here that mammalian cells lacking High Mobility Group Box 1 protein (HMGB1) contain a reduced amount of core, linker, and variant histones, and a correspondingly reduced number of nucleosomes, possibly because HMGB1 facilitates nucleosome assembly. Yeast nhp6 mutants lacking Nhp6a and -b proteins, which are related to HMGB1, also have a reduced amount of histones and fewer nucleosomes. Nucleosome limitation in both mammalian and yeast cells increases the sensitivity of DNA to damage, increases transcription globally, and affects the relative expression of about 10% of genes. In yeast nhp6 cells the loss of more than one nucleosome in four does not affect the location of nucleosomes and their spacing, but nucleosomal occupancy. The decrease in nucleosomal occupancy is non-uniform and can be modelled assuming that different nucleosomal sites compete for available histones. Sites with a high propensity to occupation are almost always packaged into nucleosomes both in wild type and nucleosome-depleted cells; nucleosomes on sites with low propensity to occupation are disproportionately lost in nucleosome-depleted cells. We suggest that variation in nucleosome number, by affecting nucleosomal occupancy both genomewide and gene-specifically, constitutes a novel layer of epigenetic regulation