NaNet: a Low-Latency, Real-Time, Multi-Standard Network Interface Card with GPUDirect Features

While the GPGPU paradigm is widely recognized as an effective approach to high performance computing, its adoption in low-latency, real-time systems is still in its early stages. Although GPUs typically show deterministic behaviour in terms of latency in executing computational kernels as soon as data is available in their internal memories, assessment of real-time features of a standard GPGPU system needs careful characterization of all subsystems along data stream path. The networking subsystem results in being the most critical one in terms of absolute value and fluctuations of its response latency. Our envisioned solution to this issue is NaNet, a FPGA-based PCIe Network Interface Card (NIC) design featuring a configurable and extensible set of network channels with direct access through GPUDirect to NVIDIA Fermi/Kepler GPU memories. NaNet design currently supports both standard - GbE (1000BASE-T) and 10GbE (10Base-R) - and custom - 34~Gbps APElink and 2.5~Gbps deterministic latency KM3link - channels, but its modularity allows for a straightforward inclusion of other link technologies. To avoid host OS intervention on data stream and remove a possible source of jitter, the design includes a network/transport layer offload module with cycle-accurate, upper-bound latency, supporting UDP, KM3link Time Division Multiplexing and APElink protocols. After NaNet architecture description and its latency/bandwidth characterization for all supported links, two real world use cases will be presented: the GPU-based low level trigger for the RICH detector in the NA62 experiment at CERN and the on-/off-shore data link for KM3 underwater neutrino telescope

High-speed data transfer with FPGAs and QSFP+ modules

We present test results and characterization of a data transmission system based on a last generation FPGA and a commercial QSFP+ (Quad Small Form Pluggable +) module. QSFP+ standard defines a hot-pluggable transceiver available in copper or optical cable assemblies for an aggregated bandwidth of up to 40 Gbps. We implemented a complete testbench based on a commercial development card mounting an Altera Stratix IV FPGA with 24 serial transceivers at 8.5 Gbps, together with a custom mezzanine hosting three QSFP+ modules. We present test results and signal integrity measurements up to an aggregated bandwidth of 12 Gbps.Comment: 5 pages, 3 figures, Published on JINST Journal of Instrumentation proceedings of Topical Workshop on Electronics for Particle Physics 2010, 20-24 September 2010, Aachen, Germany(R Ammendola et al 2010 JINST 5 C12019

Status of the EPIC thin and medium filters on-board XMM-Newton after more than 10 years of operation II: analysis of in-flight data

After more than ten years of operation of the EPIC camera on board the X-ray observatory XMM-Newton we have reviewed the status of its thin and medium filters by performing both analysis of data collected in-flight and laboratory measurements on on-ground back-up filters. We have investigated the status of the EPIC thin and medium filters by performing an analysis of the optical loading in the PN offset maps to gauge variations in the optical and UV transmission of the filters. We both investigated repeated observations of single optically bright targets and performed a statistical analysis of the extent of loading versus visual magnitude at different epochs. We report the results of these measurements

GPU-based Real-time Triggering in the NA62 Experiment

Over the last few years the GPGPU (General-Purpose computing on Graphics Processing Units) paradigm represented a remarkable development in the world of computing. Computing for High-Energy Physics is no exception: several works have demonstrated the effectiveness of the integration of GPU-based systems in high level trigger of different experiments. On the other hand the use of GPUs in the low level trigger systems, characterized by stringent real-time constraints, such as tight time budget and high throughput, poses several challenges. In this paper we focus on the low level trigger in the CERN NA62 experiment, investigating the use of real-time computing on GPUs in this synchronous system. Our approach aimed at harvesting the GPU computing power to build in real-time refined physics-related trigger primitives for the RICH detector, as the the knowledge of Cerenkov rings parameters allows to build stringent conditions for data selection at trigger level. Latencies of all components of the trigger chain have been analyzed, pointing out that networking is the most critical one. To keep the latency of data transfer task under control, we devised NaNet, an FPGA-based PCIe Network Interface Card (NIC) with GPUDirect capabilities. For the processing task, we developed specific multiple ring trigger algorithms to leverage the parallel architecture of GPUs and increase the processing throughput to keep up with the high event rate. Results obtained during the first months of 2016 NA62 run are presented and discussed

Upper limb motor improvement in chronic stroke after combining botulinum toxin A injection and multi-joints robot-assisted therapy: A case report

Spasticity is one of the major complications after stroke. Botulinum toxin type A (BoNT-A) injection is commonly used to manage focal spasticity. However, it is uncertain whether BoNT-A can improve activities of daily living function of paretic arm. The recovery of functions of the affected arm is also the aim of robotic upper limb (UL) therapy. The motorized exoskeleton assists the patient in a large 3D work environment by promoting movement for the UL (shoulder, elbow, wrist, hand). The combination of the BoNT-A injection and the robotic therapy might enhance functional recovery after stroke.We reported the case of a chronic stroke patient in which the injection of BoNT-A was combined with multi-joint exoskeleton training. The patient showed improvement in the motor control of the UL, supporting the feasibility of this approach

Pilot health technology assessment study: organizational and economic impact of remote monitoring system for home automated peritoneal dialysis

Purpose Follow-up of automated peritoneal dialysis (APD) has been improved by data transmission by cellular modem and internet cloud. With the new remote patient monitoring (RPM) technology, clinical control and prescription of dialysis are performed by software (Baxter Claria-Sharesource), which allows the center to access home operational data. The objective of this pilot study was to determine the impact of RPM compared to traditional technology, in clinical, organizational, social, and economic terms in a single center. Methods We studied 21 prevalent APD patients aged 69 ± 13 years, on dialysis for a median of 9 months, for a period of 6 months with the traditional technology and 6 months with the new technology. A relevant portion of patients lived in mountainous or hilly areas. Results Our study shows more proactive calls from the center to patients after the consultation of RPM software, reduction of calls from patients and caregivers, early detection of clinical problems, a significant reduction of unscheduled visits, and a not significant reduction of hospitalizations. The analysis also highlighted how the RPM system lead to relevant economic savings, which for the health system have been calculated € 335 (mean per patient-month). With the social costs represented by the waste of time of the patient and the caregiver, we calculated € 685 (mean per patient-month). Conclusion In our pilot report, the RPM system allowed the accurate assessment of daily APD sessions to suggest significative organizational and economic advantages, and both patients and healthcare providers reported good subjective experiences in terms of safety and quality of follow-up

APEnet+: high bandwidth 3D torus direct network for petaflops scale commodity clusters

We describe herein the APElink+ board, a PCIe interconnect adapter featuring the latest advances in wire speed and interface technology plus hardware support for a RDMA programming model and experimental acceleration of GPU networking; this design allows us to build a low latency, high bandwidth PC cluster, the APEnet+ network, the new generation of our cost-effective, tens-of-thousands-scalable cluster network architecture. Some test results and characterization of data transmission of a complete testbench, based on a commercial development card mounting an Altera FPGA, are provided.Comment: 6 pages, 7 figures, proceeding of CHEP 2010, Taiwan, October 18-2

Simple and fast orotracheal intubation procedure in rat

Introduction: Endotracheal intubation in the rat is difficult because of extremely small size of anatomical structures (oral cavity, epiglottis and vocal cords), small inlet for an endotracheal tube and the lack of proper techniacal instruments. Matherial and Methods: In this study we used seventy rats weighthing 400-500 g. The equipment needed for intubation was an operating table, a longish of cotton, a cotton tip, orotracheal tube, neonatal laryngoscope KTR4, small animal ventilator, and isoflurane for inhalation anaesthesia. Premedication was carried out by medetomidine hydrochloride 1 mg/mL; then, thanks to a closed glass chamber, a mixture of oxygen and isoflurane was administered. By means of neonatal laryngoscope the orotracheal tube was advanced into the oral cavity untile the wire guide was visualized trough the vocal cords; then it was passed through them. The tube was introduced directly into into the larynx over the wire guide; successively, the guide was removed and the tube placed into the trachea. Breathing was confirmed using a glove, cut at the end of a finger, simulating a small ballon. Conclusions: We believe that our procedure is easier and faster than those previously reported in scientific literature. (www.actabiomedica.it

Distinctive features of tumor-infiltrating gd T lymphocytes in human colorectal cancer

gd T cells usually infiltrate many different types of cancer, but it is unclear whether they inhibit or promote tumor progression. Moreover, properties of tumor-infiltrating gd T cells and those in the corresponding normal tissue remain largely unknown. Here we have studied features of gd T cells in colorectal cancer, normal colon tissue and peripheral blood, and correlated their levels with clinicopathologic hallmarks. Flow cytometry and transcriptome analyses showed that the tumor comprised a highly variable rate of TILs (5-90%) and 4%gd T cells on average, with the majority expressing Vd1. Most Vd1 and Vd2 T cells showed a predominant effector memory phenotype and had reduced production of IFN-g which was likely due to yet unidentified inhibitory molecules present in cancer stem cell secretome. Transcriptome analyses revealed that patients containing abundant gd T cells had significantly longer 5-year disease free survival rate, suggesting their efficacy in controlling tumor at very early stage

Multiple Sclerosis in the Mount Etna Region: Possible Role of Volcanogenic Trace Elements

Background: Trace elements have been hypothesised to be involved in the pathogenesis of Multiple Sclerosis and volcanic degassing is the major natural sources of trace elements. Both incidence of Multiple Sclerosis in Catania and volcanic activity of Mount Etna have been significantly increased during the last 30 years. Due to prevailing trade winds direction, volcanic gases from Etna summit craters are mostly blown towards the eastern and southern sectors of the volcano. Objective: To evaluate the possible association between Multiple Sclerosis and exposure to volcanogenic trace elements. Methods: We evaluated prevalence and incidence of Multiple Sclerosis in four communities (47,234 inhabitants) located in the eastern flank and in two communities (52,210 inhabitants) located in the western flank of Mount Etna, respectively the most and least exposed area to crater gas emissions. Results: A higher prevalence was found in the population of the eastern flank compared to the population of the western one (137.6/100,000 versus 94.3/100,000; p-value 0.04). We found a borderline significantly higher incidence risk during the incidence study period (1980–2009) in the population of the eastern flank 4.6/100,000 (95% CI 3.1–5.9), compared with the western population 3.2/100,000 (95% CI 2.4–4.2) with a RR of 1.41 (95% CI 0.97–2.05; p-value 0.06). Incidence risks have increased over the time in both populations reaching a peak of 6.4/100,000 in the eastern flank and of 4.4/100.000 in the western flank during 2000–2009. Conclusion: We found a higher prevalence and incidence of Multiple Sclerosis among populations living in the eastern flank of Mount Etna. According to our data a possible role of TE cannot be ruled out as possible co-factor in the MS pathogenesis. However larger epidemiological study are needed to confirm this hypothesis.Publishede742596A. Monitoraggio ambientale, sicurezza e territorioJCR Journalope