Extreme Data-rate Scheduling for the Data Center

Designing scalable and cost-effective data center interconnect architectures based on electrical packet switches is challenging. To overcome this challenge, researchers have tried to harness the advantages of optics in data center environment. This has resulted in exploration of hybrid switching architectures that contains an optical circuit switch to serve long bursts of traffic along with an electrical packet switch serving short bursts of traffic. The performance of such hybrid switching architectures in data center is dependent on the schedulers. Building hybrid schedulers is challenging because of varying properties of data center traffic, increasing network demands, requirements imposed by hybrid network architecture etc. Slow schedulers can negatively impact the performance of the data center network because of poor resource utilization. With future demands, this problem is going to escalate motivating the need for faster schedulers. One approach to do this would be to use a hardware based scheduler. In this paper we propose a framework that can be used to explore and evaluate hardware based hybrid schedulers.This project is supported by the EPSRC INTERNET Project EP/H040536/1.This is the author accepted manuscript. The final version is available from ACM via http://dx.doi.org/10.1145/2785956.279001

Quantitative analysis of malondialdehyde-guanine adducts in genomic DNA samples by liquid chromatography tandem mass spectrometry.

RATIONALE: The lipid peroxidation product malondialdehyde forms M1 dG adducts with guanine bases in genomic DNA. The analysis of these adducts is important as a biomarker of lipid peroxidation, oxidative stress and inflammation which may be linked to disease risk or exposure to a range of chemicals. METHODS: Genomic DNA samples were subjected to acid hydrolysis to release the adducts in the base form (M1 G) alongside the other purines. A liquid chromatography-mass spectrometry method was optimised for the quantitation of the M1 G adducts in genomic DNA samples using product ion and multiple reaction mode scans. RESULTS: Product ion scans revealed four product ions from the precursor ion; m/z 188 → 160, 133, 106 and 79. The two smallest ions have not been observed previously and optimisation of the method revealed that these gave better sensitivity (LOQ m/z 79: 162 adducts per 10(7) nucleotides; m/z 106: 147 adducts per 10(7) nucleotides) than the other two ions. An MRM method gave similar sensitivity but the two smallest product ions gave better accuracy (94-95%). Genomic DNA treated with malondialdehyde showed a linear dose-response relationship. CONCLUSION: A fast reliable sample preparation method was used to release adducts in the base form rather than the nucleoside. The methods were optimised to selectively analyse the adducts in the presence of other DNA bases without the need for further sample clean-up. Analysis of genomic DNA gave results consistent with previous work and was applied to new samples. Thus, the method is suitable for the analysis of M1 (d)G adducts in biological samples

NetFPGA - Rapid prototyping of high bandwidth devices in open source

The demand-led growth of datacenter networks has meant that many constituent technologies are beyond the budget of the wider community. In order to make and validate timely and relevant new contributions, the wider community requires accessible evaluation, experimentation and demonstration environments with specification comparable to the subsystems of the most massive datacenter networks. We demonstrate NetFPGA SUME, an open-source FPGA-based PCIe board for rapid prototyping of high bandwidth devices. NetFPGA SUME has I/O capabilities for 100Gbps operation as a networking device, computing unit, or for test and measurement.This work was jointly supported by EPSRC INTERNET Project EP/H040536/1, National Science Foundation under Grant No. CNS-0855268, and Defense Advanced Research Projects Agency (DARPA) and Air Force Research Laboratory (AFRL), under contract FA8750-11-C-0249. The views, opinions, and/or findings contained in this report are those of the authors and should not be interpreted as representing the official views or policies, either expressed or implied, of the National Science Foundation, Defense Advanced Research Projects Agency or the Department of Defense. The Xilinx XUP program has been a long-standing supporter of NetFPGA and the NetFPGA SUME project is only possible with their generous support. We thank the people at Digilent Inc. We thank Micron and Cypress Semiconductor for their generous part donations.This is the author accepted manuscript. The final version is available from IEEE via http://dx.doi.org/10.1109/FPL.2015.729396

Expectations of rehabilitation following lower limb amputation: a qualitative study.

To explore the expectations of patients about to undergo prosthetic rehabilitation following a lower limb amputation

Pitch Enumeration: Failure to Subitize in Audition

Background: Subitizing involves recognition mechanisms that allow effortless enumeration of up to four visual objects, however despite ample resolution experimental data suggest that only one pitch can be reliably enumerated. This may be due to the grouping of tones according to harmonic relationships by recognition mechanisms prior to fine pitch processing. Poorer frequency resolution of auditory information available to recognition mechanisms may lead to unrelated tones being grouped, resulting in underestimation of pitch number. Methods, Results and Conclusion: We tested whether pitch enumeration is better for chords of full harmonic complex tones, where grouping errors are less likely, than for complexes with fewer and less accurately tuned harmonics. Chords of low familiarity were used to mitigate the possibility that participants would recognize the chord itself and simply recall the number of pitches. We found that accuracy of pitch enumeration was less than the visual system overall, and underestimation of pitch number increased for stimuli containing fewer harmonics. We conclude that harmonically related tones are first grouped at the poorer frequency resolution of the auditory nerve, leading to poor enumeration of more than one pitch

Early and efficient detection of Mycobacterium tuberculosis in sputum by microscopic observation of broth cultures.

Early, efficient and inexpensive methods for the detection of pulmonary tuberculosis are urgently needed for effective patient management as well as to interrupt transmission. These methods to detect M. tuberculosis in a timely and affordable way are not yet widely available in resource-limited settings. In a developing-country setting, we prospectively evaluated two methods for culturing and detecting M. tuberculosis in sputum. Sputum samples were cultured in liquid assay (micro broth culture) in microplate wells and growth was detected by microscopic observation, or in Löwenstein-Jensen (LJ) solid media where growth was detected by visual inspection for colonies. Sputum samples were collected from 321 tuberculosis (TB) suspects attending Bugando Medical Centre, in Mwanza, Tanzania, and were cultured in parallel. Pulmonary tuberculosis cases were diagnosed using the American Thoracic Society diagnostic standards. There were a total of 200 (62.3%) pulmonary tuberculosis cases. Liquid assay with microscopic detection detected a significantly higher proportion of cases than LJ solid culture: 89.0% (95% confidence interval [CI], 84.7% to 93.3%) versus 77.0% (95% CI, 71.2% to 82.8%) (p = 0.0007). The median turn around time to diagnose tuberculosis was significantly shorter for micro broth culture than for the LJ solid culture, 9 days (interquartile range [IQR] 7-13), versus 21 days (IQR 14-28) (p<0.0001). The cost for micro broth culture (labor inclusive) in our study was US $4.56 per sample, versus US$11.35 per sample for the LJ solid culture. The liquid assay (micro broth culture) is an early, feasible, and inexpensive method for detection of pulmonary tuberculosis in resource limited settings

CHERI Concentrate: Practical Compressed Capabilities

We present CHERI Concentrate, a new fat-pointer compression scheme applied to CHERI, the most developed capability-pointer system at present. Capability fat-pointers are a primary candidate for enforcing fine-grained and non-bypassable security properties in future computer systems, although increased pointer size can severely affect performance. Thus, several proposals for capability compression have been suggested but these did not support legacy instruction sets, ignored features critical to the existing software base, and also introduced design inefficiencies to RISC-style processor pipelines. CHERI Concentrate improves on the state-of-the-art region-encoding efficiency, solves important pipeline problems, and eases semantic restrictions of compressed encoding, allowing it to protect a full legacy software stack. We analyze and extend logic from the open-source CHERI prototype processor design on FPGA to demonstrate encoding efficiency, minimize delay of pointer arithmetic, and eliminate additional load-to-use delay. To verify correctness of our proposed high-performance logic, we present a HOL4 machine-checked proof of the decode and pointer-modify operations. Finally, we measure a 50%-75% reduction in L2 misses for many compiled C-language benchmarks running under a commodity operating system using compressed 128-bit and 64-bit formats, demonstrating both compatibility with and increased performance over the uncompressed, 256-bit format

The Effect of Polyhydramnios on Cervical Length in Twins: A Controlled Intervention Study in Complicated Monochorionic Pregnancies

Objective: To test the hypothesis that cervical shortening in polyhydramnios reflects the degree of excess amniotic fluid, and increases with normalisation of amniotic fluid volume. Study Design: Prospective cohort study of 40 women with monochorionic twins undergoing interventional procedures between 16-26 weeks. Cervical length was assessed via transvaginal sonography pre-procedure, 1 and 24 hours postprocedure, and results compared between amnioreduction and control procedures. Amniotic fluid index (AFI) was measured pre- and post-procedure. Results: Pre-procedural cervical length correlated with AFI (linear fit = 5.07 -0.04x, R2 = 0.17, P = 0.03) in patients with polyhydramnios (n = 28). Drainage of 2000ml fluid (range 700-3500ml), reduced AFI from 42cm to 21cm (P>0.001). Their pre-procedural cervical length did not change at one (mean Δ:-0.1cm, 95%CI, -0.4 to 0.2) or 24 hours (0.2cm, -0.1 to 0.6) after amnioreduction. There was no change in cervical length at control procedures. Conclusion: Cervical shortening in twins with polyhydramnios does not appear to be an acute process; cervical length can be measured before or after therapeutic procedures. © 2008 Engineer et al

Ferritins: furnishing proteins with iron

Ferritins are a superfamily of iron oxidation, storage and mineralization proteins found throughout the animal, plant, and microbial kingdoms. The majority of ferritins consist of 24 subunits that individually fold into 4-α-helix bundles and assemble in a highly symmetric manner to form an approximately spherical protein coat around a central cavity into which an iron-containing mineral can be formed. Channels through the coat at inter-subunit contact points facilitate passage of iron ions to and from the central cavity, and intrasubunit catalytic sites, called ferroxidase centers, drive Fe2+ oxidation and O2 reduction. Though the different members of the superfamily share a common structure, there is often little amino acid sequence identity between them. Even where there is a high degree of sequence identity between two ferritins there can be major differences in how the proteins handle iron. In this review we describe some of the important structural features of ferritins and their mineralized iron cores and examine in detail how three selected ferritins oxidise Fe2+ in order to explore the mechanistic variations that exist amongst ferritins. We suggest that the mechanistic differences reflect differing evolutionary pressures on amino acid sequences, and that these differing pressures are a consequence of different primary functions for different ferritins

Thunderclap: Exploring Vulnerabilities in Operating System IOMMU Protection via DMA from Untrustworthy Peripherals

Direct Memory Access (DMA) attacks have been known for many years: DMA-enabled I/O peripherals have complete access to the state of a computer and can fully compromise it including reading and writing all of system memory. With the popularity of Thunderbolt 3 over USB Type-C and smart internal devices, opportunities for these attacks to be performed casually with only seconds of physical access to a computer have greatly broadened. In response, commodity hardware and operating-system (OS) vendors have incorporated support for Input-Output Memory Management Units (IOMMUs), which impose memory protection on DMA, and are widely believed to protect against DMA attacks. We investigate the state-of-the-art in IOMMU protection across OSes using a novel I/O security research platform, and find that current protections fall short when faced with a functional network peripheral that uses its complex interactions with the OS for ill intent, and demonstrate compromises against macOS, FreeBSD, and Linux, which notionally utilize IOMMUs to protect against DMA attackers. Windows only uses the IOMMU in limited cases and remains vulnerable. Using Thunderclap, an open-source FPGA research platform we built, we explore a number of novel exploit techniques to expose new classes of OS vulnerability. The complex vulnerability space for IOMMU-exposed shared memory available to DMA-enabled peripherals allows attackers to extract private data (sniffing cleartext VPN traffic) and hijack kernel control flow (launching a root shell) in seconds using devices such as USB-C projectors or power adapters. We have worked closely with OS vendors to remedy these vulnerability classes, and they have now shipped substantial feature improvements and mitigations as a result of our work.DARPA I2O FA8750-10-C-0237 ("CTSRD") DARPA MTO HR0011- 18-C-0016 ("ECATS") Arm Ltd Google Inc This work was also supported by EPSRC EP/R012458/1 (“IOSEC”)