Simurgh: a fully decentralized and secure NVMM user space file system

The availability of non-volatile main memory (NVMM) has started a new era for storage systems and NVMM specific file systems can support extremely high data and metadata rates, which are required by many HPC and data-intensive applications. Scaling metadata performance within NVMM file systems is nevertheless often restricted by the Linux kernel storage stack, while simply moving metadata management to the user space can compromise security or flexibility. This paper introduces Simurgh, a hardware-assisted user space file system with decentralized metadata management that allows secure metadata updates from within user space. Simurgh guarantees consistency, durability, and ordering of updates without sacrificing scalability. Security is enforced by only allowing NVMM access from protected user space functions, which can be implemented through two proposed instructions. Comparisons with other NVMM file systems show that Simurgh improves metadata performance up to 18x and application performance up to 89% compared to the second-fastest file system.This work has been supported by the European Comission’s BigStorage project H2020-MSCA-ITN2014-642963. It is also supported by the Big Data in Atmospheric Physics (BINARY) project, funded by the Carl Zeiss Foundation under Grant No.: P2018-02-003.Peer ReviewedPostprint (author's final draft

175 GHz, 400-fs-pulse harmonically mode-locked surface emitting semiconductor laser

We report a harmonically mode-locked vertical external cavity surface emitting laser (VECSEL) producing 400 fs pulses at a repetition frequency of 175 GHz with an average output power of 300 mW. Harmonic mode-locking was established using a 300 µm thick intracavity single crystal diamond heat spreader in thermal contact with the front surface of the gain sample using liquid capillary bonding. The repetition frequency was set by the diamond microcavity and stable harmonic mode locking was achieved when the laser cavity length was tuned so that the laser operated on the 117th harmonic of the fundamental cavity. When an etalon placed intracavity next to the gain sample, but not in thermal contact was used pulse groups were observed. These contained 300 fs pulses with a spacing of 5.9 ps. We conclude that to achieve stable harmonic mode locking at repetition frequencies in the 100s of GHz range in a VECSEL there is a threshold pulse energy above which harmonic mode locking is achieved and below which groups of pulses are observed

VirMAP for Cancer: Characterization of the Intratumoral Virome in Virally-Associated Cancers and a Resource for Investigators

View full abstracthttps://openworks.mdanderson.org/leading-edge/1040/thumbnail.jp

2017 American Brachytherapy Society’s Annual Meeting Report

The American Brachytherapy Society (ABS) and its membership seeks to benefit patients by promoting the highest possible standard for brachytherapy practice, support health care professionals through the encouragement of state of the art technology and education, promote clinical and laboratory research, and advocate for the socioeconomic aspects of brachytherapy. The 2017 ABS Annual Meeting took place is Boston, Massachusetts, United States from April 20–22, 2017. The theme “The Value of Brachytherapy in Multidisciplinary Cancer Care” drew a multitude of national and international speakers to present data and debate clinical indications, advancements in practice and the value of brachytherapy. With a focus on the advancement of brachytherapy for prostate cancer and the socioeconomic benefits of brachytherapy, the globally focused program hosted 93 speakers, 506 attendees, and exhibitors from 15 countries and featured 251 abstracts for presentation and display. The ABS Annual Meeting left attendees with initial data on timely and relevant topics such as outcomes following brachytherapy for recurrent prostate cancer following external beam radiotherapy, findings of prototype algorithms capable of rapidly generating prostate brachytherapy pre-operative treatment plans and results on the socioeconomic disparities impacting the utilization of brachytherapy for common malignancies. These novel findings, among many other thoughtful and thought-provoking presentations, gave meeting attendees knowledge of the current state of brachytherapy and future directions of the specialty

A validation study of loci associated with mastitis resistance in two French dairy sheep breeds

The identification of loci associated with resistance to mastitis or of the causative mutations may be helpful in breeding programs for dairy sheep as it is for cattle worldwide. Seven genomic regions that control milk somatic cell counts, an indirect indicator of udder infection, have already been identified in sheep (Spanish Churra, French Lacaune and Italian Sardinian-Lacaune backcross populations). In this study, we used a 960 custom-designed ovine single nucleotide polymorphism (SNP) chip in Lacaune and Manech Tete Rousse dairy sheep to validate these seven genomic regions associated with mastitis. The most significant SNP (rs868996547) on Ovis aries chromosome (OAR) 3 was a previously described mutation in the suppressor of cytokine signalling 2 (SOCS2) gene. An antagonist effect of this causal candidate between health and growth in Lacaune sheep was confirmed. Effects of the mutation on the infectious status of the udder, i.e. increases in milk somatic cell counts and bacteria shedding, were also identified. This SNP was not present in the data available on Manech Tete Rousse. Three other regions associated with mastitis were also confirmed on OAR16 (Manech Tete Rousse), 19 (Lacaune) and 2 (both breeds). For the OAR2 region, we validated previously detected SNPs in several other breeds (Sarda, Churra, and Chios). For significant SNPs in the four mastitis regions, the effect varied from 0.24 to 0.67 phenotypic standard deviation of the traits. Two of the mastitis quantitative trait loci (QTL) regions (OAR2 and 16) that we validated here were also associated in opposite ways with milk production traits in both populations. These results indicate, at least in part, a genomic basis for the trade-off between milk production and mastitis resistance. Four of the seven mastitis QTL regions that were previously identified in independent populations, were confirmed in this study, which demonstrates partial sharing of mastitis-related genetic mechanisms between different distant dairy sheep populations

American Brachytherapy Task Group Report: Adjuvant vaginal brachytherapy for early-stage endometrial cancer: A comprehensive review

This article aims to review the risk stratification of endometrial cancer, treatment rationale, outcomes, treatment planning, and treatment recommendations of vaginal brachytherapy (VBT) in the post-operative management of endometrial cancer patients. The authors performed a thorough review of the literature and reference pertinent articles pertaining to the aims of this review. Adjuvant VBT for early stage endometrial cancer patients results in very low rates of vaginal recurrence (0–3.1%) with low rates of late toxicity which are primarily vaginal in nature. PORTEC-2 supports that VBT results in non-inferior rates of vaginal recurrence compared to external beam radiotherapy (EBRT) for the treatment of high-intermediate risk patients. VBT as a boost following EBRT, in combination with chemotherapy, and for high-risk histologies have shown excellent results as well though randomized data do not exist supporting VBT boost. There are many different applicators, dose-fractionation schedules, and treatment planning techniques which all result in favorable clinical outcomes and low rates of toxicity. Recommendations have been published by the American Brachytherapy Society and the American Society of Radiation Oncology to help guide practitioners in the use of VBT. Data support that patients and physicians both prefer joint decision-making regarding the use of VBT, and patients often desire additional treatment for a marginal benefit in risk of recurrence. Discussions regarding adjuvant therapy for endometrial cancer are best performed in a multi-disciplinary setting and patients should be counseled properly regarding the risks and benefits of adjuvant therapy

Pyroséquençage pour le développement d'EST et de SNP aviaires

Le but du programme est de combler les déficits en marqueurs observés pour trois espèces aviaires : la caille, le canard et la poule. La stratégie choisie est l'obtention, à partir de plusieurs individus de lignées d'intérêt, de SNP (Single Nucleotide Polymorphism, polymorphisme d'un nucléotide) par une nouvelle technologie de séquençage à haut débit (séquenceur 454 GS-FLX, Roche). Nous séquençons des représentations réduites du génome, en sélectionnant d'une part des fragments de restriction d'ADN génomique - les mêmes chez tous les individus - et d'autre part les transcrits qui représentent globalement la partie du génome correspondant aux gènes exprimés. Ces expérimentations sont réalisées à partir d'échantillons d'ADN ou d'ARN issus d'individus de lignées à l'origine de croisements existants, pour chacune des trois espèces. Les données générées par plusieurs "runs" de séquence seront traitées in silico : contigage à haut débit, recherche de SNP, comparaison avec les banques de séquences connues...En plus de l'intérêt que représente la production d'un très grand nombre de SNP nouveaux, cette technologie devrait permettre de mieux séquencer les régions riches en (G+C) correspondant aux plus petits des microchromosomes pour lesquels il n'y a pas de séquence chez la poule. La comparaison des séquences des transcrits obtenues chez la caille et le canard avec la séquence du génome de la poule permettra d'établir une "cartographie virtuelle" des SNP obtenus, grâce à la grande conservation de synténie existant entre ces trois espèces

Unraveling the temperature dependence of the yield strength in single-crystal tungsten using atomistically-informed crystal plasticity calculations

We use a physically-based crystal plasticity model to predict the yield strength of body-centered cubic (bcc) tungsten single crystals subjected to uniaxial loading. Our model captures the thermally-activated character of screw dislocation motion and full non-Schmid effects, both of which are known to play a critical role in bcc plasticity. The model uses atomistic calculations as the sole source of constitutive information, with no parameter fitting of any kind to experimental data. Our results are in excellent agreement with experimental measurements of the yield stress as a function of temperature for a number of loading orientations. The validated methodology is then employed to calculate the temperature and strain-rate dependence of the yield strength for 231 crystallographic orientations within the standard stereographic triangle. We extract the strain-rate sensitivity of W crystals at different temperatures, and finish with the calculation of yield surfaces under biaxial loading conditions that can be used to define effective yield criteria for engineering design models