Realizing Accelerated Cost-Effective Distributed RAID

The exponential growth in user and application data entails new means for providing fault tolerance and protection against data loss. High Performance Com- puting (HPC) storage systems, which are at the forefront of handling the data del- uge, typically employ hardware RAID at the backend. However, such solutions are costly, do not ensure end-to-end data integrity, and can become a bottleneck during data reconstruction. In this paper, we design an innovative solution to achieve a flex- ible, fault-tolerant, and high-performance RAID-6 solution for a parallel file system (PFS). Our system utilizes low-cost, strategically placed GPUs — both on the client and server sides — to accelerate parity computation. In contrast to hardware-based approaches, we provide full control over the size, length and location of a RAID array on a per file basis, end-to-end data integrity checking, and parallelization of RAID array reconstruction. We have deployed our system in conjunction with the widely-used Lustre PFS, and show that our approach is feasible and imposes ac- ceptable overhead.

An accelerated method of developing DBT projects using CDIO partner institutions as parallel processors

The cycle of the academic year impacts on efforts to refine and improve major group design-build-test (DBT) projects since the time to run and evaluate projects is generally a full calendar year. By definition these major projects have a high degree of complexity since they act as the vehicle for the application of a range of technical knowledge and skills. There is also often an extensive list of desired learning outcomes which extends to include professional skills and attributes such as communication and team working. It is contended that student project definition and operation, like any other designed product, requires a number of iterations to achieve optimisation. The problem however is that if this cycle takes four or more years then by the time a project’s operational structure is fine tuned it is quite possible that the project theme is no longer relevant. The majority of the students will also inevitably experience a sub-optimal project experience over the 5 year development period. It would be much better if the ratio were flipped so that in 1 year an optimised project definition could be achieved which had sufficient longevity that it could run in the same efficient manner for 4 further years. An increased number of parallel investigators would also enable more varied and adventurous project concepts to be examined than a single institution could undertake alone in the same time frame.
This work-in-progress paper describes a parallel processing methodology for the accelerated definition of new student DBT project concepts. This methodology has been devised and implemented by a number of CDIO partner institutions in the UK & Ireland region. An agreed project theme was operated in parallel in one academic year with the objective of replacing a multi-year iterative cycle. Additionally the close collaboration and peer learning derived from the interaction between the coordinating academics facilitated the development of faculty teaching skills in line with CDIO standard 10.

Measurements of high-energy radiation generation from laser-wakefield accelerated electron beams

Using high-energy (∼0.5 GeV) electron beams generated by laser wakefield acceleration (LWFA), bremsstrahlung radiation was created by interacting these beams with various solid targets. Secondary processes generate high-energy electrons, positrons, and neutrons, which can be measured shot-to-shot using magnetic spectrometers, short half-life activation, and Compton scattering. Presented here are proof-of-principle results from a high-resolution, high-energy gamma-ray spectrometer capable of single-shot operation, and high repetition rate activation diagnostics. We describe the techniques used in these measurements and their potential applications in diagnosing LWFA electron beams and measuring high-energy radiation from laser-plasma interactions.

Accelerated rehabilitation of an edentulous patient with an implant retained dental prosthesis: a case report

This case report details the successful rehabilitation of an edentulous patient using a complete upper prosthesis and a lower implant retained overdenture. The provision of care was split between a specialist centre and a primary care setting. This approach reduced inconvenience to the patient. Modern surgical and prosthodontic techniques also reduced the total delivery time. After initial consultation a new set of complete dentures was prescribed with changes in design to the originals. The patient was also planned for placement of two mandibular implants to stabilise and retain the mandibular denture. The first line of treatment involved provision of a new set of dentures constructed by the patient's general dental practitioner. Dental implants were then placed in a specialist centre and the patient returned to the dental practice for attachment of the lower denture to the dental implants. The benefits and success of mandibular implant retained dentures are well documented. With delivery of the overdenture, the patient reported increased satisfaction with his prostheses which allowed him to eat a greater range of foods and enabled him to feel confident when speaking and socialising.

Accelerated partial breast irradiation (APBI): Are breath-hold and volumetric radiation therapy techniques useful?

Background: In a selective group of patients accelerated partial breast irradiation (APBI) might be applied after conservative breast surgery to reduce the amount of irradiated healthy tissue. The role of volumetric modulated arc therapy (VMAT) and voluntary moderately deep inspiration breath-hold (vmDIBH) techniques in further reducing irradiated healthy – especially heart – tissue is investigated.

Material and methods: For 37 partial breast planning target volumes (PTVs), three-dimensional conformal radiotherapy (3D-CRT) (3 – 5 coplanar or non-coplanar 6 and/or 10 MV beams) and VMAT (two partial 6 MV arcs) plans were made on CTs acquired in free-breathing (FB) and/or in vmDIBH. Dose-volume parameters for the PTV, heart, lungs, and breasts were compared. 

Results: Better dose conformity was achieved with VMAT compared to 3D-CRT (conformity index 1.24 0.09 vs. 1.49 0.20). Non-PTV ipsilateral breast receiving 50% of the prescribed dose was on average reduced by 28% in VMAT plans compared to 3D-CRT plans. Mean heart dose (MHD) reduced from 2.0 (0.1 – 5.1) Gy in 3D-CRT(FB) to 0.6 (0.1 – 1.6) Gy in VMAT(vmDIBH). VMAT is benefi cial for MHD reduction if MHD with 3D-CRT exceeds 0.5Gy. Cardiac dose reduction as a result of VMAT increases with increasing initial MHD, and adding vmDIBH reduces the cardiac dose further. Mean dose to the ipsilateral lung decreased from 3.7 (0.7 – 8.7) to 1.8 (0.5 – 4.0) Gy with VMAT(vmDIBH) compared to 3D-CRT(FB). VMAT resulted in a slight increase in the contralateral breast dose (DMean ) always remaining 1.9 Gy). 

Conclusions: For APBI patients, VMAT improves PTV dose conformity and delivers lower doses to the ipsilateral breast and lung compared to 3D-CRT. This goes at the cost of a slight but acceptable increase of the contralateral breast dose. VMAT reduces cardiac dose if MHD exceeds 0.5 Gy for 3D-CRT. Adding vmDIBH results in a further reduction of heart and ipsilateral lung dose. 

Transport of laser accelerated proton beams and isochoric heating of matter

The acceleration of intense proton and ion beams by ultra-intense lasers has matured to a point where applications in basic research and technology are being developed. Crucial for harvesting the unmatched beam parameters driven by the relativistic electron sheath is the precise control of the beam. We report on recent experiments using the PHELIX laser at GSI, the VULCAN laser at RAL and the TRIDENT laser at LANL to control and use laser accelerated proton beams for applications in high energy density research. We demonstrate efficient collimation of the proton beam using high field pulsed solenoid magnets, a prerequisite to capture and transport the beam for applications. Furthermore we report on two campaigns to use intense, short proton bunches to isochorically heat solid targets up to the warm dense matter state. The temporal profile of the proton beam allows for rapid heating of the target, much faster than the hydrodynamic response time thereby creating a strongly coupled plasma at solid density. The target parameters are then probed by X-ray Thomson scattering (XRTS) to reveal the density and temperature of the heated volume. This combination of two powerful techniques developed during the past few years allows for the generation and investigation of macroscopic samples of matter in states present in giant planets or the interior of the earth.

Observation of the inhomogeneous spatial distribution of MeV ions accelerated by the hydrodynamic ambipolar expansion of clusters

An inhomogeneous spatial distribution of laser accelerated carbon/oxygen ions produced via the hydrodynamic ambipolar expansion of CO₂ clusters has been measured by using CR-39 detectors. An inhomogeneous etch pits spatial distribution has appeared on the etched CR-39 detector installed on the laser propagation direction, while homogeneous ones are appeared on those installed at 45°and 90°from the laser propagation direction. From the range of ions in CR-39 obtained by using the multi-step etching technique, the averaged energies of carbon/oxygen ions for all directions are determined as 0.78 ± 0.09 MeV/n. The number of ions in the laser propagation direction is about 1.5 times larger than those in other directions. The inhomogeneous etch pits spatial distribution in the laser propagation direction could originate from an ion beam collimation and modulation by the effect of electromagnetic structures created in the laser plasma.

A comparison between accelerated hypofractionation and stereotactic ablative radiotherapy (SABR) for early-stage non-small cell lung cancer (NSCLC): Results of a propensity score-matched analysis

BACKGROUND AND PURPOSE: Stereotactic ablative radiotherapy (SABR) has become standard for inoperable early-stage non-small cell lung cancer (NSCLC). However, there is no randomized evidence demonstrating benefit over more fractionated radiotherapy. We compared accelerated hypofractionation (AH) and SABR using a propensity score-matched analysis.

MATERIALS AND METHODS: From 1997-2007, 119 patients (T1-3N0M0 NSCLC) were treated with AH (48-60Gy, 12-15 fractions). Prior to SABR, this represented our institutional standard. From 2008-2012, 192 patients (T1-3N0M0 NSCLC) were treated with SABR (48-52Gy, 4-5 fractions). A total of 114 patients (57 per cohort) were matched (1:1 ratio, caliper: 0.10) using propensity scores.

RESULTS: Median follow-up (range) for the AH cohort was 36.3 (2.5-109.1) months, while that for the SABR group was 32.5 (0.3-62.6)months. Three-year overall survival (OS) and local control (LC) rates were 49.5% vs. 72.4% [p=0.024; hazard ratio (HR): 2.33 (1.28, 4.23), p=0.006] and 71.9% vs. 89.3% [p=0.077; HR: 5.56 (1.53, 20.2), p=0.009], respectively. On multivariable analysis, tumour diameter and PET staging were predictive for OS, while the only predictive factor for LC was treatment cohort.

CONCLUSIONS: OS and LC were improved with SABR, although OS is more closely related to non-treatment factors. This represents one of the few studies comparing AH to SABR for early-stage lung cancer.

Beamed neutron emission driven by laser accelerated light ions

Highly anisotropic, beam-like neutron emission with peak flux of the order of 10^9 n/sr was obtained from light nuclei reactions in a pitcher–catcher scenario, by employing MeV ions driven by subpetawatt laser. The spatial profile of the neutron beam, fully captured for the first time by employing a CR39 nuclear track detector, shows a FWHMdivergence angle of ~70 deg, with a peak flux nearly an order of magnitude higher than the isotropic component elsewhere. The observed beamed flux of neutrons is highly favourable for a wide range of applications, and indeed for further transport and moderation to thermal energies. A systematic study employing various combinations of pitcher–catcher materials indicates the dominant reactions being d(p, n+p)1Hand d(d,n)3He. Albeit insufficient cross-section data are available for modelling, the observed anisotropy in the neutrons’ spatial and spectral profiles are most likely related to the directionality and high energy of the projectile ions.

Constitutive OGG1 variant together with BRCA mutations display accelerated telomere shortening

Dissertação de mestrado, Oncobiologia, Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, 2015

Iron Overload in a Murine Model of Hereditary Hemochromatosis Is Associated with Accelerated Progression of Osteoarthritis Under Mechanical Stress

OBJECTIVE: Hereditary hemochromatosis (HH) is a disease caused by mutations in the Hfe gene characterised by systemic iron overload and associated with an increased prevalence of osteoarthritis (OA) but the role of iron overload in the development of OA is still undefined. To further understand the molecular mechanisms involved we have used a murine model of HH and studied the progression of experimental OA under mechanical stress. DESIGN: OA was surgically induced in the knee joints of 10-week-old C57BL6 (wild-type) mice and Hfe-KO mice. OA progression was assessed using histology, micro CT, gene expression and immunohistochemistry at 8 weeks after surgery. RESULTS: Hfe-KO mice showed a systemic iron overload and an increased iron accumulation in the knee synovial membrane following surgery. The histological OA score was significantly higher in the Hfe-KO mice at 8 weeks after surgery. Micro CT study of the proximal tibia revealed increased subchondral bone volume and increased trabecular thickness. Gene expression and immunohistochemical analysis showed a significant increase in the expression of matrix metallopeptidase 3 (MMP-3) in the joints of Hfe-KO mice compared with control mice at 8 weeks after surgery. CONCLUSIONS: HH was associated with an accelerated development of OA in mice. Our findings suggest that synovial iron overload has a definite role in the progression of HH-related OA