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Verifying Spatial Properties of Array Computations
Arrays computations are at the core of numerical modelling and computational science applications. However, low-level manipulation of array indices is a source of program error. Many practitioners are aware of the need to ensure program correctness, yet very few of the techniques from the programming research community are applied by scientists. We aim to change that by providing targetted lightweight veriication techniques for scientiic code. We focus on the all too common mistake of array ofset errors as a generalisation of of-by-one errors. Firstly, we report on a code analysis study on eleven real-world computational science code base, identifying common idioms of array usage and their spatial properties. This provides much needed data on array programming idioms common in scientiic code. From this data, we designed a lightweight declarative speciication language capturing the majority of array access patterns via a small set of combinators. We detail a semantic model, and the design and implementation of a veriication tool for our speciication language, which both checks and infers speciications. We evaluate our tool on our corpus of scientiic code. Using the inference mode, we found roughly 87,000 targets for speciication across roughly 1.1 million lines of code, showing that the vast majority of array computations read from arrays in a pattern with a simple, regular, static shape. We also studied the commit logs of one of our corpus packages, inding past bug ixes for which our speciication system distinguishes the change and thus could have been applied to detect such bugs.This work was supported by the EPSRC [grant number EP/M026124/1]
The chemistry of protoplanetary fragments formed via gravitational instabilities
In this paper, we model the chemical evolution of a 0.25 M
protoplanetary disc surrounding a 1 M star that undergoes
fragmentation due to self-gravity. We use Smoothed Particle Hydrodynamics
including a radiative transfer scheme, along with time-dependent chemical
evolution code to follow the composition of the disc and resulting fragments
over approximately 4000 yrs. Initially, four quasi-stable fragments are formed,
of which two are eventually disrupted by tidal torques in the disc. From the
results of our chemical modelling, we identify species that are abundant in the
fragments (e.g. HO, HS, HNO, N, NH,
OCS, SO), species that are abundant in the spiral shocks within the disc (e.g.
CO, CH, CN, CS, HCO), and species which are abundant in the
circumfragmentary material (e.g. HCO). Our models suggest that in
some fragments it is plausible for grains to sediment to the core before
releasing their volatiles into the planetary envelope, leading to changes in,
e.g., the C/O ratio of the gas and ice components. We would therefore predict
that the atmospheric composition of planets generated by gravitational
instability should not necessarily follow the bulk chemical composition of the
local disc material
A novel PKC activating molecule promotes neuroblast differentiation and delivery of newborn neurons in brain injuries
Neural stem cells are activated within neurogenic niches in response to brain injuries. This results in the production of neuroblasts, which unsuccessfully attempt to migrate toward the damaged tissue. Injuries constitute a gliogenic/non-neurogenic niche generated by the presence of anti-neurogenic signals, which impair neuronal differentiation and migration. Kinases of the protein kinase C (PKC) family mediate the release of growth factors that participate in different steps of the neurogenic process, particularly, novel PKC isozymes facilitate the release of the neurogenic growth factor neuregulin. We have demonstrated herein that a plant derived diterpene, (EOF2; CAS number 2230806-06-9), with the capacity to activate PKC facilitates the release of neuregulin 1, and promotes neuroblasts differentiation and survival in cultures of subventricular zone (SVZ) isolated cells in a novel PKC dependent manner. Local infusion of this compound in mechanical cortical injuries induces neuroblast enrichment within the perilesional area, and noninvasive intranasal administration of EOF2 promotes migration of neuroblasts from the SVZ towards the injury, allowing their survival and differentiation into mature neurons, being some of them cholinergic and GABAergic. Our results elucidate the mechanism of EOF2 promoting neurogenesis in injuries and highlight the role of novel PKC isozymes as targets in brain injury regeneration
Chronic non-freezing cold injury results in neuropathic pain due to a sensory neuropathy
Non-freezing cold injury develops after sustained exposure to cold temperatures, resulting in tissue cooling but not freezing. This can result in persistent sensory disturbance of the hands and feet including numbness, paraesthesia and chronic pain. Both vascular and neurological aetiologies of this pain have been suggested but remain unproven. We prospectively approached patients referred for clinical assessment of chronic pain following non-freezing cold injury between 12 February 2014 and 30 November 2016. Of 47 patients approached, 42 consented to undergo detailed neurological evaluations including: questionnaires to detail pain location and characteristics, structured neurological examination, quantitative sensory testing, nerve conduction studies and skin biopsy for intraepidermal nerve fibre assessment. Of the 42 study participants, all had experienced non-freezing cold injury while serving in the UK armed services and the majority were of African descent (76.2%) and male (95.2%). Many participants reported multiple exposures to cold. The median time between initial injury and referral was 3.72 years. Pain was principally localized to the hands and the feet, neuropathic in nature and in all study participants associated with cold hypersensitivity. Clinical examination and quantitative sensory testing were consistent with a sensory neuropathy. In all cases, large fibre nerve conduction studies were normal. The intraepidermal nerve fibre density was markedly reduced with 90.5% of participants having a count at or below the 0.05 centile of published normative controls. Using the Neuropathic Pain Special Interest Group of the International Association for the Study of Pain grading for neuropathic pain, 100% had probable and 95.2% definite neuropathic pain. Chronic non-freezing cold injury is a disabling neuropathic pain disorder due to a sensory neuropathy. Why some individuals develop an acute painful sensory neuropathy on sustained cold exposure is not yet known, but individuals of African descent appear vulnerable. Screening tools, such as the DN4 questionnaire, and treatment algorithms for neuropathic pain should now be used in the management of these patients
Modeling Slope Instability as Shear Rupture Propagation in a Saturated Porous Medium
When a region of intense shear in a slope is much thinner than other relevant geometric lengths, this shear failure may be approximated as localized slip, as in faulting, with strength determined by frictional properties of the sediment and effective stress normal to the failure surface. Peak and residual frictional strengths of submarine sediments indicate critical slope angles well above those of most submarine slopes—in contradiction to abundant failures. Because deformation of sediments is governed by effective stress, processes affecting pore pressures are a means of strength reduction. However, common methods of exami ning slope stability neglect dynamically variable pore pressure during failure. We examine elastic-plastic models of the capped Drucker-Prager type and derive approximate equations governing pore pressure about a slip surface when the adjacent material may deform plastically. In the process we identify an elastic-plastic hydraulic diffusivity with an evolving permeability and plastic storage term analogous to the elastic term of traditional poroelasticity. We also examine their application to a dynamically propagating subsurface rupture and find indications of downslope directivity.Earth and Planetary SciencesEngineering and Applied Science
Need-based resource allocation: different need indicators, different results?
<p>Abstract</p> <p>Background</p> <p>A key policy objective in most publicly financed health care systems is to allocate resources according to need. Many jurisdictions implement this policy objective through need-based allocation models. To date, no gold standard exists for selecting need indicators. In the absence of a gold standard, sensitivity of the choice of need indicators is of concern. The primary objective of this study was to assess the consistency and plausibility of estimates of per capita relative need for health services across Canadian provinces based on different need indicators.</p> <p>Methods</p> <p>Using the 2000/2001 Canadian Community Health Survey, we estimated relative per capita need for general practitioner, specialist, and hospital services by province using two approaches that incorporated a different set of need indicators: (1) demographics (age and sex), and (2) demographics, socioeconomic status, and health status. For both approaches, we first fitted regression models to estimate standard utilization of each of three types of health services by indicators of need. We defined the standard as average levels of utilization by needs indicators in the national sample. Subsequently, we estimated expected per capita utilization of each type of health services in each province. We compared these estimates of per capita relative need with premature mortality in each province to check their face validity.</p> <p>Results</p> <p>Both approaches suggested that expected relative per capita need for three services vary across provinces. Different approaches, however, yielded different and inconsistent results. Moreover, provincial per capita relative need for the three health services did not always indicate the same direction of need suggested by premature mortality in each province. In particular, the two approaches suggested Newfoundland had less need than the Canadian average for all three services, but it had the highest premature mortality in Canada.</p> <p>Conclusion</p> <p>Substantial differences in need for health care may exist across Canadian provinces, but the direction and magnitude of differences depend on the need indicators used. Allocations from models using survey data lacked face validity for some provinces. These results call for the need to better understand the biases that may result from the use of survey data for resource allocation.</p
Protective Efficacy and Safety of Brucella melitensis 16M mucR against Intraperitoneal and Aerosol Challenge in BALB/c Mice
Human neutrophil clearance of bacterial pathogens triggers anti-microbial gamma delta T cell responses in early infection
Human blood Vc9/Vd2 T cells, monocytes and neutrophils share a responsiveness toward inflammatory chemokines and are rapidly recruited to sites of infection. Studying their interaction in vitro and relating these findings to in vivo observations in patients may therefore provide crucial insight into inflammatory events. Our present data demonstrate that Vc9/Vd2 T cells provide potent survival signals resulting in neutrophil activation and the release of the neutrophil chemoattractant CXCL8 (IL-8). In turn, Vc9/Vd2 T cells readily respond to neutrophils harboring phagocytosed bacteria, as evidenced by expression of CD69, interferon (IFN)-c and tumor necrosis factor (TNF)-a. This response is dependent on the ability of these bacteria to produce the microbial metabolite (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMB-PP), requires cell-cell contact of Vc9/Vd2 T cells with accessory monocytes through lymphocyte function-associated antigen-1 (LFA-1), and results in a TNF-a dependent proliferation of Vc9/Vd2 T cells. The antibiotic fosmidomycin, which targets the HMB-PP biosynthesis pathway, not only has a direct antibacterial effect on most HMB-PP producing bacteria but also possesses rapid anti-inflammatory properties by inhibiting cd T cell responses in vitro. Patients with acute peritoneal-dialysis (PD)-associated bacterial peritonitis – characterized by an excessive influx of neutrophils and monocytes into the peritoneal cavity – show a selective activation of local Vc9/Vd2 T cells by HMB-PP producing but not by HMB-PP deficient bacterial pathogens. The cd T celldriven perpetuation of inflammatory responses during acute peritonitis is associated with elevated peritoneal levels of cd T cells and TNF-a and detrimental clinical outcomes in infections caused by HMB-PP positive microorganisms. Taken together, our findings indicate a direct link between invading pathogens, neutrophils, monocytes and microbe-responsive cd T cells in early infection and suggest novel diagnostic and therapeutic approaches.Martin S. Davey, Chan-Yu Lin, Gareth W. Roberts, Sinéad Heuston, Amanda C. Brown, James A. Chess, Mark A. Toleman, Cormac G.M. Gahan, Colin Hill, Tanya Parish, John D. Williams, Simon J. Davies, David W. Johnson, Nicholas Topley, Bernhard Moser and Matthias Eber
Design and feasibility testing of a novel group intervention for young women who binge drink in groups
BackgroundYoung women frequently drink alcohol in groups and binge drinking within these natural drinking groups is common. This study describes the design of a theoretically and empirically based group intervention to reduce binge drinking among young women. It also evaluates their engagement with the intervention and the acceptability of the study methods.MethodsFriendship groups of women aged 18–35 years, who had two or more episodes of binge drinking (>6 UK units on one occasion; 48g of alcohol) in the previous 30 days, were recruited from the community. A face-to-face group intervention, based on the Health Action Process Approach, was delivered over three sessions. Components of the intervention were woven around fun activities, such as making alcohol free cocktails. Women were followed up four months after the intervention was delivered. Results The target of 24 groups (comprising 97 women) was recruited. The common pattern of drinking was infrequent, heavy drinking (mean consumption on the heaviest drinking day was UK 18.1 units). Process evaluation revealed that the intervention was delivered with high fidelity and acceptability of the study methods was high. The women engaged positively with intervention components and made group decisions about cutting down. Twenty two groups set goals to reduce their drinking, and these were translated into action plans. Retention of individuals at follow up was 87%.ConclusionsThis study successfully recruited groups of young women whose patterns of drinking place them at high risk of acute harm. This novel approach to delivering an alcohol intervention has potential to reduce binge drinking among young women. The high levels of engagement with key steps in the behavior change process suggests that the group intervention should be tested in a full randomised controlled trial
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