Learning units-of-measure from scientific code

CamFort is our multi-purpose tool for lightweight analysis and verification of scientific Fortran code. One core feature provides units-of-measure verification (dimensional analysis) of programs, where users partially annotate programs with units-of-measure from which our tool checks consistency and infers any missing specifications. However, many users find it onerous to provide units-of-measure information for existing code, even in part. We have noted however that there are often many common patterns and clues about the intended units-of-measure contained within variable names, comments, and surrounding code context. In this work-in-progress paper, we describe how we are adapting our approach, leveraging machine-learning techniques to reconstruct units-of-measure information automatically thus saving programmer effort and increasing the likelihood of adoption

Learning units-of-measure from scientific code

CamFort is our multi-purpose tool for lightweight analysis and verification of scientific Fortran code. One core feature provides units-of-measure verification (dimensional analysis) of programs, where users partially annotate programs with units-of-measure from which our tool checks consistency and infers any missing specifications. However, many users find it onerous to provide units-of-measure information for existing code, even in part. We have noted however that there are often many common patterns and clues about the intended units-of-measure contained within variable names, comments, and surrounding code context. In this work-in-progress paper, we describe how we are adapting our approach, leveraging machine-learning techniques to reconstruct units-of-measure information automatically thus saving programmer effort and increasing the likelihood of adoption

Mineral sinks within ripening grape berries (Vitis vinifera L.)

Trends in the accumulation of mineral elements into the grape berry components give information about vascular flow into the berry. Shiraz berries were dissected into receptacle, skin, pulp, brush and seeds and the accumulation of 10 mineral elements into these components was followed through development. The elements were separated into two categories according to their accumulation pattern into the berry. The first group of elements continued to accumulate throughout berry growth and ripening, and was comprised of  phloem-mobile potassium, phosphorus, sulphur, magnesium, boron, iron and copper. The second group of elements accumulated mostly prior to veraison, and included the xylem-mobile minerals calcium, manganese and zinc. These results indicate that the xylem contribution to berry growth diminished after veraison. Berry fresh weight, dry weight, as well as berry sugar content, were all highly correlated with berry potassium content. While the pulp and skin were the strongest sinks for potassium and boron, seeds were the strongest sinks for calcium, phosphorus, sulphur, manganese and zinc. With the exception of calcium and manganese, seeds ceased to accumulate most elements during late ripening. The berry receptacle and brush did not accumulate any of the elements to levels above those of the other berry components at any stage of development. Therefore, they did not act as sinks for xylem- or phloem-mobile elements as vascular flow to the pulp and skin slowed.

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]

Lightning talk: Supporting software sustainability with lightweight specifications

Lightweight specifications support software maintainability by providing a way to verify that any changes to a code base preserve certain program properties. We give two examples of lightweight specifications for numerical code: $\textit{units-of-measure types}$ which specify the physical units of numerical quantities in a program; and $\textit{stencil specifications}$ which describe the pattern of data access used in array computations. Not only can we automatically verify that a program correctly implements these requirements but specifications provide documentation for future developers. Specifications can also be inferred and generated automatically in some cases, further reducing programmer effort. We finish by identifying future potential specification techniques to ease the maintenance and comprehension of scientific code.Engineering and Physical Sciences Research Council (Grant ID: EP/M026124/1)This is the final version of the article. It first appeared from CEUR Workshop Proceedings via http://ceur-ws.org/Vol-1686

Wavelength Tunability of Ion-bombardment Induced Ripples on Sapphire

A study of ripple formation on sapphire surfaces by 300-2000 eV Ar+ ion bombardment is presented. Surface characterization by in-situ synchrotron grazing incidence small angle x-ray scattering and ex-situ atomic force microscopy is performed in order to study the wavelength of ripples formed on sapphire (0001) surfaces. We find that the wavelength can be varied over a remarkably wide range-nearly two orders of magnitude-by changing the ion incidence angle. Within the linear theory regime, the ion induced viscous flow smoothing mechanism explains the general trends of the ripple wavelength at low temperature and incidence angles larger than 30. In this model, relaxation is confined to a few-nm thick damaged surface layer. The behavior at high temperature suggests relaxation by surface diffusion. However, strong smoothing is inferred from the observed ripple wavelength near normal incidence, which is not consistent with either surface diffusion or viscous flow relaxation.Comment: Revtex4, 19 pages, 10 figures with JPEG forma

Intrathecal enzyme replacement for Hurler syndrome: biomarker association with neurocognitive outcomes.

PurposeAbnormalities in cerebrospinal fluid (CSF) have been reported in Hurler syndrome, a fatal neurodegenerative lysosomal disorder. While no biomarker has predicted neurocognitive response to treatment, one of these abnormalities, glycosaminoglycan nonreducing ends (NREs), holds promise to monitor therapeutic efficacy. A trial of intrathecal enzyme replacement therapy (ERT) added to standard treatment enabled tracking of CSF abnormalities, including NREs. We evaluated safety, biomarker response, and neurocognitive correlates of change.MethodsIn addition to intravenous ERT and hematopoietic cell transplantation, patients (N = 24) received intrathecal ERT at four peritransplant time points; CSF was evaluated at each point. Neurocognitive functioning was quantified at baseline, 1 year, and 2 years posttransplant. Changes in CSF biomarkers and neurocognitive function were evaluated for an association.ResultsOver treatment, there were significant decreases in CSF opening pressure, biomarkers of disease activity, and markers of inflammation. Percent decrease in NRE from pretreatment to final intrathecal dose posttransplant was positively associated with percent change in neurocognitive score from pretreatment to 2 years posttransplant.ConclusionIntrathecal ERT was safe and, in combination with standard treatment, was associated with reductions in CSF abnormalities. Critically, we report evidence of a link between a biomarker treatment response and neurocognitive outcome in Hurler syndrome

Pedestrians with Disabilities and Town and City Streets: From Shared to Inclusive Space?

This article highlights the importance of ensuring that accessibility and inclusion for people with disabilities, as required by the UN Convention on the Rights of Persons with Disabilities, is fully embedded in efforts to reduce the dominance of cars in city streets and promote more active modes of travel (including walking, wheeling and cycling) in line with global agendas. Drawing on emerging findings from the Inclusive Public Space research project, we present and critically reflect on types of difficulty associated with streets in which what is commonly known as a ‘shared space’ design operates, and those in which all or part of the available space is designated as primarily for pedestrian use. The data on which this analysis is based is qualitative, deriving from 83 semi-structured interviews about the experiences of our participants (a substantial majority of whom identified as having a disability) in two large UK cities and their wider metropolitan areas. The types of exclusionary experience described by our participants are organised into two broad overlapping categories – first, difficulties associated with navigating environments in which kerbs have been removed; and second, difficulties associated with interacting with vehicles (including bicycles) within and at the boundaries of shared or pedestrian spaces. Our findings are in line with those of previous projects that challenge and complicate claims that ‘shared space’ design, with its removal of kerbs and controlled crossings, enhances safety and mobility for all. Further, they demonstrate that many of the concerns associated with ‘shared space’ environments are also applicable to other types of street environment intended primarily for pedestrians. As well as highlighting and raising awareness of potential types of exclusion against which action should be taken, we draw attention to measures that could reduce the risk of such exclusionary barriers arising and persisting