Precision analysis for hardware acceleration of numerical algorithms

The precision used in an algorithm affects the error and performance of individual computations, the memory usage, and the potential parallelism for a fixed hardware budget. However, when migrating an algorithm onto hardware, the potential improvements that can be obtained by tuning the precision throughout an algorithm to meet a range or error specification are often overlooked; the major reason is that it is hard to choose a number system which can guarantee any such specification can be met. Instead, the problem is mitigated by opting to use IEEE standard double precision arithmetic so as to be ‘no worse’ than a software implementation. However, the flexibility in the number representation is one of the key factors that can be exploited on reconfigurable hardware such as FPGAs, and hence ignoring this potential significantly limits the performance achievable. In order to optimise the performance of hardware reliably, we require a method that can tractably calculate tight bounds for the error or range of any variable within an algorithm, but currently only a handful of methods to calculate such bounds exist, and these either sacrifice tightness or tractability, whilst simulation-based methods cannot guarantee the given error estimate. This thesis presents a new method to calculate these bounds, taking into account both input ranges and finite precision effects, which we show to be, in general, tighter in comparison to existing methods; this in turn can be used to tune the hardware to the algorithm specifications. We demonstrate the use of this software to optimise hardware for various algorithms to accelerate the solution of a system of linear equations, which forms the basis of many problems in engineering and science, and show that significant performance gains can be obtained by using this new approach in conjunction with more traditional hardware optimisations

Solar off-limb line widths: Alfven waves, ion-cyclotron waves, and preferential heating

Alfven waves and ion-cyclotron absorption of high-frequency waves are frequently brought into models devoted to coronal heating and fast solar-wind acceleration. Signatures of ion-cyclotron resonance have already been observed in situ in the solar wind (HELIOS spacecrafts) and, recently, in the upper corona (UVCS/SOHO remote-sensing results). We propose a method to constrain both the Alfven wave amplitude and the preferential heating induced by ion-cyclotron resonance, above a partially developed polar coronal hole observed with the SUMER/SOHO spectrometer. The instrumental stray light contribution is first substracted from the spectra. By supposing that the non-thermal velocity is related to the Alfven wave amplitude, it is constrained through a density diagnostic and the gradient of the width of the Mg X 625 A line. The temperatures of several coronal ions, as functions of the distance above the limb, are then determined by substracting the non-thermal component to the observed line widths. The effect of stray light explains the apparent decrease with height in the width of several spectral lines, this decrease usually starting about 0.1-0.2 Rs above the limb. This result rules out any direct evidence of damping of the Alfven waves, often suggested by other authors. We also find that the ions with the smallest charge-to-mass ratios are the hottest ones at a fixed altitude and that they are subject to a stronger heating, as compared to the others, between 57" and 102" above the limb. This constitutes a serious clue to ion-cyclotron preferential heating.Comment: 15 pages, 12 figures, 3 table

Elevated A20 promotes TNF-induced and RIPK1-dependent intestinal epithelial cell death

Intestinal epithelial cell (IEC) death is a common feature of inflammatory bowel disease (IBD) that triggers inflammation by compromising barrier integrity. In many patients with IBD, epithelial damage and inflammation are TNF-dependent. Elevated TNF production in IBD is accompanied by increased expression of the TNFAIP3 gene, which encodes A20, a negative feedback regulator of NF-κB. A20 in intestinal epithelium from patients with IBD coincided with the presence of cleaved caspase-3, and A20 transgenic (Tg) mice, in which A20 is expressed from an IEC-specific promoter, were highly susceptible to TNF-induced IEC death, intestinal damage, and shock. A20-expressing intestinal organoids were also susceptible to TNF-induced death, demonstrating that enhanced TNF-induced apoptosis was a cell-autonomous property of A20. This effect was dependent on Receptor Interacting Protein Kinase 1 (RIPK1) activity, and A20 was found to associate with the Ripoptosome complex, potentiating its ability to activate caspase-8. A20-potentiated RIPK1-dependent apoptosis did not require the A20 deubiquitinase (DUB) domain and zinc finger 4 (ZnF4), which mediate NF-κB inhibition in fibroblasts, but was strictly dependent on ZnF7 and A20 dimerization. We suggest that A20 dimers bind linear ubiquitin to stabilize the Ripoptosome and potentiate its apoptosis-inducing activity

Prediction of enteric methane production, yield and intensity in dairy cattle using an intercontinental database

Enteric methane (CH4) production from cattle contributes to global greenhouse gas emissions. Measurement of enteric CH4 is complex, expensive and impractical at large scales; therefore, models are commonly used to predict CH4 production. However, building robust prediction models requires extensive data from animals under different management systems worldwide. The objectives of this study were to (1) collate a global database of enteric CH4 production from individual lactating dairy cattle; (2) determine the availability of key variables for predicting enteric CH4 production (g/d per cow), yield [g/kg dry matter intake (DMI)], and intensity (g/kg energy corrected milk) and their respective relationships; (3) develop intercontinental and regional models and cross-validate their performance; and (4) assess the trade-off between availability of on-farm inputs and CH4 prediction accuracy. The intercontinental database covered Europe (EU), the US (US), Chile (CL), Australia (AU), and New Zealand (NZ). A sequential approach was taken by incrementally adding key variables to develop models with increasing complexity. Methane emissions were predicted by fitting linear mixed models. Within model categories, an intercontinental model with the most available independent variables performed best with root mean square prediction error (RMSPE) as a percentage of mean observed value of 16.6, 14.4, and 19.8% for intercontinental, EU, and US regions, respectively. Less complex models requiring only DMI had predictive ability comparable to complex models. Enteric CH4 production, yield, and intensity prediction models developed on an intercontinental basis had similar performance across regions, however, intercepts and slopes were different with implications for prediction. Revised CH4 emission conversion factors for specific regions are required to improve CH4 production estimates in national inventories. In conclusion, information on DMI is required for good prediction, and other factors such as dietary NDF concentration, improve the prediction. For enteric CH4 yield and intensity prediction, information on milk yield and composition is required for better estimation

The impact of lidocaine plaster prescribing reduction strategies: A comparison of two national health services in Europe

AIMS: In 2017, two distinct interventions were implemented in Ireland and England to reduce prescribing of lidocaine medicated plasters. In Ireland, restrictions on reimbursement were introduced through implementation of an application system for reimbursement. In England, updated guidance on items which should not be routinely prescribed in primary care, including lidocaine plasters, was published. This study aims to compare how the interventions impacted prescribing of lidocaine plasters in these countries. METHODS: We conducted an interrupted time-series study using general practice data. For Ireland, monthly dispensing data (2015-2019) from the means-tested General Medical Services (GMS) scheme was used. For England, data covered all patients. Outcomes were the rate of dispensings, quantity and costs of lidocaine plasters, and we modelled level and trend changes from the first full month of the policy/guidance change. RESULTS: Ireland had higher rates of lidocaine dispensings compared to England throughout the study period; this was 15.22/1000 population immediately pre-intervention, and there was equivalent to a 97.2% immediate reduction following the intervention. In England, the immediate pre-intervention dispensing rate was 0.36/1000, with an immediate reduction of 0.0251/1000 (a 5.8% decrease), followed by a small but significant decrease in the monthly trend relative to the pre-intervention trend of 0.0057 per month. CONCLUSIONS: Among two different interventions aiming to decrease low-value lidocaine plaster prescribing, there was a substantially larger impact in Ireland of reimbursement restriction compared to issuing guidance in England. However, this is in the context of much higher baseline rates of use in Ireland compared to England

Prediction of nitrogen excretion from data on dairy cows fed a wide range of diets compiled in an intercontinental database: a meta-analysis

publishedVersio

Communications Biophysics

Contains research objectives and summary of research on five research projects, with ten sub-topics.National Institutes of Health (Grant 1 RO1 NS10916-01)National Institutes of Health (Grant 5 RO1 NS11000-03)National Institutes of Health (Grant 1 RO1 NS11153-01)Harvard-M.I.T. Rehabilitation Engineering CenterU. S. Department of Health, Education, and Welfare (Grant 23-P-55854)National Institutes of Health (Grant 1 RO1 NS11680-01)National Institutes of Health (Grant 5 ROI NS11080-02)M.I.T. Health Sciences FundNational Aeronautics and Space Administration (Grant NSG-2032)National Institutes of Health (Grant 5 TO1 GM01555-09)Massachusetts General Hospital Purchase Order F63853Boston City Hospital Purchase Order 4338-7543

Communications Biophysics

Contains research objectives and summary of research on thirteen research projects split into four section.National Institutes of Health (Grant 1 RO1 NS10737-01)National Institutes of Health (Grant 1 ROI NS10916-01)National Institutes of Health (Grant 5 RO1 NS11000-02)National Institutes of Health (Grant 1 RO1 NS11153-01)Harvard M.I.T. Rehabilitation Engineering CenterU. S. Department of Health, Education, and Welfare, Grant 23-P-55854National Institutes of Health (Grant 1 RO1 NS11680-01)Norlin Music, Inc.Clarence J. LeBel FundNational Institutes of Health (Grant 1 RO1 NS11080-01A1)National Institutes of Health (Grant 5 TO1 GM01555-08)M.I.T. Health Sciences FundBoston City Hospital Purchase Order 1176-05-21335-C