A Practical Hierarchial Model of Parallel Computation: The Model

We introduce a model of parallel computation that retains the ideal properties of the PRAM by using it as a sub-model, while simultaneously being more reflective of realistic parallel architectures by accounting for and providing abstract control over communication and synchronization costs. The Hierarchical PRAM (H-PRAM) model controls conceptual complexity in the face of asynchrony in two ways. First, by providing the simplifying assumption of synchronization to the design of algorithms, but allowing the algorithms to work asynchronously with each other; and organizing this control asynchrony via an implicit hierarchy relation. Second, by allowing the restriction of communication asynchrony in order to obtain determinate algorithms (thus greatly simplifying proofs of correctness). It is shown that the model is reflective of a variety of existing and proposed parallel architectures, particularly ones that can support massive parallelism. Relationships to programming languages are discussed. Since the PRAM is a sub-model, we can use PRAM algorithms as sub-algorithms in algorithms for the H-PRAM; thus results that have been established with respect to the PRAM are potentially transferable to this new model. The H-PRAM can be used as a flexible tool to investigate general degrees of locality (“neighborhoods of activity) in problems, considering communication and synchronization simultaneously. This gives the potential of obtaining algorithms that map more efficiently to architectures, and of increasing the number of processors that can efficiently be used on a problem (in comparison to a PRAM that charges for communication and synchronization). The model presents a framework in which to study the extent that general locality can be exploited in parallel computing. A companion paper demonstrates the usage of the H-PRAM via the design and analysis of various algorithms for computing the complete binary tree and the FFT/butterfly graph

Two-Dimensional Pattern Matching with k Mismatches

We give an algorithm which finds all occurrences of an m1 x m2 pattern array embedded as subarrays in an n1 x n2 array of text, where at most k mismatches are allowed per occurrence. The algorithm runs in time O((k+a)(blogb+ n1n2)), where a = min(m1m2) and b=max(m1m2). This improves upon the previously best known algorithm, and is asymptotically optimal for k ≈ a

A Practical Hierarchical Model of Parallel Computation ll: Binary Tree and FFT Algorithms

A companion paper has introduced the Hierarchical PRAM (H-PRAM) model of parallel computation, which achieves a good balance between simplicity of usage and reflectivity of realistic parallel computers. In this paper, we demonstrate the usage of the model by designing and analyzing various algorithms for computing the complete binary tree, and the FFT/butterfly graph. By concentrating on two problems, we are able to demonstrate the results of different combinations of organizational strategies and different types of sub-models of the H-PRAM. The philosophy in algorithm design is to maximize the number of processors P that are efficiently usable with respect to an input size N, and to minimize the inefficiency when efficiency is not possible (when P is too large with respect to N). This can be done because of the H-PRAM\u27s representation of general locality, i.e. both strict and neighborhood locality, and results in algorithms that can efficiently employ more processors (and are thus faster) than algorithms for models that only represent strict locality

Effective recruitment of participants to a phase I study using the internet and publicity releases through charities and patient organisations: analysis of the adaptive study of IL-2 dose on regulatory T cells in type 1 diabetes (DILT1D).

A barrier to the successful development of new disease treatments is the timely recruitment of participants to experimental medicine studies that are primarily designed to investigate biological mechanisms rather than evaluate clinical efficacy. The aim of this study was to analyse the performance of three recruitment sources and the effect of publicity events during the Adaptive study of IL-2 dose on regulatory T cells in type 1 diabetes (DILT1D).This work is funded by the JDRF (9-2011-253), the Wellcome Trust (091157) and the National Institute for Health Research (NIHR) Cambridge Biomedical Research Centre. The research leading to these results has received funding from the European Union’s Seventh Framework Programme (FP7/2007-2013) under grant agreement number 241447 (NAIMIT). The Cambridge Institute for Medical Research (CIMR) is in receipt of a Wellcome Trust Strategic Award (100140).This is the final version of the article. It first appeared from BMC via http://dx.doi.org/10.1186/s13063-015-0583-

Does mixing acute medical admissions with burn patients increase infective complications from paediatric thermal injuries?

In the winter of 2005–2006, the management at our children's hospital elected to admit ‘overspill’ acute medical admissions to the ward used for plastic surgery and burns for logistical reasons. This study was conducted to assess the effects of that change on the incidence of infective complications in thermally-injured patients. Seventy-three patients were studied, 23 in the sample winter and 50 in the two preceding control winters. The data gathered included days on IV fluids and antibiotics, transfer to the Paediatric Intensive Care Unit (PICU), microbiology and a ‘septic signs score’ – based on pyrexia, irritability, diarrhoea/vomiting, wound colonization, bacteraemia. The outcomes studied were: the maximum ‘septic signs score’; patients with a score ≥3; wound colonization; PICU admission; days on antibiotics and IV fluids. A statistically significant increase in patients with septic episodes was demonstrated by an increase in the mean septic signs score (0.66–1.48, P = 0.044) and the number of patients with a score ≥3 (4–22%, P = 0.017). Other analysed variables did not reach statistical significance although the raw data suggested a trend. It was concluded that there is an association between mixing acute medical admissions with thermally-injured patients and an increase in the incidence of infective complications in the latter group

Cystatin C is glucocorticoid responsive, directs recruitment of Trem2+ macrophages, and predicts failure of cancer immunotherapy

Cystatin C (CyC), a secreted cysteine protease inhibitor, has unclear biological functions. Many patients exhibit elevated plasma CyC levels, particularly during glucocorticoid (GC) treatment. This study links GCs with CyC’s systemic regulation by utilizing genome-wide association and structural equation modeling to determine CyC production genetics in the UK Biobank. Both CyC production and a polygenic score (PGS) capturing predisposition to CyC production were associated with increased all-cause and cancer-specific mortality. We found that the GC receptor directly targets CyC, leading to GC-responsive CyC secretion in macrophages and cancer cells. CyC-knockout tumors displayed significantly reduced growth and diminished recruitment of TREM2+ macrophages, which have been connected to cancer immunotherapy failure. Furthermore, the CyC-production PGS predicted checkpoint immunotherapy failure in 685 patients with metastatic cancer from combined clinical trial cohorts. In conclusion, CyC may act as a GC effector pathway via TREM2+ macrophage recruitment and may be a potential target for combination cancer immunotherapy.publishedVersio

Human Resource and Funding Constraints for Essential Surgery in District Hospitals in Africa: A Retrospective Cross-Sectional Survey

In the second of two papers investigating surgical provision in eight district hospitals in Saharan African countries, Margaret Kruk and colleagues describe the range of providers of surgical care and anesthesia and estimate the related costs

Regulatory T Cell Responses in Participants with Type 1 Diabetes after a Single Dose of Interleukin-2: A Non-Randomised, Open Label, Adaptive Dose-Finding Trial

BACKGROUND: Interleukin-2 (IL-2) has an essential role in the expansion and function of CD4+ regulatory T cells (Tregs). Tregs reduce tissue damage by limiting the immune response following infection and regulate autoreactive CD4+ effector T cells (Teffs) to prevent autoimmune diseases, such as type 1 diabetes (T1D). Genetic susceptibility to T1D causes alterations in the IL-2 pathway, a finding that supports Tregs as a cellular therapeutic target. Aldesleukin (Proleukin; recombinant human IL-2), which is administered at high doses to activate the immune system in cancer immunotherapy, is now being repositioned to treat inflammatory and autoimmune disorders at lower doses by targeting Tregs. METHODS AND FINDINGS: To define the aldesleukin dose response for Tregs and to find doses that increase Tregs physiologically for treatment of T1D, a statistical and systematic approach was taken by analysing the pharmacokinetics and pharmacodynamics of single doses of subcutaneous aldesleukin in the Adaptive Study of IL-2 Dose on Regulatory T Cells in Type 1 Diabetes (DILT1D), a single centre, non-randomised, open label, adaptive dose-finding trial with 40 adult participants with recently diagnosed T1D. The primary endpoint was the maximum percentage increase in Tregs (defined as CD3+CD4+CD25highCD127low) from the baseline frequency in each participant measured over the 7 d following treatment. There was an initial learning phase with five pairs of participants, each pair receiving one of five pre-assigned single doses from 0.04 × 106 to 1.5 × 106 IU/m2, in order to model the dose-response curve. Results from each participant were then incorporated into interim statistical modelling to target the two doses most likely to induce 10% and 20% increases in Treg frequencies. Primary analysis of the evaluable population (n = 39) found that the optimal doses of aldesleukin to induce 10% and 20% increases in Tregs were 0.101 × 106 IU/m2 (standard error [SE] = 0.078, 95% CI = -0.052, 0.254) and 0.497 × 106 IU/m2 (SE = 0.092, 95% CI = 0.316, 0.678), respectively. On analysis of secondary outcomes, using a highly sensitive IL-2 assay, the observed plasma concentrations of the drug at 90 min exceeded the hypothetical Treg-specific therapeutic window determined in vitro (0.015-0.24 IU/ml), even at the lowest doses (0.040 × 106 and 0.045 × 106 IU/m2) administered. A rapid decrease in Treg frequency in the circulation was observed at 90 min and at day 1, which was dose dependent (mean decrease 11.6%, SE = 2.3%, range 10.0%-48.2%, n = 37), rebounding at day 2 and increasing to frequencies above baseline over 7 d. Teffs, natural killer cells, and eosinophils also responded, with their frequencies rapidly and dose-dependently decreased in the blood, then returning to, or exceeding, pretreatment levels. Furthermore, there was a dose-dependent down modulation of one of the two signalling subunits of the IL-2 receptor, the β chain (CD122) (mean decrease = 58.0%, SE = 2.8%, range 9.8%-85.5%, n = 33), on Tregs and a reduction in their sensitivity to aldesleukin at 90 min and day 1 and 2 post-treatment. Due to blood volume requirements as well as ethical and practical considerations, the study was limited to adults and to analysis of peripheral blood only. CONCLUSIONS: The DILT1D trial results, most notably the early altered trafficking and desensitisation of Tregs induced by a single ultra-low dose of aldesleukin that resolves within 2-3 d, inform the design of the next trial to determine a repeat dosing regimen aimed at establishing a steady-state Treg frequency increase of 20%-50%, with the eventual goal of preventing T1D. TRIAL REGISTRATION: ISRCTN Registry ISRCTN27852285; ClinicalTrials.gov NCT01827735.This is the final version of the article. It first appeared from the Public Library of Science via http://dx.doi.org/10.1371/journal.pmed.100213