Parallel implementation of the TRANSIMS micro-simulation

This paper describes the parallel implementation of the TRANSIMS traffic micro-simulation. The parallelization method is domain decomposition, which means that each CPU of the parallel computer is responsible for a different geographical area of the simulated region. We describe how information between domains is exchanged, and how the transportation network graph is partitioned. An adaptive scheme is used to optimize load balancing. We then demonstrate how computing speeds of our parallel micro-simulations can be systematically predicted once the scenario and the computer architecture are known. This makes it possible, for example, to decide if a certain study is feasible with a certain computing budget, and how to invest that budget. The main ingredients of the prediction are knowledge about the parallel implementation of the micro-simulation, knowledge about the characteristics of the partitioning of the transportation network graph, and knowledge about the interaction of these quantities with the computer system. In particular, we investigate the differences between switched and non-switched topologies, and the effects of 10 Mbit, 100 Mbit, and Gbit Ethernet. keywords: Traffic simulation, parallel computing, transportation planning, TRANSIM

The dynamics of iterated transportation simulations

Iterating between a router and a traffic micro-simulation is an increasibly accepted method for doing traffic assignment. This paper, after pointing out that the analytical theory of simulation-based assignment to-date is insufficient for some practical cases, presents results of simulation studies from a real world study. Specifically, we look into the issues of uniqueness, variability, and robustness and validation. Regarding uniqueness, despite some cautionary notes from a theoretical point of view, we find no indication of ``meta-stable'' states for the iterations. Variability however is considerable. By variability we mean the variation of the simulation of a given plan set by just changing the random seed. We show then results from three different micro-simulations under the same iteration scenario in order to test for the robustness of the results under different implementations. We find the results encouraging, also when comparing to reality and with a traditional assignment result. Keywords: dynamic traffic assignment (DTA); traffic micro-simulation; TRANSIMS; large-scale simulations; urban planningComment: 24 pages, 7 figure

Elastase activity on sputum neutrophils correlates with severity of lung disease in cystic fibrosis

Neutrophil elastase (NE) is a key risk factor for severity of cystic fibrosis (CF) lung disease. Recent studies identified increased NE activity on the surface of airway neutrophils from CF-like mice and patients with CF. However, the role of surface-bound NE in CF lung disease remains unknown. We determined the relationship between surface-bound NE activity and severity of lung disease in CF.Surface-bound NE activity was measured on sputum neutrophils from 35 CF patients and eight healthy controls using novel lipidated Förster resonance energy transfer reporters and correlated with free NE activity, neutrophil counts, interleukin-8, myeloperoxidase and antiproteases in sputum supernatant, and with lung function parameters.Surface-bound NE activity was increased in CF compared to healthy controls (p&lt;0.01) and correlated with free NE activity (p&lt;0.05) and other inflammation markers (p&lt;0.001). Surface-bound and free NE activity correlated with forced expiratory volume in 1 s % predicted (p&lt;0.01 and p&lt;0.05), but only surface-bound NE activity correlated with plethysmographic functional residual capacity % pred (p&lt;0.01) in patients with CF.We demonstrate that surface-bound NE activity on airway neutrophils correlates with severity of lung disease in patients with CF. Our results suggest that surface-bound NE activity may play an important role in the pathogenesis and serve as novel biomarker in CF lung disease.</jats:p

PI3K Signaling in Normal B Cells and Chronic Lymphocytic Leukemia (CLL).

B cells provide immunity to extracellular pathogens by secreting a diverse repertoire of antibodies with high affinity and specificity for exposed antigens. The B cell receptor (BCR) is a transmembrane antibody, which facilitates the clonal selection of B cells producing secreted antibodies of the same specificity. The diverse antibody repertoire is generated by V(D)J recombination of heavy and light chain genes, whereas affinity maturation is mediated by activation-induced cytidine deaminase (AID)-mediated mutagenesis. These processes, which are essential for the generation of adaptive humoral immunity, also render B cells susceptible to chromosomal rearrangements and point mutations that in some cases lead to cancer. In this chapter, we will review the central role of PI3K s in mediating signals from the B cell receptor that not only facilitate the development of functional B cell repertoire, but also support the growth and survival of neoplastic B cells, focusing on chronic lymphocytic leukemia (CLL) B cells. Perhaps because of the central role played by PI3K in BCR signaling, B cell leukemia and lymphomas are the first diseases for which a PI3K inhibitor has been approved for clinical use

Duration of androgen deprivation therapy with postoperative radiotherapy for prostate cancer: a comparison of long-course versus short-course androgen deprivation therapy in the RADICALS-HD randomised trial

Background Previous evidence supports androgen deprivation therapy (ADT) with primary radiotherapy as initial treatment for intermediate-risk and high-risk localised prostate cancer. However, the use and optimal duration of ADT with postoperative radiotherapy after radical prostatectomy remains uncertain. Methods RADICALS-HD was a randomised controlled trial of ADT duration within the RADICALS protocol. Here, we report on the comparison of short-course versus long-course ADT. Key eligibility criteria were indication for radiotherapy after previous radical prostatectomy for prostate cancer, prostate-specific antigen less than 5 ng/mL, absence of metastatic disease, and written consent. Participants were randomly assigned (1:1) to add 6 months of ADT (short-course ADT) or 24 months of ADT (long-course ADT) to radiotherapy, using subcutaneous gonadotrophin-releasing hormone analogue (monthly in the short-course ADT group and 3-monthly in the long-course ADT group), daily oral bicalutamide monotherapy 150 mg, or monthly subcutaneous degarelix. Randomisation was done centrally through minimisation with a random element, stratified by Gleason score, positive margins, radiotherapy timing, planned radiotherapy schedule, and planned type of ADT, in a computerised system. The allocated treatment was not masked. The primary outcome measure was metastasis-free survival, defined as metastasis arising from prostate cancer or death from any cause. The comparison had more than 80% power with two-sided α of 5% to detect an absolute increase in 10-year metastasis-free survival from 75% to 81% (hazard ratio [HR] 0·72). Standard time-to-event analyses were used. Analyses followed intention-to-treat principle. The trial is registered with the ISRCTN registry, ISRCTN40814031, and ClinicalTrials.gov , NCT00541047 . Findings Between Jan 30, 2008, and July 7, 2015, 1523 patients (median age 65 years, IQR 60–69) were randomly assigned to receive short-course ADT (n=761) or long-course ADT (n=762) in addition to postoperative radiotherapy at 138 centres in Canada, Denmark, Ireland, and the UK. With a median follow-up of 8·9 years (7·0–10·0), 313 metastasis-free survival events were reported overall (174 in the short-course ADT group and 139 in the long-course ADT group; HR 0·773 [95% CI 0·612–0·975]; p=0·029). 10-year metastasis-free survival was 71·9% (95% CI 67·6–75·7) in the short-course ADT group and 78·1% (74·2–81·5) in the long-course ADT group. Toxicity of grade 3 or higher was reported for 105 (14%) of 753 participants in the short-course ADT group and 142 (19%) of 757 participants in the long-course ADT group (p=0·025), with no treatment-related deaths. Interpretation Compared with adding 6 months of ADT, adding 24 months of ADT improved metastasis-free survival in people receiving postoperative radiotherapy. For individuals who can accept the additional duration of adverse effects, long-course ADT should be offered with postoperative radiotherapy. Funding Cancer Research UK, UK Research and Innovation (formerly Medical Research Council), and Canadian Cancer Society