2,671 research outputs found
Concurrent Computing with Shared Replicated Memory
The behavioural theory of concurrent systems states that any concurrent
system can be captured by a behaviourally equivalent concurrent Abstract State
Machine (cASM). While the theory in general assumes shared locations, it
remains valid, if different agents can only interact via messages, i.e. sharing
is restricted to mailboxes. There may even be a strict separation between
memory managing agents and other agents that can only access the shared memory
by sending query and update requests to the memory agents. This article is
dedicated to an investigation of replicated data that is maintained by a memory
management subsystem, whereas the replication neither appears in the requests
nor in the corresponding answers. We show how the behaviour of a concurrent
system with such a memory management can be specified using concurrent
communicating ASMs. We provide several refinements of a high-level ground model
addressing different replication policies and internal messaging between data
centres. For all these refinements we analyse their effects on the runs such
that decisions concerning the degree of consistency can be consciously made.Comment: 23 page
GP-SUM. Gaussian Processes Filtering of non-Gaussian Beliefs
This work studies the problem of stochastic dynamic filtering and state
propagation with complex beliefs. The main contribution is GP-SUM, a filtering
algorithm tailored to dynamic systems and observation models expressed as
Gaussian Processes (GP), and to states represented as a weighted sum of
Gaussians. The key attribute of GP-SUM is that it does not rely on
linearizations of the dynamic or observation models, or on unimodal Gaussian
approximations of the belief, hence enables tracking complex state
distributions. The algorithm can be seen as a combination of a sampling-based
filter with a probabilistic Bayes filter. On the one hand, GP-SUM operates by
sampling the state distribution and propagating each sample through the dynamic
system and observation models. On the other hand, it achieves effective
sampling and accurate probabilistic propagation by relying on the GP form of
the system, and the sum-of-Gaussian form of the belief. We show that GP-SUM
outperforms several GP-Bayes and Particle Filters on a standard benchmark. We
also demonstrate its use in a pushing task, predicting with experimental
accuracy the naturally occurring non-Gaussian distributions.Comment: WAFR 2018, 16 pages, 7 figure
BASH: a tool for managing BeadArray spatial artefacts
Summary: With their many replicates and their random layouts, Illumina BeadArrays provide greater scope fordetecting spatial artefacts than do other microarray technologies. They are also robust to artefact exclusion, yet there is a lack of tools that can perform these tasks for Illumina. We present BASH, a tool for this purpose. BASH adopts the concepts of Harshlight, but implements them in a manner that utilizes the unique characteristics of the Illumina technology. Using bead-level data, spatial artefacts of various kinds can thus be identified and excluded from further analyses
Optically trapped bacteria pairs reveal discrete motile response to control aggregation upon cell–cell approach
Aggregation of bacteria plays a key role in the formation of many biofilms. The critical first step is cell–cell approach, and yet the ability of bacteria to control the likelihood of aggregation during this primary phase is unknown. Here, we use optical tweezers to measure the force between isolated Bacillus subtilis cells during approach. As we move the bacteria towards each other, cell motility (bacterial swimming) initiates the generation of repulsive forces at bacterial separations of ~3 μm. Moreover, the motile response displays spatial sensitivity with greater cell–cell repulsion evident as inter-bacterial distances decrease. To examine the environmental influence on the inter-bacterial forces, we perform the experiment with bacteria suspended in Tryptic Soy Broth, NaCl solution and deionised water. Our experiments demonstrate that repulsive forces are strongest in systems that inhibit biofilm formation (Tryptic Soy Broth), while attractive forces are weak and rare, even in systems where biofilms develop (NaCl solution). These results reveal that bacteria are able to control the likelihood of aggregation during the approach phase through a discretely modulated motile response. Clearly, the force-generating motility we observe during approach promotes biofilm prevention, rather than biofilm formation
Pulmonary Biomarkers Based on Alterations in Protein Expression after Exposure to Arsenic
OBJECTIVE: Environmental exposure to arsenic results in multiple adverse effects in the lung. Our objective was to identify potential pulmonary protein biomarkers in the lung-lining fluid of mice chronically exposed to low-dose As and to validate these protein changes in human populations exposed to As. METHODS: Mice were administered 10 or 50 ppb As (sodium arsenite) in their drinking water for 4 weeks. Proteins in the lung-lining fluid were identified using two-dimensional gel electrophoresis (n = 3) or multidimensional protein identification technology (MUDPIT) (n = 2) coupled with mass spectrometry. Lung-induced sputum samples were collected from 57 individuals (tap water As ranged from ~ 5 to 20 ppb). Protein levels in sputum were determined by ELISA, and As species were analyzed in first morning void urine. RESULTS: Proteins in mouse lung-lining fluid whose expression was consistently altered by As included glutathione-S-transferase (GST)-omega-1, contraspin, apolipoprotein A-I and A-IV, enolase-1, peroxiredoxin-6, and receptor for advanced glycation end products (RAGE). Validation of the putative biomarkers was carried out by evaluating As-induced alterations in RAGE in humans. Regression analysis demonstrated a significant negative correlation (p = 0.016) between sputum levels of RAGE and total urinary inorganic As, similar to results seen in our animal model. CONCLUSION: Combinations of proteomic analyses of animal models followed by specific analysis of human samples provide an unbiased determination of important, previously unidentified putative biomarkers that may be related to human disease
Muscle invasive bladder cancer in Upper Egypt: the shift in risk factors and tumor characteristics
<p>Abstract</p> <p>Background</p> <p>In Egypt, where bilharziasis is endemic, bladder cancer is the commonest cancer in males and the 2<sup>nd </sup>in females; squamous cell carcinoma (SCC) is the commonest type found, with a peculiar mode of presentation. The aim of this study is to identify and rank the risk factors of muscle invasive bladder cancer (MIBC) in Upper Egypt and describe its specific criteria of presentation and histopathology.</p> <p>Methods</p> <p>This is an analytical, hospital based, case controlled study conducted in south Egypt cancer institute through comparing MIBC cases (n = 130) with age, sex and residence matched controls (n = 260) for the presence of risk factors of MIBC. Data was collected by personal interview using a well designed questionnaire. Patients' records were reviewed for histopathology and Radiologic findings.</p> <p>Results</p> <p>The risk factors of MIBC were positive family history [Adjusted odds ratio (AOR) = 7.7], exposure to pesticides [AOR = 6.2], bladder stones [AOR = 5], consanguinity [AOR = 3.9], recurrent cystitis [AOR = 3.1], bilharziasis [odds ratio (OR) = 5.8] and smoking [OR = 5.3]. SCC represented 67.6% of cases with burning micturition being the presenting symptom in 73.8%.</p> <p>Conclusion</p> <p>MIBC in Upper Egypt is usually of the SCC type (although its percentage is decreasing), occurs at a younger age and presents with burning micturition rather than hematuria. Unlike the common belief, positive family history, parents' consanguinity, exposure to pesticides and chronic cystitis seem to play now more important roles than bilharziasis and smoking in the development of this disease in this area.</p
Family history of colorectal cancer in Iran
BACKGROUND: Previous reports show a high proportion of young CRC patients in Iran. In this study we aim to look for the clustering of colorectal cancer in families of a series of CRC patients from Iran. METHODS: The family history of cancer is traced in 449 CRC patients of which 112 were 45 yrs or younger and 337 were older than 45 yrs at time of diagnosis. The patients were admitted in two hospitals in Tehran, during a 4-year period. RESULTS: Clinical diagnosis of HNPCC was established in 21 (4.7%) probands. Family history of CRC was more frequently reported by early-onset than by late-onset patients (29.5% vs. 12.8%, p < 0.001). Distribution of tumor site differed significantly between those with and without family history of CRC. Right colon cancer was the most frequent site (23/45, 35.4%) observed in patients with positive family history of colorectal cancer. CONCLUSION: The relatively high frequency of CRC clustering along with HNPCC in our patients should be further confirmed with larger sample size population-based and genetic studies to establish a cost effective molecular screening for the future
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