PI-FLAME: A parallel immune system simulator using the FLAME graphic processing unit environment

Agent-based models (ABMs) are increasingly being used to study population dynamics in complex systems, such as the human immune system. Previously, Folcik et al. (The basic immune simulator: an agent-based model to study the interactions between innate and adaptive immunity. Theor Biol Med Model 2007; 4: 39) developed a Basic Immune Simulator (BIS) and implemented it using the Recursive Porous Agent Simulation Toolkit (RePast) ABM simulation framework. However, frameworks such as RePast are designed to execute serially on central processing units and therefore cannot efficiently handle large model sizes. In this paper, we report on our implementation of the BIS using FLAME GPU, a parallel computing ABM simulator designed to execute on graphics processing units. To benchmark our implementation, we simulate the response of the immune system to a viral infection of generic tissue cells. We compared our results with those obtained from the original RePast implementation for statistical accuracy. We observe that our implementation has a 13× performance advantage over the original RePast implementation

Femtosecond photoelectron diffraction: A new approach to image molecular structure during photochemical reactions.

Continuing technical advances in the creation of (sub-) femtosecond VUV and X-ray pulses with Free-Electron Lasers and laser-based high-harmonic-generation sources have created new opportunities for studying ultrafast dynamics during chemical reactions. Here, we present an approach to image the geometric structure of gas-phase molecules with fewfemtosecond temporal and sub-Ångström spatial resolution using femtosecond photoelectron diffraction. This technique allows imaging the molecules “from within” by analyzing the diffraction of inner-shell photoelectrons that are created by femtosecond VUV and X-ray pulses. Using pump-probe schemes, ultrafast structural changes during photochemical reactions can thus be directly visualized with a temporal resolution that is only limited by the pulse durations of the pump and the probe pulse and the synchronization of the two light pulses. Here, we illustrate the principle of photoelectron diffraction using a simple, geometric scattering model and present results from photoelectron diffraction experiments on laser-aligned molecules using X-ray pulses from a Free-Electron Laser

Effect of firing temperature on the particles size of Gd2O3: Eu doped nanophosphors

The paper reports that synthesis and characterization of Eu2+ doped Gd2O3 nanophosphors prepared by combustion synthesis. It has been reported that the effect of synthesis temperature on particle size dependence phenomenon of rare earth doped nanophosphors. The sample was characterized by XRD pattern and FTIR study. Synthesized sample shows cubic structure verified by the XRD results.  Size of the particle was caculated by scherer equation the avarage size obtained 15, 23 and 55 at 4000C, 5000C and 6000C respectively. In this synthesis urea used as a fuel for created reducing atmosphere during sample preparation.&nbsp

Thermoluminescence and Mechanoluminescence studies of (Cd0.95 Zn0.05)S: Ag doped phosphor

Through the execution of experimental investigation, mechanoluminescence of (Cd,Zn)S: Ag phosphor was studied which is synthesized by solid state reaction. In the observation, the peak value of ML depends on different concentration. It is seen that ML intensity increases with Ag ion concentration in (Cd, Zn)S phosphor. The peak value of TL depends on the different UV-irradiation time. It is seen that as UV-irradiation exposure increases the TL intensity also increases

Assessment of Adenosine Deaminase Level and the Utility of Polymerase Chain Reaction in Diagnosis of Tuberculous Pleural Effusion

Background: Extrapulmonary tuberculosis is one of the major causes of exudative pleural effusion. The paucibacillary nature of effusion suggests the need of markers and methodologies for accurate diagnosis and prognosis of tuberculosis as well as to differentiate it from other non-tubercular causes of pleural effusion. Objectives: This study was focused to evaluate the utility of polymerase chain reaction (PCR) in detection of tuberculosis antigen and to assess the level of Adenosine Deaminase (ADA) in tubercular pleural effusion (TPE) and contrast it with other causes. Methods: This is a cross-sectional study where 100 samples of pleural effusion suspected to be tuberculosis were analyzed by PCR for the detection of IS6110 segment of DNA. The level of ADA was then determined and compared in both PCR positive and negative samples. The cut-off value of ADA was >40 U/L for TPE. Student t test was applied to compare the means with statistical significance set at p<0.05. Results: Out of 100 samples analyzed, 45% were positive for TPE and remaining 55% were non-tuberculosis pleural effusion as detected by PCR. The level of ADA was above cut-off (>40 U/L) in 43% TPE samples whereas all the non-tuberculosis effusion had ADA <40 U/L (p<0.001). Conclusion: The ADA level was significantly higher in TPE than in non-tuberculosis cases, and PCR was able to detect suspected cases of tuberculosis effusion in almost half of the cases. This finding suggests the diagnostic utility of combined use of ADA and PCR in diagnosis of TPE.  J-GMC-N | Volume 11 | Issue 01 | January-June 2018, Page: 5-

Comparison of Results of Calibration of Isolation Current Transformer by Conventional Method Two Power Comparator Method

This paper describes the calibration of Isolation Current Transformer by two methods, by conventional method and by two comparator based calibration method. A conventional method has limitations that we get fixed ratios and hence can go up to lower value of 1A. The uncertainties of the calibration system are in the order of 0.005 % for the ratio error and 0.01 crad for the phase displacement of the current transformer at 50 Hz. The power comparator based measurements can be done at test currents from 10 mA to 160A

Healthcare Utilization Patterns for Acute Febrile Illness in Bangladesh, Nepal, and Pakistan: Results from the Surveillance for Enteric Fever in Asia Project

Background: Characterizing healthcare-seeking patterns for acute febrile illness is critical for generating population-based enteric fever incidence estimates from facility-based surveillance data. Methods: We used a hybrid model in the Surveillance for Enteric Fever in Asia Project (SEAP) to assess incidence of enteric fever at 6 study hospitals in 3 countries. We recruited individuals presenting to the hospitals and obtained blood cultures to evaluate for enteric fever. For this analysis, we undertook cluster random household surveys in Dhaka, Bangladesh (2 sites); Karachi, Pakistan; Kathmandu, Nepal; and Kavrepalanchok, Nepal between January 2017 and February 2019, to ascertain care-seeking behavior for individuals with 1) fever for ≥3 consecutive days within the past 8 weeks; or 2) fever resulting in hospitalization within the past year. We also collected data about disease severity and household demographics and assets. We used mixed-effect multivariable logistic regression models to identify determinants of healthcare seeking at study hospitals and determinants of culture-confirmed enteric fever. Results: We enrolled 31 841 households (53926 children) in Bangladesh, 25510 households (84196 children and adults) in Nepal, and 21310 households (108031 children and adults) in Pakistan. Children <5 years were most likely to be taken to the study hospitals for febrile illness at all sites. Household wealth was positively correlated with healthcare seeking in 4 of 5 study sites, and at least one marker of disease severity was positively associated with healthcare seeking in 3 of 5 catchment areas. Wealth and disease severity were variably predictive of blood culture-confirmed enteric fever. Conclusions: Age, household wealth, and disease severity are important determinants of healthcare seeking for acute febrile illness and enteric fever risk in these communities, and should be incorporated into estimation models for enteric fever incidence

Dose-response model of murine typhus (Rickettsia typhi): time post inoculation and host age dependency analysis

<p>Abstract</p> <p>Background</p> <p><it>Rickettsia typhi (R. mooseri) </it>is the causative agent of murine typhus. It is one of the most widely distributed flea-borne diseases with a relatively mild febrile initial illness with six to 14 days of incubation period. The bacterium is gram negative and an obligate intracellular pathogen. The disease is transmitted to humans and vertebrate host through fleabites or via contact with infected feces. This paper develops dose-response models of different routes of exposure for typhus in rodents.</p> <p>Methods</p> <p>Data from published articles were analyzed using parametric dose-response relationship models. Dose-response relationships were fit to data using the method of maximum likelihood estimation (MLE).</p> <p>Results</p> <p>Dose-response models quantifying the effects of different ages of rats and time post inoculation in BALB/c mice were analyzed in the study. Both the adult rats (inoculated intradermally) and newborn rats (inoculated subcutaneously) were best fit by exponential models and both distributions could be described by a single dose-response relationship. The BALB/C mice inoculated subcutaneously were best fit by Beta-Poisson models. The time post inoculation analysis showed that there was a definite time and response relationship existed in this case.</p> <p>Conclusions</p> <p>Intradermally or subcutaneously inoculated rats (adult and newborn) models suggest that less than 1 plaque-forming unit (PFU) (1.33 to 0.38 in 95% confidence limits) of the pathogen is enough to seroconvert 50% of the exposed population on average. For the BALB/c mouse time post inoculation model, an average dose of 0.28 plaque-forming units (PFU) (0.75 to 0.11 in 95% confidence limits) will seroconvert 50% of the exposed mice.</p

Viral and Cell Cycle–Regulated Kinases in Cytomegalovirus-Induced Pseudomitosis and Replication

A process of pseudomitosis occurs during human cytomegalovirus infection that appears similar to cellular mitosis but involves the formation of multiple spindle poles, abnormal condensation, and mislocalization of chromosomal DNA. The relationship of this process to viral replication and cell cycle regulation during infection has been poorly understood. Pseudomitosis consistently peaks at late times of infection in all viral strains examined but at overall highest frequencies (30% to 35% of cells) using one common laboratory strain variant (AD169varATCC). Cyclin-dependent kinase 1 (Cdk1) plays a crucial role in pseudomitosis, mirroring its role in conventional mitosis. Dominant negative Cdk1 inhibits and wild-type Cdk1 stimulates this process; however, viral yields remain the same regardless of pseudomitosis levels. Broad inhibition of cell cycle−regulated kinases (Cdk1/Cdk2/Cdk5/Cdk9) with indirubin-3′-monoxime substantially decreases viral yields and synergizes with the viral UL97 kinase inhibitor, maribavir. Thus, Cdk1 is necessary and sufficient to drive pseudomitosis, whereas a combination of viral and cell cycle−regulated kinases is important during viral replication