A comparative performance analysis of the phase recovery algorithm for microstructure reconstruction

This thesis explores the high-performance implementation of a phase recovery algorithm for microstructure reconstruction of materials. Implementations on a variety of high-performance computing platforms, including multi-core and Graphics Processing Unit (GPU), were investigated and compared. The phase recovery algorithm is an iterative process requiring multiple Discrete Fourier Transform (DFT) computations each iteration. In order to achieve high-performance, it is necessary to use highly optimized fast Fourier transform (FFT) code to compute the DFTs. In our investigation, several FFT libraries, including FFTW, the Intel R Math Kernel Library (MKL), the CUFFT library for the NVIDIAR GPU, and the SPIRAL generated code, were used and compared. The SPIRAL system provides an extensible framework for generating and automatically optimizing implementations of DSP (digital signal processing) algorithms described using mathematical formulas, and is the most extensible of the platforms investigated here. The phas recovery algorithm intersperses FFT computations with point-wise computations, and while the FFTs are the dominant computation, the point-wise operations can have a signi cant impact on the overall performance. Therefore, simply relying on the performance of an optimized FFT library is insu cient to obtain optimal performance. Unlike the FFTW, MKL, and CUFFT libraries, the SPIRAL system allows the FFTs to be combined with the point-wise operations and the entire algorithm to be optimized. In this thesis, we obtained a mathematical formula representing the phase recovery algorithm that can be incorporated into the SPIRAL framework and utilize SPIRAL's parallel and vector code generation and optimization facilities. The SPIRAL code generated in this thesis is sequential. We estimate that with a vectorized and parallelized SPIRAL implementation, it is possible to obtain a 1.5-fold speedup for two-dimensional (2D) phase recovery and 1.88-fold speed up for 3D phase recovery over the MKL implementation.M.S., Computer Engineering -- Drexel University, 200

Mejora de los niveles de conciencia y salud periodontal entre pacientes sometidos a terapia con aparatos de ortodoncia fijos con gingivitis establecida y programa de mantenimiento de la salud periodontal: Un estudio basado en cuestionarios.

Objetive: Home oral care practices in patients undergoing orthodontic therapy are often ineffective in maintaining optimal plaque control. The aim of the present study was to assess the effectiveness of periodontal maintenance program in subjects with established gingivitis undergoing fixed orthodontic appliance therapy for one year. Material and Methods: Forty patients undergoing fixed orthodontic appliance therapy with established chronic gingivitis were recruited for the study. As a part of a periodontal maintenance program, a pre-validated structured questionnaire evaluating oral hygiene and periodontal health was administered at the baseline as well as at the end of the study. At the baseline Gingival Bleeding Index, Gingival Index, and Bonded Bracket Plaque Index scores were recorded, Scaling and polishing procedure was performed followed by a customised Oral Hygiene Advice (OHA) session was conducted for all the study subjects. Clinical indices were assessed and OHA was conducted at the 3rd, 6th, 9th, and 12th months of orthodontic treatment visits. Results: There was significant improvement in the clinical indices and awareness regarding oral hygiene and periodontal health level in the patients at the end of the 12th month. Conclusion: The periodontal maintenance program appeared to be effective in improving the periodontal health and awareness health awareness level about oral hygiene among patients undergoing fixed orthodontic therapy at the end of 12 months in our study population.Objetivo: Las prácticas de cuidado bucal en el hogar en pacientes sometidos a terapia de ortodoncia suelen ser ineficaces para mantener un control óptimo de la placa. El objetivo del presente estudio fue evaluar la efectividad del programa de mantenimiento periodontal en sujetos con gingivitis establecida sometidos a terapia con aparatos de ortodoncia fijos durante un año. Material y Métodos: Se reclutó para el estudio a 40 pacientes sometidos a terapia con aparatos de ortodoncia fijos y con gingivitis crónica establecida. Como parte de un programa de mantenimiento periodontal, se administró un cuestionario estructurado pre-validado que evaluaba la higiene bucal y la salud periodontal al inicio y al final del estudio. En la línea de base, se registraron las puntuaciones del índice de sangrado gingival, el índice gingival y el índice de placa de soporte adherido, se realizó el procedimiento de raspado y pulido seguido de una sesión personalizada de consejos de higiene oral (CHO) para todos los sujetos del estudio. Se evaluaron los índices clínicos y se llevó a cabo la CHO a los 3, 6, 9 y 12 meses durante las visitas de tratamiento de ortodoncia. Resultados: Hubo una mejora significativa en los índices clínicos y la conciencia sobre la higiene oral y el nivel de salud periodontal en los pacientes al final del 12º mes. Conclusión: El programa de mantenimiento periodontal pareció ser eficaz para mejorar la salud periodontal y el nivel de conciencia de la salud sobre la higiene bucal entre los pacientes sometidos a terapia de ortodoncia fija al final de los 12 meses en nuestra población de estudio

HIV Infection Among Partners of HIV-Infected Black Men Who Have Sex with Men — North Carolina, 2011–2013

The incidence of human immunodeficiency virus (HIV) infection has significantly increased among black men who have sex with men (MSM) in the United States, and young black MSM have been disproportionately affected. HIVinfected black MSM are also less likely to engage in HIV care and achieve viral suppression than MSM of other races/ethnicities. Engaging in care and achieving viral suppression is a multistep process that starts with diagnosis. Diagnosing persons unaware of their HIV status traditionally has been a critical component of HIV partner services, but partner services also provide an important opportunity to reengage HIVinfected partners in medical care. One approach for partner services involves contacting partners of persons with newly diagnosed HIV infection and using sexual and social network and molecular phylogenetic data to improve the continuum of HIV care among black MSM. To evaluate the effectiveness of that approach, results from a prospective partner services study conducted in North Carolina were examined, and one of the partner networks identified through this study was evaluated in depth. Overall, partner services were provided to 30 black, HIV-infected MSM who named 95 sex partners and social contacts, of whom 39 (41%) previously had been diagnosed with HIV infection. The partner network evaluation demonstrated that HIV-infected and HIV-negative partners were frequently in the same network, and that the majority of HIV-infected partners were already aware of their diagnosis but had not achieved viral suppression. Using partner services to ensure that HIV-infected partners are linked to care and treatment might reduce HIV transmission and might improve outcomes along the continuum of care

Beyond Bushmeat:Animal Contact, Injury, and Zoonotic Disease Risk in Western Uganda

Zoonotic pathogens cause an estimated 70% of emerging and re-emerging infectious diseases in humans. In sub-Saharan Africa, bushmeat hunting and butchering is considered the primary risk factor for human-wildlife contact and zoonotic disease transmission, particularly for the transmission of simian retroviruses. However, hunting is only one of many activities in sub-Saharan Africa that bring people and wildlife into contact. Here, we examine human-animal interaction in western Uganda, identifying patterns of injuries from animals and contact with nonhuman primates. Additionally, we identify individual-level risk factors associated with contact. Nearly 20% (246/ 1,240) of participants reported either being injured by an animal or having contact with a primate over their lifetimes. The majority (51.7%) of injuries were dog bites that healed with no long term medical consequences. The majority (76.8%) of 125 total primate contacts involved touching a carcass; however, butchering (20%), hunting (10%), and touching a live primate (10%) were also reported. Red colobus (Piliocolobus rufomitratus tephrosceles) accounted for most primate contact events. Multivariate logistic regression indicated that men who live adjacent to forest fragments are at elevated risk of animal contact and specifically primate contact. Our results provide a useful comparison to West and Central Africa where “bushmeat hunting” is the predominant paradigm for human-wildlife contact and zoonotic disease transmission

Effect of molybdenum trioxide nanoparticle-mediated seed priming on the productivity of green gram (Vigna radiata L.)

A field experiment was undertaken in the post-Rabi season of 2019-2020 to reveal the response of greengram (Vigna radiata L.) to seed dressing and seed priming with nano molybdenum trioxide (MoO3). The experiment was laid out in randomized block design (RBD) consisting of 10 different treatments i.e., M0 (no seed treatment with Mo); M1 (seed dressing with Sodium molybdate @ 400 ppm); M2, M3, M4, and M5 (seed dressing with nano Molybdenum trioxide-MoO3 @ 50, 100, 200 and 400 ppm, respectively); and M6, M7, M8 and M9 (seed priming with nano MoO3 @ 50, 100, 200 and 400 ppm, respectively). Inoculation of greengram seeds cv. Shreya (IPM 2-14) with Rhizobium sps. was undertaken in all treatments as per the recommended practice, except in M0 (control). The MoO3 nanoparticles (NPs) synthesized from Ammonium molybdate through calcination at 600 0C for 5 hours indicated globular-shaped NPs of 68.55 nm in TEM and XRD. Nanopriming with MoO3 @ 200 ppm (M8) was most promising in recording significantly superior growth and yield attributing parameters and yield, whereas Mo (control) produced the least. Crop height, number of branches, root length, shoot dry matter, pods/plant and seeds/plant and root nodulation at harvest in M8 were 39.4% and 22.6%; 39% and 5.6%; 23% and 9.3%; 43.9%, and 16.3%; 28.2% and 5.3%; 28.1% and 0.8%, and 73.3% and 36.5% higher than M0 (control) and M1 (farmers’ practice), respectively. Superior growth and yield attributing characters in M8 treatment produced the highest grain and stover yield of 0.88 and 3.74 t/ ha that was 32.53% and 8.37%, and 35.5% and 14.7% higher than M0 (control) and M1 (farmers’ practice), respectively. Seed priming with nano MoO3 @ 400 ppm (M9) and seed dressing with nano MoO3 @ 400 ppm (M5) were of second and third order in recording grain and stover yield but M0 recorded the lowest among all the treatments

Detection of Murine Leukemia Virus or Mouse DNA in Commercial RT-PCR Reagents and Human DNAs

The xenotropic murine leukemia virus (MLV)-related viruses (XMRV) have been reported in persons with prostate cancer, chronic fatigue syndrome, and less frequently in blood donors. Polytropic MLVs have also been described in persons with CFS and blood donors. However, many studies have failed to confirm these findings, raising the possibility of contamination as a source of the positive results. One PCR reagent, Platinum Taq polymerase (pol) has been reported to contain mouse DNA that produces false-positive MLV PCR results. We report here the finding of a large number of PCR reagents that have low levels of MLV sequences. We found that recombinant reverse-transcriptase (RT) enzymes from six companies derived from either MLV or avian myeloblastosis virus contained MLV pol DNA sequences but not gag or mouse DNA sequences. Sequence and phylogenetic analysis showed high relatedness to Moloney MLV, suggesting residual contamination with an RT-containing plasmid. In addition, we identified contamination with mouse DNA and a variety of MLV sequences in commercially available human DNAs from leukocytes, brain tissues, and cell lines. These results identify new sources of MLV contamination and highlight the importance of careful pre-screening of commercial specimens and diagnostic reagents to avoid false-positive MLV PCR results

No Evidence of Murine Leukemia Virus-Related Viruses in Live Attenuated Human Vaccines

The association of xenotropic murine leukemia virus (MLV)-related virus (XMRV) in prostate cancer and chronic fatigue syndrome reported in previous studies remains controversial as these results have been questioned by recent data. Nonetheless, concerns have been raised regarding contamination of human vaccines as a possible source of introduction of XMRV and MLV into human populations. To address this possibility, we tested eight live attenuated human vaccines using generic PCR for XMRV and MLV sequences. Viral metagenomics using deep sequencing was also done to identify the possibility of other adventitious agents.All eight live attenuated vaccines, including Japanese encephalitis virus (JEV) (SA-14-14-2), varicella (Varivax), measles, mumps, and rubella (MMR-II), measles (Attenuvax), rubella (Meruvax-II), rotavirus (Rotateq and Rotarix), and yellow fever virus were negative for XMRV and highly related MLV sequences. However, residual hamster DNA, but not RNA, containing novel endogenous gammaretrovirus sequences was detected in the JEV vaccine using PCR. Metagenomics analysis did not detect any adventitious viral sequences of public health concern. Intracisternal A particle sequences closest to those present in Syrian hamsters and not mice were also detected in the JEV SA-14-14-2 vaccine. Combined, these results are consistent with the production of the JEV vaccine in Syrian hamster cells.We found no evidence of XMRV and MLV in eight live attenuated human vaccines further supporting the safety of these vaccines. Our findings suggest that vaccines are an unlikely source of XMRV and MLV exposure in humans and are consistent with the mounting evidence on the absence of these viruses in humans