A Reconfigurable Vector Instruction Processor for Accelerating a Convection Parametrization Model on FPGAs

High Performance Computing (HPC) platforms allow scientists to model computationally intensive algorithms. HPC clusters increasingly use General-Purpose Graphics Processing Units (GPGPUs) as accelerators; FPGAs provide an attractive alternative to GPGPUs for use as co-processors, but they are still far from being mainstream due to a number of challenges faced when using FPGA-based platforms. Our research aims to make FPGA-based high performance computing more accessible to the scientific community. In this work we present the results of investigating the acceleration of a particular atmospheric model, Flexpart, on FPGAs. We focus on accelerating the most computationally intensive kernel from this model. The key contribution of our work is the architectural exploration we undertook to arrive at a solution that best exploits the parallelism available in the legacy code, and is also convenient to program, so that eventually the compilation of high-level legacy code to our architecture can be fully automated. We present the three different types of architecture, comparing their resource utilization and performance, and propose that an architecture where there are a number of computational cores, each built along the lines of a vector instruction processor, works best in this particular scenario, and is a promising candidate for a generic FPGA-based platform for scientific computation. We also present the results of experiments done with various configuration parameters of the proposed architecture, to show its utility in adapting to a range of scientific applications.Comment: This is an extended pre-print version of work that was presented at the international symposium on Highly Efficient Accelerators and Reconfigurable Technologies (HEART2014), Sendai, Japan, June 911, 201

In-vitro application of pentoxifylline preserved ultrastructure of spermatozoa after vitrification in asthenozoospermic patients

Abstract PURPOSE: To evaluate the effect of in vitro application of pentoxifylline (PX) on sperm parameters and ultrastructure after vitrification in asthenozoospermic patients. MATERIALS AND METHODS: A total of 30 asthenozoospermic semen samples (aged 25-45 years) were divided into four groups before vitrification, after vitrification, control (without PX) and experimental (with PX). In experimental group, each sample was exposed for 30 min to 3.6mmol/l PX and the control group without any treatment apposing in 370C for 30 min. After incubation, the samples were washed and analyzed again. Vitrification was done according to straw method. Eosin-nigrosin and Papanicolaou staining were applied for assessment of sperm viability and morphology, respectively. The samples without PX and post treatment with PX were assessed by transmission electron microscopy (TEM). RESULTS: A significant decrease in sperm motility (P ≤ .001), morphology (11.47 ± 2.9 versus 6.73 ± 2.01) and viability (73.37 ± 6.26 versus 54.67 ± 6.73) was observed post vitrification, but sperm motility (19.85 ± 4.75 versus 32.07 ± 5.58, P ≤ .001) was increased significantly following application of PX. This drug had no significant (P >.05) detrimental neither negative effect on ultrastructure acrosome, plasma membrane and coiled tail statues of spermatozoa. CONCLUSION: Vitrification had detrimental effects on sperm parameters, but PX reversed detrimental effects on sperm motility. However, PX had no alteration on ultrastructure morphology of human spermatozoa after vitrification

Chromosome 9p deletion in clear cell renal cell carcinoma predicts recurrence and survival following surgery

BACKGROUND: Wider clinical applications of 9p status in clear cell renal cell carcinoma (ccRCC) are limited owing to the lack of validation and consensus for interphase fluorescent in situ hybridisation (I-FISH) scoring technique. The aim of this study was to analytically validate the applicability of I-FISH in assessing 9p deletion in ccRCC and to clinically assess its long-term prognostic impact following surgical excision of ccRCC. METHODS: Tissue microarrays were constructed from 108 renal cell carcinoma (RCC) tumour paraffin blocks. Interphase fluorescent in situ hybridisation analysis was undertaken based on preset criteria by two independent observers to assess interobserver variability. 9p status in ccRCC tumours was determined and correlated to clinicopathological variables, recurrence-free survival and disease-specific survival. RESULTS: There were 80 ccRCCs with valid 9p scoring and a median follow-up of 95 months. Kappa statistic for interobserver variability was 0.71 (good agreement). 9p deletion was detected in 44% of ccRCCs. 9p loss was associated with higher stage, larger tumours, necrosis, microvascular and renal vein invasion, and higher SSIGN (stage, size, grade and necrosis) score. Patients with 9p-deleted ccRCC were at a higher risk of recurrence (P=0.008) and RCC-specific mortality (P=0.001). On multivariate analysis, 9p deletion was an independent predictor of recurrence (hazard ratio 4.323; P=0.021) and RCC-specific mortality (hazard ratio 4.603; P=0.007). The predictive accuracy of SSIGN score improved from 87.7% to 93.1% by integrating 9p status to the model (P=0.001). CONCLUSIONS: Loss of 9p is associated with aggressive ccRCC and worse prognosis in patients following surgery. Our findings independently confirm the findings of previous reports relying on I-FISH to detect 9p (CDKN2A) deletion

Risk-stratified breast cancer screening incorporating a polygenic risk score: a survey of UK General Practitioners’ knowledge and attitudes

A polygenic risk score (PRS) quantifies the aggregated effects of common genetic variants in an individual. A ‘personalised breast cancer risk assessment’ combines PRS with other genetic and nongenetic risk factors to offer risk-stratified screening and interventions. Large-scale studies are evaluating the clinical utility and feasibility of implementing risk-stratified screening; however, General Practitioners’ (GPs) views remain largely unknown. This study aimed to explore GPs’: (i) knowledge of risk-stratified screening; (ii) attitudes towards risk-stratified screening; and (iii) preferences for continuing professional development. A cross-sectional online survey of UK GPs was conducted between July–August 2022. The survey was distributed by the Royal College of General Practitioners and via other mailing lists and social media. In total, 109 GPs completed the survey; 49% were not familiar with the concept of PRS. Regarding risk-stratified screening pathways, 75% agreed with earlier and more frequent screening for women at high risk, 43% neither agreed nor disagreed with later and less screening for women at lower-than-average risk, and 55% disagreed with completely removing screening for women at much lower risk. In total, 81% felt positive about the potential impact of risk-stratified screening towards patients and 62% felt positive about the potential impact on their practice. GPs selected training of healthcare professionals as the priority for future risk-stratified screening implementation, preferring online formats for learning. The results suggest limited knowledge of PRS and risk-stratified screening amongst GPs. Training—preferably using online learning formats—was identified as the top priority for future implementation. GPs felt positive about the potential impact of risk-stratified screening; however, there was hesitance and disagreement towards a low-risk screening pathway

Novel removal of Anthracene from oil-contaminated water by synthesized modified magnetic nano-particles

Novel magnetic nanoparticles (MNPs) modified with (3-mercaptopropyl)-trimethoxysilane (MPTMS), grafted with allyl glycidyl ether and coupled with beta naphthol, were prepared for removal of anthracene in aqueous solutions. The grafted MNPs were characterized by transmission electron microscopy (TEM), infrared spectroscopy (FT-IR) and thermogravimetric analysis (TGA). The modified MNPs contributed to enhancement of the adsorption capacity and were prepared by co-precipitation. The modified MNPs were characterized by TEM, FT-IR and TGA and the adsorption and kinetic behavior of anthracene on the modified MNPs was examined. It was shown that the nano-adsorbent optimized adsorption capacity is at pH 7. Three kinetics models: pseudo-first-order, pseudo-second-order, and intraparticle diffusion were used to investigate the adsorption mechanism of the anthracene onto the modified MNPs. The best fit was obtained for the pseudo-second-order model. The synthesized nano adsorbent can be considered as a new method for anthracene adsorption in contaminated water with the benefit of fast removal by applying a magnetic field

Polyp in concha bullosa: a case report and review of the literature

Polyp originating within a concha bullosa is uncommon; we report only the third such case in the English literature. A 45-year-old man presented with nasal obstruction and headache. Examination of the nose revealed right septal deviation and a hypertrophic left middle concha. Computed tomography confirmed right septal deviation and identified left concha bullosa with thickening of the mucosa covering this lesion. The lateral lamella of the affected turbinate was removed and a mass was excised. Histopathologic examination of the excised mass revealed polypoid hyperplasia. The rare finding of polyp in concha bullosa is discussed with a review of the literature. In any case of concha bullosa, computed tomography images should be carefully evaluated before surgery to check for other pathologies that might have arisen within the lesion

Lead-free Magnetic Double Perovskites for Photovoltaic and Photocatalysis Applications

The magnetic spin degrees of freedom in magnetic materials serve as additional capability to tune materials properties, thereby invoking magneto-optical response. Herein, we report the magneto-optoelectronic properties of a family of lead-free magnetic double perovskites Cs_{2}AgTX_{6} (T = Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu; X=Cl, Br, I). This turns out to provide an extremely fertile series, giving rise to potential candidate materials for photovoltaic(PV) applications. In conjunction with high absorption coefficient and high simulated power conversion efficiency for PV applications, few compounds in this series exhibit novel magnetic character useful for spintronic applications. The interaction between magnetism and light can have far-reaching results on the photovoltaic properties as a consequence of the shift in the defect energy levels due to Zeeman effect. This subsequently affects the recombination rate of minority carriers, and hence the photoconversion efficiency. Moreover, the distinct ferromagnetic and anti-ferromagnetic ordering driven by hybridization and super-exchange mechanism can play a significant role to break the time-reversal and/or inversion symmetry. Such a coalescence of magnetism and efficient optoelectronic response has the potential to trigger magnetic/spin anomalous photovoltaic (non-linear Optical) effect in this Cs$_{2}$AgTX$_{6}$ family. These insights can thus channelize the advancement of lead-free double perovskites in magnetic/spin anomalous photovoltaic field as well.Comment: 9 pages, 5 figures, 1 tabl

Fine-Grid Calculations for Stellar Electron and Positron Capture Rates on Fe-Isotopes

The acquisition of precise and reliable nuclear data is a prerequisite to success for stellar evolution and nucleosynthesis studies. Core-collapse simulators find it challenging to generate an explosion from the collapse of the core of massive stars. It is believed that a better understanding of the microphysics of core-collapse can lead to successful results. The weak interaction processes are able to trigger the collapse and control the lepton-to-baryon ratio ($Y_{e}$) of the core material. It is suggested that the temporal variation of $Y_{e}$ within the core of a massive star has a pivotal role to play in the stellar evolution and a fine-tuning of this parameter at various stages of presupernova evolution is the key to generate an explosion. During the presupernova evolution of massive stars, isotopes of iron, mainly $^{54,55,56}$Fe, are considered to be key players in controlling $Y_{e}$ ratio via electron capture on these nuclide. Recently an improved microscopic calculation of weak interaction mediated rates for iron isotopes was introduced using the proton-neutron quasiparticle random phase approximation (pn-QRPA) theory. The pn-QRPA theory allows a microscopic \textit{state-by-state} calculation of stellar capture rates which greatly increases the reliability of calculated rates. The results were suggestive of some fine-tuning of the $Y_{e}$ ratio during various phases of stellar evolution. Here we present for the first time the fine-grid calculation of the electron and positron capture rates on $^{54,55,56}$Fe. Core-collapse simulators may find this calculation suitable for interpolation purposes and for necessary incorporation in the stellar evolution codes.Comment: 21 pages, 6 ps figures and 2 table

Programas educativos modulares basados en competencias

It has been established that the basic documents on the development of higher education of the Republic of Kazakhstan declared the principles of competence approach and modular learning, but in practice, their implementation is faced with certain difficulties and that it is particularly difficult to implement the competency-based approach in the absence of professional standards. In this regard, the goal was set to develop a methodology for the formation of integrated standards and implement it for a modular educational program of any specialty. The essence of this methodology consists in that the development of an integrated standard is not a single process. It is divided because at the initial stage the representatives of the education sphere determine only the expanded list of competencies, then the employers enter the process independently on them, and the faculty formulates the learning outcomes only after specification of the competences’ list. To achieve this goal, an algorithm for the development of modular educational programs has been created, methods of document analysis, retrospective analysis and questionnaires were applied, experimental work on the formation of the list of competencies was carried out. The experts who participated in assessing the competencies importance showed the high qualifications, good knowledge in the labor market and the skill to formulate the required data. On the basis of this list, the list of necessary competencies for “Computer science and software” specialty has been compiled.Se ha establecido que los documentos básicos sobre el desarrollo de la educación superior de la República de Kazajstán declaran los principios del enfoque de competencia y el aprendizaje modular, pero en la práctica su implementación enfrenta ciertas dificultades y que es particularmente difícil implementar el enfoque basado en la competencia. enfoque en ausencia de estándares profesionales. En este sentido, se estableció el objetivo de desarrollar una metodología para la formación de estándares integrados e implementarla para un programa educativo modular de cualquier especialidad. La esencia de esta metodología consiste en que el desarrollo de estándares integrados no es un proceso único. Se divide porque en la etapa inicial, los representantes de la esfera de la educación determinan solo la lista ampliada de competencias, luego los empleadores ingresan al proceso de forma independiente en ellas y el profesorado formula los resultados del aprendizaje solo después de la especificación de la lista de competencias. Para lograr este objetivo, se creó un algoritmo para el desarrollo de programas educativos modulares, se aplicaron métodos de análisis de documentos, análisis retrospectivos y cuestionarios, se realizó un trabajo experimental sobre la formación de la lista de competencias. Los expertos que participaron en la evaluación de la importancia de las competencias mostraron las altas calificaciones, buen conocimiento en el mercado laboral y la habilidad para formular los datos requeridos. Sobre la base de esta lista, se ha compilado la lista de competencias necesarias para la especialidad «Informática y software»

Function of Serum Complement in Drinking Water Arsenic Toxicity

Serum complement function was evaluated in 125 affected subjects suffering from drinking water arsenic toxicity. Their mean duration of exposure was 7.4 ± 5.3 yrs, and the levels of arsenic in drinking water and urine samples were 216 ± 211 and 223 ± 302 μg/L, respectively. The mean bactericidal activity of complement from the arsenic patients was 92% and that in the unexposed controls was 99% (P < 0.01), but heat-inactivated serum showed slightly elevated activity than in controls. In patients, the mean complement C3 was 1.56 g/L, and C4 was 0.29 g/L compared to 1.68 g/L and 0.25 g/L, respectively, in the controls. The mean IgG in the arsenic patients was 24.3 g/L that was highly significantly elevated (P < 0.001). Arsenic patients showed a significant direct correlation between C3 and bactericidal activity (P = 0.014). Elevated levels of C4 indicated underutilization and possibly impaired activity of the classical complement pathway. We conclude reduced function of serum complement in drinking water arsenic toxicity