315 research outputs found
A framework for enabling high-end high performance computing resources as a service
No full textIn an era of data explosion and analysis, researchers across the globe are trying to convert massive quantities of complex data into useful knowledge using Computational and Data-Enabled Science and Engineering (CDS&E) applications. CDS&E applications are gaining traction as an important dimension of Science, Technology, Engineering, and Mathematics research. These applications require powerful processors with fast interconnects, extreme large scale, and elastic resources. While high-end High Performance Computing (HPC) resources provide the necessary requirements, the complexity of such systems has grown exponentially. Furthermore, due to their high cost, limited availability, and high demand, the queue wait times to run applications on these systems is in the order of months. All of the above challenges prevent their adoption as a mainstream solution. On the other hand, Cloud computing is emerging as a dominant computing paradigm that offers many advantages. Consequently, early adopters have looked into using Clouds to solve the HPC model challenges. Initially, CDS&E applications were run on commodity Clouds, but this was found to be appropriate only for certain classes of applications. Other approaches explored complementing HPC resources with Clouds but failed to address all challenges in the HPC environment. Cloud providers also tried to provide HPC as a Cloud using small HPC clusters connected to form a larger Cloud but were hindered by small scale and limited performance. These approaches fall short of providing the high performance necessary for CDS&E applications. In this document, we propose a new approach to achieve the notion of HPC as a Service. This approach targets existing high-end HPC resources and investigates how a Cloud abstraction can be applied to provide a simple interface and support real-world applications. In particular, the application of Clouds to supercomputers is discussed, tested, and validated on an IBM Blue Gene/P supercomputer. The proposed framework transforms Blue Gene/P into an elastic cloud by bridging multiple systems to create HPC federated Clouds, supporting dynamic provisioning and efficient utilization, and maximizing ease-of-use through an as a Service abstraction. In order to effectively illustrate the benefits of such a concept, the proposed framework is demonstrated using a real-world ensemble application.M.S.Includes bibliographical referencesby Moustafa AbdelBak
Genetic engineering of tumour-infiltrating monocytes to inhibit metastatic breast cancer
No full textEffect of chain length on the photophysical properties of pyrene-based molecules substituted with extended chains
No full textThe important role played by organic conjugated compounds in the ?elds of electronics and optoelectronics has led to a vast ?eld of research concerned with synthesizing various complex structures where π-π stacking plays a vital role. Pyrene-based molecules are examples of compounds which allow ef?cient charge transfer through π-π molecular stacking. Photophysical studies of such compounds have shown similar behavior as that of pyrene, even though they bear two additional conjugated rings and four long alkyl chains. Chain length may have played an effective role in in?uencing the π-π molecular stacking of such molecules. In continuation of our earlier work(Moustafa, R. M.; Degheili, J. A.; Patra, D.; Kaafarani, B. R. J. Phys. Chem. A 2008, 113, 1235-1243), we hereby synthesize and investigate the role of the chain lengths on the photophysical aspects of 2,11-di-tert-butyl-6,7,15,16- tetrakis(alkoxy-alkythio)quinoxaline-[2′,3′:9,10]phenanthro[4, 5-ab-c]phenazine, TQPP-[t-Bu]2-[XR]4(X O, S; R C nH2n+1). Various photophysical parameters such as Stokes shift, ?uorescence lifetime, ?uorescence quantum yield, and radiative and nonradiative rate constants are evaluated for TQPP-[t-Bu]2-[OR] 4 and TQPP-[t-Bu]2-[SR]4 in tetrahydrofuran. The variation of the Stokes shift, ?uorescence quantum yield, and lifetime are also correlated with the number of carbons in the alkyl chain R for TQPP-[t-Bu]2-[OR]4 and TQPP-[t-Bu]2-[SR] 4. © 2009 American Chemical Society.Anthony JE, 2008, ANGEW CHEM INT EDIT, V47, P452, DOI 10.1002-anie.200604045; Boden N, 1999, J MATER CHEM, V9, P2081, DOI 10.1039-a903005k; Chen MC, 2008, J MATER CHEM, V18, P1029, DOI 10.1039-b715746k; Chen ZH, 2006, ORG LETT, V8, P273, DOI 10.1021-ol0526468; Katsuhara M, 2005, SYNTHETIC MET, V149, P219, DOI 10.1016-j.synthmet.2005.01.005; Kumar S, 2006, CHEM SOC REV, V35, P83, DOI 10.1039-b506619k; Lakowicz J. R., 1999, PRINCIPLES FLUORESCE; Mitzi DB, 2004, J MATER CHEM, V14, P2355, DOI 10.1039-b403482a; MOUSTAFA RM, J PHYS CHEM A UNPUB; Naraso, 2005, J AM CHEM SOC, V127, P10142, DOI 10.1021-ja051755e; Oukachmih M, 2005, SOL ENERG MAT SOL C, V85, P535, DOI 10.1016-j.solmat.2004.05.012; Palilis LC, 2003, ORG ELECTRON, V4, P113, DOI 10.1016-j.orgel.2003.08.006; Parker C.A., 1968, PHOTOLUMINESCENCE SO; Petritsch K, 1999, SYNTHETIC MET, V102, P1776, DOI 10.1016-S0379-6779(98)01035-2; Ponomarenko SA, 2003, ADV FUNCT MATER, V13, P591, DOI 10.1002-adfm.200304363; Subuddhi U, 2006, PHOTOCH PHOTOBIO SCI, V5, P459, DOI 10.1039-b600009f; Sun YG, 2007, ADV MATER, V19, P1897, DOI 10.1002-adma.200602223; van de Craats AM, 1999, ADV MATER, V11, P1469, DOI 10.1002-(SICI)1521-4095(199912)11:171469::AID-ADMA14693.0.CO;2-K; WARIS R, 1988, APPL SPECTROSC, V42, P1525, DOI 10.1366-000370288442980513131
COMPARATIVE GENOTOXICOLOGICAL ANALYSIS OF OCCUPATIONAL PESTICIDE EXPOSURES: AN EXPERIMENTAL APPROACH AND SYSTEMATIC REVIEW
No full textThis dissertation investigates the genotoxic and cytotoxic effects of pesticide exposure through three complementary research components: a systematic review of occupational pesticide exposure in Arab countries (AraSys), a systematic review on encapsulated versus conventional pesticide formulations (Encap-Sys), and experimental toxicological assessments of various pesticide formulations in human cell lines (Pyr-Ex). This experimental component includes cytotoxicity assays using propidium iodide and DNA damage assessments via alkaline comet assays in HL60 and HepG2 cell lines exposed to pyrethroid insecticides and glyphosate-based formulations.
The AraSys systematic review revealed a critical positive association between occupational pesticide exposure and DNA damage in agricultural workers in Arab countries, consistent with findings from other global regions. However, the scarcity of research in this geographical area—with only five eligible studies from three countries— highlights a significant knowledge gap that limits comprehensive risk assessment. The included studies employed various methods to evaluate DNA damage but often lacked specificity regarding pesticide compositions, exposure parameters, and routes. Methodological limitations included the absence of female participants in all studies, inadequate control of confounding factors like smoking, and inconsistent reporting of control population characteristics, presenting challenges for interpretation and generalizability.
The Encap-Sys systematic review evaluated whether encapsulated pesticide product formulations present lower health risks than conventional alternatives by analyzing in vitro and in vivo animal model studies. While encapsulated formulations generally demonstrated reduced toxicity compared to conventional pesticides, the results varied considerably depending on encapsulation material, pesticide type, and experimental conditions. Chitosan-based and silica-based encapsulations frequently showed promising reductions in toxicity, but some polymeric formulations and lipid nanoparticles showed similar or even increased toxicity in certain assays. The significant variations in dose selection, exposure durations (from acute to chronic), encapsulation techniques, and evaluation endpoints created challenges for definitive conclusions, highlighting the need for standardized protocols, more comprehensive chronic exposure studies, and real-world environmental assessments.
The Pyr-Ex experimental component provided original data on the cytotoxicity and genotoxicity of various pesticide formulations in HL60 and HepG2 human cell lines. The study on cyphenothrin revealed consistent patterns across different concentrations where the encapsulated formulation Bombex Farumy exhibited the lowest genotoxicity in both cell lines, followed by released Bombex Farumy, while the cyphenothrin active ingredient alone consistently induced the greatest DNA damage. This suggests encapsulation technology effectively mitigates the genotoxic potential of cyphenothrin formulations, with HepG2 cells demonstrating greater resistance to both cytotoxic and genotoxic effects compared to the more susceptible HL60 cells. Evaluation of glyphosate-based herbicide formulations revealed complex, formulation-specific, and cell type-specific toxicity profiles. In HL60 cells, Roundup Mega demonstrated remarkable genotoxic potential in tail length at concentrations as low as 0.1 μM, well below cytotoxic thresholds, suggesting direct DNA-damaging mechanisms independent of cell death. In contrast, HepG2 cells showed different patterns, with Glyfos demonstrating genotoxic effects at the lowest concentration (100 μM) across multiple parameters, while Roundup Mega exhibited significant genotoxicity with the largest effect size only at higher concentrations (500 μM). Co-formulants like ROKAmin SR22 and Embigen BB showed varying cytotoxicity but generally lower genotoxicity when tested alone. This ability to induce genotoxicity at subcytotoxic levels emphasizes the need for independent assessments of genetic damage, particularly for complete formulations rather than ingredients in isolation. This dissertation contributes to our understanding of pesticide-related health risks by highlighting the genotoxic potential of occupational pesticide exposure, the complex and variable safety profiles of encapsulated pesticide formulations, and the critical role of formulation technology in modulating pesticide toxicity. The findings emphasize the need for formulation-specific risk assessment approaches, multi-cell line toxicity evaluations, and improved safety measures for agricultural workers, particularly in developing regions. These insights have significant implications for pesticide regulation, occupational health policies, and the development of safer formulation technologies
The effect of exercise training on biventricular myocardial strain in heart failure with preserved ejection fraction
No full textabstract: Aims
High-intensity interval training (HIIT) improves peak oxygen uptake and left ventricular diastology in patients with heart failure with preserved ejection fraction (HFpEF). However, its effects on myocardial strain in HFpEF remain unknown. We explored the effects of HIIT and moderate-intensity aerobic continuous training (MI-ACT) on left and right ventricular strain parameters in patients with HFpEF. Furthermore, we explored their relationship with peak oxygen uptake (VO[subscript 2peak]).
Methods and results
Fifteen patients with HFpEF (age = 70 ± 8.3 years) were randomized to either: (i) HIIT (4 × 4 min, 85–90% peak heart rate, interspersed with 3 min of active recovery; n = 9) or (ii) MI-ACT (30 min at 70% peak heart rate; n = 6). Patients were trained 3 days/week for 4 weeks and underwent VO[subscript 2peak] testing and 2D echocardiography at baseline and after completion of the 12 sessions of supervised exercise training. Left ventricular (LV) and right ventricular (RV) average global peak systolic longitudinal strain (GLS) and peak systolic longitudinal strain rate (GSR) were quantified. Paired t-tests were used to examine within-group differences and unpaired t-tests used for between-group differences (α = 0.05). Right ventricular average global peak systolic longitudinal strain improved significantly in the HIIT group after training (pre = −18.4 ± 3.2%, post = −21.4 ± 1.7%; P = 0.02) while RV-GSR, LV-GLS, and LV-GSR did not (P > 0.2). No significant improvements were observed following MI-ACT. No significant between-group differences were observed for any strain measure. ΔLV-GLS and ΔRV-GLS were modestly correlated with ΔVO[subscript 2peak] (r = −0.48 and r = −0.45; P = 0.1, respectively).
Conclusions
In patients with HFpEF, 4 weeks of HIIT significantly improved RV-GLS.The final version of this article, as published in ESC Heart Failure, can be viewed online at: http://onlinelibrary.wiley.com/doi/10.1002/ehf2.12149/abstract
Effects of biochar amendment on sorption, dissipation, and uptake of fenamiphos and cadusafos nematicides in sandy soil
No full textBACKGROUND: The application of biochar to soil is supposed to alter its adsorption/desorption potential toward pesticides, thereby affecting their bioavailability and efficacy. This is particularly relevant in the case of nematicides because these pesticides are directly applied to soil. RESULTS: Biochar was produced from date palm (PB) and eucalyptus (EB) waste at 450 °C and added at a rate of 1% to a sandy soil. The half-life (t1⁄2) of fenamiphos was increased from 2.7 to 18.3 and 18.6 days in PB- and EB-amended soils, respectively. By contrast, the half-life of cadusafos was unaffected. Freundlich Kf values increased from 1.22 and 0.39 (μg1–Nf g−1 mLNf) to 4.49 and 6.84 in 1% PB-amended soil, and to 3.49 and 4.62 in 1% EB-amended soil for cadusafos and fenamiphos, respectively. Plant uptake of both nematicides in tomato seedlings was reduced by approximately 97% (cadusafos) and 85% (fenamiphos). Although nematicide efficacy against Meloidogyne incognita was not altered at the recommended dosage, it was negatively affected at a half-dose rate. Under these conditions, it decreased from 43.1% in unamended sandy soil to only 18.3% in 1% PB-amended soil. CONCLUSIONS: Biochar addition increased the sorption capacity of soil. This resulted in a decrease of nematicide bioavailability, together with a reduction of both the dissipation rate and uptake by tomato plants. © 2018 Society of Chemical Industry
The Current State of Artificial Intelligence on Detecting Pulmonary Embolism via Computerised Tomography Pulmonary Angiogram: A Systematic Review.
No full textCopyright: © 2025 The Author(s).
https://creativecommons.org/licenses/by-nc/4.0/Pulmonary embolism (PE) is a life-threatening condition with significant diagnostic challenges due to high rates of missed or delayed detection. Computed tomography pulmonary angiography (CTPA) is the current standard for diagnosing PE, however, demand for imaging places strain on healthcare systems and increases error rates. This systematic review aims to assess the diagnostic accuracy and clinical applicability of artificial intelligence (AI)-based models for PE detection on CTPA, exploring their potential to enhance diagnostic reliability and efficiency across clinical settings. A systematic review was conducted in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Excerpta Medica Database (EMBASE), Medical Literature Analysis and Retrieval System Online (MEDLINE), Cochrane, PubMed, and Google Scholar were searched for original articles from inception to September 2024. Articles were included if they reported successful AI integration, whether partial or full, alongside CTPA scans for PE detection in patients. The literature search identified 919 articles, with 745 remaining after duplicate removal. Following rigorous screening and appraisal aligned with inclusion and exclusion criteria, 12 studies were included in the final analysis. A total of three primary AI modalities emerged: convolutional neural networks (CNNs), segmentation models, and natural language processing (NLP), collectively used in the analysis of 341,112 radiographic images. CNNs were the most frequently applied modality in this review. Models such as AdaBoost and EmbNet have demonstrated high sensitivity, with EmbNet achieving 88-90.9% per scan and reducing false positives to 0.45 per scan. AI shows significant promise as a diagnostic tool for identifying PE on CTPA scans, particularly when combined with other forms of clinical data. However, challenges remain, including ensuring generalisability, addressing potential bias, and conducting rigorous external validation. Variability in study methodologies and the lack of standardised reporting of key metrics complicate comparisons. Future research must focus on refining models, improving peripheral emboli detection, and validating performance across diverse settings to realise AI's potential fully
Fame bias in editorial choice: Yes or No?
No full textRecently, Scientometrics has published a paper titled “Is there bias in editorial choice? Yes” (Moustafa 2015) in which some comments are given on our published paper in Nature titled “Is there fame bias in editorial choice?” (Mahian et al. 2015). Unfortunately, the author of above mentioned paper and many other readers might misunderstand the main aim of our correspondence. Here, we try to give some explanations to clarify the main goal of analysis presented in the paper
Programming and managing distributed software-defined environments
No full textThe amount of data generated by applications and digital sources is rising to unprecedented scales. To keep pace, applications and workflows tasked with transforming the data to insight are becoming increasingly dynamic and inherently data-driven. Furthermore, the computational services, i.e., compute, data, and communication, required to run this emerging class of applications are often just as dynamic and heterogeneous. As data sizes continue to grow, one must find new ways of harnessing these services to meet the needs of emerging data-driven workloads. Building a computational environment capable of supporting these applications presents many complex challenges. For example, there are requirements and dynamic behaviors set forth by multiple components of the environment, i.e., users, service providers, applications, and computational services. Accordingly, an environment must be capable of (1) providing a way for these components to express their requirements at any time in the application lifecycle and (2) reacting in real-time to changes set forth by any of these components by adjusting the service composition. While cloud computing provides the flexibility and diversity of services required by such an environment, determining which services to compose to meet application needs and when to compose them is not supported by current service models and infrastructure. To address these challenges, this dissertation presents a programming system to enable the creation of a distributed Software-Defined Environment (dSDE); the resulting environment can seamlessly and symbiotically combine compute, data sources, data storage, and network resources. Specifically, this work makes the following contributions: (1) it enables the on-demand aggregation of distributed services while facilitating the continuous deployment of applications on top of them; (2) it provides programming abstractions that allow users, resource providers, and applications to dynamically compose different services based on constraints or requirements; (3) it introduces a runtime framework that can autonomously adapt to changes from any of the components in the environment; and (4) it sets forth a quantification model for application performance and expected quality of service of the resulting distributed Software-Defined Environment, which allows users to reason about trade-offs and requirements with respect to throughput, latency, cost, deadline, etc. The applicability of this work to real-world scientific applications is validated through a series of experiments where heterogeneous, geographically distributed services are composed based on user, resource provider, and application specifications. The results establish the potential impact of a system capable of real-time adaptability to changes in mixed resource environments, including multiple clouds, grids, clusters, supercomputers, and traditional data centers.Ph.D.Includes bibliographical referencesby Moustafa H. AbdelBak
- …
