ahmed fahmi - Academia.edu (original) (raw)

Papers by ahmed fahmi

Prunus Armeniaca (Egyptian apricot) is the plant of Rosaceae family which is widely known for its... more Prunus Armeniaca (Egyptian apricot) is the plant of Rosaceae family which is widely known for its fruit. It has high nutritional value as it contains essential amino acids, proteins, carbohydrates, and lipids. Kernel oil extracted from it was found to have antibacterial, antifungal, antioxidant, and anti-inflammatory effects. Its therapeutic effect is still under research. Apricot extracts were found to inhibit in vitro growth of breast cancer and hepatocellular carcinoma. Objectives: Evaluating the effect of Prunus Armeniaca (PA) extract on Oral Squamous cell carcinoma (OSCC) Methods: Egyptian PA seeds were macerated and added to 90% methanol for 7 day for alcohol extract preparations. OSCC cell line of human tongue were cultured and divided onto 2 groups. Group − 1 was treated with the PA alcohol extract. Group-2 were untreated cell line of the OSCC human tongue as a negative control group. Caspase-3 and − 8 activity assay, Cell viability and cytotoxicity, and Cell cycle analysis ...

Egyptian Dental Journal, 2020

Egyptian Dental Journal, 2020

Background and Objectives: Oral squamous cell carcinoma (OSCC) is a major oral cancer representat... more Background and Objectives: Oral squamous cell carcinoma (OSCC) is a major oral cancer representative. Squamous cell carcinoma antigen (Scc-AG) is detected in squamous cell carcinoma of oral tissues and other different tissues. It has been used as a biomarker for OSCC and hence the aim of this study was to detect if Scc-Ag can differentiate between malignant lesions and suspicious chronic inflammatory lesions.. Methods: Forty-five participants divided into OSCC group and two control groups: oral lichen planus as an inflammatory disease (positive control) and healthy volunteers (negative control). Clinical staging and grading of OSCC was recorded. A double-antibody sandwich enzyme-linked immunosorbent assay was used to evaluate the level of Scc-AG in serum and saliva. Results: Statistically significant difference for serum and salivary Scc-Ag, was found between the groups; OSCC, OLP on one hand and healthy controls on the other hand. No statistically significant difference was found between OSCC and OLP control groups in serum levels, while for salivary Scc-Ag a statistically significant difference was found between these two groups, with the higher values in OLP. Staging and grading in OSCC group were not found to be related to Scc-Ag level. Conclusion: Serum Scc-Ag cannot be used as a biomarker to differentiate between oral malignant and chronic inflammatory lesions. Salivary Scc-Ag is more reliable than serum Scc-Ag in differential diagnosis of OSCC.

arXiv (Cornell University), Aug 14, 2020

Spurred by widening gap between data processing speed and data communication speed in Von-Neumann... more Spurred by widening gap between data processing speed and data communication speed in Von-Neumann computing architectures, some bioinformatic applications have harnessed the computational power of Processing-in-Memory (PIM) platforms. However, the performance of PIMs unavoidably diminishes when dealing with such complex applications seeking bulk bit-wise comparison or addition operations. In this work, we present an efficient Processing-in-MRAM Accelerated De Bruijn Graph based DNA Assembly platform named PANDA based on an optimized and hardware-friendly genome assembly algorithm. PANDA is able to assemble large-scale DNA sequence data-set from all-pair overlaps. We first design PANDA platform that exploits MRAM as a computational memory and converts it to a potent processing unit for genome assembly. PANDA can execute not only efficient bulk bit-wise X(N)ORbased comparison/addition operations heavily required for the genome assembly task but a full-set of 2-/3-input logic operations inside MRAM chip. We then develop a highly parallel and stepby-step hardware-friendly DNA assembly algorithm for PANDA that only requires the developed in-memory logic operations. The platform is then configured with a novel data partitioning and mapping technique that provides local storage and processing to fully utilize the algorithm-level's parallelism. The cross-layer simulation results demonstrate that PANDA reduces the run time and power, respectively, by a factor of 18 and 11 compared with CPU. Besides, speed-ups of up-to 2-4× can be obtained over recent processing-in-MRAM platforms to perform the same task.

Egyptian Dental Journal, 2019

Objectives To evaluate the effect of a single-dose local administration versus the systemic admin... more Objectives To evaluate the effect of a single-dose local administration versus the systemic administration of Erythropoietin on bone healing in calvarial bone defects Material & Methods Critical-size cranial osteotomy defects were created in 30 rabbits. The animals were randomly divided into 3 groups. The animals were randomly divided into 3 groups (n= 10 animals in each group). In the Group I, the bone defect was only filled with a collagen sponge soaked with erythropoietin. In the Group II, it was filled with a collagen sponge and erythropoietin injected systemically. While in the Group III, the defect was filled with a collagen sponge. The groups were further split in two for euthanasia 10-and 21-days post-surgery. New bone formation and neovascularization were evaluated by hematoxylin-eosin. For the 10-days samples, all the groups analyzed for area percent of blood vessels while on the 21-day samples, the area of new bone formation was calculated. Differences between groups were analyzed by one-way ANOVA. Results At 10 days post-surgery, the histological analysis showed that the erythropoietin Groups exhibited a significantly higher percentage of bone formation compared with the other Group. At 21 days post-surgery, a higher percentage of new bone was observed in the erythropoietin group. Conclusions The results suggest that both local and systemic administration of erythropoietin hormone encouraged the bone healing in critical-size calvarial defects in Rabbits.

Egyptian Dental Journal, 2017

Aim of the study: The aim of the current study was to assess the vitality of autogenous bone graf... more Aim of the study: The aim of the current study was to assess the vitality of autogenous bone grafts harvested from rabbits` calvaria following decontamination of the grafts using three different antimicrobial agents. Materials and Methods: Autogenous bone grafts were harvested from the calvaria of twenty four white New Zealand male rabbits. The grafts were allowed a five minutes contact time with normal saline (Group I), 2% chlorhexidine (Group II), Clindamycine (Group III) and Oleozone gel (Group IV). The grafts were then reinserted into the previously created graft beds. Animals were sacrificed at 10 and 21 days post surgery, dual energy x-ray absorptiometry (DEXA) scans were performed for the skull of the rabbits and bone specimens were collected for histological examination. Results: Histomorphometric analysis showed a superior results in favor of the ozone treated group represented as a significantly higher percentage of normal osteocytes and marked increase in area percentage of new bone formation. Additionally, DEXA scan revealed a significant increase in bone mineral density and bone mineral concentration of the ozone treated group compared to the other studied groups. Conclusion: The ozone treated grafts showed a distinguished preservation of osteoblastic vitality, which may indicate a superior biocompatibility compared to chlorhexidine and clindamycin.

Science, Technology and Arts Research Journal, 2016

The objective of this study was to assess the status and challenges of wetlands management in Bul... more The objective of this study was to assess the status and challenges of wetlands management in Bule Hora Woreda so as to enhance the sustainability of the wetlands to increase the advantages of wetland beneficiaries and ecological health. Results of the study Indicates that, Bule Hora woreda has many wetlands, which they use for different purposes including for grazing, for traditional house making, for fresh water supply, for cultivation of some crops and for other purposes. However, the areal coverage, their distribution, their benefits, as well as their management practices are not studied in the Woreda. According to this study, some of the degrading factors of these wetlands include unplanned settlement, eucalyptus plantation, deforestation, agricultural practices, overgrazing and gold extraction particularly for Rophi Megada wetlands. In addition, to describe the trend of change of these wetlands Landsat TM 1986, Landsat ETM 2000 and SPOT 2006 were used to show the declining pattern of these resources. As a result degradation of these resources many local communities experienced with scarcity of some of their basic livelihood such as scarcity of fresh water supply , scarcity of some crops as well as some important edible plants like Syzygium guineense var. (Wild.) DC. (Myrtaceae), Olea europaea subsp. cuspidata (Wall. Ex G. Don) Cif., (Oleaceae) and others. Furthermore, due to the degradation of these wetlands, many wetland were disappeared. The information gathered from elders also revealed that some wildlife species such as duicker, aardvark, porcupine, bushback, Trign (and pig are under threat due to the destruction of these Cattle Egret, Great White Egret, Hadada Ibis, Egyptian Goose, Egyptian Vultur , Abyssinian Ground Hornbill, and Laughing Dove are also disappeared from these wetlands.

2020 57th ACM/IEEE Design Automation Conference (DAC), 2020

In this paper, for the first time, we propose a high-throughput and energy-efficient Processing-i... more In this paper, for the first time, we propose a high-throughput and energy-efficient Processing-in-DRAMaccelerated genome assembler called PIM-Assembler based on an optimized and hardware-friendly genome assembly algorithm. PIM-Assembler can assemble large-scale DNA sequence dataset from all-pair overlaps. We first develop PIM-Assembler platform that harnesses DRAM as computational memory and transforms it to a fundamental processing unit for genome assembly. PIM-Assembler can perform efficient X(N)OR-based operations inside DRAM incurring low cost on top of commodity DRAM designs (∼5% of chip area). PIM-Assembler is then optimized through a correlated data partitioning and mapping methodology that allows local storage and processing of DNA short reads to fully exploit the genome assembly algorithm-level's parallelism. The simulation results show that PIM-Assembler achieves on average 8.4× and 2.3× higher throughput for performing bulk bitwise XNOR-based comparison operations compared with CPU and recent processing-in-DRAM platforms, respectively. As for comparison/addition-extensive genome assembly application, it reduces the execution time and power by ∼5× and ∼7.5× compared to GPU.

The primary aim of this research paper is to analyse and discuss how the implementation of Public... more The primary aim of this research paper is to analyse and discuss how the implementation of Public-Private Partnerships (PPPs) can maximize the impact of capacity building in scientific research and in turn, contribute to the implementation of the Sustainable Development Goals (SDGs). It is discussed that there has been a movement towards an evolution of PPPs systems, particularly in regard to new financial methods for education and scientific research. This paper demonstrates that international organisations such as the United Nations (UN) are increasingly encouraging the adoption of PPPs. Also discussed are the challenges faced during the cooperation between the private sector and multilateral organisations during the adoption of PPPs. Practical casework from the African continent is also explored. This article showcases joint-initiatives (such as the UNESCO-Merck Africa Research Summit) that aim to create fertile ground for spillover effects, such as North-South and South-South scientific cooperation, as well as gender empowerment in research. Following controversial literature, PPPs can catalyse stronger relationships among heterogeneous actors which include international organisations, industry, research centres and universities. L'obiettivo primario di questo studio è analizzare e discutere come lo sviluppo di partenariati pubblico-privati (PPP) possa massimizzare l'impatto di progetti legati al "rafforzamento delle capacità" nella ricerca scientifica e, allo stesso tempo, contribuire al raggiungimento degli obiettivi di sviluppo sostenibile sanciti dall'Agenda 2030. Negli ultimi decenni si è sviluppato un notevole interesse sull'evoluzione di sistemi di PPP, soprattutto in relazione ai meccanismi di finanziamento dell'educazione e della ricerca scientifica. Viene qui inoltre descritto il ruolo di organizzazioni internazionali, quali le Nazioni Unite, nell'incoraggiare l'adozione di PPP per perseguire i propri obiettivi di § The authors of this paper have been in collaboration in creating and implementing the joint initiative, among UNESCO, Merck Foundation and the African Union, which constitutes the background of the research. The opinions expressed in this paper are the author's own and do not reflect the view of UNESCO, the African Union, or the Merck Foundation.

Prunus Armeniaca (Egyptian apricot) is the plant of Rosaceae family which is widely known for its... more Prunus Armeniaca (Egyptian apricot) is the plant of Rosaceae family which is widely known for its fruit. It has high nutritional value as it contains essential amino acids, proteins, carbohydrates, and lipids. Kernel oil extracted from it was found to have antibacterial, antifungal, antioxidant, and anti-inflammatory effects. Its therapeutic effect is still under research. Apricot extracts were found to inhibit in vitro growth of breast cancer and hepatocellular carcinoma. Objectives: Evaluating the effect of Prunus Armeniaca (PA) extract on Oral Squamous cell carcinoma (OSCC) Methods: Egyptian PA seeds were macerated and added to 90% methanol for 7 day for alcohol extract preparations. OSCC cell line of human tongue were cultured and divided onto 2 groups. Group − 1 was treated with the PA alcohol extract. Group-2 were untreated cell line of the OSCC human tongue as a negative control group. Caspase-3 and − 8 activity assay, Cell viability and cytotoxicity, and Cell cycle analysis ...

Egyptian Dental Journal, 2020

Egyptian Dental Journal, 2020

Background and Objectives: Oral squamous cell carcinoma (OSCC) is a major oral cancer representat... more Background and Objectives: Oral squamous cell carcinoma (OSCC) is a major oral cancer representative. Squamous cell carcinoma antigen (Scc-AG) is detected in squamous cell carcinoma of oral tissues and other different tissues. It has been used as a biomarker for OSCC and hence the aim of this study was to detect if Scc-Ag can differentiate between malignant lesions and suspicious chronic inflammatory lesions.. Methods: Forty-five participants divided into OSCC group and two control groups: oral lichen planus as an inflammatory disease (positive control) and healthy volunteers (negative control). Clinical staging and grading of OSCC was recorded. A double-antibody sandwich enzyme-linked immunosorbent assay was used to evaluate the level of Scc-AG in serum and saliva. Results: Statistically significant difference for serum and salivary Scc-Ag, was found between the groups; OSCC, OLP on one hand and healthy controls on the other hand. No statistically significant difference was found between OSCC and OLP control groups in serum levels, while for salivary Scc-Ag a statistically significant difference was found between these two groups, with the higher values in OLP. Staging and grading in OSCC group were not found to be related to Scc-Ag level. Conclusion: Serum Scc-Ag cannot be used as a biomarker to differentiate between oral malignant and chronic inflammatory lesions. Salivary Scc-Ag is more reliable than serum Scc-Ag in differential diagnosis of OSCC.

arXiv (Cornell University), Aug 14, 2020

Spurred by widening gap between data processing speed and data communication speed in Von-Neumann... more Spurred by widening gap between data processing speed and data communication speed in Von-Neumann computing architectures, some bioinformatic applications have harnessed the computational power of Processing-in-Memory (PIM) platforms. However, the performance of PIMs unavoidably diminishes when dealing with such complex applications seeking bulk bit-wise comparison or addition operations. In this work, we present an efficient Processing-in-MRAM Accelerated De Bruijn Graph based DNA Assembly platform named PANDA based on an optimized and hardware-friendly genome assembly algorithm. PANDA is able to assemble large-scale DNA sequence data-set from all-pair overlaps. We first design PANDA platform that exploits MRAM as a computational memory and converts it to a potent processing unit for genome assembly. PANDA can execute not only efficient bulk bit-wise X(N)ORbased comparison/addition operations heavily required for the genome assembly task but a full-set of 2-/3-input logic operations inside MRAM chip. We then develop a highly parallel and stepby-step hardware-friendly DNA assembly algorithm for PANDA that only requires the developed in-memory logic operations. The platform is then configured with a novel data partitioning and mapping technique that provides local storage and processing to fully utilize the algorithm-level's parallelism. The cross-layer simulation results demonstrate that PANDA reduces the run time and power, respectively, by a factor of 18 and 11 compared with CPU. Besides, speed-ups of up-to 2-4× can be obtained over recent processing-in-MRAM platforms to perform the same task.

Egyptian Dental Journal, 2019

Objectives To evaluate the effect of a single-dose local administration versus the systemic admin... more Objectives To evaluate the effect of a single-dose local administration versus the systemic administration of Erythropoietin on bone healing in calvarial bone defects Material & Methods Critical-size cranial osteotomy defects were created in 30 rabbits. The animals were randomly divided into 3 groups. The animals were randomly divided into 3 groups (n= 10 animals in each group). In the Group I, the bone defect was only filled with a collagen sponge soaked with erythropoietin. In the Group II, it was filled with a collagen sponge and erythropoietin injected systemically. While in the Group III, the defect was filled with a collagen sponge. The groups were further split in two for euthanasia 10-and 21-days post-surgery. New bone formation and neovascularization were evaluated by hematoxylin-eosin. For the 10-days samples, all the groups analyzed for area percent of blood vessels while on the 21-day samples, the area of new bone formation was calculated. Differences between groups were analyzed by one-way ANOVA. Results At 10 days post-surgery, the histological analysis showed that the erythropoietin Groups exhibited a significantly higher percentage of bone formation compared with the other Group. At 21 days post-surgery, a higher percentage of new bone was observed in the erythropoietin group. Conclusions The results suggest that both local and systemic administration of erythropoietin hormone encouraged the bone healing in critical-size calvarial defects in Rabbits.

Egyptian Dental Journal, 2017

Aim of the study: The aim of the current study was to assess the vitality of autogenous bone graf... more Aim of the study: The aim of the current study was to assess the vitality of autogenous bone grafts harvested from rabbits` calvaria following decontamination of the grafts using three different antimicrobial agents. Materials and Methods: Autogenous bone grafts were harvested from the calvaria of twenty four white New Zealand male rabbits. The grafts were allowed a five minutes contact time with normal saline (Group I), 2% chlorhexidine (Group II), Clindamycine (Group III) and Oleozone gel (Group IV). The grafts were then reinserted into the previously created graft beds. Animals were sacrificed at 10 and 21 days post surgery, dual energy x-ray absorptiometry (DEXA) scans were performed for the skull of the rabbits and bone specimens were collected for histological examination. Results: Histomorphometric analysis showed a superior results in favor of the ozone treated group represented as a significantly higher percentage of normal osteocytes and marked increase in area percentage of new bone formation. Additionally, DEXA scan revealed a significant increase in bone mineral density and bone mineral concentration of the ozone treated group compared to the other studied groups. Conclusion: The ozone treated grafts showed a distinguished preservation of osteoblastic vitality, which may indicate a superior biocompatibility compared to chlorhexidine and clindamycin.

Science, Technology and Arts Research Journal, 2016

The objective of this study was to assess the status and challenges of wetlands management in Bul... more The objective of this study was to assess the status and challenges of wetlands management in Bule Hora Woreda so as to enhance the sustainability of the wetlands to increase the advantages of wetland beneficiaries and ecological health. Results of the study Indicates that, Bule Hora woreda has many wetlands, which they use for different purposes including for grazing, for traditional house making, for fresh water supply, for cultivation of some crops and for other purposes. However, the areal coverage, their distribution, their benefits, as well as their management practices are not studied in the Woreda. According to this study, some of the degrading factors of these wetlands include unplanned settlement, eucalyptus plantation, deforestation, agricultural practices, overgrazing and gold extraction particularly for Rophi Megada wetlands. In addition, to describe the trend of change of these wetlands Landsat TM 1986, Landsat ETM 2000 and SPOT 2006 were used to show the declining pattern of these resources. As a result degradation of these resources many local communities experienced with scarcity of some of their basic livelihood such as scarcity of fresh water supply , scarcity of some crops as well as some important edible plants like Syzygium guineense var. (Wild.) DC. (Myrtaceae), Olea europaea subsp. cuspidata (Wall. Ex G. Don) Cif., (Oleaceae) and others. Furthermore, due to the degradation of these wetlands, many wetland were disappeared. The information gathered from elders also revealed that some wildlife species such as duicker, aardvark, porcupine, bushback, Trign (and pig are under threat due to the destruction of these Cattle Egret, Great White Egret, Hadada Ibis, Egyptian Goose, Egyptian Vultur , Abyssinian Ground Hornbill, and Laughing Dove are also disappeared from these wetlands.

2020 57th ACM/IEEE Design Automation Conference (DAC), 2020

In this paper, for the first time, we propose a high-throughput and energy-efficient Processing-i... more In this paper, for the first time, we propose a high-throughput and energy-efficient Processing-in-DRAMaccelerated genome assembler called PIM-Assembler based on an optimized and hardware-friendly genome assembly algorithm. PIM-Assembler can assemble large-scale DNA sequence dataset from all-pair overlaps. We first develop PIM-Assembler platform that harnesses DRAM as computational memory and transforms it to a fundamental processing unit for genome assembly. PIM-Assembler can perform efficient X(N)OR-based operations inside DRAM incurring low cost on top of commodity DRAM designs (∼5% of chip area). PIM-Assembler is then optimized through a correlated data partitioning and mapping methodology that allows local storage and processing of DNA short reads to fully exploit the genome assembly algorithm-level's parallelism. The simulation results show that PIM-Assembler achieves on average 8.4× and 2.3× higher throughput for performing bulk bitwise XNOR-based comparison operations compared with CPU and recent processing-in-DRAM platforms, respectively. As for comparison/addition-extensive genome assembly application, it reduces the execution time and power by ∼5× and ∼7.5× compared to GPU.

The primary aim of this research paper is to analyse and discuss how the implementation of Public... more The primary aim of this research paper is to analyse and discuss how the implementation of Public-Private Partnerships (PPPs) can maximize the impact of capacity building in scientific research and in turn, contribute to the implementation of the Sustainable Development Goals (SDGs). It is discussed that there has been a movement towards an evolution of PPPs systems, particularly in regard to new financial methods for education and scientific research. This paper demonstrates that international organisations such as the United Nations (UN) are increasingly encouraging the adoption of PPPs. Also discussed are the challenges faced during the cooperation between the private sector and multilateral organisations during the adoption of PPPs. Practical casework from the African continent is also explored. This article showcases joint-initiatives (such as the UNESCO-Merck Africa Research Summit) that aim to create fertile ground for spillover effects, such as North-South and South-South scientific cooperation, as well as gender empowerment in research. Following controversial literature, PPPs can catalyse stronger relationships among heterogeneous actors which include international organisations, industry, research centres and universities. L'obiettivo primario di questo studio è analizzare e discutere come lo sviluppo di partenariati pubblico-privati (PPP) possa massimizzare l'impatto di progetti legati al "rafforzamento delle capacità" nella ricerca scientifica e, allo stesso tempo, contribuire al raggiungimento degli obiettivi di sviluppo sostenibile sanciti dall'Agenda 2030. Negli ultimi decenni si è sviluppato un notevole interesse sull'evoluzione di sistemi di PPP, soprattutto in relazione ai meccanismi di finanziamento dell'educazione e della ricerca scientifica. Viene qui inoltre descritto il ruolo di organizzazioni internazionali, quali le Nazioni Unite, nell'incoraggiare l'adozione di PPP per perseguire i propri obiettivi di § The authors of this paper have been in collaboration in creating and implementing the joint initiative, among UNESCO, Merck Foundation and the African Union, which constitutes the background of the research. The opinions expressed in this paper are the author's own and do not reflect the view of UNESCO, the African Union, or the Merck Foundation.