The construction of artificial systems by drawing inspiration from nat- ural systems is not a new... more The construction of artificial systems by drawing inspiration from nat- ural systems is not a new idea. The Artificial Neural Network (ANN) and Genetic Algorithms (GAs) are good examples of successful applications of the biological metaphor to the solution of computational problems. The study of artificial immune systems is a relatively new field that tries to exploit the mechanisms of the natural immune system (NIS) in order to develop problem- solving techniques. In this re- search, we have combined the artificial immune system with the genetic algorithms in one hybrid algorithm. We proposed a modification to the clonal selection algo- rithm, which is inspired from the clonal selection principle and affinity maturation of the human immune responses, by hybridizing it with the crossover operator, which is imported from GAs to increase the exploration of the search space. We also in- troduced the adaptability of the mutation rates by applying a degrading function so that the mutation rates decrease with time where the affinity of the population in- creases, the hybrid algorithm used for evolving a fuzzy rule system to solve the well- known Wisconsin Breast Cancer Diagnosis problem (WBCD). Our evolved system exhibits two important characteristics; first, it attains high classification performance, with the possibility of attributing a confidence measure to the output diagnosis; sec- ond, the system has a simple fuzzy rule system; therefore, it is human interpretable. The hybrid algorithm overcomes both the GAs and the AIS, so that it reached the classification ratio 97.36, by only one rule, in the earlier generations than the two other algorithms. The learning and memory acquisition of our algorithm was ver- ified through its application to a binary character recognition problem. The hybrid algorithm overcomes also GAs and AIS and reached the convergence point before
Post-translational histone modifications are known to be altered in cancer cells, and loss of sel... more Post-translational histone modifications are known to be altered in cancer cells, and loss of selected histone acetylation and methylation marks has recently been shown to predict patient outcome in human carcinoma. Immunohistochemistry was used to detect a series of histone lysine acetylation (H3K9ac, H3K18ac, H4K12ac, and H4K16ac), lysine methylation (H3K4me2 and H4K20me3), and arginine methylation (H4R3me2) marks in a well-characterized series of human breast carcinomas (n = 880). Tissue staining intensities were assessed using blinded semiquantitative scoring. Validation studies were done using immunofluorescence staining and Western blotting. Our analyses revealed low or absent H4K16ac in the majority of breast cancer cases (78.9%), suggesting that this alteration may represent an early sign of breast cancer. There was a highly significant correlation between histone modifications status, tumor biomarker phenotype, and clinical outcome, where high relative levels of global histone acetylation and methylation were associated with a favorable prognosis and detected almost exclusively in luminal-like breast tumors (93%). Moderate to low levels of lysine acetylation (H3K9ac, H3K18ac, and H4K12ac), lysine (H3K4me2 and H4K20me3), and arginine methylation (H4R3me2) were observed in carcinomas of poorer prognostic subtypes, including basal carcinomas and HER-2-positive tumors. Clustering analysis identified three groups of histone displaying distinct pattern in breast cancer, which have distinct relationships to known prognostic factors and clinical outcome. This study identifies the presence of variations in global levels of histone marks in different grades, morphologic types, and phenotype classes of invasive breast cancer and shows that these differences have clinical significance. [Cancer Res 2009;69(9):3802-9]
An experimental investigation is presented on free convection of air around the outer surface of ... more An experimental investigation is presented on free convection of air around the outer surface of a constant heat flux elliptic tube. The local and average Nusselt number distribution is reported for different values of Rayleigh number and different tube inclination angles. The test Rayleigh number, based on input heat flux, ranges from 1:1 Â 10 7 to 8 Â 10 7 . Average Nusselt numbers are evaluated and correlated with Rayleigh number for the elliptic tube with vertical major axis. Comparison between the convection characteristics of isothermal and constant heat flux elliptic tubes has been presented. Also, the effect of elliptic tube orientation on the average Nusselt number is shown. It is found that a higher value of average Nusselt number is achieved when the major axis of the tube is vertical.
we have treated a number of 45 male patients diagnosed with idiopathic male infertility. The medi... more we have treated a number of 45 male patients diagnosed with idiopathic male infertility. The median age was 33.4 years (25)(26)(27)(28)(29)(30)(31)(32)(33)(34)(35)(36)(37)(38). We have excluded from the treatment group the patients with a large varicocele, and those with chronic UTI, prostatitis. The therapeutic protocol included a number of 10 to 15 acupuncture sessions at an interval of 2-3 days. The needles were introduced into the selected points, then mobilized until the deqi sensation was elicited and then left in place for half an hour. From each patient two spermograms were obtained; one just prior to the beginning of the treatment and one two to three weeks after its conclusion. Acupuncture points that we have used with predilection were mostly from the Kidney, Liver, Spleen, Urinary Bladder, DuMai and RenMai meridians -respectively Lv3, Sp6, Sp8, Sp9, Ren2, Ren3, Ren4, Du4, Ub23, Ub52 and Ub31, Ub32. Results: We have seen a marked increase in all of the followed parameters. The overall sperm count/ejaculate has risen three to ten fold. The functional sperm/ ejaculate rose 2.5 to 3 times. The percentage of mobile sperm increased 3-4 times. The percentage of normal sperm morphology has risen from a median value of 3% to 12%. Conclusion: We consider these results to be of significance. The present study needs to be continued with a complete hormonal workup before and after the treatment. In some of the presented cases that we could investigate, we have observed a decrease of the prolactine levels and an increase in the testosterone levels. We strongly believe that in selected cases, acupuncture is a valuable treatment of the male infertility, with high success rates. We have noted 12 pregnancies with subsequent child birth in the couples of the patients included in this study.
We identified involved lymph node groups in patients with oropharyngeal carcinoma and radiologica... more We identified involved lymph node groups in patients with oropharyngeal carcinoma and radiologically N0 disease, aiming to define the clinical target volume, and to assess the negative predictive value of CT neck and correlate it to the tumor site, stage, and grade. Between 1988 and 2000, we evaluated 53 patients who satisfied all of the following criteria: 1) oropharyngeal carcinoma diagnosis; 2) NO stage based on CT; 3) no prior treatment; and 4) primary surgical resection including ipsi-lateral neck dissection. The pathology reports were reviewed to identify the exact site of lymph node involvement. Twenty patients (37.7%) were found to have pathologically positive lymph nodes, yielding a negative predictive value of 62.3% for CT neck. Node levels II, III, and IV were the most commonly involved (26%, 17%, and 11% of all patients, respectively). Fifty percent of patients with T3 and T4 tumors had positive lymph nodes versus 20% of patients with T1 and T2 (P = 0.036). Tumor grade and site were insignificant (P > 0.05). Ipsilateral neck levels II-IV should be included during elective nodal irradiation in patients with N0-stage oropharyngeal carcinoma, regardless of the primary tumor site, stage, and grade.
The pattern of cytokines secreted by T cells at the site of viral replication may influence the f... more The pattern of cytokines secreted by T cells at the site of viral replication may influence the final outcome of HCV infection. The aim of this study was to assess whether there is a preferential production of Th1 or Th2 associated cytokines in the course of acute and chronic HCV infection. Serum level of IL2, INF gamma (Th1 associated cytokines) and IL1O (Th2 associated cyto- kines) were measured in 21 chronic HCV cases, 20 acute HCV cases and 19 healthy volunteers. Mean serum level of IL2 was significantly higher in chronic hepatitis C (267.3 ± 76.13) than in acute cases (147.09 ± 54.9) and controls (116.11 ± 33.45). Acute HCV cases had a higher mean ILIO level (13.3 ± 4.12) than controls (10.64 ± 0.84) and chronic HCV cases had a higher mean ILIO level (36.87 ± 6.58) than acute HCV cases. Mean serum level of INF gamma where nearly equal in all three groups. There was a trend to negative correlation between IL2 and IL 10 and positive correlation between IL2 and INF gamma. However these trends were not statistically significant. In conclusion this study suggests weak response of Th1 cells in acute HCV infection and a possible suppressive Th2 cell response in chronic HCV, which might explain the failure of viral clearance and a weak cellular immune response.
The automatic diagnosis of breast cancer is an important, real-world medical problem. In this pap... more The automatic diagnosis of breast cancer is an important, real-world medical problem. In this paper we give an introduction to fuzzy systems, genetic algorithms and artificial immune system, and then we introduce a hybrid algorithm that gathers the genetic algorithms with the artificial immune system in one algorithm. The genetic algorithm, the artificial immune system and the hybrid algorithm were implemented and tested on the Wisconsin breast cancer diagnosis (WBCD) problem in order to generate a fuzzy rule system for breast cancer diagnosis. The hybrid algorithm generated a fuzzy system which reached the maximum classification ratio earlier than the two other ones. The motivations of using fuzzy rules incorporate with evolutionary algorithms in the underline problem are attaining high classification performance with the possibility of attributing a confidence measure (degree of benignity or malignancy) to the output diagnosis beside the simplicity of the diagnosis system which means that the system is human interpretable.
Treatment of tumor-bearing mice with LD 12.5 values of iodoacetate; IAA (1.84 mg/100g b.w.) and/o... more Treatment of tumor-bearing mice with LD 12.5 values of iodoacetate; IAA (1.84 mg/100g b.w.) and/or dimethylsulphoxide; DMSO (350 mg/ 100g b.w.) significantly increased the cumulative mean survival time and percentage of survivors and reduced the mean tumor weight, compared to tumor-bearing controls, however, a more pronounced effect is recorded in the combined treatment. Also, an increase in the life span (ILS%) and tumor growth inhibition ratio (T/C%) are reported and amounted to 145.78 and 43.80%, 195.54 and 61.30% and 220.77 and 78.40% in IAA, DMSO and combined-treated groups, respectively. Results obtained from biochemical studies reveal that a single IAA treatment of tumor-bearing mice significantly increased the levels of plasma lactate dehydrogenase (LDH) activity, while it also significantly decreased the levels of plasma glucose and liver total protein, RNA and DNA, compared to normal controls. On the other hand, a single DMSO treatment significantly elevated the activities of blood antioxidant enzymes, i.e. glutathione peroxidase (GP x ) and glucose-6-phosphate dehydrogenase (G6PDH) and decreased the liver RNA and DNA levels. Combined treatment increased significantly the levels of plasma LDH and erythrocytes G6PDH activities, as well as liver glycogen, and in contrast it decreased the levels of liver total protein, RNA and DNA, compared to normal controls.
Analytical formula for the resonance frequencies of circular, square, and hexagonal MEMS resonato... more Analytical formula for the resonance frequencies of circular, square, and hexagonal MEMS resonators are extracted based on the analytical model for extensional vibrations of MEMS resonators. Material properties for the MEMS resonators are then extracted based on the analytical formula. Experimental measurement is done to extract the material properties of single crystal silicon MEMS resonators to verify the extraction method.
The construction of artificial systems by drawing inspiration from nat- ural systems is not a new... more The construction of artificial systems by drawing inspiration from nat- ural systems is not a new idea. The Artificial Neural Network (ANN) and Genetic Algorithms (GAs) are good examples of successful applications of the biological metaphor to the solution of computational problems. The study of artificial immune systems is a relatively new field that tries to exploit the mechanisms of the natural immune system (NIS) in order to develop problem- solving techniques. In this re- search, we have combined the artificial immune system with the genetic algorithms in one hybrid algorithm. We proposed a modification to the clonal selection algo- rithm, which is inspired from the clonal selection principle and affinity maturation of the human immune responses, by hybridizing it with the crossover operator, which is imported from GAs to increase the exploration of the search space. We also in- troduced the adaptability of the mutation rates by applying a degrading function so that the mutation rates decrease with time where the affinity of the population in- creases, the hybrid algorithm used for evolving a fuzzy rule system to solve the well- known Wisconsin Breast Cancer Diagnosis problem (WBCD). Our evolved system exhibits two important characteristics; first, it attains high classification performance, with the possibility of attributing a confidence measure to the output diagnosis; sec- ond, the system has a simple fuzzy rule system; therefore, it is human interpretable. The hybrid algorithm overcomes both the GAs and the AIS, so that it reached the classification ratio 97.36, by only one rule, in the earlier generations than the two other algorithms. The learning and memory acquisition of our algorithm was ver- ified through its application to a binary character recognition problem. The hybrid algorithm overcomes also GAs and AIS and reached the convergence point before
Post-translational histone modifications are known to be altered in cancer cells, and loss of sel... more Post-translational histone modifications are known to be altered in cancer cells, and loss of selected histone acetylation and methylation marks has recently been shown to predict patient outcome in human carcinoma. Immunohistochemistry was used to detect a series of histone lysine acetylation (H3K9ac, H3K18ac, H4K12ac, and H4K16ac), lysine methylation (H3K4me2 and H4K20me3), and arginine methylation (H4R3me2) marks in a well-characterized series of human breast carcinomas (n = 880). Tissue staining intensities were assessed using blinded semiquantitative scoring. Validation studies were done using immunofluorescence staining and Western blotting. Our analyses revealed low or absent H4K16ac in the majority of breast cancer cases (78.9%), suggesting that this alteration may represent an early sign of breast cancer. There was a highly significant correlation between histone modifications status, tumor biomarker phenotype, and clinical outcome, where high relative levels of global histone acetylation and methylation were associated with a favorable prognosis and detected almost exclusively in luminal-like breast tumors (93%). Moderate to low levels of lysine acetylation (H3K9ac, H3K18ac, and H4K12ac), lysine (H3K4me2 and H4K20me3), and arginine methylation (H4R3me2) were observed in carcinomas of poorer prognostic subtypes, including basal carcinomas and HER-2-positive tumors. Clustering analysis identified three groups of histone displaying distinct pattern in breast cancer, which have distinct relationships to known prognostic factors and clinical outcome. This study identifies the presence of variations in global levels of histone marks in different grades, morphologic types, and phenotype classes of invasive breast cancer and shows that these differences have clinical significance. [Cancer Res 2009;69(9):3802-9]
An experimental investigation is presented on free convection of air around the outer surface of ... more An experimental investigation is presented on free convection of air around the outer surface of a constant heat flux elliptic tube. The local and average Nusselt number distribution is reported for different values of Rayleigh number and different tube inclination angles. The test Rayleigh number, based on input heat flux, ranges from 1:1 Â 10 7 to 8 Â 10 7 . Average Nusselt numbers are evaluated and correlated with Rayleigh number for the elliptic tube with vertical major axis. Comparison between the convection characteristics of isothermal and constant heat flux elliptic tubes has been presented. Also, the effect of elliptic tube orientation on the average Nusselt number is shown. It is found that a higher value of average Nusselt number is achieved when the major axis of the tube is vertical.
we have treated a number of 45 male patients diagnosed with idiopathic male infertility. The medi... more we have treated a number of 45 male patients diagnosed with idiopathic male infertility. The median age was 33.4 years (25)(26)(27)(28)(29)(30)(31)(32)(33)(34)(35)(36)(37)(38). We have excluded from the treatment group the patients with a large varicocele, and those with chronic UTI, prostatitis. The therapeutic protocol included a number of 10 to 15 acupuncture sessions at an interval of 2-3 days. The needles were introduced into the selected points, then mobilized until the deqi sensation was elicited and then left in place for half an hour. From each patient two spermograms were obtained; one just prior to the beginning of the treatment and one two to three weeks after its conclusion. Acupuncture points that we have used with predilection were mostly from the Kidney, Liver, Spleen, Urinary Bladder, DuMai and RenMai meridians -respectively Lv3, Sp6, Sp8, Sp9, Ren2, Ren3, Ren4, Du4, Ub23, Ub52 and Ub31, Ub32. Results: We have seen a marked increase in all of the followed parameters. The overall sperm count/ejaculate has risen three to ten fold. The functional sperm/ ejaculate rose 2.5 to 3 times. The percentage of mobile sperm increased 3-4 times. The percentage of normal sperm morphology has risen from a median value of 3% to 12%. Conclusion: We consider these results to be of significance. The present study needs to be continued with a complete hormonal workup before and after the treatment. In some of the presented cases that we could investigate, we have observed a decrease of the prolactine levels and an increase in the testosterone levels. We strongly believe that in selected cases, acupuncture is a valuable treatment of the male infertility, with high success rates. We have noted 12 pregnancies with subsequent child birth in the couples of the patients included in this study.
We identified involved lymph node groups in patients with oropharyngeal carcinoma and radiologica... more We identified involved lymph node groups in patients with oropharyngeal carcinoma and radiologically N0 disease, aiming to define the clinical target volume, and to assess the negative predictive value of CT neck and correlate it to the tumor site, stage, and grade. Between 1988 and 2000, we evaluated 53 patients who satisfied all of the following criteria: 1) oropharyngeal carcinoma diagnosis; 2) NO stage based on CT; 3) no prior treatment; and 4) primary surgical resection including ipsi-lateral neck dissection. The pathology reports were reviewed to identify the exact site of lymph node involvement. Twenty patients (37.7%) were found to have pathologically positive lymph nodes, yielding a negative predictive value of 62.3% for CT neck. Node levels II, III, and IV were the most commonly involved (26%, 17%, and 11% of all patients, respectively). Fifty percent of patients with T3 and T4 tumors had positive lymph nodes versus 20% of patients with T1 and T2 (P = 0.036). Tumor grade and site were insignificant (P > 0.05). Ipsilateral neck levels II-IV should be included during elective nodal irradiation in patients with N0-stage oropharyngeal carcinoma, regardless of the primary tumor site, stage, and grade.
The pattern of cytokines secreted by T cells at the site of viral replication may influence the f... more The pattern of cytokines secreted by T cells at the site of viral replication may influence the final outcome of HCV infection. The aim of this study was to assess whether there is a preferential production of Th1 or Th2 associated cytokines in the course of acute and chronic HCV infection. Serum level of IL2, INF gamma (Th1 associated cytokines) and IL1O (Th2 associated cyto- kines) were measured in 21 chronic HCV cases, 20 acute HCV cases and 19 healthy volunteers. Mean serum level of IL2 was significantly higher in chronic hepatitis C (267.3 ± 76.13) than in acute cases (147.09 ± 54.9) and controls (116.11 ± 33.45). Acute HCV cases had a higher mean ILIO level (13.3 ± 4.12) than controls (10.64 ± 0.84) and chronic HCV cases had a higher mean ILIO level (36.87 ± 6.58) than acute HCV cases. Mean serum level of INF gamma where nearly equal in all three groups. There was a trend to negative correlation between IL2 and IL 10 and positive correlation between IL2 and INF gamma. However these trends were not statistically significant. In conclusion this study suggests weak response of Th1 cells in acute HCV infection and a possible suppressive Th2 cell response in chronic HCV, which might explain the failure of viral clearance and a weak cellular immune response.
The automatic diagnosis of breast cancer is an important, real-world medical problem. In this pap... more The automatic diagnosis of breast cancer is an important, real-world medical problem. In this paper we give an introduction to fuzzy systems, genetic algorithms and artificial immune system, and then we introduce a hybrid algorithm that gathers the genetic algorithms with the artificial immune system in one algorithm. The genetic algorithm, the artificial immune system and the hybrid algorithm were implemented and tested on the Wisconsin breast cancer diagnosis (WBCD) problem in order to generate a fuzzy rule system for breast cancer diagnosis. The hybrid algorithm generated a fuzzy system which reached the maximum classification ratio earlier than the two other ones. The motivations of using fuzzy rules incorporate with evolutionary algorithms in the underline problem are attaining high classification performance with the possibility of attributing a confidence measure (degree of benignity or malignancy) to the output diagnosis beside the simplicity of the diagnosis system which means that the system is human interpretable.
Treatment of tumor-bearing mice with LD 12.5 values of iodoacetate; IAA (1.84 mg/100g b.w.) and/o... more Treatment of tumor-bearing mice with LD 12.5 values of iodoacetate; IAA (1.84 mg/100g b.w.) and/or dimethylsulphoxide; DMSO (350 mg/ 100g b.w.) significantly increased the cumulative mean survival time and percentage of survivors and reduced the mean tumor weight, compared to tumor-bearing controls, however, a more pronounced effect is recorded in the combined treatment. Also, an increase in the life span (ILS%) and tumor growth inhibition ratio (T/C%) are reported and amounted to 145.78 and 43.80%, 195.54 and 61.30% and 220.77 and 78.40% in IAA, DMSO and combined-treated groups, respectively. Results obtained from biochemical studies reveal that a single IAA treatment of tumor-bearing mice significantly increased the levels of plasma lactate dehydrogenase (LDH) activity, while it also significantly decreased the levels of plasma glucose and liver total protein, RNA and DNA, compared to normal controls. On the other hand, a single DMSO treatment significantly elevated the activities of blood antioxidant enzymes, i.e. glutathione peroxidase (GP x ) and glucose-6-phosphate dehydrogenase (G6PDH) and decreased the liver RNA and DNA levels. Combined treatment increased significantly the levels of plasma LDH and erythrocytes G6PDH activities, as well as liver glycogen, and in contrast it decreased the levels of liver total protein, RNA and DNA, compared to normal controls.
Analytical formula for the resonance frequencies of circular, square, and hexagonal MEMS resonato... more Analytical formula for the resonance frequencies of circular, square, and hexagonal MEMS resonators are extracted based on the analytical model for extensional vibrations of MEMS resonators. Material properties for the MEMS resonators are then extracted based on the analytical formula. Experimental measurement is done to extract the material properties of single crystal silicon MEMS resonators to verify the extraction method.
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