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Papers by Mohamed saeed Helmy
In this study, we present the results of the first large-scale multinational study (36,220 partic... more In this study, we present the results of the first large-scale multinational study (36,220 participants) that measures vaccine hesitancy among Arab-speaking subjects. Our analysis shows a significant rate of vaccine hesitancy among Arabs in and outside the Arab region (83% and 81%, respectively). The most cited reasons for hesitancy are concerns about side effects and distrust in healthcare policies, vaccine expedited production, published studies and vaccine producing companies. We also found that female participants, participants 30-59 year-old, those with no chronic diseases, those with lower-level of academic education, and those who do not know the type of vaccine authorized in their countries are more hesitant to receive COVID-19 vaccination. On the other hand, participants who regularly receive the influenza vaccine, health care workers, and those from countries with higher rates of COVID-19 infections showed more vaccination willingness. Interactive representation of our res...
eLife, 2021
Background:Vaccine hesitancy can limit the benefits of available vaccines in halting the spread o... more Background:Vaccine hesitancy can limit the benefits of available vaccines in halting the spread of COVID-19 pandemic. Previously published studies paid little attention to Arab countries, which has a population of over 440 million. In this study, we present the results of the first large-scale multinational study that measures vaccine hesitancy among Arab-speaking subjects.Methods:An online survey in Arabic was conducted from 14 January 2021 to 29 January 2021. It consisted of 17 questions capturing demographic data, acceptance of COVID-19 vaccine, attitudes toward the need for COVID-19 vaccination and associated health policies, and reasons for vaccination hesitancy. R software v.4.0.2 was used for data analysis and visualization.Results:The survey recruited 36,220 eligible participants (61.1% males, 38.9% females, mean age 32.6 ± 10.8 years) from all the 23 Arab countries and territories (83.4%) and 122 other countries (16.6%). Our analysis shows a significant rate of vaccine hesi...
Journal of the Egyptian Society of Parasitology, 2008
The bile duct injuries rose from 0.1%-0.2% to 0.4%-0.7% from the era of open cholecystectomy to t... more The bile duct injuries rose from 0.1%-0.2% to 0.4%-0.7% from the era of open cholecystectomy to the era of laparoscopic cholecystectomy. Many classifications categorized the biliary tract injury, but none was universally accepted. In this study, 10 patients with iatrogenic major bile duct injuries were managed in Al Rahba General Hospital, UAE (April 2003 to December 2007). They were 8 females & 2 males with a mean age of 46.5 years and a mean hospital stay of 19.4 days. Four patients were initially operated upon for laparoscopic cholecystectomy and six were initially operated on elsewhere. Intraoperative bile duct injury was discovered in only 2 cases, and in 8 patients, bile duct injury was discovered in the postoperative period. Roux en Y hepaticojejunostomy was the treatment of choice for 6 patients, and 4 patients was choledochodudenostomy in one patient, left hepaticojejunostomy in another, end to end anastomosis of common bile duct over a T tube in a third patient, and remova...
Frontiers in Plant Science, 2012
Our recently developed rice proteogenomics database (OryzaPG-DB) is the first sustainable resourc... more Our recently developed rice proteogenomics database (OryzaPG-DB) is the first sustainable resource for rice shotgun-based proteogenomics, providing information on peptides identified in rice protein digested peptides measured by means of liquid chromatographytandem mass spectrometry (LC-MS/MS), and mapping of the peptides to their genomic origins and the genomic novelty of each peptide. The sequences of the peptides, proteins, cDNAs and genes, and the gene annotations are available for download in FASTA and GFF3 formats, respectively. Further, an annotated visualization of the gene models, corresponding peptides, and genomic novelty is available for each gene, and MS/MS spectra are available for each peptide. In this article, we discuss the utilization of OryzaPG-DB and report on its development, recent content expansions, and newly added features in the current version (OryzaPG-DB v1.1).
PLoS ONE, 2009
The Toll-like receptor (TLR) 3 plays a critical role in mammalian innate immune response against ... more The Toll-like receptor (TLR) 3 plays a critical role in mammalian innate immune response against viral attacks by recognizing double-stranded RNA (dsRNA) or its synthetic analog polyinosinic-polycytidylic acid (poly (I:C)). This leads to the activation of MAP kinases and NF-kB which results in the induction of type I interferons and proinflammatory cytokines to combat the viral infection. To understand the complex interplay of the various intracellular signaling molecules in the regulation of NF-kB and MAP kinases, we developed a computational TLR3 model based upon perturbation-response approach. We curated literature and databases to determine the TLR3 signaling topology specifically for murine macrophages. For initial model creation, we used wildtype temporal activation profiles of MAP kinases and NF-kB and, for model testing, used TRAF6 KO and TRADD KO data. From dynamic simulations we predict i) the existence of missing intermediary steps between extracellular poly (I:C) stimulation and intracellular TLR3 binding, and ii) the presence of a novel pathway which is essential for JNK and p38, but not NF-kB, activation. Our work shows activation dynamics of signaling molecules can be used in conjunction with perturbation-response models to decipher novel signaling features of complicated immune pathways.
Genes to Cells, 2012
We have developed a novel bioinformatics method called mass spectrum sequential subtraction (MSSS... more We have developed a novel bioinformatics method called mass spectrum sequential subtraction (MSSS) to search large peptide spectra datasets produced by liquid chromatography/mass spectrometry (LC-MS/MS) against protein and large-sized nucleotide sequence databases. The main principle in MSSS is to search the peptide spectra set against the protein database, followed by removal of the spectra corresponding to the identified peptides to create a smaller set of the remaining peptide spectra for searching against the nucleotide sequences database. Therefore, we reduce the number of spectra to be searched to limit the peptide search space. Comparing MSSS and conventional search approach using a dataset of 27 LC-MS/MS runs of rice culture cells indicated that MSSS reduced the search queries to 50% and the search time to 75% on average. In addition, MSSS had no effect on the identification false-positive rate (FPR) or the novel peptide sequences identification ability. We used MSSS to analyze another dataset of 34 LC-MS/MS runs, resulting in identifying additional 74 novel peptides. Proteogenomic analysis with these additional peptides yielded 47 new genomic features in 24 rice genes plus 24 intergenic peptides. These results show that the utility of MSSS in searching large databases with large MS/MS datasets for proteogenomics.
BMC Plant Biology, 2011
Background Proteogenomics aims to utilize experimental proteome information for refinement of gen... more Background Proteogenomics aims to utilize experimental proteome information for refinement of genome annotation. Since mass spectrometry-based shotgun proteomics approaches provide large-scale peptide sequencing data with high throughput, a data repository for shotgun proteogenomics would represent a valuable source of gene expression evidence at the translational level for genome re-annotation. Description Here, we present OryzaPG-DB, a rice proteome database based on shotgun proteogenomics, which incorporates the genomic features of experimental shotgun proteomics data. This version of the database was created from the results of 27 nanoLC-MS/MS runs on a hybrid ion trap-orbitrap mass spectrometer, which offers high accuracy for analyzing tryptic digests from undifferentiated cultured rice cells. Peptides were identified by searching the product ion spectra against the protein, cDNA, transcript and genome databases from Michigan State University, and were mapped to the rice genome...
Proceedings of 10th International Conference on Molecular Systems Biology, 2008
We constructed dynamic in silico Toll-like receptor (TLR) 4 models constituting the Myeloid Diffe... more We constructed dynamic in silico Toll-like receptor (TLR) 4 models constituting the Myeloid Differentiation factor 88 (MyD88)-dependent and–independent pathways and investigated the experimental induction of MyD88-dependent pathway genes Tnf, Il1β, Cxcl1 and the MyD88-independent pathway genes Ccl5, Cxcl10, Ifit1 in wildtype and several knock-out (KO) conditions. By fitting our model with wildtype experimental data and analysing with MyD88 KO, TRIF KO and MyD88 and TRIF (double) KO conditions, we infer ...
BMJ case reports, Jan 8, 2017
Pituitary abscess is an uncommon pituitary lesion. Its clinical diagnosis can be difficult to dis... more Pituitary abscess is an uncommon pituitary lesion. Its clinical diagnosis can be difficult to distinguish from other pituitary lesions. This pathology is characterised by vague symptoms of headaches, generalised tiredness and hypopituitarism manifestations. A history of recent meningitis, paranasal sinusitis or head surgery can be a suggestive of the source of infection.A 20-year-old man was admitted to neurosurgery department with complain of headache, fatigue, polyuria, polydipsia, blurred vision and sexual dysfunction. MRI of the head revealed a suprasellar mass that was centrally hyperintense lesion on T2-weighted images with peripheral hypointensity and isointense centrally on T1 images with peripheral hyperintensity images. Treatment of this lesion pituitary abscess was surgical drainage of the pituitary area through a trans-sphenoidal approach and broad spectrum antibiotic therapy with ceftriaxone, metronidazole and vancomycin for 6 weeks. The patient continues to have pituit...
In this study, we present the results of the first large-scale multinational study (36,220 partic... more In this study, we present the results of the first large-scale multinational study (36,220 participants) that measures vaccine hesitancy among Arab-speaking subjects. Our analysis shows a significant rate of vaccine hesitancy among Arabs in and outside the Arab region (83% and 81%, respectively). The most cited reasons for hesitancy are concerns about side effects and distrust in healthcare policies, vaccine expedited production, published studies and vaccine producing companies. We also found that female participants, participants 30-59 year-old, those with no chronic diseases, those with lower-level of academic education, and those who do not know the type of vaccine authorized in their countries are more hesitant to receive COVID-19 vaccination. On the other hand, participants who regularly receive the influenza vaccine, health care workers, and those from countries with higher rates of COVID-19 infections showed more vaccination willingness. Interactive representation of our res...
eLife, 2021
Background:Vaccine hesitancy can limit the benefits of available vaccines in halting the spread o... more Background:Vaccine hesitancy can limit the benefits of available vaccines in halting the spread of COVID-19 pandemic. Previously published studies paid little attention to Arab countries, which has a population of over 440 million. In this study, we present the results of the first large-scale multinational study that measures vaccine hesitancy among Arab-speaking subjects.Methods:An online survey in Arabic was conducted from 14 January 2021 to 29 January 2021. It consisted of 17 questions capturing demographic data, acceptance of COVID-19 vaccine, attitudes toward the need for COVID-19 vaccination and associated health policies, and reasons for vaccination hesitancy. R software v.4.0.2 was used for data analysis and visualization.Results:The survey recruited 36,220 eligible participants (61.1% males, 38.9% females, mean age 32.6 ± 10.8 years) from all the 23 Arab countries and territories (83.4%) and 122 other countries (16.6%). Our analysis shows a significant rate of vaccine hesi...
Journal of the Egyptian Society of Parasitology, 2008
The bile duct injuries rose from 0.1%-0.2% to 0.4%-0.7% from the era of open cholecystectomy to t... more The bile duct injuries rose from 0.1%-0.2% to 0.4%-0.7% from the era of open cholecystectomy to the era of laparoscopic cholecystectomy. Many classifications categorized the biliary tract injury, but none was universally accepted. In this study, 10 patients with iatrogenic major bile duct injuries were managed in Al Rahba General Hospital, UAE (April 2003 to December 2007). They were 8 females & 2 males with a mean age of 46.5 years and a mean hospital stay of 19.4 days. Four patients were initially operated upon for laparoscopic cholecystectomy and six were initially operated on elsewhere. Intraoperative bile duct injury was discovered in only 2 cases, and in 8 patients, bile duct injury was discovered in the postoperative period. Roux en Y hepaticojejunostomy was the treatment of choice for 6 patients, and 4 patients was choledochodudenostomy in one patient, left hepaticojejunostomy in another, end to end anastomosis of common bile duct over a T tube in a third patient, and remova...
Frontiers in Plant Science, 2012
Our recently developed rice proteogenomics database (OryzaPG-DB) is the first sustainable resourc... more Our recently developed rice proteogenomics database (OryzaPG-DB) is the first sustainable resource for rice shotgun-based proteogenomics, providing information on peptides identified in rice protein digested peptides measured by means of liquid chromatographytandem mass spectrometry (LC-MS/MS), and mapping of the peptides to their genomic origins and the genomic novelty of each peptide. The sequences of the peptides, proteins, cDNAs and genes, and the gene annotations are available for download in FASTA and GFF3 formats, respectively. Further, an annotated visualization of the gene models, corresponding peptides, and genomic novelty is available for each gene, and MS/MS spectra are available for each peptide. In this article, we discuss the utilization of OryzaPG-DB and report on its development, recent content expansions, and newly added features in the current version (OryzaPG-DB v1.1).
PLoS ONE, 2009
The Toll-like receptor (TLR) 3 plays a critical role in mammalian innate immune response against ... more The Toll-like receptor (TLR) 3 plays a critical role in mammalian innate immune response against viral attacks by recognizing double-stranded RNA (dsRNA) or its synthetic analog polyinosinic-polycytidylic acid (poly (I:C)). This leads to the activation of MAP kinases and NF-kB which results in the induction of type I interferons and proinflammatory cytokines to combat the viral infection. To understand the complex interplay of the various intracellular signaling molecules in the regulation of NF-kB and MAP kinases, we developed a computational TLR3 model based upon perturbation-response approach. We curated literature and databases to determine the TLR3 signaling topology specifically for murine macrophages. For initial model creation, we used wildtype temporal activation profiles of MAP kinases and NF-kB and, for model testing, used TRAF6 KO and TRADD KO data. From dynamic simulations we predict i) the existence of missing intermediary steps between extracellular poly (I:C) stimulation and intracellular TLR3 binding, and ii) the presence of a novel pathway which is essential for JNK and p38, but not NF-kB, activation. Our work shows activation dynamics of signaling molecules can be used in conjunction with perturbation-response models to decipher novel signaling features of complicated immune pathways.
Genes to Cells, 2012
We have developed a novel bioinformatics method called mass spectrum sequential subtraction (MSSS... more We have developed a novel bioinformatics method called mass spectrum sequential subtraction (MSSS) to search large peptide spectra datasets produced by liquid chromatography/mass spectrometry (LC-MS/MS) against protein and large-sized nucleotide sequence databases. The main principle in MSSS is to search the peptide spectra set against the protein database, followed by removal of the spectra corresponding to the identified peptides to create a smaller set of the remaining peptide spectra for searching against the nucleotide sequences database. Therefore, we reduce the number of spectra to be searched to limit the peptide search space. Comparing MSSS and conventional search approach using a dataset of 27 LC-MS/MS runs of rice culture cells indicated that MSSS reduced the search queries to 50% and the search time to 75% on average. In addition, MSSS had no effect on the identification false-positive rate (FPR) or the novel peptide sequences identification ability. We used MSSS to analyze another dataset of 34 LC-MS/MS runs, resulting in identifying additional 74 novel peptides. Proteogenomic analysis with these additional peptides yielded 47 new genomic features in 24 rice genes plus 24 intergenic peptides. These results show that the utility of MSSS in searching large databases with large MS/MS datasets for proteogenomics.
BMC Plant Biology, 2011
Background Proteogenomics aims to utilize experimental proteome information for refinement of gen... more Background Proteogenomics aims to utilize experimental proteome information for refinement of genome annotation. Since mass spectrometry-based shotgun proteomics approaches provide large-scale peptide sequencing data with high throughput, a data repository for shotgun proteogenomics would represent a valuable source of gene expression evidence at the translational level for genome re-annotation. Description Here, we present OryzaPG-DB, a rice proteome database based on shotgun proteogenomics, which incorporates the genomic features of experimental shotgun proteomics data. This version of the database was created from the results of 27 nanoLC-MS/MS runs on a hybrid ion trap-orbitrap mass spectrometer, which offers high accuracy for analyzing tryptic digests from undifferentiated cultured rice cells. Peptides were identified by searching the product ion spectra against the protein, cDNA, transcript and genome databases from Michigan State University, and were mapped to the rice genome...
Proceedings of 10th International Conference on Molecular Systems Biology, 2008
We constructed dynamic in silico Toll-like receptor (TLR) 4 models constituting the Myeloid Diffe... more We constructed dynamic in silico Toll-like receptor (TLR) 4 models constituting the Myeloid Differentiation factor 88 (MyD88)-dependent and–independent pathways and investigated the experimental induction of MyD88-dependent pathway genes Tnf, Il1β, Cxcl1 and the MyD88-independent pathway genes Ccl5, Cxcl10, Ifit1 in wildtype and several knock-out (KO) conditions. By fitting our model with wildtype experimental data and analysing with MyD88 KO, TRIF KO and MyD88 and TRIF (double) KO conditions, we infer ...
BMJ case reports, Jan 8, 2017
Pituitary abscess is an uncommon pituitary lesion. Its clinical diagnosis can be difficult to dis... more Pituitary abscess is an uncommon pituitary lesion. Its clinical diagnosis can be difficult to distinguish from other pituitary lesions. This pathology is characterised by vague symptoms of headaches, generalised tiredness and hypopituitarism manifestations. A history of recent meningitis, paranasal sinusitis or head surgery can be a suggestive of the source of infection.A 20-year-old man was admitted to neurosurgery department with complain of headache, fatigue, polyuria, polydipsia, blurred vision and sexual dysfunction. MRI of the head revealed a suprasellar mass that was centrally hyperintense lesion on T2-weighted images with peripheral hypointensity and isointense centrally on T1 images with peripheral hyperintensity images. Treatment of this lesion pituitary abscess was surgical drainage of the pituitary area through a trans-sphenoidal approach and broad spectrum antibiotic therapy with ceftriaxone, metronidazole and vancomycin for 6 weeks. The patient continues to have pituit...