166 results on '"Habibi, E"'
Search Results
2. Genomics facilitates evaluation and monitoring of McCloud River Redband Trout (Oncorhynchus mykiss stonei)
- Author
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Habibi, E, Habibi, E, Miller, MR, Gille, D, Sanders, L, Rodzen, J, Aurniger, GM, Stephens, M, Finger, AJ, Habibi, E, Habibi, E, Miller, MR, Gille, D, Sanders, L, Rodzen, J, Aurniger, GM, Stephens, M, and Finger, AJ
- Abstract
The McCloud River Redband Trout (MRRT; Oncorhynchus mykiss stonei) is a unique subspecies of rainbow trout that inhabits the isolated Upper McCloud River of Northern California. A major threat to MRRT is introgressive hybridization with non-native rainbow trout from historical stocking and contemporary unauthorized introductions. To help address this concern, we collected RAD-sequencing data on 308 total individuals from MRRT and other California O. mykiss populations and examined population structure using Principal Component and admixture analyses. Our results are consistent with previous studies; we found that populations of MRRT in Sheepheaven, Swamp, Edson, and Moosehead creeks are nonintrogressed. Additionally, we saw no evidence of introgression in Dry Creek, and suggest further investigation to determine if it can be considered a core MRRT conservation population. Sheepheaven Creek was previously thought to be the sole historical lineage of MRRT, but our analysis identified three: Sheepheaven, Edson, and Dry creeks, all of which should be preserved. Finally, we discovered diagnostic and polymorphic SNP markers for monitoring introgression and genetic diversity in MRRT. Collectively, our results provide a valuable resource for the conservation and management of MRRT.
- Published
- 2022
3. Investigation of Correlation Result of NORDIC Questionnaire (wrist & hand) with DASH Questionnaire
- Author
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Ordudari, Z, primary and Habibi, E, additional
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- 2022
- Full Text
- View/download PDF
4. Additional file 1 of Urate-induced epigenetic modifications in myeloid cells
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Badii, M., Gaal, O. I., Cleophas, M. C., Klück, V., Davar, R., Habibi, E., Keating, S. T., Novakovic, B., Helsen, M. M., Dalbeth, N., Stamp, L. K., Macartney-Coxson, D., Phipps-Green, A. J., Stunnenberg, H. G., Dinarello, C. A., Merriman, T. R., Netea, M. G., Crişan, T. O., and Joosten, L. A. B.
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Data_FILES - Abstract
Additional file 1.
- Published
- 2021
- Full Text
- View/download PDF
5. Relationship between Anxiety and Depression with Musculoskeletal Disorders in Military Personnel
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Habibi. E, Ghanbary Sartang. A, Ashnagar. M, and Rezaei. N
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Military personnel ,medicine.medical_specialty ,business.industry ,General Engineering ,Medicine ,Anxiety ,medicine.symptom ,business ,Psychiatry ,Depression (differential diagnoses) - Published
- 2017
6. Chromatin-Based Classification of Genetically Heterogeneous AMLs into Two Distinct Subtypes with Diverse Stemness Phenotypes
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Yi, G., Wierenga, A., Petraglia, F., Narang, P., Janssen-Megens, E., Mandoli, A., Merkel, A., Berentsen, K., Kim, B., Matarese, F., Singh, A., Habibi, E., Prange, K., Mulder, A., Jansen, J., Clarke, L., Heath, S., van der Reijden, B., Flicek, P., Yaspo, M., Gut, I., Bock, C., Schuringa, J., Altucci, L., Vellenga, E., Stunnenberg, H., Martens, J., H., A., Yi, Guoqiang, Wierenga, Albertus T. J., Petraglia, Francesca, Narang, Pankaj, Janssen-Megens, Eva M., Mandoli, Amit, Merkel, Angelika, Berentsen, Kim, Kim, Bowon, Matarese, Filomena, Singh, Abhishek A., Habibi, Ehsan, Prange, Koen H. M., Mulder, André B., Jansen, Joop H., Clarke, Laura, Heath, Simon, van der Reijden, Bert A., Flicek, Paul, Yaspo, Marie-Laure, Gut, Ivo, Bock, Christoph, Schuringa, Jan Jacob, Altucci, Lucia, Vellenga, Edo, Stunnenberg, Hendrik G., Martens, Joost H. A., Medical Biochemistry, ACS - Atherosclerosis & ischemic syndromes, Stem Cell Aging Leukemia and Lymphoma (SALL), and Guided Treatment in Optimal Selected Cancer Patients (GUTS)
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Spliceosome ,NPM1 ,Oncogene Proteins, Fusion ,chromatin state ,Cancer development and immune defence Radboud Institute for Molecular Life Sciences [Radboudumc 2] ,DNA accessibility ,epigenome ,Biology ,acute myeloid leukemia ,Article ,General Biochemistry, Genetics and Molecular Biology ,stemness ,03 medical and health sciences ,chemistry.chemical_compound ,All institutes and research themes of the Radboud University Medical Center ,0302 clinical medicine ,AML ,hemic and lymphatic diseases ,Humans ,chromatin states ,histone mark ,Molecular Biology ,030304 developmental biology ,Genetics ,0303 health sciences ,Biochemistry, Genetics and Molecular Biology (all) ,histone marks ,Nuclear Proteins ,Myeloid leukemia ,Epigenome ,Phenotype ,Chromatin ,stemne ,Leukemia, Myeloid, Acute ,Histone ,RUNX1 ,chemistry ,030220 oncology & carcinogenesis ,Core Binding Factor Alpha 2 Subunit ,Mutation ,biology.protein ,transcriptome ,Nucleophosmin ,human activities - Abstract
Summary Global investigation of histone marks in acute myeloid leukemia (AML) remains limited. Analyses of 38 AML samples through integrated transcriptional and chromatin mark analysis exposes 2 major subtypes. One subtype is dominated by patients with NPM1 mutations or MLL-fusion genes, shows activation of the regulatory pathways involving HOX-family genes as targets, and displays high self-renewal capacity and stemness. The second subtype is enriched for RUNX1 or spliceosome mutations, suggesting potential interplay between the 2 aberrations, and mainly depends on IRF family regulators. Cellular consequences in prognosis predict a relatively worse outcome for the first subtype. Our integrated profiling establishes a rich resource to probe AML subtypes on the basis of expression and chromatin data.
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- 2019
7. The alarmin S100A9 hampers osteoclast differentiation from human circulating precursors by reducing the expression of RANK
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Di Ceglie, I., Blom, A.B., Davar, R., Logie, C., Martens, J.H.A., Habibi, E., Kraan, P.M. van der, Lent, P.L. van, Bosch, M.H.J. van den, Di Ceglie, I., Blom, A.B., Davar, R., Logie, C., Martens, J.H.A., Habibi, E., Kraan, P.M. van der, Lent, P.L. van, and Bosch, M.H.J. van den
- Abstract
Contains fulltext : 207346.pdf (publisher's version ) (Closed access)
- Published
- 2019
8. Epigenetic modulation of a hardwired 3D chromatin landscape in two naive states of pluripotency
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Atlasi, Y., Megchelenbrink, Wout, Peng, T., Habibi, E., Joshi, O.K., Wang, S., Wang, C., Logie, Colin, Marks, Hendrik, Stunnenberg, Hendrik G., Atlasi, Y., Megchelenbrink, Wout, Peng, T., Habibi, E., Joshi, O.K., Wang, S., Wang, C., Logie, Colin, Marks, Hendrik, and Stunnenberg, Hendrik G.
- Abstract
Contains fulltext : 203684.pdf (Publisher’s version ) (Closed access)
- Published
- 2019
9. Multi-omics profiling reveals a distinctive epigenome signature for high-risk acute promyelocytic leukemia.
- Author
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Singh, A.A., Petraglia, F., Nebbioso, A., Yi, G., Mandoli, A., Lindeboom, R.G.H., Kerstens, H.H.D., Janssen-Megens, E.M., Habibi, E., Berentsen, K., Kim, B., Logie, C., Stunnenberg, H.G., Martens, J.H.A., Jansen, J.H., Singh, A.A., Petraglia, F., Nebbioso, A., Yi, G., Mandoli, A., Lindeboom, R.G.H., Kerstens, H.H.D., Janssen-Megens, E.M., Habibi, E., Berentsen, K., Kim, B., Logie, C., Stunnenberg, H.G., Martens, J.H.A., and Jansen, J.H.
- Abstract
Contains fulltext : 197503.pdf (publisher's version ) (Open Access), Epigenomic alterations have been associated with both pathogenesis and progression of cancer. Here, we analyzed the epigenome of two high-risk APL (hrAPL) patients and compared it to non-high-risk APL cases. Despite the lack of common genetic signatures, we found that human hrAPL blasts from patients with extremely poor prognosis display specific patterns of histone H3 acetylation, specifically hyperacetylation at a common set of enhancer regions. In addition, unique profiles of the repressive marks H3K27me3 and DNA methylation were exposed in high-risk APLs. Epigenetic comparison with low/intermediate-risk APLs and AMLs revealed hrAPL-specific patterns of histone acetylation and DNA methylation, suggesting these could be further developed into markers for clinical identification. The epigenetic drug MC2884, a newly generated general HAT/EZH2 inhibitor, induces apoptosis of high-risk APL blasts and reshapes their epigenomes by targeting both active and repressive marks. Together, our analysis uncovers distinctive epigenome signatures of hrAPL patients, and provides proof of concept for use of epigenome profiling coupled to epigenetic drugs to 'personalize' precision medicine.
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- 2018
10. Increased H3K9 methylation and impaired expression of Protocadherins are associated with the cognitive dysfunctions of the Kleefstra syndrome
- Author
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Iacono, G., Dubos, A., Meziane, H., Benevento, M., Habibi, E., Mandoli, A., Riet, F., Selloum, M., Feil, R., Zhou, H., Kleefstra, T., Nadif Kasri, N., Bokhoven, H. van, Herault, Y., Stunnenberg, H., Iacono, G., Dubos, A., Meziane, H., Benevento, M., Habibi, E., Mandoli, A., Riet, F., Selloum, M., Feil, R., Zhou, H., Kleefstra, T., Nadif Kasri, N., Bokhoven, H. van, Herault, Y., and Stunnenberg, H.
- Abstract
Contains fulltext : 193230.pdf (publisher's version ) (Open Access), Kleefstra syndrome, a disease with intellectual disability, autism spectrum disorders and other developmental defects is caused in humans by haploinsufficiency of EHMT1. Although EHMT1 and its paralog EHMT2 were shown to be histone methyltransferases responsible for deposition of the di-methylated H3K9 (H3K9me2), the exact nature of epigenetic dysfunctions in Kleefstra syndrome remains unknown. Here, we found that the epigenome of Ehmt1+/- adult mouse brain displays a marked increase of H3K9me2/3 which correlates with impaired expression of protocadherins, master regulators of neuronal diversity. Increased H3K9me3 was present already at birth, indicating that aberrant methylation patterns are established during embryogenesis. Interestingly, we found that Ehmt2+/- mice do not present neither the marked increase of H3K9me2/3 nor the cognitive deficits found in Ehmt1+/- mice, indicating an evolutionary diversification of functions. Our finding of increased H3K9me3 in Ehmt1+/- mice is the first one supporting the notion that EHMT1 can quench the deposition of tri-methylation by other Histone methyltransferases, ultimately leading to impaired neurocognitive functioning. Our insights into the epigenetic pathophysiology of Kleefstra syndrome may offer guidance for future developments of therapeutic strategies for this disease.
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- 2018
11. Dynamics of Transcription Regulation in Human Bone Marrow Myeloid Differentiation to Mature Blood Neutrophils.
- Author
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Grassi, L., Pourfarzad, F., Ullrich, S., Merkel, A., Were, F., Carrillo-de-Santa-Pau, E., Yi, G., Hiemstra, I.H., Tool, A.T., Mul, E., Perner, J., Janssen-Megens, E.M., Berentsen, K., Kerstens, H.H.D., Habibi, E., Gut, M., Yaspo, M.L., Linser, M., Lowy, E., Datta, A., Clarke, L., Flicek, P., Vingron, M., Roos, D., Berg, T.K. van den, Heath, S., Rico, D., Frontini, M., Kostadima, M., Gut, I., Valencia, A., Ouwehand, W.H., Stunnenberg, H., Martens, J.H.A., Kuijpers, T.W., Grassi, L., Pourfarzad, F., Ullrich, S., Merkel, A., Were, F., Carrillo-de-Santa-Pau, E., Yi, G., Hiemstra, I.H., Tool, A.T., Mul, E., Perner, J., Janssen-Megens, E.M., Berentsen, K., Kerstens, H.H.D., Habibi, E., Gut, M., Yaspo, M.L., Linser, M., Lowy, E., Datta, A., Clarke, L., Flicek, P., Vingron, M., Roos, D., Berg, T.K. van den, Heath, S., Rico, D., Frontini, M., Kostadima, M., Gut, I., Valencia, A., Ouwehand, W.H., Stunnenberg, H., Martens, J.H.A., and Kuijpers, T.W.
- Abstract
Contains fulltext : 195014.pdf (publisher's version ) (Open Access), Neutrophils are short-lived blood cells that play a critical role in host defense against infections. To better comprehend neutrophil functions and their regulation, we provide a complete epigenetic overview, assessing important functional features of their differentiation stages from bone marrow-residing progenitors to mature circulating cells. Integration of chromatin modifications, methylation, and transcriptome dynamics reveals an enforced regulation of differentiation, for cellular functions such as release of proteases, respiratory burst, cell cycle regulation, and apoptosis. We observe an early establishment of the cytotoxic capability, while the signaling components that activate these antimicrobial mechanisms are transcribed at later stages, outside the bone marrow, thus preventing toxic effects in the bone marrow niche. Altogether, these data reveal how the developmental dynamics of the chromatin landscape orchestrate the daily production of a large number of neutrophils required for innate host defense and provide a comprehensive overview of differentiating human neutrophils.
- Published
- 2018
12. Validation of a questionnaire for heat strain evaluation in women workers
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Dehghan, H., Habibi, E., Habibi, P., and Mohammad Reza Maracy
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questionnaire ,lcsh:R ,lcsh:Medicine ,Original Article ,Heat strain ,women - Abstract
Introduction: Physiological, anthropometrical and thermal perceptual are the most important factors affecting thermoregulation of men and women in workplaces. The purpose of this study was determining the validity of a questionnaire method for assessing women′s heat strain in workplaces. Methods: This cross-sectional study was carried out on 96 healthy women. Data were continuously collected over a period of 3 months (July-September) in 2012. Mean ± (SD) of age was found to be 31.5 ± 7.48 years, of height 1.61 ± 0.05 m, of weight 61.55 ± 10.35 kg, and of body mass index 23.52 ± 3.75 kg/m 2 in different workplaces. Heart rate and oral temperature were measured by heart rate monitoring and a medical digital thermometer, respectively. Subjects completed a draft questionnaire about the effective factors in the onset of heat strain. After collecting the questionnaires, the data were analyzed by applying Cronbach′sa calculation, factor analysis method, Pearson correlation and receiver operator characteristic curves using the SPSS 18 software. Results: The value for Cronbach′s α was found to be 0.68. The factor analysis method on items of draft questionnaire extracted three subscale (16 variables) which they explained 63.6% of the variance. According to the results of receiver operator characteristic curve analysis, the cut-off questionnaire score for separating people with heat strain from people with no heat strain was obtained to be 17. Conclusions: The results of this research indicated that this quantitative questionnaire has an acceptable reliability and validity, and a cut-off point. Therefore it could be used in the preliminary screening of heat strain in women in warm workplaces, when other heat stress evaluation methods are not available.
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- 2013
13. Transcriptional and epigenetic control in mouse pluripotency: Lessons from in vivo and in vitro studies
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Habibi, E., Stunnenberg, H., Habibi, E., and Stunnenberg, H.
- Abstract
Contains fulltext : 178028.pdf (Publisher’s version ) (Open Access)
- Published
- 2017
14. Epigenetic plasticity in pluripotent and mature cells
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Habibi, E., Stunnenberg, H.G., and Radboud University Nijmegen
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Molecular Biology - Abstract
Contains fulltext : 161964.pdf (Publisher’s version ) (Open Access) Radboud University, 22 december 2016 Promotor : Stunnenberg, H.G. 161 p.
- Published
- 2016
15. Evaluation of work-related Psychosocial and Ergonomics factors in relation to Low back discomfort in emergency unit nurses
- Author
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Habibi, E., Siamak Pourabdian, Atabaki, A. K., and Hoseini, M.
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Emergency unit nurses ,lcsh:R ,population characteristics ,work-related psychosocial factors ,lcsh:Medicine ,Original Article ,ergonomics factors ,health care economics and organizations ,low back pain - Abstract
Background and Aim: High prevalence of low back pain is one of the most common problems among nurses. The aim of this study was to evaluate the relation of the intensity of low back discomfort to two low back pain contributor factors (Ergonomics risk factors and psychosocial factors). Methods: This cross-sectional survey was conducted on 120 emergency unit nurses in Esfahan. Job content, ergonomics hazards and nordic questionnaire were used in that order for daily assessment of Psychosocial and Ergonomics factors and the intensity of low back discomfort. Nurses were questioned during a 5-week period, at the end of each shift work. The final results were analyzed with SPSS software18/PASW by using Spearman, Mann-Whitney and Kolmogorov-Smirnove test. Results: There was a significant relationship between work demand, job content, social support and intensity of low back discomfort (P value
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- 2012
16. Proportion of elementary school pupils’ anthropometric characteristics with dimensions of classroom furniture in Isfahan, Iran
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Habibi, E., Asaadi, Z., and Mohsen Hosseini
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Anthropometry ,Short Communication ,Furniture ,lcsh:R ,lcsh:Medicine ,Ergonomics - Abstract
Background: This study is aimed to examine the appropriacy of school furniture to Iranian pupils′ anthropometric features. Methods: The participants in this cross-sectional study were 493 boys and 489 girls with the age-range of 7 to 12 years who were selected through a multistage random cluster sampling procedure. Age, weight, height, and anthropometric dimensions were determined. Results: This study indicates that there is a significant difference between the minimum and maximum acceptable dimensions and those of the available furniture (p < 0.001). Conclusions: In designing suitable furniture for pupils the anthropometric differences of age and gender must be tak-en into account.
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- 2011
17. Prevalence of Musculoskeletal Disorders and Associated Lost Work Days in Steel Making Industry
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Habibi, E., Fereidan, M., Molla Aghababai, A., and Siamak Pourabdian
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lcsh:Public aspects of medicine ,fungi ,lcsh:RA1-1270 ,Lost workdays ,Steelmaking industry - Abstract
Background: The study aims at clarifying prevalence of work-related musculoskeletal disorders (WMSDs) among steel making workers and employees as well as associated lost work days.Methods: A detailed questionnaire based on Nordic ergonomic questionnaire describing work history, ergonomic conditions at work, sign and symptoms of musculoskeletal system with in previous12 months was applied to the investigation among1030 male workers and employees in a steel making plant in Isfahan, Iran, 2004.Results: The prevalence of low back pain ranked top, regardless of job titles followed by knee pain. The age groups (24-35) and (34-45) manifested the most frequent number of (MSDs) and MSDs related lost workdays.Conclusion: This is almost in harmony with the prevalence of MSDs among general population and statistics presented by Bureau of Labor Statistics, the U.S Department of Labor.
- Published
- 2008
18. Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells
- Author
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Chen, L., Ge, B., Casale, F.P., Vasquez, L., Kwan, T., Garrido-Martin, D., Watt, S., Yan, Y., Kundu, K., Ecker, S., Datta, A., Richardson, D., Burden, F., Mead, D., Mann, A.L., Fernandez, J.M., Rowlston, S., Wilder, S.P., Farrow, S., Shao, X., Lambourne, J.J., Redensek, A., Albers, C.A., Amstislavskiy, V., Ashford, S., Berentsen, K., Bomba, L., Bourque, G., Bujold, D., Busche, S., Caron, M., Chen, S.H., Cheung, W., Delaneau, O., Dermitzakis, E.T., Elding, H., Colgiu, I., Bagger, F.O., Flicek, P., Habibi, E., Iotchkova, V., Janssen-Megens, E., Kim, B., Lehrach, H., Lowy, E., Mandoli, A., Matarese, F., Maurano, M.T., Morris, J.A., Pancaldi, V., Pourfarzad, F., Rehnstrom, K., Rendon, A., Risch, T., Sharifi, N., Simon, M.M., Sultan, M., Valencia, A., Walter, K., Wang, S.Y., Frontini, M., Antonarakis, S.E., Clarke, L., Yaspo, M.L., Beck, S., Guigo, R., Rico, D., Martens, J.H., Ouwehand, W.H., Kuijpers, T.W., Paul, D.S., Stunnenberg, H.G., Stegle, O., Downes, K., Pastinen, T., Soranzo, N., Chen, L., Ge, B., Casale, F.P., Vasquez, L., Kwan, T., Garrido-Martin, D., Watt, S., Yan, Y., Kundu, K., Ecker, S., Datta, A., Richardson, D., Burden, F., Mead, D., Mann, A.L., Fernandez, J.M., Rowlston, S., Wilder, S.P., Farrow, S., Shao, X., Lambourne, J.J., Redensek, A., Albers, C.A., Amstislavskiy, V., Ashford, S., Berentsen, K., Bomba, L., Bourque, G., Bujold, D., Busche, S., Caron, M., Chen, S.H., Cheung, W., Delaneau, O., Dermitzakis, E.T., Elding, H., Colgiu, I., Bagger, F.O., Flicek, P., Habibi, E., Iotchkova, V., Janssen-Megens, E., Kim, B., Lehrach, H., Lowy, E., Mandoli, A., Matarese, F., Maurano, M.T., Morris, J.A., Pancaldi, V., Pourfarzad, F., Rehnstrom, K., Rendon, A., Risch, T., Sharifi, N., Simon, M.M., Sultan, M., Valencia, A., Walter, K., Wang, S.Y., Frontini, M., Antonarakis, S.E., Clarke, L., Yaspo, M.L., Beck, S., Guigo, R., Rico, D., Martens, J.H., Ouwehand, W.H., Kuijpers, T.W., Paul, D.S., Stunnenberg, H.G., Stegle, O., Downes, K., Pastinen, T., and Soranzo, N.
- Abstract
Contains fulltext : 167824.pdf (Publisher’s version ) (Open Access)
- Published
- 2016
19. beta-Glucan Reverses the Epigenetic State of LPS-Induced Immunological Tolerance
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Novakovic, B., Habibi, E., Wang, S.Y., Arts, R.J., Davar, R., Megchelenbrink, W., Kim, B., Kuznetsova, T., Kox, M., Zwaag, J., Matarese, F., Heeringen, S.J. van, Janssen-Megens, E.M., Sharifi, N., Wang, C., Keramati, F., Schoonenberg, V., Flicek, P., Clarke, L., Pickkers, P., Heath, S., Gut, I., Netea, M.G., Martens, J.H., Logie, C., Stunnenberg, H.G., Novakovic, B., Habibi, E., Wang, S.Y., Arts, R.J., Davar, R., Megchelenbrink, W., Kim, B., Kuznetsova, T., Kox, M., Zwaag, J., Matarese, F., Heeringen, S.J. van, Janssen-Megens, E.M., Sharifi, N., Wang, C., Keramati, F., Schoonenberg, V., Flicek, P., Clarke, L., Pickkers, P., Heath, S., Gut, I., Netea, M.G., Martens, J.H., Logie, C., and Stunnenberg, H.G.
- Abstract
Contains fulltext : 165879.pdf (publisher's version ) (Open Access), Innate immune memory is the phenomenon whereby innate immune cells such as monocytes or macrophages undergo functional reprogramming after exposure to microbial components such as lipopolysaccharide (LPS). We apply an integrated epigenomic approach to characterize the molecular events involved in LPS-induced tolerance in a time-dependent manner. Mechanistically, LPS-treated monocytes fail to accumulate active histone marks at promoter and enhancers of genes in the lipid metabolism and phagocytic pathways. Transcriptional inactivity in response to a second LPS exposure in tolerized macrophages is accompanied by failure to deposit active histone marks at promoters of tolerized genes. In contrast, beta-glucan partially reverses the LPS-induced tolerance in vitro. Importantly, ex vivo beta-glucan treatment of monocytes from volunteers with experimental endotoxemia re-instates their capacity for cytokine production. Tolerance is reversed at the level of distal element histone modification and transcriptional reactivation of otherwise unresponsive genes. VIDEO ABSTRACT.
- Published
- 2016
20. Vitamin C and L-Proline Antagonistic Effects Capture Alternative States in the Pluripotency Continuum
- Author
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D'Aniello, C., Habibi, E., Cermola, F., Paris, D., Russo, F., Fiorenzano, A., Di Napoli, G., Melck, D.J., Cobellis, G., Angelini, C., Fico, A., Blelloch, R., Motta, A., Stunnenberg, H.G., De Cesare, D., Patriarca, E.J., Minchiotti, G., D'Aniello, C., Habibi, E., Cermola, F., Paris, D., Russo, F., Fiorenzano, A., Di Napoli, G., Melck, D.J., Cobellis, G., Angelini, C., Fico, A., Blelloch, R., Motta, A., Stunnenberg, H.G., De Cesare, D., Patriarca, E.J., and Minchiotti, G.
- Abstract
Contains fulltext : 165841.pdf (publisher's version ) (Open Access)
- Published
- 2016
21. Impairment of DNA Methylation Maintenance Is the Main Cause of Global Demethylation in Naive Embryonic Stem Cells
- Author
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Meyenn, F. von, Iurlaro, M., Habibi, E., Liu, N., Salehzadeh-Yazdi, A., Santos, F., Petrini, E., Milagre, I., Yu, M., Xie, Z., Kroeze, L.I., Nesterova, T.B., Jansen, J.H., Xie, H., He, C., Reik, W., Stunnenberg, H., Meyenn, F. von, Iurlaro, M., Habibi, E., Liu, N., Salehzadeh-Yazdi, A., Santos, F., Petrini, E., Milagre, I., Yu, M., Xie, Z., Kroeze, L.I., Nesterova, T.B., Jansen, J.H., Xie, H., He, C., Reik, W., and Stunnenberg, H.
- Abstract
Contains fulltext : 172769.pdf (Publisher’s version ) (Open Access)
- Published
- 2016
22. Epigenetic plasticity in pluripotent and mature cells
- Author
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Stunnenberg, H.G., Habibi, E., Stunnenberg, H.G., and Habibi, E.
- Abstract
Radboud University, 22 december 2016, Promotor : Stunnenberg, H.G., Contains fulltext : 161964.pdf (publisher's version ) (Open Access)
- Published
- 2016
23. Glutaminolysis and Fumarate Accumulation Integrate Immunometabolic and Epigenetic Programs in Trained Immunity
- Author
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Arts, R.J., Novakovic, B., Horst, R. ter, Carvalho, A., Bekkering, S., Lachmandas, E., Rodrigues, F., Silvestre, R., Cheng, S.C., Wang, S.Y., Habibi, E., Goncalves, L.G., Mesquita, I., Cunha, C., Laarhoven, A. van, Veerdonk, F.L. van de, Williams, D.L., Meer, J.W.M. van der, Logie, C., O'Neill, L.A., Dinarello, C.A., Riksen, N.P., Crevel, R. van, Clish, C., Notebaart, R.A., Joosten, L.A., Stunnenberg, H.G., Xavier, R.J., Netea, M.G., Arts, R.J., Novakovic, B., Horst, R. ter, Carvalho, A., Bekkering, S., Lachmandas, E., Rodrigues, F., Silvestre, R., Cheng, S.C., Wang, S.Y., Habibi, E., Goncalves, L.G., Mesquita, I., Cunha, C., Laarhoven, A. van, Veerdonk, F.L. van de, Williams, D.L., Meer, J.W.M. van der, Logie, C., O'Neill, L.A., Dinarello, C.A., Riksen, N.P., Crevel, R. van, Clish, C., Notebaart, R.A., Joosten, L.A., Stunnenberg, H.G., Xavier, R.J., and Netea, M.G.
- Abstract
Contains fulltext : 165651.pdf (publisher's version ) (Open Access), Induction of trained immunity (innate immune memory) is mediated by activation of immune and metabolic pathways that result in epigenetic rewiring of cellular functional programs. Through network-level integration of transcriptomics and metabolomics data, we identify glycolysis, glutaminolysis, and the cholesterol synthesis pathway as indispensable for the induction of trained immunity by beta-glucan in monocytes. Accumulation of fumarate, due to glutamine replenishment of the TCA cycle, integrates immune and metabolic circuits to induce monocyte epigenetic reprogramming by inhibiting KDM5 histone demethylases. Furthermore, fumarate itself induced an epigenetic program similar to beta-glucan-induced trained immunity. In line with this, inhibition of glutaminolysis and cholesterol synthesis in mice reduced the induction of trained immunity by beta-glucan. Identification of the metabolic pathways leading to induction of trained immunity contributes to our understanding of innate immune memory and opens new therapeutic avenues.
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- 2016
24. Protecting OT environments against targeted cyber attacks.
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AJAYI, V., CARROLL, M., CHEVIS, M., GIL-ORTEGA, A. V., HABIBI, E., KLOTZ, T., LAAS, J., and WILCOX, S.
- Subjects
CYBERTERRORISM ,RANSOMWARE ,PROGRAMMABLE controllers ,BACK up systems - Abstract
The article offers information on the protection of operational technology (OT) environments against targeted cyber attacks in the hydrocarbon processing industry. It mentions that experts on the front lines of OT cybersecurity risk mitigation share their strategies for making control systems more secure.
- Published
- 2022
25. Dynamic Reorganization of Extremely Long-Range Promoter-Promoter Interactions between Two States of Pluripotency
- Author
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Joshi, O.K., Wang, S., Kuznetsova, T., Atlasi, Y., Peng, T., Fabre, P.J., Habibi, E., Shaik, J., Saeed, S., Handoko, L.L., Richmond, T.B., Spivakov, M., Burgess, D., Stunnenberg, H.G., Joshi, O.K., Wang, S., Kuznetsova, T., Atlasi, Y., Peng, T., Fabre, P.J., Habibi, E., Shaik, J., Saeed, S., Handoko, L.L., Richmond, T.B., Spivakov, M., Burgess, D., and Stunnenberg, H.G.
- Abstract
Contains fulltext : 149510.pdf (Publisher’s version ) (Closed access)
- Published
- 2015
26. Occupational stress among male employees of esfahan steel company, iran: prevalence and associated factors
- Author
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Lotfizadeh, M., Babak Moazen, Habibi, E., and Hassim, N.
- Subjects
male ,manpower ,lcsh:R ,lcsh:Medicine ,Burnout ,Original Article ,Iran ,professional - Abstract
Background: Lack of data on occupational stress among Iranian industrial employees persuaded us to design and conduct this study to evaluate the prevalence and associated parameters of occupational stress among male employees of the Esfahan Steel Company (ESCO), one of the biggest industrial units in Iran. Methods: In this cross-sectional study, 400 male employees were sampled from the operational divisions of the company. Socio-demographic data and stress-related variables were entered into a logistic regression to determine significant associated factors of occupational stress among the participants. Results: From all samples, 53% were found as stressful. A monthly salary of less than $600 (OR = 1.88, 95% confidence interval [CI] = 1.21-2.94), family-related problems (OR = 2.75, 95% CI = 1.22-6.21), work environment (OR = 3.09, 95% CI = 1.78-5.33) and having a second job (OR = 2.68, 95% CI = 1.78-6.78) were significantly associated with the outcome. Conclusions: Attention to some variables, especially economic problems and the work environment of employees, might play a protective role against the prevalence of occupational stress, not only among the employees of ESCO but also among all industrial employees in Iran.
- Published
- 2012
27. Targeted Radiotherapy of Metastatic Carcinoid Tumors using a High Fixed Dose of I-131-MIBG: Disease Control and Beneficial Long Term Effect with Low Toxicity
- Author
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Ezziddin, S, Logvinski, T, Ahmadzadehfar, H, Lutterbey, G, Reinhardt, MJ, Habibi, E, Palmedo, H, and Biersack, HJ
- Subjects
ddc: 610 - Published
- 2006
28. Metastatic Gastroenteropancreatic Neuroendocrine Tumors: The Revised WHO Classification and its Correlation with Somatostatin Analog Uptake
- Author
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Ezziddin, S, Yong-Hing, C, Ahmadzadehfar, H, Fischer, HP, Habibi, E, Leifeld, L, and Biersack, HJ
- Subjects
ddc: 610 - Published
- 2006
29. Whole-genome bisulfite sequencing of two distinct interconvertible DNA methylomes of mouse embryonic stem cells
- Author
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Habibi, E., Brinkman, A.B., Arand, J., Kroeze, L., Kerstens, H.H., Matarese, F., Lepikhov, K., Gut, M., Brun-Heath, I., Hubner, N.C., Benedetti, R., Altucci, L., Jansen, J.H., Walter, J., Gut, I.G., Marks, H., Stunnenberg, H.G., Habibi, E., Brinkman, A.B., Arand, J., Kroeze, L., Kerstens, H.H., Matarese, F., Lepikhov, K., Gut, M., Brun-Heath, I., Hubner, N.C., Benedetti, R., Altucci, L., Jansen, J.H., Walter, J., Gut, I.G., Marks, H., and Stunnenberg, H.G.
- Abstract
Contains fulltext : 128583.pdf (Publisher’s version ) (Closed access), The use of two kinase inhibitors (2i) enables derivation of mouse embryonic stem cells (ESCs) in the pluripotent ground state. Using whole-genome bisulfite sequencing (WGBS), we show that male 2i ESCs are globally hypomethylated compared to conventional ESCs maintained in serum. In serum, female ESCs are hypomethyated similarly to male ESCs in 2i, and DNA methylation is further reduced in 2i. Regions with elevated DNA methylation in 2i strongly correlate with the presence of H3K9me3 on endogenous retroviruses (ERVs) and imprinted loci. The methylome of male ESCs in serum parallels postimplantation blastocyst cells, while 2i stalls ESCs in a hypomethylated, ICM-like state. WGBS analysis during adaptation of 2i ESCs to serum suggests that deposition of DNA methylation is largely random, while loss of DNA methylation during reversion to 2i occurs passively, initiating at TET1 binding sites. Together, our analysis provides insight into DNA methylation dynamics in cultured ESCs paralleling early developmental processes.
- Published
- 2013
30. The radiotracer99m Tc-MIBI is not genotoxic for human peripheral blood lymphocytes at diagnostic radioactive dose
- Author
-
Hosseinimehr, S.J., primary, Ahmadi, A., additional, Beiki, D., additional, Mahmoudzadeh, A., additional, Babaei, M., additional, and Habibi, E., additional
- Published
- 2009
- Full Text
- View/download PDF
31. The effect of noise on error rate and performance rate by using the experiment of two-hand coordination.
- Author
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Habibi, E. A., Dehghan, H., Eshraghy Dehkordy, S., and Maracy, M. R.
- Published
- 2013
32. Clinicians’ knowledge and practices regarding family planning and intrauterine devices in China, Kazakhstan, Laos and Mexico
- Author
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Hoffman, Steven J., Guindon, G. Emmanuel, Lavis, John N., Randhawa, Harkanwal, Becerra-Posada, Francisco, Boupha, Boungnong, Shi, Guang, Turdaliyeva, Botagoz S., Cameron, David, Qiu, Tinglin, Osei, Eric J. A., Dovlo, Kudjoe, Yesudian, C. A. K., Ramachandran, P., Malek-Afzali, Hossein, Dejman, M., Falahat, K., Baradaran, M., Habibi, E., Kohanzad, H., Nasehi, M., Salek, S., Akanov, A. A., Turdaliyeva, B. S., Hamzina, N. K., Tulebaev, K. A., Clazhneva, T. I., Battakova, G., Kounnavong, Sengchanh, Siengsounthone, Latsamy, Ramos, Leticia Alfaro, Mejia, Israel, Akhtar, Tasleem, Khan, M. Mubashir A., Sidibe, Mintou Fall, Sidibe, Awa, Ndiaye, Djiby, Ndossi, Godwin D., Massaga, Julius, Sadana, Ritu, and Pang, Tikki
- Subjects
Family planning ,Intrauterine device ,Global health ,Knowledge translation ,Health professionals ,Medical education ,Systematic reviews ,Health systems ,Health human resources - Abstract
Background: It is widely agreed that the practices of clinicians should be based on the best available research evidence, but too often this evidence is not reliably disseminated to people who can make use of it. This “know-do” gap leads to ineffective resource use and suboptimal provision of services, which is especially problematic in low- and middle-income countries (LMICs) which face greater resource limitations. Family planning, including intrauterine device (IUD) use, represents an important area to evaluate clinicians’ knowledge and practices in order to make improvements. Methods: A questionnaire was developed, tested and administered to 438 individuals in China (n = 115), Kazakhstan (n = 110), Laos (n = 105), and Mexico (n = 108). The participants responded to ten questions assessing knowledge and practices relating to contraception and IUDs, and a series of questions used to determine their individual characteristics and working context. Ordinal logistic regressions were conducted with knowledge and practices as dependent variables. Results: Overall, a 96 % response rate was achieved (n = 438/458). Only 2.8 % of respondents were able to correctly answer all five knowledge-testing questions, and only 0.9 % self-reported “often” undertaking all four recommended clinical practices and “never” performing the one practice that was contrary to recommendation. Statistically significant factors associated with knowledge scores included: 1) having a masters or doctorate degree; and 2) often reading scientific journals from high-income countries. Significant factors associated with recommended practices included: 1) training in critically appraising systematic reviews; 2) training in the care of patients with IUDs; 3) believing that research performed in their own country is above average or excellent in quality; 4) being based in a facility operated by an NGO; and 5) having the view that higher quality available research is important to improving their work. Conclusions: This analysis supports previous work emphasizing the need for improved knowledge and practices among clinicians concerning the use of IUDs for family planning. It also identifies areas in which targeted interventions may prove effective. Assessing opportunities for increasing education and training programs for clinicians in research and IUD provision could prove to be particularly effective.
- Published
- 2016
- Full Text
- View/download PDF
33. Medical publications (2002-2009) of Islamic countries; a Medline-based study compared to non-Islamic countries [corrected] [published erratum appears in IRANIAN J MED SCI 2010 Dec;35(4):344].
- Author
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Habibi E, Mirhosseini Z, and Majidi M
- Published
- 2010
34. The Analysis of Health Research System Evaluation in Medical Sciences Universities.
- Author
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Djalalinia, Sh, Peykari, N., Owlia, P., Eftekhari, M. Baradaran, Habibi, E., Falahat, K., Mojarrab, Sh, Malekafzali, H., and Ghanei, M.
- Abstract
Background: Based on Iran by 2025 defined vision, we must to receive the first grade of science position in south western Asian region. Thus we need to have a comprehensive evaluation program. Methods: A comprehensive WHO Health Research System Analysis (HRSA)- based evaluation system was developed to evaluate the HRS in Iran. This article has explored the results of the five-year evaluation (2003-2008) and aims to introduce this method to other developing countries. Here we explore the results of research performance evaluation from 2002 to 2010 and by comparing the results with previous available information, we reveal the probable role of this method in research promotion and proposed approach to facilitate and expedite achieving the prospects for goals of health research based on the visions of Iran by 2025. Results: All of the indicators of stewardship and capacity building axes are received to their predefined levels. Moreover all of the medical science university research policies are based on their strategic plannings which are extracted from national visions of Iran by 2025. Most of the predefined goals in knowledge production domain had a significant grow trend but for more growth for commitments they should be closely follow. Conclusion: We developed an HRS-based comprehensive evaluation program to our national vision as well as our regional and international research competition. [ABSTRACT FROM AUTHOR]
- Published
- 2013
35. Trend of Knowledge Production of Research Centers in the Field of Medical Sciences in Iran.
- Author
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Falahat, K., Eftekhari, M. B., Habibi, E., Djalalinia, Sh, Peykari, N., Owlia, P., Malekafzali, H., Ghanei, M., and Mojarrab, Sh
- Abstract
Establishment of medical research centers at universities and health-related organizations and annually evaluation of their research activities was one of the strategic policies which followed by governmental organization in last decade in order to strengthening the connections between health research system and health system. The aim of this study is to scrutinize the role of medical research centers in medical science production in Iran. This study is a cross sectional which has been performed based on existing reports on national scientometrics and evaluation results of research performance of medical research centers between years 2001 to 2010. During last decade number of medical research centers increased from 53 in 2001 to 359 in 2010. Simultaneous scientific output of medical research centers has been increased especially articles indexed in ISI (web of science). Proper policy implementation in the field of health research system during last decades led to improving capacity building and growth knowledge production of medical science in recent years in Iran. The process embedding research into the health systems requires planning up until research products improves health outcomes and health equity in country. [ABSTRACT FROM AUTHOR]
- Published
- 2013
36. Health Research Evaluation and its Role on Knowledge Production.
- Author
-
Djalalinia, Sh, Owlia, P, Setareh Forouzan, A, Habibi, E, Dejman, M, Baradaran Eftekhari, M, Ghanei, M, Malekafzali, H, and Peykari, N
- Abstract
Background: Knowledge production and evaluation are two important functions of health research system (HRS). In this article, we aimed to reveal the correlation between evaluation of health research organizations and health knowledge production promotion. Methods: A comprehensive evaluation system was developed to evaluate the academic performance of national medical science universities on an annual basis. It assess following domains; stewardship, capacity building and knowledge production. Measurable indicators for each domain were assigned, a 'research profile' for each department was provided. In this study, we compared the results of annually national Health Research System evaluation findings during 2005-2008. Results: The number of scientific articles has been increased from 4672 to 8816 during 2005 to 2008. It is mentionable that, the number of articles which has been published in indexed data bases has risen too. This fact could be related to directed policy for more international publication of scientific articles from Iran. The proportion of total articles to the number of academic members was 1.14 in 2008, comparing to 0.84 in 2005. It means that this proportion have increased about twice (0.7 Vs 0.45) during mentioned time. Moreover, other scientific products such as authored books based on domestic researches and cited articles in textbooks have increased according to special attention to knowledge production by policy makers. Conclusion: We conclude that Health System Research evaluation could be used as a mean for implementing policies and promoting knowledge production. [ABSTRACT FROM AUTHOR]
- Published
- 2012
37. Health research governance: Introduction of a new web-based research evaluation model in Iran: One-decade experience
- Author
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Malekzadeh, R., Akhondzadeh, S., Ebadifar, A., Baradaran Eftekhari, M., Parviz Owlia, Ghanei, M., Fala-Hat, K., Habibi, E., Sobhani, Z., Djalalinia, S., Paykari, N., Mojarrab, S., Eltemasi, M., and Laali, R.
- Subjects
Governance ,Research evaluation ,lcsh:Public aspects of medicine ,lcsh:RA1-1270 ,Web-based model - Abstract
Background: Governance is one of the main functions of Health Research System (HRS) that consist of four essential elements such as setting up evaluation system. The goal of this study was to introduce a new web based research evaluation model in Iran. Methods: Based on main elements of governance, research indicators have been clarified and with cooperation of technical team, appropriate software was designed. Three main steps in this study consist of developing of mission-oriented program, creating enabling environment and set up Iran Research Medical Portal as a center for research evaluation. Results: Fifty-two universities of medical sciences in three types have been participated. After training the evaluation focal points in all of medical universities, access to data entry and uploading all of documents were provided. Regarding to mission – based program, the contribution of medical universities in knowledge production was 60% for type one, 31% for type two and 9% for type three. The research priorities based on Essential National Health Research (ENHR) approach and mosaic model were gathered from universities of medical sciences and aggregated to nine main areas as national health research priorities. Ethical committees were established in all of medical universities. Conclusion: Web based research evaluation model is a comprehensive and integrated system for data collection in research. This system is appropriate tool to national health research ranking.
38. Evaluation of the effect of noise on the rate of errors and speed of work by the ergonomic test of two-hand co-ordination
- Author
-
Habibi, E., Dehghan, H., Dehkordy, S. E., and Mohammad Reza Maracy
- Subjects
noise ,lcsh:R ,lcsh:Medicine ,Original Article ,Ergonomics ,rate of error ,speed of work ,two-hand coordination - Abstract
Background: Among the most important and effective factors affecting the efficiency of the human workforce are accuracy, promptness, and ability. In the context of promoting levels and quality of productivity, the aim of this study was to investigate the effects of exposure to noise on the rate of errors, speed of work, and capability in performing manual activities. Methods: This experimental study was conducted on 96 students (52 female and 44 male) of the Isfahan Medical Science University with the average and standard deviations of age, height, and weight of 22.81 (3.04) years, 171.67 (8.51) cm, and 65.05 (13.13) kg, respectively. Sampling was conducted with a randomized block design. Along with controlling for intervening factors, a combination of sound pressure levels [65 dB (A), 85 dB (A), and 95 dB (A)] and exposure times (0, 20, and 40) were used for evaluation of precision and speed of action of the participants, in the ergonomic test of two-hand coordination. Data was analyzed by SPSS18 software using a descriptive and analytical statistical method by analysis of covariance (ANCOVA) repeated measures. Results: The results of this study showed that increasing sound pressure level from 65 to 95 dB in network ′A′ increased the speed of work (P < 0.05). Increase in the exposure time (0 to 40 min of exposure) and gender showed no significant differences statistically in speed of work (P > 0.05). Male participants got annoyed from the noise more than females. Also, increase in sound pressure level increased the rate of error (P < 0.05). Conclusions: According to the results of this research, increasing the sound pressure level decreased efficiency and increased the errors and in exposure to sounds less than 85 dB in the beginning, the efficiency decreased initially and then increased in a mild slope.
39. Trend of knowledge production of research centers in the field of medical sciences in iran
- Author
-
Falahat, K., Eftekhari, M. B., Habibi, E., Djalalinia, S., Niloofar Peykari, Owlia, P., Malekafzali, H., Ghanei, M., and Mojarrab, S.
- Subjects
National Report ,lcsh:Public aspects of medicine ,Knowledge Production ,Medical Research Center ,lcsh:RA1-1270 ,Health System - Abstract
Establishment of medical research centers at universities and health-related organizations and annually evaluation of their research activities was one of the strategic policies which followed by governmental organization in last decade in order to strengthening the connections between health research system and health system. The aim of this study is to scrutinize the role of medical research centers in medical science production in Iran. This study is a cross sectional which has been performed based on existing reports on national scientometrics and evaluation results of research performance of medical research centers between years 2001 to 2010. During last decade number of medical research centers increased from 53 in 2001 to 359 in 2010. Simultaneous scientific output of medical research centers has been increased especially articles indexed in ISI (web of science). Proper policy implementation in the field of health research system during last decades led to improving capacity building and growth knowledge production of medical science in recent years in Iran. The process embedding research into the health systems requires planning up until research products improves health outcomes and health equity in country.
40. Health research evaluation and its role on knowledge production
- Author
-
Djalalinia, S., Parviz Owlia, Setareh Forouzan, A., Habibi, E., Dejman, M., Baradaran Eftekhari, M., Ghanei, M., Malekafzali, H., and Peykari, N.
- Subjects
Knowledge ,Health ,Research ,lcsh:Public aspects of medicine ,Production ,Original Article ,lcsh:RA1-1270 ,Iran ,Evaluation - Abstract
Background: Knowledge production and evaluation are two important functions of health research system (HRS). In this article, we aimed to reveal the correlation between evaluation of health research organizations and health knowledge production promotion. Methods: A comprehensive evaluation system was developed to evaluate the academic performance of national medical science universities on an annual basis. It assess following domains; stewardship, capacity building and knowledge production. Measurable indicators for each domain were assigned, a ‘research profile’ for each department was provided. In this study, we compared the results of annually national Health Research System evaluation findings during 2005–2008. Results: The number of scientific articles has been increased from 4672 to 8816 during 2005 to 2008. It is mentionable that, the number of articles which has been published in indexed data bases has risen too. This fact could be related to directed policy for more international publication of scientific articles from Iran. The proportion of total articles to the number of academic members was 1.14 in 2008, comparing to 0.84 in 2005. It means that this proportion have increased about twice (0.7 Vs 0.45) during mentioned time. Moreover, other scientific products such as authored books based on domestic researches and cited articles in textbooks have increased according to special attention to knowledge production by policy makers. Conclusion: We conclude that Health System Research evaluation could be used as a mean for implementing policies and promoting knowledge production.
41. Designing and validation a visual fatigue questionnaire for video display terminals operators
- Author
-
Rajabi-Vardanjani, H., Habibi, E., Pourabdian, S., Dehghan, H., and Mohammad Reza Maracy
- Subjects
validity ,visual fatigue questionnaire ,lcsh:R ,lcsh:Medicine ,Original Article ,Reliability ,visual display terminals - Abstract
Background: Along with the rapid growth of technology its related tools such as computer, monitors and video display terminals (VDTs) grow as well. Based on the studies, the most common complaint reported is of the VDT users. Methods: This study attempts to design a proper tool to assess the visual fatigue of the VDT users. First draft of the questionnaire was prepared after a thorough study on the books, papers and similar questionnaires. The validity and reliability of the questionnaire was confirmed using the content validity index (CVI) beside that of the Cronbach′s Coefficient Alpha. Then, a cross-sectional study was carried out on 248 of the VDT users in different professions. A theoretical model with four categories of symptoms of visual fatigue was derived from the previous studies and questionnaires. Having used the AMOS 16 software, the construct validity of the questionnaire was evaluated using the confirmatory factor analysis. The correlation co-efficiency of the internal domains was calculated using the SPSS 11.5 software. To assess the quality check index and determining the visual fatigue levels, visual fatigue of the VDT users was measured by the questionnaire and visual fatigue meter (VFM) device. Cut-off points were identified by receiver operating characteristic curves. Results: CVI and reliability co-efficiency were both equal to 0.75. Model fit indices including root mean of squared error approximation, goodness of fit index and adjusted goodness of fit index were obtained 0.026, 0.96 and 0.92 respectfully. The correlation between the results measured with the questionnaire and VFM-90.1 device was −0.87. Cut-off points of the questionnaire were 0.65, 2.36 and 3.88. The confirmed questionnaire consists of four main areas: Eye strain (4 questions), visual impairment (5 questions) and the surface impairment of the eye (3 questions) and the out of eye problems (3 questions). Conclusions: The visual fatigue questionnaire contains 15 questions and has a very remarkable validity and reliability. Using this questionnaire and its findings, one will be able to identify, assess and finally prevent the effective factors of VDT users′ visual fatigue.
42. The epidemiologic study on hearing standard threshold shift using audiometric data and noise level among workers of Isfehan metal industry
- Author
-
Pourabdiyan, S., Ghotbi, M., Yousefi, H. A., Habibi, E., and mohsen zare
- Subjects
Isfehan Metal Industries ,lcsh:R5-920 ,lcsh:R ,lcsh:Medicine ,Audiometer ,lcsh:Medicine (General) ,STS ,Noise Measurement - Abstract
Introduction: Standard threshold shifts (STS) as an important indicator for identifying hearing lossin industries that they perform hearing conservation programs. The aim of this study is theinvestigation of the occurrence of standard threshold shift (STS) among workers of Isfehan metalindustry using audiometric data and noise measurement level.Materials and Methods: This is a cross-sectional and descriptive study that performed among 2016of workers in Isfehan Metal Industry. All of subjects were men and the rate of using personalprotective equipment among workers were sometime=189, often=865 and always=962. At the first wedetermined the parts of plant that exposed to non permissible noise level and then measured exposureto 8 hour equivalent noise level. Finally in regard to basic audiometric and current audiometric, theoccurrences of STS were examined.Results: This study showed that 29.9 % of workers have a STS in these workplaces. There aresignificance relationship between age, exposure time, noise level, wearing time and number ofworkers with STS. But there is no relation between precedence of work and STS statistically.Conclusion: Findings of this study indicated that occurrences of STS among workers exposed tonoise are high. Thus, it is concluded that hearing conservation programs in these industries wasunsuccessful.
43. The analysis of health research system evaluation in medical sciences universities
- Author
-
Djalalinia, S., Peykari, N., Parviz Owlia, Baradaran Eftekhari, M., Habibi, E., Falahat, K., Mojarrab, S., Malekafzali, H., and Ghanei, M.
- Subjects
System ,Health ,Research ,lcsh:Public aspects of medicine ,Original Article ,lcsh:RA1-1270 ,Iran ,Evaluation - Abstract
Background: Based on Iran by 2025 defined vision, we must to receive the first grade of science position in south western Asian region. Thus we need to have a comprehensive evaluation program. Methods: A comprehensive WHO Health Research System Analysis (HRSA)- based evaluation system was developed to evaluate the HRS in Iran. This article has explored the results of the five-year evaluation (2003–2008) and aims to introduce this method to other developing countries. Here we explore the results of research performance evaluation from 2002 to 2010 and by comparing the results with previous available information, we reveal the probable role of this method in research promotion and proposed approach to facilitate and expedite achieving the prospects for goals of health research based on the visions of Iran by 2025. Results: All of the indicators of stewardship and capacity building axes are received to their predefined levels. Moreover all of the medical science university research policies are based on their strategic plannings which are extracted from national visions of Iran by 2025. Most of the predefined goals in knowledge production domain had a significant grow trend but for more growth for commitments they should be closely follow. Conclusion: We developed an HRS-based comprehensive evaluation program to our national vision as well as our regional and international research competition.
44. Research assessment of Iranian medical universities, an experience from a developing country
- Author
-
Malekafzali, H., Eftekhari, M. B., Peykari, N., Gholami, F. S., Djalali Nia, S., Owlia, P., Habibi, E., Bita Mesgarpour, and Vasei, M.
- Subjects
WHO ,University Ranking ,lcsh:Public aspects of medicine ,lcsh:RA1-1270 ,Iran ,Health Research System - Abstract
"nInternational ranking of universities by bibliometric assays has received a great attention in recent years. The developing countries have commenced to build their own infrastructure of research and post graduate training during the past couple of years. In 2000, the Ministry of Health and Medical Education of Iran began an annual national survey for assessing research activities in medical universities and their affiliated institutions by applying a customized ranking method. Research indicators were scored in three topics; Stewardship, Capacity Building, and Knowledge Production. In 2000, there were about 300 published medical articles in ISI/Thomson and PUBMED from the whole country. This number increased up to 3376 in 2007. The score of indexed papers in international databases per academic member rose from 0.1 in 2000 to 0.63 in 2007. The share of global articles (in the field of Medicine) grew from 0.06% in 2000 to 0.55% in 2007. This rising in article output led to a change from grade 57th in 2000 to 27th in 2007 in the ranking system of Scopus database. The number of local medical journals, which were 53 in 2000, increased to 141 at the end of 2008. This rising scores was ongoing while the growth of the total staff of the academic members was about 25% (from 9086 in 2000 to 11324 in 2007). The number of the short training courses rose from 458 in 2000 to 1097 in 2007. The registered research projects in health topic rose from less than 3878 in 2000 to 6816 in 2007.
45. Epigenetic modulation of a hardwired 3D chromatin landscape in two naive states of pluripotency
- Author
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Cheng Wang, Ehsan Habibi, Onkar Joshi, Tianran Peng, Hendrik G. Stunnenberg, Hendrik Marks, Yaser Atlasi, Colin Logie, Shuang-Yin Wang, Ina Poser, Wout Megchelenbrink, Atlasi, Y., Megchelenbrink, W., Peng, T., Habibi, E., Joshi, O., Wang, S. -Y., Wang, C., Logie, C., Poser, I., Marks, H., and Stunnenberg, H. G.
- Subjects
Biology ,Epigenesis, Genetic ,03 medical and health sciences ,Mice ,0302 clinical medicine ,Gene expression ,CRISPR-Cas System ,Epigenetics ,Induced pluripotent stem cell ,Enhancer ,Promoter Regions, Genetic ,Transcription factor ,Molecular Biology ,030304 developmental biology ,0303 health sciences ,Pluripotent Stem Cell ,Animal ,Cell Differentiation ,Mouse Embryonic Stem Cell ,Cell Biology ,Epigenome ,Chromatin ,Cell biology ,Histone ,Enhancer Elements, Genetic ,Spatiotemporal gene expression ,Receptors, Estrogen ,030220 oncology & carcinogenesis ,Transcriptome - Abstract
The mechanisms underlying enhancer activation and the extent to which enhancer-promoter rewiring contributes to spatiotemporal gene expression are not well understood. Using integrative and time-resolved analyses we show that the extensive transcriptome and epigenome resetting during the conversion between 'serum' and '2i' states of mouse embryonic stem cells (ESCs) takes place with minimal enhancer-promoter rewiring that becomes more evident in primed-state pluripotency. Instead, differential gene expression is strongly linked to enhancer activation via H3K27ac. Conditional depletion of transcription factors and allele-specific enhancer analysis reveal an essential role for Esrrb in H3K27 acetylation and activation of 2i-specific enhancers. Restoration of a polymorphic ESRRB motif using CRISPR-Cas9 in a hybrid ESC line restores ESRRB binding and enhancer H3K27ac in an allele-specific manner but has no effect on chromatin interactions. Our study shows that enhancer activation in serum- and 2i-ESCs is largely driven by transcription factor binding and epigenetic marking in a hardwired network of chromatin interactions.
- Published
- 2019
46. beta-Glucan Reverses the Epigenetic State of LPS-Induced Immunological Tolerance
- Author
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Mihai G. Netea, Cheng Wang, Filomena Matarese, Hendrik G. Stunnenberg, Joost H.A. Martens, Ivo Gut, Paul Flicek, Laura Clarke, Colin Logie, Jelle Zwaag, Ehsan Habibi, Robab Davar, Eva M. Janssen-Megens, Nilofar Sharifi, Vivien Schoonenberg, Wout Megchelenbrink, Matthijs Kox, Rob J.W. Arts, Tatyana Kuznetsova, Peter Pickkers, Simon J. van Heeringen, Farid Keramati, Boris Novakovic, Simon Heath, Shuang-Yin Wang, Bowon Kim, Novakovic, B., Habibi, E., Wang, S. -Y., Arts, R. J. W., Davar, R., Megchelenbrink, W., Kim, B., Kuznetsova, T., Kox, M., Zwaag, J., Matarese, F., van Heeringen, S. J., Janssen-Megens, E. M., Sharifi, N., Wang, C., Keramati, F., Schoonenberg, V., Flicek, P., Clarke, L., Pickkers, P., Heath, S., Gut, I., Netea, M. G., Martens, J. H. A., Logie, C., and Stunnenberg, H. G.
- Subjects
0301 basic medicine ,Epigenomics ,Lipopolysaccharides ,beta-Glucans ,Lipopolysaccharide ,Transcription, Genetic ,Macrophage ,medicine.medical_treatment ,epigenome ,lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4] ,human monocytes ,Monocyte ,Monocytes ,human monocyte ,chemistry.chemical_compound ,histone modification ,Gene Regulatory Networks ,GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries) ,Gene Regulatory Network ,biology ,histone modifications ,BLUEPRINT ,lipopolysaccharide ,Cell Differentiation ,Cell biology ,macrophages ,Histone Code ,Histone ,Cytokine ,Reprogramming ,Human ,Epigenomic ,Sepsi ,β-glucan ,beta-Glucan ,General Biochemistry, Genetics and Molecular Biology ,Article ,03 medical and health sciences ,trained innate immunity ,endotoxin tolerance ,Sepsis ,medicine ,Immune Tolerance ,Humans ,Epigenetics ,Molecular Biology ,Innate immune system ,Biochemistry, Genetics and Molecular Biology(all) ,Epigenome ,DNA Methylation ,Immunity, Innate ,030104 developmental biology ,chemistry ,Immunology ,biology.protein ,Immunologic Memory ,transcriptome - Abstract
Contains fulltext : 165879.pdf (Publisher’s version ) (Open Access) Innate immune memory is the phenomenon whereby innate immune cells such as monocytes or macrophages undergo functional reprogramming after exposure to microbial components such as lipopolysaccharide (LPS). We apply an integrated epigenomic approach to characterize the molecular events involved in LPS-induced tolerance in a time-dependent manner. Mechanistically, LPS-treated monocytes fail to accumulate active histone marks at promoter and enhancers of genes in the lipid metabolism and phagocytic pathways. Transcriptional inactivity in response to a second LPS exposure in tolerized macrophages is accompanied by failure to deposit active histone marks at promoters of tolerized genes. In contrast, beta-glucan partially reverses the LPS-induced tolerance in vitro. Importantly, ex vivo beta-glucan treatment of monocytes from volunteers with experimental endotoxemia re-instates their capacity for cytokine production. Tolerance is reversed at the level of distal element histone modification and transcriptional reactivation of otherwise unresponsive genes. VIDEO ABSTRACT.
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- 2016
47. Whole-genome bisulfite sequencing of two distinct interconvertible DNA methylomes of mouse embryonic stem cells
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Marta Gut, Ehsan Habibi, Rosaria Benedetti, Isabelle Brun-Heath, Arie B. Brinkman, Hendrik Marks, Joop H. Jansen, Filomena Matarese, Leonie I. Kroeze, Lucia Altucci, Hindrik H. D. Kerstens, Ivo Gut, Konstantin Lepikhov, Julia Arand, Hendrik G. Stunnenberg, Nina C. Hubner, Jörn Walter, Habibi, E, Brinkman, Ab, Arand, J, Kroeze, Li, Kerstens, Hh, Matarese, F, Lepikhov, K, Gut, M, Brun Heath, I, Hubner, Nc, Benedetti, Rosaria, Altucci, Lucia, Jansen, Jh, Walter, J, Gut, Ig, Marks, H, and Stunnenberg, H. G.
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Male ,Bisulfite sequencing ,Endogenous retrovirus ,Leukemia Inhibitory Factor ,Fetal Development ,Histones ,chemistry.chemical_compound ,Mice ,0302 clinical medicine ,Cells, Cultured ,reproductive and urinary physiology ,Histone Demethylases ,0303 health sciences ,Immune Regulation Translational research [NCMLS 2] ,Genome ,Methylation ,DNA-Binding Proteins ,medicine.anatomical_structure ,DNA methylation ,embryonic structures ,Molecular Medicine ,Female ,Whole-Genome Bisulfite Sequencing ,Stem cell ,biological phenomena, cell phenomena, and immunity ,Pluripotent Stem Cells ,Biology ,03 medical and health sciences ,Proto-Oncogene Proteins ,medicine ,Genetics ,Animals ,Sulfites ,Blastocyst ,Protein Kinase Inhibitors ,Molecular Biology ,Embryonic Stem Cells ,030304 developmental biology ,urogenital system ,Sequence Analysis, DNA ,Cell Biology ,DNA Methylation ,Embryonic stem cell ,Molecular biology ,stem cell ,chemistry ,030217 neurology & neurosurgery ,DNA - Abstract
Contains fulltext : 128583.pdf (Publisher’s version ) (Closed access) The use of two kinase inhibitors (2i) enables derivation of mouse embryonic stem cells (ESCs) in the pluripotent ground state. Using whole-genome bisulfite sequencing (WGBS), we show that male 2i ESCs are globally hypomethylated compared to conventional ESCs maintained in serum. In serum, female ESCs are hypomethyated similarly to male ESCs in 2i, and DNA methylation is further reduced in 2i. Regions with elevated DNA methylation in 2i strongly correlate with the presence of H3K9me3 on endogenous retroviruses (ERVs) and imprinted loci. The methylome of male ESCs in serum parallels postimplantation blastocyst cells, while 2i stalls ESCs in a hypomethylated, ICM-like state. WGBS analysis during adaptation of 2i ESCs to serum suggests that deposition of DNA methylation is largely random, while loss of DNA methylation during reversion to 2i occurs passively, initiating at TET1 binding sites. Together, our analysis provides insight into DNA methylation dynamics in cultured ESCs paralleling early developmental processes.
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- 2013
48. Expansion in situ genome sequencing links nuclear abnormalities to hotspots of aberrant euchromatin repression.
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Labade AS, Chiang ZD, Comenho C, Reginato PL, Payne AC, Earl AS, Shrestha R, Duarte FM, Habibi E, Zhang R, Church GM, Boyden ES, Chen F, and Buenrostro JD
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Microscopy and genomics are both used to characterize cell function, but approaches to connect the two types of information are lacking, particularly at subnuclear resolution. While emerging multiplexed imaging methods can simultaneously localize genomic regions and nuclear proteins, their ability to accurately measure DNA-protein interactions is constrained by the diffraction limit of optical microscopy. Here, we describe expansion in situ genome sequencing (ExIGS), a technology that enables sequencing of genomic DNA and superresolution localization of nuclear proteins in single cells. We applied ExIGS to fibroblast cells derived from an individual with Hutchinson-Gilford progeria syndrome to characterize how variation in nuclear morphology affects spatial chromatin organization. Using this data, we discovered that lamin abnormalities are linked to hotspots of aberrant euchromatin repression that may erode cell identity. Further, we show that lamin abnormalities heterogeneously increase the repressive environment of the nucleus in tissues and aged cells. These results demonstrate that ExIGS may serve as a generalizable platform for connecting nuclear abnormalities to changes in gene regulation across disease contexts.
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- 2024
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49. The effect of Polygonum hyrcanicum Rech. f. hydroalcoholic extract on oxidative stress and nephropathy in alloxan-induced diabetic mice.
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Arabnozari H, Shaki F, Najjari A, Sharifianjazi F, Sarker SD, Habibi E, and Nahar L
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- Animals, Mice, Male, Alloxan, Lipid Peroxidation drug effects, Tumor Necrosis Factor-alpha metabolism, Glutathione metabolism, Kidney drug effects, Kidney metabolism, Kidney pathology, Interleukin-6 metabolism, Interleukin-6 blood, Oxidative Stress drug effects, Plant Extracts pharmacology, Plant Extracts chemistry, Diabetes Mellitus, Experimental drug therapy, Diabetes Mellitus, Experimental metabolism, Diabetic Nephropathies drug therapy, Diabetic Nephropathies metabolism, Antioxidants pharmacology, Polygonum chemistry
- Abstract
Diabetic nephropathy, characterized by inflammation and oxidative stress, poses a management challenge. This study investigates the effect of Polygonum hyrcanicum extract on diabetic nephropathy in alloxan-induced diabetic mice. In this experimental animal study, the P. hyrcanicum extract was prepared using continuous macerations. Thirty male Albino mice, divided into five groups, were induced with alloxan-induced diabetes. They received intraperitoneal injections of the plant extract (100 and 200 mg/kg) and metformin (300 mg/kg) for four weeks. Kidney and blood samples were collected to assess protein carbonyl, glutathione, lipid peroxidation, TNF-α and IL-6 levels. The amount of total flavonoid and phenolic content in the hydroalcoholic extract of P. hyrcanicum were 7.5 ± 0.3 mg of quercetin and 88.2 ± 1.3 mg gallic acid per gram of extract respectively. The antioxidant activity level of the hydroalcoholic extract was determined to be 1.78 ± 0.51 mM equivalent per gram of extract. Alloxan administration resulted in a significant reduction in glutathione levels and a significant increase in protein carbonyl, lipid peroxidation, TNF-α, and IL-6 levels. Hydroalcoholic extract of P. hyrcanicum effectively reduced oxidative stress markers and inflammatory cytokines (TNF-α, IL-6), indicating its potential in mitigating diabetic nephropathy. However, no significant difference in efficacy was observed between the 100 mg/kg and 200 mg/kg doses in terms of reducing these toxicities., (© 2024. The Author(s).)
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- 2024
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50. Corrigendum: The neuroprotective effects of fisetin, a natural flavonoid in neurodegenerative diseases: focus on the role of oxidative stress.
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Hassan SSU, Samanta S, Dash R, Karpiński TM, Habibi E, Sadiq A, Ahmadi A, and Bungau SG
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[This corrects the article DOI: 10.3389/fphar.2022.1015835.]., (Copyright © 2024 Hassan, Samanta, Dash, Karpiński, Habibi, Sadiq, Ahmadi and Bungau.)
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- 2024
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