29 results on '"B. HAMIDI"'
Search Results
2. Field Guide for Research in Community Settings : Tools, Methods, Challenges and Strategies
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M. R. Islam, Niaz A. Khan, Siti H.A.B. Ah, Haris A. Wahab, Mashitah B. Hamidi, M. R. Islam, Niaz A. Khan, Siti H.A.B. Ah, Haris A. Wahab, and Mashitah B. Hamidi
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- Sociology--Fieldwork
- Abstract
This insightful book offers practical advice to fieldworkers in social research, enabling robust and judicious applications of research methods and techniques in data collection. It also outlines data collection challenges that are commonly faced when working in the field.Authors address key strategies to tackle the major challenges to fieldwork, including advice on using indigenous or innovative skills and making intelligent use of the advantages already available within standard research methodologies. International contributors provide a hands-on account of research methodologies as applied in the field, with particular focus on research ethics and community culture and interactions. The book offers a number of useful case studies, featuring examples of the application of research techniques in different cultural and socio-economic contexts.Utilizing an innovative and dynamic ‘storytelling'method, this book will be a useful research tool for fieldworkers engaging in social science research in community settings, as well as students in the field learning the core techniques of fieldwork.
- Published
- 2021
3. Memory: The Majestic Case of an Amnestic Trace
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Anahita B. Hamidi and Steve Ramirez
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0301 basic medicine ,Cognitive science ,Trace (semiology) ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,Biology ,General Agricultural and Biological Sciences ,030217 neurology & neurosurgery ,General Biochemistry, Genetics and Molecular Biology ,Childhood amnesia - Abstract
Summary Memories formed during infancy are forgotten in adulthood, a phenomenon called ‘infantile amnesia’. New research suggests that these memories can be artificially recovered in adulthood, suggesting that they were never completely lost in the first place.
- Published
- 2018
4. Corrigendum to 'Insight meditation and telomere biology: The effects of intensive retreat and the moderating role of personality' [Brain Behav. Immun. 70 (2018) 233-245]
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Perla Kaliman, Brandon G. King, Jue Lin, Quinn A Conklin, Elissa S. Epel, Marta Cosín-Tomás, Anahita B. Hamidi, María Jesús Álvarez-López, Jennifer J. Pokorny, Anthony P. Zanesco, Colin Huang, and Clifford D. Saron
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Endocrine and Autonomic Systems ,Telomere biology ,media_common.quotation_subject ,Immunology ,MEDLINE ,030227 psychiatry ,03 medical and health sciences ,Behavioral Neuroscience ,0302 clinical medicine ,Personality ,Meditation ,Psychology ,030217 neurology & neurosurgery ,Clinical psychology ,media_common - Published
- 2018
5. Artificially Enhancing and Suppressing Hippocampus-Mediated Memories
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Yosif Zaki, Olivia McKissick, Abby Basya Finkelstein, Steve Ramirez, Nathen J. Murawski, Emily Doucette, Anahita B. Hamidi, Briana K. Chen, Emily Merfeld, Monika Shpokayte, Amanda Fortin, Stephanie L. Grella, and Christine Cincotta
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0301 basic medicine ,Male ,Conditioning, Classical ,Hippocampus ,Stimulation ,Engram ,Optogenetics ,Hippocampal formation ,Biology ,General Biochemistry, Genetics and Molecular Biology ,Article ,03 medical and health sciences ,Mice ,Random Allocation ,0302 clinical medicine ,Memory ,medicine ,Animals ,Neurons ,Cognition ,Fear ,Mice, Inbred C57BL ,Freezing behavior ,030104 developmental biology ,medicine.anatomical_structure ,Mental Recall ,General Agricultural and Biological Sciences ,Neuroscience ,030217 neurology & neurosurgery ,Basolateral amygdala - Abstract
Emerging evidence indicates that distinct hippocampal domains differentially drive cognition and emotion [1, 2]; dorsal regions encode spatial, temporal, and contextual information [3-5], whereas ventral regions regulate stress responses [6], anxiety-related behaviors [7, 8], and emotional states [8-10]. Although previous studies demonstrate that optically manipulating cells in the dorsal hippocampus can drive the behavioral expression of positive and negative memories, it is unknown whether changes in cellular activity in the ventral hippocampus can drive such behaviors [11-14]. Investigating the extent to which distinct hippocampal memories across the longitudinal axis modulate behavior could aid in the understanding of stress-related psychiatric disorders known to affect emotion, memory, and cognition [15]. Here, we asked whether tagging and stimulating cells along the dorsoventral axis of the hippocampus could acutely, chronically, and differentially promote context-specific behaviors. Acute reactivation of both dorsal and ventral hippocampus cells that were previously active during memory formation drove freezing behavior, place avoidance, and place preference. Moreover, chronic stimulation of dorsal or ventral hippocampal fear memories produced a context-specific reduction or enhancement of fear responses, respectively, thus demonstrating bi-directional and context-specific modulation of memories along the longitudinal axis of the hippocampus. Fear memory suppression was associated with a reduction in hippocampal cells active during retrieval, while fear memory enhancement was associated with an increase in basolateral amygdala activity. Together, our data demonstrate that discrete sets of cells throughout the hippocampus provide key nodes sufficient to bi-directionally reprogram both the neural and behavioral expression of memory.
- Published
- 2018
6. Insight meditation and telomere biology: The effects of intensive retreat and the moderating role of personality
- Author
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Elissa S. Epel, Marta Cosín-Tomás, Quinn A Conklin, Anthony P. Zanesco, María Jesús Álvarez-López, Colin Huang, Jue Lin, Jennifer J. Pokorny, Anahita B. Hamidi, Clifford D. Saron, Perla Kaliman, and Brandon G. King
- Subjects
Adult ,Male ,0301 basic medicine ,Agreeableness ,Telomerase ,media_common.quotation_subject ,Immunology ,Biological Psychology ,education ,MindRxiv|Social and Behavioral Sciences ,MindRxiv|Social and Behavioral Sciences|Psychology ,Social and Behavioral Sciences ,03 medical and health sciences ,Behavioral Neuroscience ,0302 clinical medicine ,Humans ,Personality ,Psychology ,Meditation ,Big Five personality traits ,media_common ,Neuroticism ,bepress|Social and Behavioral Sciences|Psychology ,Endocrine and Autonomic Systems ,MindRxiv|Social and Behavioral Sciences|Psychology|Biological Psychology ,Telomere Homeostasis ,bepress|Social and Behavioral Sciences|Psychology|Biological Psychology ,Telomere ,humanities ,FOS: Psychology ,030104 developmental biology ,bepress|Social and Behavioral Sciences ,Female ,Cell aging ,Stress, Psychological ,030217 neurology & neurosurgery ,Clinical psychology - Abstract
A growing body of evidence suggests that meditation training may have a range of salubrious effects, including improved telomere regulation. Telomeres and the enzyme telomerase interact with a variety of molecular components to regulate cell-cycle signaling cascades, and are implicated in pathways linking psychological stress to disease. We investigated the effects of intensive meditation practice on these biomarkers by measuring changes in telomere length (TL), telomerase activity (TA), and telomere-related gene (TRG) expression during a 1-month residential Insight meditation retreat. Multilevel analyses revealed an apparent TL increase in the retreat group, compared to a group of experienced meditators, similarly comprised in age and gender, who were not on retreat. Moreover, personality traits predicted changes in TL, such that retreat participants highest in neuroticism and lowest in agreeableness demonstrated the greatest increases in TL. Changes observed in TRGs further suggest retreat-related improvements in telomere maintenance, including increases in Gar1 and HnRNPA1, which encode proteins that bind telomerase RNA and telomeric DNA. Although no group-level changes were observed in TA, retreat participants’ TA levels at post-assessment were inversely related to several indices of retreat engagement and prior meditation experience. Neuroticism also predicted variation in TA across retreat. These findings suggest that meditation training in a retreat setting may have positive effects on telomere regulation, which are moderated by individual differences in personality and meditation experience. (ClinicalTrials.gov #NCT03056105).
- Published
- 2018
7. La pancréatite aigüe révélant une tuberculose péritonéale chez une jeune fille de 20 ans
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Z. Samlani, K. Krati, Sofia Oubaha, B. Hamidi, F. Hlili, and A. Diffaa
- Subjects
Infectious Diseases ,Hepatology ,Gastroenterology - Abstract
La pancreatite aigue est une presentation exceptionnelle de la tuberculose pancreatique. Elle est particulierement exceptionnelle chez l’immunocompetent. Nous rapportons le cas d’une patiente de 20 ans sans antecedents medicaux. Elle consultait pour des epigastralgies atypiques calmees par la position anteflechie qui evoluaient depuis 15 jours dans un contexte de fievre non chiffree. L’examen trouvait une fievre a 39°C, une sensibilite epigastrique et une ascite. La biologie notait une hyperleucytose a 12.000 elements/mm3 a predominance polynucleaire, les hemocultures, les prelevements urinaires et la radiographie thoracique etaient normaux. La lipasemie etait a 423 ui/l. Le scanner abdominal trouvait l’aspect de pancreatite aigue classee stade C selon la classification de Balthazard et l’echoendoscopie ne trouvait pas d’obstacle sur la voie biliaire principale. Le liquide d’ascite etait riche en lymphocyte (89%), en protide a 58g/l, en lipase: 325 UI/l et en adenosine desaminase a 65g/l. L’origine tuberculeuse a ete evoquee et l’intradermoreaction a la tuberculine etait positive a 17 mm. La recherche d’autre localisation de tuberculose etait negative. La patiente a recu le traitement antibacillaire pendant 9 mois et l’evolution clinique et radiologique etait bonne. Le diagnostic de tuberculose pancreatique etait retenu a posteriori sur la bonne evolution sous traitement medical. Nous allons faire le point sur cette pathologie exceptionnelle chez l’adulte immunocompetent.
- Published
- 2012
8. Acute d-serine treatment produces antidepressant-like effects in rodents
- Author
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Anahita B. Hamidi, Daniel R. Austin, Zhenzhong Cui, Gregory R. Rompala, Kazu Nakazawa, Gang Wang, Husseini K. Manji, Carlos A. Zarate, Tyson Tragon, W. Scott Young, Oz Malkesman, and Guang Chen
- Subjects
Male ,Learned helplessness ,Motor Activity ,Phenylenediamines ,Hippocampus ,Rats, Inbred WKY ,Receptors, N-Methyl-D-Aspartate ,Article ,Mice ,Glutamatergic ,Helplessness, Learned ,Escape Reaction ,Serine ,Animals ,Pharmacology (medical) ,RNA, Messenger ,Swimming ,Mice, Knockout ,Pharmacology ,Analysis of Variance ,Depression ,Glutamate receptor ,Immobility Response, Tonic ,Antidepressive Agents ,Rats ,Mice, Inbred C57BL ,Disease Models, Animal ,Psychiatry and Mental health ,Synaptic plasticity ,Exploratory Behavior ,Antidepressant ,NMDA receptor ,Female ,Ketamine ,Serotonin ,Calcium-Calmodulin-Dependent Protein Kinase Type 2 ,Psychology ,Excitatory Amino Acid Antagonists ,Neuroscience ,Behavioural despair test - Abstract
Research suggests that dysfunctional glutamatergic signalling may contribute to depression, a debilitating mood disorder affecting millions of individuals worldwide. Ketamine, a N-methyl-D-aspartate (NMDA) receptor antagonist, exerts rapid antidepressant effects in approximately 70% of patients. Glutamate evokes the release of D-serine from astrocytes and neurons, which then acts as a co-agonist and binds at the glycine site on the NR1 subunit of NMDA receptors. Several studies have implicated glial deficits as one of the underlying facets of the neurobiology of depression. The present study tested the hypothesis that D-serine modulates behaviours related to depression. The behavioural effects of a single, acute D-serine administration were examined in several rodent tests of antidepressant-like effects, including the forced swim test (FST), the female urine sniffing test (FUST) following serotonin depletion, and the learned helplessness (LH) paradigm. D-serine significantly reduced immobility in the FST without affecting general motor function. Both D-serine and ketamine significantly rescued sexual reward-seeking deficits caused by serotonin depletion in the FUST. Finally, D-serine reversed LH behaviour, as measured by escape latency, number of escapes, and percentage of mice developing LH. Mice lacking NR1 expression in forebrain excitatory neurons exhibited a depression-like phenotype in the same behavioural tests, and did not respond to D-serine treatment. These findings suggest that D-serine produces antidepressant-like effects and support the notion of complex glutamatergic dysfunction in depression. It is unclear whether D-serine has a convergent influence on downstream synaptic plasticity cascades that may yield a similar therapeutic profile to NMDA antagonists like ketamine.
- Published
- 2011
9. THE EFFECT OF FILTER TYPE, CONCENTRATION, AND TYPE OF CARBON NANOTUBE ON THE BUCKYPAPER SURFACE QUALITY
- Author
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M. Madhkhan, Ali Vahedi, M. Kamalvand, Saeed Ziaei-Rad, M. A. Vaziri, and B. Hamidi
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Yield (engineering) ,Materials science ,Bioengineering ,Buckypaper ,Carbon nanotube ,Surface finish ,Condensed Matter Physics ,Computer Science Applications ,law.invention ,Filter (video) ,law ,Frit compression ,General Materials Science ,Electrical and Electronic Engineering ,Composite material ,Suspension (vehicle) ,Filtration ,Biotechnology - Abstract
Buckypaper is a thin sheet fabricated from the aggregation of carbon nanotubes. The generally accepted method for forming such carbon nanotube (CNT) films involves the use of stable suspension of carbon nanotubes in water. These suspensions can then be membrane-filtered under pressure to yield uniform films. After preparation of a stable solution, it should be membrane-filtrated on the surface of a filter. Usually, the quality of a buckypaper depends on sonication time and power, surfactant type and concentration, filter type, and concentration of carbon nanotube. In order to investigate the surface quality of buckypapers, low-magnification images could give rather useful information about the roughness of surface. Analysis of the 100 × images clearly shows that with increasing the suspension concentration, the smoothness of buckypaper surface will decrease. Therefore, from this viewpoint, decreasing the concentration can enhance the quality of the buckypaper. Surface of the filter also affects on the buckypaper quality. Therefore, for filtration of the suspension, a filter with suitable material, pore sizes, and surface should be used. As the pore sizes of the filter are usually small, the filtration process may be very time-consuming. Since the process is carring out under pressure and also due to the brittle nature of the buckypaper, removal of the buckypaper from the surface of the filter is a very serious and important stage and depends on the filter type, concentration, and type of CNTs. The buckypaper usually can be removed from the filter mechanically. The type of CNTs (MWNT or SWNT) may change the above-mentioned factors.
- Published
- 2011
10. Stable isotope-resolved metabolomic analysis of lithium effects on glial-neuronal metabolism and interactions
- Author
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Yun Wang, Husseini K. Manji, Rima Kaddurah-Daouk, Peixiong Yuan, Anahita B. Hamidi, Xavier Guitart, Richard M. Higashi, Andrew N. Lane, Guang Chen, Teresa W.-M. Fan, and Rulun Zhou
- Subjects
Lithium (medication) ,Chemistry ,Endocrinology, Diabetes and Metabolism ,Clinical Biochemistry ,Metabolism ,Biochemistry ,Article ,Glutamine ,Citric acid cycle ,Metabolic pathway ,Lactate oxidation ,Extracellular ,medicine ,Glycolysis ,medicine.drug - Abstract
Despite the long-established therapeutic efficacy of lithium in the treatment of bipolar disorder (BPD), its molecular mechanism of action remains elusive. Newly developed stable isotope-resolved metabolomics (SIRM) is a powerful approach that can be used to elucidate systematically how lithium impacts glial and neuronal metabolic pathways and activities, leading ultimately to deciphering its molecular mechanism of action. The effect of lithium on the metabolism of three different (13)C-labeled precursors ([U-(13)C]-glucose, (13)C-3-lactate or (13)C-2,3-alanine) was analyzed in cultured rat astrocytes and neurons by nuclear magnetic resonance (NMR) spectroscopy and gas chromatography mass spectrometry (GC-MS). Using [U-(13)C]-glucose, lithium was shown to enhance glycolytic activity and part of the Krebs cycle activity in both astrocytes and neurons, particularly the anaplerotic pyruvate carboxylation (PC). The PC pathway was previously thought to be active in astrocytes but absent in neurons. Lithium also stimulated the extracellular release of (13)C labeled-lactate, -alanine (Ala), -citrate, and -glutamine (Gln) by astrocytes. Interrogation of neuronal pathways using (13)C-3-lactate or (13)C-2,3-Ala as tracers indicated a high capacity of neurons to utilize lactate and Ala in the Krebs cycle, particularly in the production of labeled Asp and Glu via PC and normal cycle activity. Prolonged lithium treatment enhanced lactate metabolism via PC but inhibited lactate oxidation via the normal Krebs cycle in neurons. Such lithium modulation of glycolytic, PC and Krebs cycle activity in astrocytes and neurons as well as release of fuel substrates by astrocytes should help replenish Krebs cycle substrates for Glu synthesis while meeting neuronal demands for energy. Further investigations into the molecular regulation of these metabolic traits should provide new insights into the pathophysiology of mood disorders and early diagnostic markers, as well as new target(s) for effective therapies.
- Published
- 2010
11. Analysis of composite skin/stiffener debounding and failure under uniaxial loading
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Bijan Mohammadi, Hamid Reza Ovesy, Hossein Hosseini-Toudeshky, and B. Hamidi
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Fiber pull-out ,Materials science ,business.industry ,Tension (physics) ,Delamination ,Fracture mechanics ,Structural engineering ,Flange ,Finite element method ,Stress (mechanics) ,Composite construction ,Ceramics and Composites ,Composite material ,business ,Civil and Structural Engineering - Abstract
In this paper, damage mechanisms in the composite bounded skin/stiffener constructions under monotonic tension loading are investigated. The approach uses experiments to detect the failure mechanisms, two and three-dimensional stress analysis to determine the location of first matrix cracking and computational fracture mechanics to investigate the potential for cracks and delamination growth. The laminates strength and damage mechanisms obtained from both experimental and finite elements analysis are presented for several laminates lay-up configurations. Observations on the performed experiments show matrix crack initiation and propagation in the skin and near the flange tip, causing the flange to almost fully debounded from the skin in some cases, interlaminar debounding and fiber breakage up to the failure of the components. The finite elements analysis is also show that the matrix cracks are initiated in the first skin layer for most of the cases. With increasing the applied load the matrix cracks are propagated through the thickness to reach the next layer and causes delamination between the two layers. With increasing the applied load this delamination is propagated up to the occurrence of unstable delamination growth or the first fiber breakage known as the final failure of the component. The obtained experimental failure loads are compared with those calculated by the finite elements analysis.
- Published
- 2006
12. Telomere lengthening after three weeks of an intensive insight meditation retreat
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Clifford D. Saron, Elissa S. Epel, Anahita B. Hamidi, Quinn A Conklin, Jennifer J. Pokorny, Elizabeth H. Blackburn, Brandon G. King, Jue Lin, and Anthony P. Zanesco
- Subjects
Gerontology ,Psychiatry and Mental health ,Telomere Lengthening ,Endocrinology ,Psychotherapist ,Endocrine and Autonomic Systems ,Endocrinology, Diabetes and Metabolism ,media_common.quotation_subject ,Meditation ,Psychology ,Biological Psychiatry ,media_common - Published
- 2015
13. The anterior cingulate ERK pathway contributes to regulation of behavioral excitement and hedonic activity
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Husseini K. Manji, Yanlei Hao, Min Zhuo, Sharon Engel, Anahita B. Hamidi, Guang Chen, Thomas K. Creson, and Yi Shen
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MAPK/ERK pathway ,Male ,Microinjections ,Transfection ,Gyrus Cinguli ,Rats, Sprague-Dawley ,medicine ,Animals ,Enzyme Inhibitors ,Amphetamine ,Prefrontal cortex ,Extracellular Signal-Regulated MAP Kinases ,Maze Learning ,Biological Psychiatry ,PI3K/AKT/mTOR pathway ,Anterior cingulate cortex ,Cells, Cultured ,Swimming ,Cerebral Cortex ,Flavonoids ,Neurons ,Mitogen-Activated Protein Kinase 3 ,Behavior, Animal ,Kinase ,medicine.disease ,Embryo, Mammalian ,Rats ,Psychiatry and Mental health ,medicine.anatomical_structure ,Mood disorders ,Gene Expression Regulation ,Mutation ,Exploratory Behavior ,Central Nervous System Stimulants ,Signal transduction ,Psychology ,Neuroscience ,medicine.drug ,Signal Transduction - Abstract
Objectives: Several intracellular signaling cascades, such as the extracellular signal-regulated kinase (ERK), Wnt-signaling/GSK-3, PLC/PKC, and PI3K pathways, have been shown to be affected directly or indirectly by mood stabilizers. Clinical imaging studies reveal that mood disorders are associated with structural and/or metabolic changes in specific brain regions such as the anterior cingulate cortex (ACC). Here we investigated the extent to which perturbation of one of the affected pathways, the ERK pathway, in the ACC influences affective-related behavior. Methods: The regional perturbation was induced by two means: local continuous infusion of PD98059, an ERK pathway inhibitor, and microinjection of a lentiviral-mediated gene delivery system encoding functional negative ERK1. The outcomes were monitored with a battery of affective-related tests similar to those used in several previous studies. Results: Compared to their respective controls, rats infused with PD98059 or injected with the lentiviral negative ERK1 construct displayed hyperactivities in multiple tests, exhibited preferentially more open-arm activity in the elevated-plus-maze test, consumed more sweetened liquid in a saccharin preference test, and showed heightened response to amphetamine. Conclusions: These data support a role for the ACC ERK pathway in the regulation of affective-related behaviors. However, the medial prefrontal cortex (mPFC) comprises at least three other regions that will need to be similarly examined before specific roles of the ACC ERK pathway can be definitively attributed to affective behaviors. Additionally, responses of other signaling pathways to mood stabilizers in these mPFC regions, as well as the limbic regions to which they project, will be important to examine.
- Published
- 2009
14. Finite Element Based Prediction of Failure in Laminated Composite Plates
- Author
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H. R. Ovesi, B. Hamidi, Hossein Hosseini-Toudeshky, and Bijan Mohammadi
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Optimal design ,Strain energy release rate ,Matrix (mathematics) ,Materials science ,Ultimate tensile strength ,Composite number ,Composite material ,Matrix cracking ,Finite element method - Abstract
Damage accumulation in laminated composite is a major concern in the design and use of composite structures. Accumulated damage can affect laminated response and ultimate strength, which are critical to design of load-carrying structural components. For the optimal design of composite structures, laminate response beyond the point of initial matrix cracking must be known, and subsequent damage and failure modes induced by accumulated matrix crack must be understood.
- Published
- 2008
15. P-120 – Syndrome d'hyper-IgM chez un frère et sa sœur
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J. Najib, B. Hamidi, S. Bassit, Aziz Bousfiha, Fatima Ailal, I. Benhssaine, and M. Zniber
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Pediatrics, Perinatology and Child Health - Published
- 2015
16. MODELING, SIMULATION AND SENSITIVE ANALYZING OF THE TERRAIN VEHICLE SUSPENSION SYSTEM.
- Author
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LAJQI, Sh., PEHAN, S., LAJQI, N., and B. HAMIDI
- Subjects
COMPUTER simulation ,ALL terrain vehicles ,AUTOMOBILE springs & suspension ,MATHEMATICAL models ,AUTOMOBILE acceleration - Abstract
Effective method for analyzing of the terrain vehicle suspension performance is presented. The key objective of this approach is to make quick analyses of the vehicle suspension system performance. The vehicle is simplified by mathematical modeling of a quarter of it and equations of motion are solved by using Matlab software. To verify the reliability of the proposed method a comparison with one of the simply commercial software is done. The usefulness of the proposed method on the real terrain vehicle is presented in order to analyze the sensitivity of the several suspension parameters such as spring stiffness coefficient, damping coefficient, tire stiffness coefficient, sprung and un-sprung masses. The sensitivity of the suspension parameters is determined by considering of the vehicle body acceleration, vertical tire force and suspension travel that directly influences on the driving comfort and driving safety. [ABSTRACT FROM AUTHOR]
- Published
- 2013
17. Periodontal Inflammation and Dysbiosis Relate to Microbial Changes in the Gut.
- Author
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Kamer AR, Pushalkar S, Hamidi B, Janal MN, Tang V, Annam KRC, Palomo L, Gulivindala D, Glodzik L, and Saxena D
- Abstract
Periodontal disease (PerioD) is a chronic inflammatory disease of dysbiotic etiology. Animal models and few human data showed a relationship between oral bacteria and gut dysbiosis. However, the effect of periodontal inflammation and subgingival dysbiosis on the gut is unknown. We hypothesized that periodontal inflammation and its associated subgingival dysbiosis contribute to gut dysbiosis even in subjects free of known gut disorders. We evaluated and compared elderly subjects with Low and High periodontal inflammation (assessed by Periodontal Inflamed Surface Area (PISA)) for stool and subgingival derived bacteria (assayed by 16S rRNA sequencing). The associations between PISA/subgingival dysbiosis and gut dysbiosis and bacteria known to produce short-chain fatty acid (SCFA) were assessed. LEfSe analysis showed that, in Low PISA, species belonging to Lactobacillus , Roseburia, and Ruminococcus taxa and Lactobacillus zeae were enriched, while species belonging to Coprococcus , Clostridiales , and Atopobium were enriched in High PISA. Regression analyses showed that PISA associated with indicators of dysbiosis in the gut mainly reduced abundance of SCFA producing bacteria (Radj = -0.38, p = 0.03). Subgingival bacterial dysbiosis also associated with reduced levels of gut SCFA producing bacteria (Radj = -0.58, p = 0.002). These results suggest that periodontal inflammation and subgingival microbiota contribute to gut bacterial changes.
- Published
- 2024
- Full Text
- View/download PDF
18. Application of Spatial Analysis for Electronic Health Records: Characterizing Patient Phenotypes and Emerging Trends.
- Author
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Mollalo A, Hamidi B, Lenert L, and Alekseyenko AV
- Abstract
Background: Electronic health records (EHR) commonly contain patient addresses that provide valuable data for geocoding and spatial analysis, enabling more comprehensive descriptions of individual patients for clinical purposes. Despite the widespread use of EHR in clinical decision support and interventions, no systematic review has examined the extent to which spatial analysis is used to characterize patient phenotypes., Objective: This study reviews advanced spatial analyses that employed individual-level health data from EHR within the US to characterize patient phenotypes., Methods: We systematically evaluated English-language peer-reviewed articles from PubMed/MEDLINE, Scopus, Web of Science, and Google Scholar databases from inception to August 20, 2023, without imposing constraints on time, study design, or specific health domains., Results: Only 49 articles met the eligibility criteria. These articles utilized diverse spatial methods, with a predominant focus on clustering techniques, while spatiotemporal analysis (frequentist and Bayesian) and modeling were relatively underexplored. A noteworthy surge (n = 42, 85.7%) in publications was observed post-2017. The publications investigated a variety of adult and pediatric clinical areas, including infectious disease, endocrinology, and cardiology, using phenotypes defined over a range of data domains, such as demographics, diagnoses, and visits. The primary health outcomes investigated were asthma, hypertension, and diabetes. Notably, patient phenotypes involving genomics, imaging, and notes were rarely utilized., Conclusions: This review underscores the growing interest in spatial analysis of EHR-derived data and highlights knowledge gaps in clinical health, phenotype domains, and spatial methodologies. Additionally, this review proposes guidelines for harnessing the potential of spatial analysis to enhance the context of individual patients for future clinical decision support., Competing Interests: Conflicts of interest None declared. Additional Declarations: The authors declare no competing interests.
- Published
- 2024
- Full Text
- View/download PDF
19. The hidden microbiome of hospital infection surveillance testing: biomarkers of health outcomes in MRSA and VRE colonization.
- Author
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Hamidi B, Steed LL, Curry SR, Salgado CD, and Alekseyenko AV
- Abstract
Background: Hospital-acquired infections present a major concern for healthcare systems in the U.S. and worldwide. Drug-resistant infections result in increased costs and prolonged hospital stays. Methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE) are responsible for many drug-resistant infections in the U.S. We undertook two parallel studies aimed to investigate the differences in the microbial communities of individuals colonized with MRSA (or VRE) as compared to their respective non-colonized counterparts matched for age, sex, race, ethnicity, unit of admission, and diagnostic-related group, when available., Results: The VRE study showed considerably more Enterococcus genus communities in the VRE colonized samples. Our findings for both MRSA and VRE studies suggest a strong association between 16S rRNA gene alpha diversity, beta diversity, and colonization status. When we assessed the colonized microbial communities in isolation, the differences disappeared, suggesting that the colonized microbial communities drove the change. Isolating Staphylococcus, we saw significant differences expressed across colonization in specific sequence variants., Conclusions: The differences seen in the microbial communities from MRSA (or VRE) colonized samples as compared to non-colonized match-pairs are driven by the isolated communities of the Staphylococcus (or Enterococcus) genus, the removal of which results in the disappearance of any differences in the diversity observed across the match-pairs., Competing Interests: Declarations Competing Interests The authors declare that no competing interests.
- Published
- 2023
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20. Periodontal Inflamed Surface Area (PISA) associates with composites of salivary cytokines.
- Author
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Tang V, Hamidi B, Janal MN, Barber CA, Godder B, Palomo L, and Kamer AR
- Subjects
- Humans, Cytokines, Cross-Sectional Studies, Inflammation, Saliva, Periodontitis, Periodontal Diseases
- Abstract
Background: Periodontal disease (PerioD) is a chronic, complex inflammatory condition resulting from the interaction between subgingival dysbiotic bacteria and the host immune response leading to local inflammation. Since periodontal inflammation is characterized by multiple cytokines effects we investigated whether Periodontal Inflamed Surface Area (PISA), a continuous measure of clinical periodontal inflammation is a predictor of composite indexes of salivary cytokines., Methods and Findings: In a cross-sectional study of 67 healthy, well-educated individuals, we evaluated PISA and several cytokines expressed in whole stimulated saliva. Two salivary cytokine indexes were constructed using weighted and unweighted approaches based on a Principal Component Analysis [named Cytokine Component Index (CCI)] or averaging the (standardized) level of all cytokines [named Composite Inflammatory Index (CII)]. In regression analysis we found that PISA scores were significantly associated with both salivary cytokine constructs, (CCI: part R = 0.51, p<0.001; CII: part R = 0.40, p = 0.001) independent of age, gender and BMI showing that single scores summarizing salivary cytokines correlated with severity of clinical periodontal inflammation., Conclusions: Clinical periodontal inflammation may be reflected by a single score encompassing several salivary cytokines. These results are consistent with the complexity of interactions characterizing periodontal disease. In addition, Type I error is likely to be avoided., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Tang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
- Published
- 2023
- Full Text
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21. Not all phenotypes are created equal: covariates of success in e-phenotype specification.
- Author
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Hamidi B, Flume PA, Simpson KN, and Alekseyenko AV
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- Phenotype, Electronic Health Records, Mental Processes, Research Design
- Abstract
Background: Electronic (e)-phenotype specification by noninformaticist investigators remains a challenge. Although validation of each patient returned by e-phenotype could ensure accuracy of cohort representation, this approach is not practical. Understanding the factors leading to successful e-phenotype specification may reveal generalizable strategies leading to better results., Materials and Methods: Noninformaticist experts (n = 21) were recruited to produce expert-mediated e-phenotypes using i2b2 assisted by a honest data-broker and a project coordinator. Patient- and visit-sets were reidentified and a random sample of 20 charts matching each e-phenotype was returned to experts for chart-validation. Attributes of the queries and expert characteristics were captured and related to chart-validation rates using generalized linear regression models., Results: E-phenotype validation rates varied according to experts' domains and query characteristics (mean = 61%, range 20-100%). Clinical domains that performed better included infectious, rheumatic, neonatal, and cancers, whereas other domains performed worse (psychiatric, GI, skin, and pulmonary). Match-rate was negatively impacted when specification of temporal constraints was required. In general, the increase in e-phenotype specificity contributed positively to match-rate., Discussions and Conclusions: Clinical experts and informaticists experience a variety of challenges when building e-phenotypes, including the inability to differentiate clinical events from patient characteristics or appropriately configure temporal constraints; a lack of access to available and quality data; and difficulty in specifying routes of medication administration. Biomedical query mediation by informaticists and honest data-brokers in designing e-phenotypes cannot be overstated. Although tools such as i2b2 may be widely available to noninformaticists, successful utilization depends not on users' confidence, but rather on creating highly specific e-phenotypes., (© The Author(s) 2022. Published by Oxford University Press on behalf of the American Medical Informatics Association.)
- Published
- 2023
- Full Text
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22. Revisiting rigid overdenture design following traditional removable prosthetic concepts: a case report.
- Author
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Kang M, Chu CW, Trushkowsky RD, Hamidi B, and Goldstein GR
- Subjects
- Dental Prosthesis, Implant-Supported, Denture Retention, Denture, Overlay, Humans, Mastication, Dental Implants, Jaw, Edentulous
- Abstract
The inability to place a sufficient number of implants posteriorly may limit tooth and soft tissue replacement because of the cantilever effects that would result from the unsupported prosthesis. Fabrication of a fixed removable overdenture that is implant retained and supported by both implants and soft tissue allows adequate replacement of teeth and soft tissue for optimal mastication and esthetics. This case report describes a design for implant overdentures that conforms to fundamental removable prosthetic principles by using a rigid bar with bilateral locking passive attachments. The rigid implant overdenture provides extra retention via the locking attachments while maintaining stability with proper extensions and full soft tissue support posteriorly. This removable implant overdenture design is a suitable treatment option for patients who desire the sensation of a fixed prosthesis but are unable to receive fully implant-supported prostheses., Competing Interests: The authors report no conflicts of interest pertaining to any of the products or companies discussed in this article.
- Published
- 2022
23. Each patient is a research biorepository: informatics-enabled research on surplus clinical specimens via the living BioBank.
- Author
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Alekseyenko AV, Hamidi B, Faith TD, Crandall KA, Powers JG, Metts CL, Madory JE, Carroll SL, Obeid JS, and Lenert LA
- Subjects
- Data Warehousing, Humans, Microbiota genetics, Surveys and Questionnaires, Biological Specimen Banks organization & administration, Databases, Factual, Phenotype, Translational Research, Biomedical
- Abstract
The ability to analyze human specimens is the pillar of modern-day translational research. To enhance the research availability of relevant clinical specimens, we developed the Living BioBank (LBB) solution, which allows for just-in-time capture and delivery of phenotyped surplus laboratory medicine specimens. The LBB is a system-of-systems integrating research feasibility databases in i2b2, a real-time clinical data warehouse, and an informatics system for institutional research services management (SPARC). LBB delivers deidentified clinical data and laboratory specimens. We further present an extension to our solution, the Living µBiome Bank, that allows the user to request and receive phenotyped specimen microbiome data. We discuss the details of the implementation of the LBB system and the necessary regulatory oversight for this solution. The conducted institutional focus group of translational investigators indicates an overall positive sentiment towards potential scientific results generated with the use of LBB. Reference implementation of LBB is available at https://LivingBioBank.musc.edu., (© The Author(s) 2020. Published by Oxford University Press on behalf of the American Medical Informatics Association.)
- Published
- 2021
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24. MODIMA, a Method for Multivariate Omnibus Distance Mediation Analysis, Allows for Integration of Multivariate Exposure-Mediator-Response Relationships.
- Author
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Hamidi B, Wallace K, and Alekseyenko AV
- Subjects
- Animals, Computer Simulation, Datasets as Topic, Humans, Mice, Multivariate Analysis, Computational Biology methods, Gastrointestinal Microbiome, Models, Statistical
- Abstract
Many important exposure-response relationships, such as diet and weight, can be influenced by intermediates, such as the gut microbiome. Understanding the role of these intermediates, the mediators, is important in refining cause-effect theories and discovering additional medical interventions (e.g., probiotics, prebiotics). Mediation analysis has been at the heart of behavioral health research, rapidly gaining popularity with the biomedical sciences in the last decade. A specific analytic challenge is being able to incorporate an entire 'omics assay as a mediator. To address this challenge, we propose a hypothesis testing framework for multivariate omnibus distance mediation analysis (MODIMA). We use the power of energy statistics, such as partial distance correlation, to allow for analysis of multivariate exposure-mediator-response triples. Our simulation results demonstrate the favorable statistical properties of our approach relative to the available alternatives. Finally, we demonstrate the application of the proposed methods in two previously published microbiome datasets. Our framework adds a new tool to the toolbox of approaches to the integration of 'omics big data.
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- 2019
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25. Longitudinal changes during pregnancy in gut microbiota and methylmercury biomarkers, and reversal of microbe-exposure correlations.
- Author
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Rothenberg SE, Wagner CL, Hamidi B, Alekseyenko AV, and Andrea Azcarate-Peril M
- Subjects
- Female, Humans, Infant, Newborn, Pregnancy, RNA, Ribosomal, 16S genetics, Time, Biomarkers analysis, Environmental Exposure analysis, Gastrointestinal Microbiome drug effects, Gastrointestinal Microbiome physiology, Mercury toxicity, Methylmercury Compounds toxicity
- Abstract
Objective: Gut microorganisms contribute to the metabolism of environmental toxicants, including methylmercury (MeHg). Our main objective was to investigate whether associations between biomarkers for prenatal MeHg exposure and maternal gut microbiota differed between early and late gestation., Methods: Maternal blood and stool samples were collected during early (8.3-17 weeks, n=28) and late (27-36 weeks, n=24) gestation. Total mercury and MeHg concentrations were quantified in biomarkers, and inorganic mercury was estimated by subtraction. The diversity and structure of the gut microbiota were investigated using 16S rRNA gene profiling (n = 52). Biomarkers were dichotomized, and diversity patterns were compared between high/low mercury concentrations. Spearman's correlation was used to assess bivariate associations between MeHg biomarkers (stool, blood, and meconium), and 23 gut microbial taxa (genus or family level, >1% average relative abundance)., Results: Within-person and between-person diversity patterns in gut microbiota differed between early/late gestation. The overall composition of the microbiome differed between high/low MeHg concentrations (in blood and stool) during early gestation, but not late gestation. Ten (of 23) taxa were significantly correlated with MeHg biomarkers (increasing or decreasing); however, associations differed, depending on whether the sample was collected during early or late gestation. A total of 43% of associations (69/161) reversed the direction of correlation between early/late gestation., Conclusions: The time point at which a maternal fecal sample is collected may yield different associations between gut microorganisms and MeHg biomarkers, which may be due in part to remodeling of maternal microbiota during pregnancy. Our results suggest the effectiveness of dietary interventions to reduce prenatal MeHg exposure may differ between early and late gestation., (Copyright © 2019 Elsevier Inc. All rights reserved.)
- Published
- 2019
- Full Text
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26. W ∗ d -test: robust distance-based multivariate analysis of variance
- Author
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Hamidi B, Wallace K, Vasu C, and Alekseyenko AV
- Subjects
- Computer Simulation, Humans, Multivariate Analysis, Software, Computational Biology methods, Microbiota
- Abstract
Background: Community-wide analyses provide an essential means for evaluation of the effect of interventions or design variables on the composition of the microbiome. Applications of these analyses are omnipresent in microbiome literature, yet some of their statistical properties have not been tested for robustness towards common features of microbiome data. Recently, it has been reported that PERMANOVA can yield wrong results in the presence of heteroscedasticity and unbalanced sample sizes., Findings: We develop a method for multivariate analysis of variance, [Formula: see text], based on Welch MANOVA that is robust to heteroscedasticity in the data. We do so by extending a previously reported method that does the same for two-level independent factor variables. Our approach can accommodate multi-level factors, stratification, and multiple post hoc testing scenarios. An R language implementation of the method is available at https://github.com/alekseyenko/WdStar ., Conclusion: Our method resolves potential for confounding of location and dispersion effects in multivariate analyses by explicitly accounting for the differences in multivariate dispersion in the data tested. The methods based on [Formula: see text] have general applicability in microbiome and other 'omics data analyses.
- Published
- 2019
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27. Social Media Use Among Living Kidney Donors and Recipients: Survey on Current Practice and Potential.
- Author
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Kazley AS, Hamidi B, Balliet W, and Baliga P
- Subjects
- Aged, Cross-Sectional Studies, Female, Health Status, Humans, Living Donors, Male, Middle Aged, Surveys and Questionnaires, United States, Health Education methods, Kidney Transplantation, Social Media statistics & numerical data
- Abstract
Background: In the United States, there is a national shortage of organs donated for transplant. Among the solid organs, most often kidneys are donated by living donors, but the lack of information and complicated processes limit the number of individuals who serve as living kidney donors. Social media can be a tool for advocacy, educating the public about the need, process, and outcomes of live kidney donors, yet little is known about social media use by kidney transplant patients., Objective: The purpose of this study was to examine the social media use of potential kidney transplant patients and their willingness to use social media and their networks to advocate and educate about living kidney donation., Methods: Using a validated survey, we modified the instrument to apply to the patient population of interest attending the Medical University of South Carolina, Charleston, SC, USA. The questions on the survey inquired about current social media use, sites visited, frequency and duration of social media use, and willingness to use social media to share the need for living kidney donors. We asked patients who had received a transplant and those awaiting a transplant to complete the survey during an office visit. Participation was voluntary., Results: A total of 199 patients completed the survey. Approximately half of all kidney transplant patients surveyed used social media (104/199, 52.3%), and approximately one-third (66/199, 33.2%) had more than 100 friends in their social media network. Facebook was the most popular site, and 51% (102/199) reported that they would be willing to post information about living kidney donation on their social networks. More than a quarter of the sample (75/199, 37.7%) had posted about their health status in the past., Conclusions: Social media holds great promise for health-related education and awareness. Our study shows the current social media use of kidney transplant patients. In turn, such information can be used to design interventions to ensure appropriate decision making about live kidney donation. Transplant programs can help increase the number of living donors by providing guidance to kidney transplant patients in how to use social media, to be advocates, and to provide information about living kidney donation to their social network., Competing Interests: Conflicts of Interest: None declared., (©Abby Swanson Kazley, Bashir Hamidi, Wendy Balliet, Prabhakar Baliga. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 20.12.2016.)
- Published
- 2016
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28. Investigation of amino acid-polymer aqueous biphasic systems.
- Author
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Sadeghi R, Hamidi B, and Ebrahimi N
- Subjects
- Phase Transition, Temperature, Thermodynamics, Amino Acids chemistry, Polymers chemistry, Salts chemistry, Water chemistry
- Abstract
Aiming at gathering further information to evaluate the recently proposed1,2 mechanism of the salt effect in aqueous polymer solutions, experimental vapor-liquid equilibria (VLE), liquid-liquid equilibria (LLE), and volumetric-compressibility measurements were carried out for several polymer-amino acid aqueous systems. The constant water activity lines (obtained through the isopiestic method at 298.15 K) of aqueous polypropylene glycol 400 (PPG400) + alanine or glycine systems, which form aqueous biphasic systems (salting-out effect), have a concave and convex slope, respectively, in the one-phase and two-phase regions. However, all the investigated polyethylene glycols (PEG400, PEG2000, PEG6000, and PEG10000) do not form aqueous biphasic systems with alanine or glycine (salting-in effect) and their constant water activity lines have a convex slope. In the second part of this work, the apparent molar volume and isentropic compressibility of transfer of alanine and glycine from water to aqueous solutions of PEG200, PEG2000, PEG10000, and PPG400 were studied at different temperatures. The third part of this work is concerned with the determination of LLE phase diagrams for several ternary polymer-amino acid aqueous systems containing polymers PPG400 and PPG725 and amino acids alanine, glycine, serine, and proline at different temperatures. On the basis of the obtained cloud point values of aqueous solutions of PPG725 in the absence and presence of various amino acids, it was found that all the investigated amino acids have a salting-out effect on PPG725 in aqueous solutions and entropy is the driving force for biphasic formation.
- Published
- 2014
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29. Pulmonary symptoms and spirometric values in Kangan Sour Gas Refinery workers.
- Author
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Mostaghni AA, Nabipour I, Dianat M, and Hamidi B
- Subjects
- Adult, Case-Control Studies, Cross-Sectional Studies, Environmental Monitoring, Epidemiological Monitoring, Humans, Incidence, Iran epidemiology, Lung Diseases epidemiology, Male, Middle Aged, Occupational Diseases epidemiology, Predictive Value of Tests, Risk Factors, Spirometry, Surveys and Questionnaires, Chemical Industry, Gasoline adverse effects, Lung Diseases chemically induced, Lung Diseases diagnosis, Occupational Diseases chemically induced, Occupational Diseases diagnosis
- Abstract
In this study, the author measured the frequency of symptoms and/or alterations in respiratory functions in workers of the sour gas refining industry. All workers (n = 62) were employed in the most-exposed units of the Kangan Sour Gas Refinery. The refinery is approximately 250 km east of Bushehr Port along the Persian Gulf. This cross-sectional study involved a comprehensive health questionnaire, standardized clinical examinations by physicians blinded to subjects' symptoms and concerns, and multiple spirometric values. Although gas refinery workers experienced more respiratory symptoms than the 30 controls (i.e., 37.7% vs. 23.3%, respectively), who were matched for age and smoking status, pulmonary function data were not statistically different (p > .05) between the groups. The authors concluded, therefore, that in Kangan Sour Gas Refinery workers there were no respiratory or spirometric values associated with chronic low-dose exposure to sour gas plant emissions, including hydrogen sulfide.
- Published
- 2000
- Full Text
- View/download PDF
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