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Article ; Online: Inflammation scintigraphy imaging through a novel antimicrobial peptide labeled with technetium-99m in an animal model.

Mazaheri Tehrani, Maryam / Erfani, Mostafa / Goudarzi, Mostafa

International journal of radiation biology

2022 Volume 99, Issue 4, Page(s) 673–680

Abstract: Purpose: Antimicrobial peptides (AMPs), due to their biological properties, have great potential for radiopharmaceutical development. In this research, a new antimicrobial peptide, derived from a 21-residue antimicrobial peptide microcinJ25 (MccJ25), ... ...

Abstract	Purpose: Antimicrobial peptides (AMPs), due to their biological properties, have great potential for radiopharmaceutical development. In this research, a new antimicrobial peptide, derived from a 21-residue antimicrobial peptide microcinJ25 (MccJ25), was utilized to diagnose inflamed sites in mice bodies after labeling with [ Materials and methods: An antimicrobial peptide derivative was connected with an efficient chelator, hydrazinonicotinamide, and then labeled with [ Results: High radiochemical purity (>98%) was obtained for [ Conclusion: Based on our results this new designed [
MeSH term(s)	Mice ; Animals ; Technetium/chemistry ; Antimicrobial Peptides ; Radionuclide Imaging ; Inflammation/diagnostic imaging ; Inflammation/metabolism ; Models, Animal ; Radiopharmaceuticals
Chemical Substances	Technetium (7440-26-8) ; Antimicrobial Peptides ; Radiopharmaceuticals
Language	English
Publishing date	2022-08-18
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3065-x
ISSN	1362-3095 ; 0020-7616 ; 0955-3002
ISSN (online)	1362-3095
ISSN	0020-7616 ; 0955-3002
DOI	10.1080/09553002.2022.2110298
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Article ; Online: Synthesis, radiolabeling and evaluation of [

Dinmohammadi, Fahimeh / Erfani, Mostafa / Shamsaei, Mojtaba / Shirmardi, Seyed Pezhman / Goudarzi, Mostafa

Bioorganic chemistry

2022 Volume 130, Page(s) 106237

Abstract: Amino acid metabolism is recognized as a target for medical imaging due to its increase in malignant cells. Several radiotracers with primary achievement and possible subsequent chances have been designed and tested to image amino acid metabolism. Here, ... ...

Abstract	Amino acid metabolism is recognized as a target for medical imaging due to its increase in malignant cells. Several radiotracers with primary achievement and possible subsequent chances have been designed and tested to image amino acid metabolism. Here, we report a new amino acid conjugate, with the purpose of extending [
MeSH term(s)	Animals ; Rats ; Glioblastoma/diagnostic imaging ; Amino Acids ; Tissue Distribution ; Diagnostic Imaging ; Ethylenediamines ; Glioma ; Radiopharmaceuticals/pharmacology
Chemical Substances	Amino Acids ; EDDA (5657-17-0) ; ethylenediamine (60V9STC53F) ; Ethylenediamines ; acetoacetic acid (4ZI204Y1MC) ; Radiopharmaceuticals
Language	English
Publishing date	2022-11-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	120080-x
ISSN	1090-2120 ; 0045-2068
ISSN (online)	1090-2120
ISSN	0045-2068
DOI	10.1016/j.bioorg.2022.106237
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Article ; Online: Food protein-derived antihypertensive peptides in the COVID-19 pandemic: friends of foes?

Goudarzi, Mostafa / Garavand, Farhad / Madadlou, Ashkan / Fogliano, Vincenzo

Journal of hypertension

2020 Volume 38, Issue 8, Page(s) 1614–1616

Keywords	covid19
Language	English
Publishing date	2020-05-29
Publishing country	England
Document type	Journal Article
ZDB-ID	605532-1
ISSN	1473-5598 ; 0263-6352 ; 0952-1178
ISSN (online)	1473-5598
ISSN	0263-6352 ; 0952-1178
DOI	10.1097/HJH.0000000000002534
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Article ; Online: SVNN: an efficient PacBio-specific pipeline for structural variations calling using neural networks.

Akbarinejad, Shaya / Hadadian Nejad Yousefi, Mostafa / Goudarzi, Maziar

BMC bioinformatics

2021 Volume 22, Issue 1, Page(s) 335

Abstract: Background: Once aligned, long-reads can be a useful source of information to identify the type and position of structural variations. However, due to the high sequencing error of long reads, long-read structural variation detection methods are far from ...

Abstract	Background: Once aligned, long-reads can be a useful source of information to identify the type and position of structural variations. However, due to the high sequencing error of long reads, long-read structural variation detection methods are far from precise in low-coverage cases. To be accurate, they need to use high-coverage data, which in turn, results in an extremely time-consuming pipeline, especially in the alignment phase. Therefore, it is of utmost importance to have a structural variation calling pipeline which is both fast and precise for low-coverage data. Results: In this paper, we present SVNN, a fast yet accurate, structural variation calling pipeline for PacBio long-reads that takes raw reads as the input and detects structural variants of size larger than 50 bp. Our pipeline utilizes state-of-the-art long-read aligners, namely NGMLR and Minimap2, and structural variation callers, videlicet Sniffle and SVIM. We found that by using a neural network, we can extract features from Minimap2 output to detect a subset of reads that provide useful information for structural variation detection. By only mapping this subset with NGMLR, which is far slower than Minimap2 but better serves downstream structural variation detection, we can increase the sensitivity in an efficient way. As a result of using multiple tools intelligently, SVNN achieves up to 20 percentage points of sensitivity improvement in comparison with state-of-the-art methods and is three times faster than a naive combination of state-of-the-art tools to achieve almost the same accuracy. Conclusion: Since prohibitive costs of using high-coverage data have impeded long-read applications, with SVNN, we provide the users with a much faster structural variation detection platform for PacBio reads with high precision and sensitivity in low-coverage scenarios.
MeSH term(s)	Diagnostic Tests, Routine ; High-Throughput Nucleotide Sequencing ; Neural Networks, Computer ; Sequence Analysis, DNA ; Software
Language	English
Publishing date	2021-06-19
Publishing country	England
Document type	Journal Article
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-021-04184-7
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Article ; Online: SVNN

Shaya Akbarinejad / Mostafa Hadadian Nejad Yousefi / Maziar Goudarzi

BMC Bioinformatics, Vol 22, Iss 1, Pp 1-

an efficient PacBio-specific pipeline for structural variations calling using neural networks

2021 Volume 17

Abstract: Abstract Background Once aligned, long-reads can be a useful source of information to identify the type and position of structural variations. However, due to the high sequencing error of long reads, long-read structural variation detection methods are ... ...

Abstract	Abstract Background Once aligned, long-reads can be a useful source of information to identify the type and position of structural variations. However, due to the high sequencing error of long reads, long-read structural variation detection methods are far from precise in low-coverage cases. To be accurate, they need to use high-coverage data, which in turn, results in an extremely time-consuming pipeline, especially in the alignment phase. Therefore, it is of utmost importance to have a structural variation calling pipeline which is both fast and precise for low-coverage data. Results In this paper, we present SVNN, a fast yet accurate, structural variation calling pipeline for PacBio long-reads that takes raw reads as the input and detects structural variants of size larger than 50 bp. Our pipeline utilizes state-of-the-art long-read aligners, namely NGMLR and Minimap2, and structural variation callers, videlicet Sniffle and SVIM. We found that by using a neural network, we can extract features from Minimap2 output to detect a subset of reads that provide useful information for structural variation detection. By only mapping this subset with NGMLR, which is far slower than Minimap2 but better serves downstream structural variation detection, we can increase the sensitivity in an efficient way. As a result of using multiple tools intelligently, SVNN achieves up to 20 percentage points of sensitivity improvement in comparison with state-of-the-art methods and is three times faster than a naive combination of state-of-the-art tools to achieve almost the same accuracy. Conclusion Since prohibitive costs of using high-coverage data have impeded long-read applications, with SVNN, we provide the users with a much faster structural variation detection platform for PacBio reads with high precision and sensitivity in low-coverage scenarios.
Keywords	Structural variation calling ; PacBio ; Long reads ; Neural networks ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Biology (General) ; QH301-705.5
Subject code	006
Language	English
Publishing date	2021-06-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
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Article ; Online: Healthcare priority-setting criteria and social values in Iran: an investigation of local evidence.

Goudarzi, Zahra / Bijlmakers, Leon / Nouhi, Mojtaba / Jahangiri, Reza / Heydari, Majid / Simangolwa, Warren / Hakimzadeh, Seyyed Mostafa / Jara, Karen Trujillo

International journal of technology assessment in health care

2023 Volume 39, Issue 1, Page(s) e37

Abstract: Introduction: Integrating social values into health technology assessment processes is an important component of proper healthcare priority setting. This study aims to identify social values related to healthcare priority setting in Iran.: Method: A ... ...

Abstract	Introduction: Integrating social values into health technology assessment processes is an important component of proper healthcare priority setting. This study aims to identify social values related to healthcare priority setting in Iran. Method: A scoping review was conducted on original studies that investigating social values in the healthcare system in Iran. The databases of PubMed, EMBASE, and EBSCO were searched with no restrictions on time and language. The reported criteria were clustered using Sham's framework of social value analysis in health policy. Results: Twenty-one studies published between 2008 and 2022 met the inclusion criteria. Fourteen of the included studies followed a quantitative approach with different methods to identify criteria, and the remaining seven studies used a qualitative approach. A total of fifty-five criteria were extracted and clustered into necessity, quality, sustainability, and process categories. Only six studies found criteria that were related to processes. Only three studies used public opinions as a source of value identification and eleven studies investigated the weight of criteria. None of the included studies explored the interdependency of the criteria. Conclusion: Evidence suggests that several criteria other than cost per health unit also need to be considered in healthcare priority setting. Previous studies have paid little attention to the social values that underlie priority setting and policy-making processes. To reach consensus on social values related to healthcare priority setting, future researches need to involve broader stakeholders' perspectives as a valuable source of social values in a fair process.
MeSH term(s)	Health Priorities ; Social Values ; Iran ; Delivery of Health Care ; Policy Making
Language	English
Publishing date	2023-06-19
Publishing country	England
Document type	Review ; Journal Article
ZDB-ID	632573-7
ISSN	1471-6348 ; 0266-4623
ISSN (online)	1471-6348
ISSN	0266-4623
DOI	10.1017/S0266462323000302
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Article ; Online: Sumatriptan mitigates bleomycin-induced lung fibrosis in male rats: Involvement of inflammation, oxidative stress and α-SMA.

Bahramifar, Ayda / Jafari, Razieh Mohammad / Sheibani, Mohammad / Manavi, Mohammad Amin / Rashidian, Amir / Tavangar, Seyed Mohammad / Akbariani, Mostafa / Mohammadi Hamaneh, Amirabbas / Goudarzi, Ramin / Shadboorestan, Amir / Dehpour, Ahmad Reza

Tissue & cell

2024 Volume 88, Page(s) 102349

Abstract: Introduction: Idiopathic pulmonary fibrosis (IPF) is a fibrotic lung condition that produces symptoms including coughing which may cause by excessive accumulation of scar tissue inflammatory and oxidative stress exacerbation. Sumatriptan, utilized for ... ...

Abstract	Introduction: Idiopathic pulmonary fibrosis (IPF) is a fibrotic lung condition that produces symptoms including coughing which may cause by excessive accumulation of scar tissue inflammatory and oxidative stress exacerbation. Sumatriptan, utilized for migraine treatment as a selective 5-HT Materials & methods: Thirty-five male Wistar rats were divided to five group, including: Sham (without IPF induction), control (BLM 5 mg/kg, intraperitoneally), and three fibrosis group with sumatriptan (0.5, 1, and 3 mg/kg, i.p. for 2 weeks) administration. IPF was induced by injection of BLM (single dose, 5 mg/kg intratracheally). Lung tissues were separated for measurement of myeloperoxidase (MPO) as an oxidative stress hallmark, and tumor necrosis factor-α (TNF-α), interleukin-1β (IL-β), and transforming growth factor-β (TGF-β) as inflammatory markers as well as alpha smooth muscle actin (α-SMA). Also, for histological investigations, tissue damages were assessed by Hematoxylin-eosin (H&E) and Masson's trichrome staining method. Results: BLM-induced fibrosis could increase α-SMA, MPO, TNF-α, IL-1β, and TGF-β, while treatment with sumatriptan has reversed the α-SMA, MPO, and IL-1β levels. Moreover, the results of H&E and Masson's trichrome staining indicated that sumatriptan (1 and 3 mg/kg) reduced tissue damages, alveolar wall thickness, collagen accumulation, and pulmonary fibrosis induced by BLM. Conclusion: According to the data achieved from this study, Sumatriptan appears to have therapeutic benefits in IPF, possibly via reducing α-SMA as well as inflammation and the toxicity caused by oxidative stress.
Language	English
Publishing date	2024-03-12
Publishing country	Scotland
Document type	Journal Article
ZDB-ID	204424-9
ISSN	1532-3072 ; 0040-8166
ISSN (online)	1532-3072
ISSN	0040-8166
DOI	10.1016/j.tice.2024.102349
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Article ; Online: 4D microvelocimetry reveals multiphase flow field perturbations in porous media.

Bultreys, Tom / Ellman, Sharon / Schlepütz, Christian M / Boone, Matthieu N / Pakkaner, Gülce Kalyoncu / Wang, Shan / Borji, Mostafa / Van Offenwert, Stefanie / Moazami Goudarzi, Niloofar / Goethals, Wannes / Winardhi, Chandra Widyananda / Cnudde, Veerle

Proceedings of the National Academy of Sciences of the United States of America

2024 Volume 121, Issue 12, Page(s) e2316723121

Abstract: Many environmental and industrial processes depend on how fluids displace each other in porous materials. However, the flow dynamics that govern this process are still poorly understood, hampered by the lack of methods to measure flows in optically ... ...

Abstract	Many environmental and industrial processes depend on how fluids displace each other in porous materials. However, the flow dynamics that govern this process are still poorly understood, hampered by the lack of methods to measure flows in optically opaque, microscopic geometries. We introduce a 4D microvelocimetry method based on high-resolution X-ray computed tomography with fast imaging rates (up to 4 Hz). We use this to measure flow fields during unsteady-state drainage, injecting a viscous fluid into rock and filter samples. This provides experimental insight into the nonequilibrium energy dynamics of this process. We show that fluid displacements convert surface energy into kinetic energy. The latter corresponds to velocity perturbations in the pore-scale flow field behind the invading fluid front, reaching local velocities more than 40 times faster than the constant pump rate. The characteristic length scale of these perturbations exceeds the characteristic pore size by more than an order of magnitude. These flow field observations suggest that nonlocal dynamic effects may be long-ranged even at low capillary numbers, impacting the local viscous-capillary force balance and the representative elementary volume. Furthermore, the velocity perturbations can enhance unsaturated dispersive mixing and colloid transport and yet, are not accounted for in current models. Overall, this work shows that 4D X-ray velocimetry opens the way to solve long-standing fundamental questions regarding flow and transport in porous materials, underlying models of, e.g., groundwater pollution remediation and subsurface storage of CO
Language	English
Publishing date	2024-03-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2316723121
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Article ; Online: Effect of long-term exposure to PM

Moradi, Maryam / Hadei, Mostafa / Yazdani, Mohsen / Goudarzi, Mohammad / Baboli, Zeynab / Tahmasebi Birgani, Yaser / Neisi, Abdolkazem / Goudarzi, Gholamreza

Environmental geochemistry and health

2021 Volume 43, Issue 8, Page(s) 3229–3235

Abstract: From a public health point of view, years of life lost (YLL) is a more important index than the number of deaths to evaluate the effect of risk factors. The objective of the present study was to estimate the burden of disease including years of life lost ...

Abstract	From a public health point of view, years of life lost (YLL) is a more important index than the number of deaths to evaluate the effect of risk factors. The objective of the present study was to estimate the burden of disease including years of life lost (YLL) and expected life remaining (ELR) attributed to long-term exposure to PM
MeSH term(s)	Air Pollutants/analysis ; Air Pollution/analysis ; Cities ; Environmental Exposure/analysis ; Female ; Humans ; Male ; Particulate Matter/analysis
Chemical Substances	Air Pollutants ; Particulate Matter
Language	English
Publishing date	2021-02-05
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	52039-1
ISSN	1573-2983 ; 0142-7245 ; 0269-4042
ISSN (online)	1573-2983
ISSN	0142-7245 ; 0269-4042
DOI	10.1007/s10653-021-00827-z
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Article ; Online: Evaluation of the effect of intratracheal ketamine on sore throat after intubation in patients undergoing strabismus surgery

Mehdi Sanatkar / Mehrdad Goudarzi / Mostafa Mohammadi / Ebrahim Espahbodi

Tehran University Medical Journal, Vol 78, Iss 8, Pp 493-

2020 Volume 499

Abstract: Background: Sore throat after endotracheal intubation during general anesthesia is a common complaint of patients especially in children. Strabismus surgery in one of the common procedures in child patients. The present study investigates the use of ... ...

Abstract	Background: Sore throat after endotracheal intubation during general anesthesia is a common complaint of patients especially in children. Strabismus surgery in one of the common procedures in child patients. The present study investigates the use of intratracheal ketamine administration in reducing sore throat after strabismus surgery. Methods: This study was performed on 60 patients undergoing elective strabismus surgery under general anesthesia from December 2019 to February 2020 in Farabi eye hospital, Tehran University of medical sciences, Tehran, Iran. These cases were referred to our center for strabismus operation from other centers of our country. Patients were randomly divided into two equal groups. After sufficient depth of anesthesia with sevoflurane and injection of fentanyl, endotracheal intubation was performed. In the control group, the endotracheal tube was inserted and 2 ml of ketamine solution at a concentration of 5 mg/ml were administered in endotracheal tube. The severity of sore throat, length of stay in recovery, incidence of delirium in recovery, satisfaction of recovery nurses and their parents and other complications were compared between the two groups. Results: Mean age, sex and weight were not significantly different between the two groups and were comparable. The mean duration of stay in recovery was higher in the case group than in the control group. The mean postoperative sore throat was significantly higher in the control group. Moreover, the mean incidence of delirium in the postoperative phase was higher in the case group. Besides, the rate of nurse satisfaction in the control group was higher than the case group. The incidence of bronchospasm, laryngospasm, and postoperative nausea and vomiting was not significantly different between the two groups. Conclusion: Intratracheal ketamine can reduce postoperative sore throat and the need for postoperative analgesic medications. Postoperative complications were not increased with this strategy, but the length of recovery stay ...
Keywords	intratracheal ; intratracheal intubation ; ketamine ; sore throat ; Medicine (General) ; R5-920
Subject code	616
Language	Persian
Publishing date	2020-10-01T00:00:00Z
Publisher	Tehran University of Medical Sciences
Document type	Article ; Online
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