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  1. Article ; Online: Reverse Vaccinology and Immunoinformatic Approach for Designing a Bivalent Vaccine Candidate Against Hepatitis A and Hepatitis B Viruses.

    Ahmadi, Neda / Aghasadeghi, Mohammadreza / Hamidi-Fard, Mojtaba / Motevalli, Fatemeh / Bahramali, Golnaz

    Molecular biotechnology

    2023  

    Abstract: Hepatitis A and B are two crucial viral infections that still dramatically affect public health worldwide. Hepatitis A Virus (HAV) is the main cause of acute hepatitis, whereas Hepatitis B Virus (HBV) leads to the chronic form of the disease, possibly ... ...

    Abstract Hepatitis A and B are two crucial viral infections that still dramatically affect public health worldwide. Hepatitis A Virus (HAV) is the main cause of acute hepatitis, whereas Hepatitis B Virus (HBV) leads to the chronic form of the disease, possibly cirrhosis or liver failure. Therefore, vaccination has always been considered the most effective preventive method against pathogens. At this moment, we aimed at the immunoinformatic analysis of HAV-Viral Protein 1 (VP1) as the major capsid protein to come up with the most conserved immunogenic truncated protein to be fused by HBV surface antigen (HBs Ag) to achieve a bivalent vaccine against HAV and HBV using an AAY linker. Various computational approaches were employed to predict highly conserved regions and the most immunogenic B-cell and T-cell epitopes of HAV-VP1 capsid protein in both humans and BALB/c. Moreover, the predicted fusion protein was analyzed regarding primary and secondary structures and also homology validation. Afterward, the three-dimensional structure of vaccine constructs docked with various toll-like receptors (TLR) 2, 4 and 7. According to the bioinformatics tools, the region of 99-259 amino acids of VP1 was selected with high immunogenicity and conserved epitopes. T-cell epitope prediction showed that this region contains 32 antigenic peptides for Human leukocyte antigen (HLA) class I and 20 antigenic peptides in terms of HLA class II which are almost fully conserved in the Iranian population. The vaccine design includes 5 linear and 4 conformational B-cell lymphocyte (BCL) epitopes to induce humoral immune responses. The designed VP1-AAY-HBsAg fusion protein has the potency to be constructed and expressed to achieve a bivalent vaccine candidate, especially in the Iranian population. These findings led us to claim that the designed vaccine candidate provides potential pathways for creating an exploratory vaccine against Hepatitis A and Hepatitis B Viruses with high confidence for the identified strains.
    Language English
    Publishing date 2023-09-16
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 1193057-3
    ISSN 1559-0305 ; 1073-6085
    ISSN (online) 1559-0305
    ISSN 1073-6085
    DOI 10.1007/s12033-023-00867-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Book ; Online: GEMTrans

    Mokhtari, Masoud / Ahmadi, Neda / Tsang, Teresa S. M. / Abolmaesumi, Purang / Liao, Renjie

    A General, Echocardiography-based, Multi-Level Transformer Framework for Cardiovascular Diagnosis

    2023  

    Abstract: Echocardiography (echo) is an ultrasound imaging modality that is widely used for various cardiovascular diagnosis tasks. Due to inter-observer variability in echo-based diagnosis, which arises from the variability in echo image acquisition and the ... ...

    Abstract Echocardiography (echo) is an ultrasound imaging modality that is widely used for various cardiovascular diagnosis tasks. Due to inter-observer variability in echo-based diagnosis, which arises from the variability in echo image acquisition and the interpretation of echo images based on clinical experience, vision-based machine learning (ML) methods have gained popularity to act as secondary layers of verification. For such safety-critical applications, it is essential for any proposed ML method to present a level of explainability along with good accuracy. In addition, such methods must be able to process several echo videos obtained from various heart views and the interactions among them to properly produce predictions for a variety of cardiovascular measurements or interpretation tasks. Prior work lacks explainability or is limited in scope by focusing on a single cardiovascular task. To remedy this, we propose a General, Echo-based, Multi-Level Transformer (GEMTrans) framework that provides explainability, while simultaneously enabling multi-video training where the inter-play among echo image patches in the same frame, all frames in the same video, and inter-video relationships are captured based on a downstream task. We show the flexibility of our framework by considering two critical tasks including ejection fraction (EF) and aortic stenosis (AS) severity detection. Our model achieves mean absolute errors of 4.15 and 4.84 for single and dual-video EF estimation and an accuracy of 96.5 % for AS detection, while providing informative task-specific attention maps and prototypical explainability.

    Comment: To be published in MLMI 2023
    Keywords Computer Science - Computer Vision and Pattern Recognition ; Computer Science - Machine Learning
    Subject code 006
    Publishing date 2023-08-25
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Economic Analysis of Water Demand in Greenhouses of Khash Township

    Shahraki, Javad / AliAhmadi, Neda

    2014  

    Abstract: The main goal of this study was to investigate the way of affecting of water in production of cucumber. From aspect of econometrics, mutual relationships of production function and expenses have been analysed in which Translog cost function has been used. ...

    Abstract The main goal of this study was to investigate the way of affecting of water in production of cucumber. From aspect of econometrics, mutual relationships of production function and expenses have been analysed in which Translog cost function has been used. This function has been estimated using the conditional input demand functions, the shefard theorem, chemical fertilizer, animal fertilizer, labour force, seed, and pesticide in the framework of a system of equations by taking advantage of the irrelevant regression method. Applied inputs is for 151 cucumber Beneficiaries in Khash in farming year of 2011-12 that insider and crossing tendency of input demand for this product has been investigated through collecting questionnaires and using obtained coefficients. The results show that the translog cost model is a good fit compared to the data of research. According to the reviews, demand for water has a minor Insidersuccession tendency more than one which shows possible stretch of demand function rather than the price of the inputs. Hence, appropriate pricing policies can be used to take a positive step in preventing the extreme usage of this input and directing beneficiaries for optimum use of these inputs.
    Keywords Irrigation water demand ; Price elasticity of demand ; Succession elasticity of demand ; Translog cost function ; Land Economics/Use ; Resource /Energy Economics and Policy
    Subject code 670
    Language English
    Publishing country us
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Costello syndrome and the importance of cancer screening.

    Ahmadi, Neda / Harley, Earl

    Archives of otolaryngology--head & neck surgery

    2010  Volume 136, Issue 10, Page(s) 1028–1029

    MeSH term(s) Chemotherapy, Adjuvant ; Child, Preschool ; Costello Syndrome/complications ; Endoscopy ; Humans ; Male ; Nasopharyngeal Neoplasms/diagnosis ; Nasopharyngeal Neoplasms/genetics ; Nasopharyngeal Neoplasms/therapy ; Radiotherapy, Adjuvant ; Rhabdomyosarcoma/diagnosis ; Rhabdomyosarcoma/genetics ; Rhabdomyosarcoma/therapy
    Language English
    Publishing date 2010-10
    Publishing country United States
    Document type Case Reports ; Journal Article
    ZDB-ID 632721-7
    ISSN 1538-361X ; 0886-4470 ; 2168-6181
    ISSN (online) 1538-361X
    ISSN 0886-4470 ; 2168-6181
    DOI 10.1001/archoto.2010.160
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Facial nerve hemangioma: a rare case involving the vertical segment.

    Ahmadi, Neda / Newkirk, Kenneth / Kim, H Jeffrey

    The Laryngoscope

    2013  Volume 123, Issue 2, Page(s) 499–502

    Abstract: This case report and literature review reports on a rare case of facial nerve hemangioma (FNH) involving the vertical facial nerve (FN) segment, and discusses the clinical presentation, imaging, pathogenesis, and management of these rare lesions. A 53- ... ...

    Abstract This case report and literature review reports on a rare case of facial nerve hemangioma (FNH) involving the vertical facial nerve (FN) segment, and discusses the clinical presentation, imaging, pathogenesis, and management of these rare lesions. A 53-year-old male presented with a 10-year history of right hemifacial twitching and progressive facial paresis (House-Brackmann grading score V/VI). The computed tomography and magnetic resonance imaging studies confirmed an expansile lesion along the vertical FN segment. Excision and histopathologic examination demonstrated FNH. FNHs involving the vertical FN segment are extremely rare. Despite being rare lesions, we believe that familiarity with the presentation and management of FNHs are imperative. Laryngoscope, 2012.
    MeSH term(s) Contrast Media ; Cranial Nerve Neoplasms/diagnosis ; Cranial Nerve Neoplasms/pathology ; Cranial Nerve Neoplasms/surgery ; Diagnosis, Differential ; Facial Nerve/pathology ; Hemangioma/diagnosis ; Hemangioma/pathology ; Hemangioma/surgery ; Humans ; Magnetic Resonance Imaging ; Male ; Middle Aged ; Reconstructive Surgical Procedures ; Tomography, X-Ray Computed
    Chemical Substances Contrast Media
    Language English
    Publishing date 2013-02
    Publishing country United States
    Document type Case Reports ; Journal Article
    ZDB-ID 80180-x
    ISSN 1531-4995 ; 0023-852X
    ISSN (online) 1531-4995
    ISSN 0023-852X
    DOI 10.1002/lary.23431
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Patterns of cervical lymph node metastases in primary and recurrent papillary thyroid cancer.

    Ahmadi, Neda / Grewal, Ameet / Davidson, Bruce J

    Journal of oncology

    2011  Volume 2011, Page(s) 735678

    Abstract: The incidence of thyroid cancer is rising in the United States with papillary thyroid cancer (PTC) being the most common type. We performed a retrospective study of 49 patients with PTC who underwent 57 lateral neck dissections (NDs). The extent of NDs ... ...

    Abstract The incidence of thyroid cancer is rising in the United States with papillary thyroid cancer (PTC) being the most common type. We performed a retrospective study of 49 patients with PTC who underwent 57 lateral neck dissections (NDs). The extent of NDs varied, but 29 of 57 (51%) consisted of levels II-V. Twelve of 57 (21%) NDs consisted of levels I-V. Twelve of 57 (21%) NDs consisted of levels II-IV. One of 57 (1.8%) necks involved only levels I-IV. One of 57(1.8%) necks involved only levels I-V. One of 57(1.8%) necks involved only levels III-V. Two (3.5%) double-level (III-IV) neck surgeries were also performed. Metastatic PTC adenopathy was confirmed pathologically in 2%-level-I, 45%-level-II, 57%-level-III, 60%-level-IV, and 22%-level-V necks. Level-V was positive in 21% of primary and 24% of recurrent groups (P = 0.76). Comparing primary and recurrent disease, there was no difference in nodal distribution or frequency for levels I, II, III, and V. Level-IV was more common in the recurrent cases (P = 0.05). Based on the pathologic distribution of nodes, dissection should routinely include levels II-IV and extend to level-V in primary and recurrent cases. Our data does not suggest routine dissection of level-I.
    Language English
    Publishing date 2011-11-17
    Publishing country Egypt
    Document type Journal Article
    ZDB-ID 2461349-6
    ISSN 1687-8469 ; 1687-8450
    ISSN (online) 1687-8469
    ISSN 1687-8450
    DOI 10.1155/2011/735678
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Melanocytic nevi with Spitz differentiation: diagnosis and management.

    Ahmadi, Neda / Davison, Steven P / Kauffman, Catharine L

    The Laryngoscope

    2010  Volume 120, Issue 12, Page(s) 2385–2390

    Abstract: Objectives: Melanocytic proliferations with Spitz differentiation present a difficult clinicopathologic dilemma, as their spectrum ranges from benign to malignant. Distinct entities include Spitz nevus, atypical Spitz nevus, and Spitzoid melanoma. Their ...

    Abstract Objectives: Melanocytic proliferations with Spitz differentiation present a difficult clinicopathologic dilemma, as their spectrum ranges from benign to malignant. Distinct entities include Spitz nevus, atypical Spitz nevus, and Spitzoid melanoma. Their histopathologic differentiation can be challenging, and cases of Spitzoid melanoma initially diagnosed as benign Spitz nevi are reported in the literature. The goal of this article is to discuss the diagnostic tools (including comparative genomic hybridization), which may be helpful in differentiating benign Spitz nevi from malignant melanoma with Spitzoid features, and to propose an appropriate management strategy for each entity.
    Study design: Retrospective case reports.
    Methods: Medical records of patients referred for suspicious nevi were reviewed. Data regarding demographics, site, pathology reports, and treatment were reviewed.
    Results: Four patients with three distinct diagnoses involving Spitz differentiation were identified. The pathologic interpretation of these biopsies was difficult and multiple dermatopathologists were involved. All four patients underwent excision with or without sentinel node biopsy.
    Conclusions: Otolaryngologists, plastic surgeons and dermatopathologists will encounter patients who have melanocytic lesions with Spitz differentiation at some point in their career. The management of these patients is significantly impacted by the histopathologic diagnosis, and should not be undertaken until it is confirmed, possibly with comparative genomic hybridization. In our experience, it is not unusual to have multiple independent pathologic examinations. We believe that a team approach between the surgeon and the dermatopathologist is crucial when diagnosing and managing patients with Spitz lesions.
    MeSH term(s) Adult ; Arm ; Back ; Biopsy ; Cell Differentiation ; Child ; Child, Preschool ; Dermis/pathology ; Diagnosis, Differential ; Female ; Follow-Up Studies ; Humans ; Male ; Neoplasm Staging/methods ; Nevus, Epithelioid and Spindle Cell/pathology ; Nevus, Epithelioid and Spindle Cell/surgery ; Retrospective Studies ; Sentinel Lymph Node Biopsy ; Skin Neoplasms/pathology ; Skin Neoplasms/surgery
    Language English
    Publishing date 2010-12
    Publishing country United States
    Document type Case Reports ; Journal Article
    ZDB-ID 80180-x
    ISSN 1531-4995 ; 0023-852X
    ISSN (online) 1531-4995
    ISSN 0023-852X
    DOI 10.1002/lary.21149
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Decreased risk of squamous cell carcinoma of the head and neck in users of nonsteroidal anti-inflammatory drugs.

    Ahmadi, Neda / Goldman, Radoslav / Seillier-Moiseiwitsch, Françoise / Noone, Anne-Michelle / Kosti, Ourania / Davidson, Bruce J

    International journal of otolaryngology

    2010  Volume 2010, Page(s) 424161

    Abstract: We evaluated the chemopreventive effect of nonsteroidal anti-inflammatory drug (NSAID) use in head and neck squamous cell carcinomas (HNSCC) by conducting a case-control study based on the administration of a standardized questionnaire to 71 incident ... ...

    Abstract We evaluated the chemopreventive effect of nonsteroidal anti-inflammatory drug (NSAID) use in head and neck squamous cell carcinomas (HNSCC) by conducting a case-control study based on the administration of a standardized questionnaire to 71 incident HNSCC cases and same number of healthy controls. NSAID use was associated with a 75% reduction in risk of developing HNSCC. A significant risk reduction was noted in association with frequency of NSAID use. Restricting the analysis to aspirin users revealed a significant 90% reduction in risk of developing HNSCC. This study provides evidence for a significant reduction in the risk of developing HNSCC in users of NSAIDs, and specifically aspirin users.
    Language English
    Publishing date 2010-06-03
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2503281-1
    ISSN 1687-921X ; 1687-9201
    ISSN (online) 1687-921X
    ISSN 1687-9201
    DOI 10.1155/2010/424161
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Cryopyrin-associated periodic syndromes: otolaryngologic and audiologic manifestations.

    Ahmadi, Neda / Brewer, Carmen C / Zalewski, Christopher / King, Kelly A / Butman, John A / Plass, Nicole / Henderson, Cailin / Goldbach-Mansky, Raphaela / Kim, H Jeffrey

    Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery

    2011  Volume 145, Issue 2, Page(s) 295–302

    Abstract: Objective: Cryopyrin-associated periodic syndromes (CAPS) represent a spectrum of CIAS1 gene-mediated autoinflammatory diseases characterized by recurrent systemic inflammation. The clinical spectrum of CAPS varies from mild to severe and includes the ... ...

    Abstract Objective: Cryopyrin-associated periodic syndromes (CAPS) represent a spectrum of CIAS1 gene-mediated autoinflammatory diseases characterized by recurrent systemic inflammation. The clinical spectrum of CAPS varies from mild to severe and includes the syndromes historically described as familial cold autoinflammatory syndrome (FCAS), Muckle-Wells syndrome (MWS), and neonatal-onset multisystem inflammatory disease (NOMID). This article presents the largest cohort of patients with CAPS. The objective is to describe the pathogenesis, otolaryngologic, and audiologic manifestations of CAPS.
    Study design: Prospective (2003-2009).
    Setting: National Institutes of Health.
    Subjects and methods: Fifty-seven patients with a diagnosis of CAPS were identified (31 NOMID, 11 NOMID/MWS, 9 MWS, and 6 FCAS). Comprehensive data regarding clinical manifestations, audiologic phenotype, and fluid attenuation inversion recovery MRI (FLAIR-MRI) of the brain and inner ear were obtained.
    Results: Complete audiologic data obtained on 70% of ears revealed conductive hearing loss in 4 (11%) NOMID ears and mixed hearing loss in 5 (13%) NOMID and 2 (14%) NOMID/MWS ears. Sensorineural hearing loss (SNHL), worse in higher frequencies, was the most common type of hearing loss and was present in 23 (61%) NOMID, 10 (71%) NOMID/MWS, and 4 (33%) MWS ears. All of the patients with FCAS had normal hearing except 2, who had SNHL from 4 to 8 kHz. On FLAIR-MRI sequence, cochlear enhancement was noted in 26 of 29 (90%) NOMID, 6 of 11 (55%) NOMID/MWS, 3 of 9 (33%) MWS, and 1 of 6 (17%) FCAS patients and was significantly associated with the presence of hearing loss. Maxillary sinus hypoplasia and mucosal thickening were found in 39% and 86% of the cohort, respectively.
    Conclusion: CIAS1 pathway–mediated CAPS is associated with unregulated autoinflammation mediated by interleukin-1 in the cochlea and hearing loss. Timely diagnosis is crucial to initiate early treatment with interleukin-1 receptor antagonists.
    MeSH term(s) Adolescent ; Adult ; Aged ; Audiometry, Pure-Tone ; Bone Conduction ; Child ; Child, Preschool ; Cochlea/metabolism ; Cryopyrin-Associated Periodic Syndromes/complications ; Cryopyrin-Associated Periodic Syndromes/diagnosis ; Cryopyrin-Associated Periodic Syndromes/physiopathology ; Female ; Follow-Up Studies ; Hearing/physiology ; Hearing Loss, Mixed Conductive-Sensorineural/diagnosis ; Hearing Loss, Mixed Conductive-Sensorineural/etiology ; Hearing Loss, Mixed Conductive-Sensorineural/physiopathology ; Hearing Loss, Sensorineural/diagnosis ; Hearing Loss, Sensorineural/etiology ; Hearing Loss, Sensorineural/physiopathology ; Humans ; Hyperplasia ; Infant ; Interleukin-1/biosynthesis ; Magnetic Resonance Imaging ; Male ; Maxillary Sinus/pathology ; Middle Aged ; Paranasal Sinus Diseases/etiology ; Paranasal Sinus Diseases/pathology ; Prognosis ; Prospective Studies ; Respiratory Mucosa/pathology ; Young Adult
    Chemical Substances Interleukin-1
    Language English
    Publishing date 2011-02-10
    Publishing country England
    Document type Comparative Study ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural
    ZDB-ID 392085-9
    ISSN 1097-6817 ; 0161-6439 ; 0194-5998
    ISSN (online) 1097-6817
    ISSN 0161-6439 ; 0194-5998
    DOI 10.1177/0194599811402296
    Database MEDical Literature Analysis and Retrieval System OnLINE

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