678 results on '"Sabeti, P"'
Search Results
202. 89. Real-world Safety and Efficacy of Teriflunomide (Tebazio®) in Iranian Females with Relapsing-Remitting Multiple Sclerosis.
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Sabeti, Fatemeh and Etemadifar, Masoud
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Multiple sclerosis (MS) is a neuroinflammatory disease that significantly impacts young women, often leading to disability. Teriflunomide – an FDA-approved and once-daily oral disease-modifying therapy (DMT) – serves as a first-line treatment for relapsing-remitting multiple sclerosis (RRMS). Observational studies on the efficacy and outcomes of teriflunomide in Iranian patients, particularly in female-only cohorts, remain scarce. In this study, we present the findings from a cohort of female RRMS patients treated with Tebazio – the latest teriflunomide brand in Iran, manufactured by Zistdaru Danesh Corporation since 2018. This was a single-center case study involving a cohort of female RRMS patients registered at the Isfahan MS Center in Isfahan, Iran. Patients who were initiated on Tebazio (14 mg once daily) were enrolled at the start of their treatment and subsequently followed for at least 18 months. We included female patients who were either beyond child-bearing age or not planning for pregnancy in the foreseeable future and instructed them to use at least two effective contraception methods. Throughout the follow-up period, we collected subjects' background, clinical and paraclinical data through in-person interviews, neurological examinations, and standardized checklists. The data were then analyzed using SPSS version 26. We enrolled 49 female RRMS patients with a mean age of 44.97 ± 8.83 years and a mean disease duration of 112.83 ± 12.31 months. Two of our subjects (4%) were eventually lost to follow-up (none due to adverse effects or disease progression). Among the 47 patients who completed the follow-up, only five (10.6%) experienced a relapse, and seven (14.9%) developed new T2-weighted lesions on their final brain MRI. We also observed a significant reduction in the mean Expanded Disability Status Scale (EDSS) scores, from 1.53 ± 0.61 at the initial visit to 1.39 ± 0.57 at the final follow-up visit (P-value = 0.001). The most frequent side effects of Tebazio were hair thinning in 68.1% (n=32), GI upset in 36.1% (n=17), and elevated LFT in 29.8% (n=14) of the patients. Additionally, no cases of life-threatening adverse effects (malignancies or progressive leukoencephalopathy) were reported. Tebazio demonstrates robust safety and efficacy in Iranian female RRMS patients of child-bearing age who are not considering pregnancy. The therapy shows low relapse rates, minimal disease progression, and manageable side effects, supporting its role as a viable treatment option. [ABSTRACT FROM AUTHOR]
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- 2024
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203. Intra-operative ultrasound facilitates the localization of the calcific deposit during arthroscopic treatment of calcifying tendinitis
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Sabeti-Aschraf, M., Gonano, C., Nemecek, E., Cichocki, L., and Schueller-Weidekamm, C.
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- 2010
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204. FURTHER INVESTIGATION OF ASSOCIATION BETWEEN BIPOLAR DISORDER AND BDNF: CHARACTERIZATION OF POPULATION GENETIC STRUCTURE AND HAPLOTYPE ASSOCIATION STUDIES IN FOUR PATIENT SAMPLES
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Petryshen, T. L., Sabeti, P. C., Aldinger, K. A., Tahl, A. R., Frye, B., Waggoner, S. G., Lim, Y., Daly, M. J., McInnis, M. G., DePaulo, R. J., Smoller, J. W., Pulver, A. E., and Sklar, P.
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- 2009
205. Evaluation of the Cytotoxicity of Two Types of Triple Antibiotic Paste on Human Permanent Dental Apical Papilla Stem Cells: an in vitro Study.
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Rafatjou, Rezvan, Sabeti, Arghavan Kamali, Ahmadi, Bahar, Asl, Sara Soleimani, and Farhadian, Maryam
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ANTIBIOTICS ,IN vitro studies ,INTERDENTAL papilla ,CIPROFLOXACIN ,CLINDAMYCIN ,METRONIDAZOLE ,MINOCYCLINE ,CELL survival ,STEM cells ,CELL surface antigens ,OINTMENTS ,IMMUNODIAGNOSIS ,PERMANENT dentition - Abstract
Statement of the Problem: The use of a new antimicrobial combination in the regenerative endodontic treatment of immature teeth pulp necrosis is a well-known method. Concerns have been raised about the destructive effect of this combination on the stem cells from the apical papilla of permanent human teeth, and there is a study gap. Purpose: The main objective of the present study was to investigate the cytotoxic effect of modified triple antibiotic paste (mTAP) on stem cells from the apical papilla (SCAPs) of permanent human teeth. Materials and Method: In this in vitro study, stem cells were removed from the immature teeth. After cultivation and third passage, metronidazole, ciprofloxacin, minocycline, and clindamycin were placed in the cell culture medium alone, paired, and in combinations as triple antibiotic paste (TAP) (metronidazole, ciprofloxacin, and minocycline) and mTAP (metronidazole, ciprofloxacin, clindamycin) with doses of 25, 50, 100, 200, 400μg/ml. After 1 and 3 days, cell viability in the culture medium was assessed using the MTT method ([4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide). SPSS software version 24, descriptive statistics methods, and statistical tests such as Kruskal-Wallis and Mann-Whitney tests were adopted to analyze the data. Results: Analysis of MTT findings indicated that the use of mTAP at 100μg/ml and TAP at 200μg/ml had no adverse cytotoxic effect on stem cells in the first 24 hours, compared to the control group. The cell viability decreased at higher concentrations, although it was not statistically significant. After 72 hours, the toxicity of concentrations higher than 100μg/ml of mTAP and 400 μg/ml of TAP significantly mitigated the percentage of viable cells. Conclusion: The obtained results demonstrated that the concentration of 100 μg/ml of mTAP could replace TAP in regenerative endodontic treatments at the studied time intervals without worrying about the toxicity. [ABSTRACT FROM AUTHOR]
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- 2022
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206. Bioterrorism: An analysis of biological agents used in terrorist events.
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Tin, Derrick, Sabeti, Pardis, and Ciottone, Gregory R.
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Background: The Covid19 pandemic has reignited debates and discussions around healthcare systems' biosecurity vulnerabilities and cast a spotlight on the potential weaponization of biological agents. Terrorist and violent extremist groups have already attempted to incite the intentional spread of Covid19 and to use it as an improvised form of a biological weapon. This study aims to provide an epidemiological description of all terrorism-related attacks using biological agents sustained between 1970 and 2019.Methods: Data collection was performed using a retrospective database search through the Global Terrorism Database (GTD). The GTD was searched using the internal database search functions for all events using biological weapons between January 1, 1970 - December 31, 2019.Results: 33 terrorist attacks involving biological agents were recorded between 1970 and 2019, registering 9 deaths and 806 injuries. 21 events occurred in the United States, 3 in Kenya, 2 each in both the United Kingdom and Pakistan and a single event in Japan, Columbia, Israel, Russia and Tunisia.Conclusion: The reported use of biological agents as a terrorist weapon is extremely rare and accounts for 0.02% of all historic terrorist attacks. Despite its apparent rarity, however, bioterrorism has the ability to inflict mass injuries unmatched by conventional weapons. Anthrax has been the most commonly used in previous bioterrorism events with the vast majority of reported attacks occurring in the United States by a single suspected perpetrator. Counter-Terrorism Medicine (CTM) and Disaster Medicine (DM) specialists need to be proactive in delivering ongoing educational sessions on biological events to first responder communities, and anticipate emerging novel biotechnology threats. [ABSTRACT FROM AUTHOR]- Published
- 2022
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207. Frozen versus fresh corneal graft carriers in Boston keratoprosthesis surgery: 10-year outcomes.
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Sabeti, Saama, Daoud, Roy, Robert, Marie-Claude, and Harissi-Dagher, Mona
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Copyright of Canadian Journal of Ophthalmology is the property of Elsevier B.V. and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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- 2022
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208. FURTHER INVESTIGATION OF ASSOCIATION BETWEEN BIPOLAR DISORDER AND BDNF: CHARACTERIZATION OF POPULATION GENETIC STRUCTURE AND HAPLOTYPE ASSOCIATION STUDIES IN FOUR PATIENT SAMPLES
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Petryshen, T. L., Sabeti, P. C., Aldinger, K. A., Tahl, A. R., Frye, B., Waggoner, S. G., Lim, Y., Daly, M. J., McInnis, M. G., DePaulo, R. J., Smoller, J. W., Pulver, A. E., and Sklar, P.
- Published
- 2005
209. YAP1Rearrangement in Parotid Sclerosing Mucoepidermoid Carcinoma
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El-Nagdy, Sherif Y., Shetty, Pushparaja, Abdullah, Bacem, and Sabeti, Shahram
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ABSTRACTObjectiveThis study investigates to investigate Yes-associated protein 1 (YAP1) rearrangement status in a six-case of sclerosing mucoepidermoid carcinoma (SMEC) series with reference to 20 conventional mucoepidermoid carcinomas.MethodA retrospective analysis was conducted on a cohort of patients diagnosed with SMEC from 2018 to 2022. The presence of YAP1rearrangement was determined using fluorescence in situ hybridization (FISH) analysis targeting the YAP1gene located at 11q22.1-q22.2. Clinical data, including patient outcomes, were collected and analyzed. Next-generation sequencing (NGS) was performed to identify the fusion partner involved in the YAP1rearrangement.ResultsA total of six cases of SMEC were included in the study, of YAP1::MAML2fusion was detected and five cases showed YAP1rearrangement on FISH testing.ConclusionYAP1alteration may explain the indolent nature of SMECs, especially in cases with low cellularity. Further studies incorporating NGS analysis are warranted to unravel the fusion partner associated with YAP1rearrangement, providing a deeper understanding of the molecular mechanisms underlying the positive outcomes observed in these patients.
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- 2024
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210. Reconstructing the 1968 River Chew flash flood: merging a HEC-RAS 2D hydraulic modelling approach with historical evidence
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Sabeti, Ramtin, Stamataki, Ioanna, and Kjeldsen, Thomas Rodding
- Abstract
AbstractThe devastating 1968 flash flood in the River Chew, South-West of England, serves as a stark reminder of the unpredictable nature of such natural disasters and highlights the importance of natural hazard assessments. The uncertain and often incomplete historical data, and the limited field measurements at the time hindered our understanding of this event. By integrating historical evidence, including technical reports, newspapers, literature, and eyewitness accounts, with advanced hydraulic modelling (HEC-RAS 2D), this study reconstructs the 1968 flash flood. A sensitivity analysis of the computational methodologies in HEC-RAS, examining various governing equations and numerical methods, introduces an additional dimension to this research. The results verify a maximum flow rate of 165 m3/s at the Compton Dando hydrometric station, marking a 65% increase from the previous official estimate. This update aligns with over 90% of the historical flood marks observed. Findings suggest recalibrating hydrological models, revising risk assessments, and updating flood frequency analyses in the study area. This novel framework confronts the challenges of uncertain and incomplete historical records through a reverse engineering methodology to reconstruct missing peak discharges. The study also presents a new methodological blueprint that can be replicated for reconstructing historical flash flood events in various regions.
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- 2024
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211. STAT3 GAIN-OF-FUNCTION MUTATION IN AN ADULT FEMALE
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Sabeti, S. and Naderi, A.
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STAT3 gain-of-function (GOF) disease is a genetic disorder of the immune system and a multisystem disease. Given the variability of clinical symptoms, diagnosis is challenging. We present a case of a patient who was initially diagnosed with common variable immunodeficiency (CVID) and was later found to have STAT3 GOF disease.
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- 2024
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212. A hybrid risk assessment approach for assessing the earthquake risks in worn-out urban fabrics: a case study in Iran
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Sadeghi, Jalal, Oghabi, Mohsen, Sarvari, Hadi, Sabeti, Mohammad Sediegh, Kashefi, Hamidreza, Chan, Daniel W.M., and Lotfata, Aynaz
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Purpose: To reduce financial and human losses, managing risks associated with earthquakes is essential in practice. However, in using common risk management methods, experts are often faced with ambiguities that can create profound challenges for risk management. Therefore, it is necessary to develop a logical and straightforward risk assessment model to provide scientific and accurate answers to complex problems. This study aims to recommend an innovative combined method based on the probability-impact (P-I) approach and intuitionistic fuzzy set theory to identify and prioritize the essential earthquake risks associated with worn-out urban fabrics in the context of Iran. Design/methodology/approach: The opinions of 15 experts in the fields of civil engineering and urban construction were gathered during brainstorming sessions. These brainstorming sessions were conducted to determine the probability of risks and the effect of identified risks. After calculating the severity of risks using the P-I approach and converting them to intuitionistic fuzzy sets, the risks were measured and prioritized based on their individual scores. Findings: The study results indicated that risk of damage due to buildings’ age and flooding risk had the highest and lowest priorities in causes of financial damage, respectively. Furthermore, the risk of damage due to building quality (demolition) and building age was the most important. The risk of flooding and damage to communication networks has the lowest importance among causes of fatalities in worn-out urban fabrics. Originality/value: The study findings and recommendations can be served as a policy and consultative instrument for the relevant stakeholders in the area of urban management.
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- 2022
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213. The Effects of the COVID-19 Pandemic on Burn Clinic
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Sabeti, Sara, Ochtli, Ché R, Tay-Lasso, Erika, Whelton, Melissa, Burton, Kimberly, Bernal, Nicole O, Joe, Victor C, and Chin, Theresa L
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The COVID-19 pandemic has led to anxiety and fears for the general public. It is unclear how the behavior of people with acute burns and the services available to them has changed during the pandemic. The aim of our observational study was to evaluate our clinic’s experience with patients presenting with burns during the first 10 months of the COVID-19 pandemic and determine if delays in presentation and healthcare delivery exist within our burn population. Patients referred to our clinic from March 1, 2020 to December 15, 2020 were reviewed for time of presentation after injury. We defined a true delay in presentation of >5 days from date of injury to date of referral for patients who were not inpatients at our facility or received initial care elsewhere prior to referral. Of the 246 patients who were referred to our clinic, during this time period, 199 patients (80.89%) attended their appointments. Our in-person clinic volume from referrals increased in July 2020 with a sharp decrease in August 2020. Our total clinic volume decreased in 2020 from 2019 by about 14%. Referrals to our clinic decreased in 2020 from 2019 by about 34%. Video telehealth visits did not account for the decrease in visits. There was low incidence of delays in presentation to our clinic during the pandemic. Additional investigation is necessary to see if the incidence of burn injury decreased. Despite the pandemic, our clinic remained ready and open to serve the burn population.
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- 2022
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214. Prognosis of Vital Pulp Therapy on Permanent Dentition: A Systematic Review and Meta-analysis of Randomized Controlled Trials.
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Sabeti, Mohammad, Huang, Yujie, Chung, Yoo Jung, and Azarpazhooh, Amir
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PERMANENT dentition ,RANDOMIZED controlled trials ,DENTAL pulp capping ,MINERAL aggregates ,GREY literature ,PROGNOSIS - Abstract
The aim of this systematic review was to evaluate the existing randomized controlled trials (RCTs) on the safety and efficacy of vital pulp therapy (VPT) and to analyze the outcomes of VPT performed with a variety of pulp-capping materials and techniques. MEDLINE (PubMed), Embase, Cochrane Library, and gray literature were searched (January 2000–March 2021). Study selection and data extraction were performed in duplicate. Eligible RCTs were critically appraised for risk of bias and quality of evidence and were meta-analyzed to estimate the treatment effects. Fourteen studies were included. The pooled success rate of VPT using contemporary capping materials such as mineral trioxide aggregate (MTA) or calcium silicate–based materials (CSMs) was 93.2% (95% confidence interval [CI], 91.6%–94.9%). Multiple subgroup analyses by different etiologies, procedure types, developmental stages of teeth, and preoperative diagnoses were performed. Analyses presented low certainty of evidence. No significant difference was noted between MTA and CSM at 12 months or a longer follow-up (risk ratio = 0.99; 95% CI, 0.95–1.03) with low certainty of evidence. Laser-assisted VPT failed to show significantly better outcomes than conventional VPT (risk ratio = 1.19; 95% CI, 0.99–1.49) with very low certainty of evidence. When MTA or CSM was used as a capping material, VPT was 93% successful. The techniques, etiologies, developmental stages of teeth, and preoperative diagnosis had no significant influence on treatment outcomes. No major adverse effects (except discoloration associated with the use of MTA) were identified. The overall quality of evidence was low. [ABSTRACT FROM AUTHOR]
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- 2021
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215. Valacyclovir in Pain Management of Acute Apical Abscesses: A Randomized Placebo-Controlled Double-Blind Pilot Study.
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Sabeti, Mohammad, Zhong, John, Hildebrandt, Kevin, and Slots, Jørgen
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VALACYCLOVIR ,PAIN management ,GRAM-negative anaerobic bacteria ,ABSCESSES ,TAKOTSUBO cardiomyopathy ,DRUGS ,PERIAPICAL diseases - Abstract
The acute (symptomatic) apical abscess is characterized by pulp necrosis, rapid onset, spontaneous pain, percussion pain, pus formation, and tissue swelling. The etiopathology of acute apical abscesses includes active (lytic) herpesviruses and gram-negative anaerobic bacteria. The present study examined the potential of valacyclovir, an anti-herpesvirus agent, and systemic amoxicillin to manage the pain of acute apical abscesses. Twenty emergency patients with moderate to severe apical abscess pain received randomly either amoxicillin (1 g immediate dose followed by 500 mg, 4 times a day, totally 7 days) + valacyclovir (2 g immediate dose followed by 500 mg, twice a day, totally 3 days) ("valacyclovir" group, 10 patients) OR amoxicillin (1 g immediate dose followed by 500 mg, 4 times a day, totally 7 days) + placebo ("placebo" group, 10 patients). Daily telephone calls during the 6-day follow-up period assessed pain level on a numeric rating scale and analgesic intake. The Mann-Whitney and the Friedman statistical tests analyzed the outcome data. At the baseline examination, all 10 valacyclovir and 9 placebo patients exhibited moderate to severe pain and 18 patients needed pain medication. On the first day after baseline, the valacyclovir group showed 2 patients with moderate/severe pain and 1 patient on pain medication, but the placebo group revealed as many as 8 patients with moderate/severe pain and 9 patients on pain medication. The difference in pain level and analgesic usage between the valacyclovir and the placebo group remained statistically significant during the entire post-baseline study period (P <.05). The present study points to valacyclovir as a promising adjunctive agent in pain control with acute apical abscesses. [ABSTRACT FROM AUTHOR]
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- 2021
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216. Clinical and Histological Evaluation of Tissue Healing in Beveled or Perpendicular Vertical Releasing Incision.
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Sabeti, Mohammad, Moeintaghavi, Amir, Shiezadeh, Farid, Salari Sedigh, Hamideh, Tay, Ronney, and Torabinejad, Mahmoud
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HEALING ,CONNECTIVE tissues ,WOUND healing ,TISSUES ,CUSPIDS ,CAPILLARY electrophoresis - Abstract
The aim of this investigation was to evaluate the clinical and histological differences in wound healing between beveled and perpendicular vertical releasing incisions in dogs. Four male mongrel dogs were used in this investigation. In each quadrant, a vertical releasing incision was made on either the mesial or the distal aspect of the cuspid teeth of each animal all on the same day. The sites were randomly selected to either receive a beveled incision or a perpendicular incision. A sulcular muco-periosteal flap was raised, reapproximated, and then sutured using 3-0 Vicryl. The animals were evaluated daily for the first week, and then at different time intervals during this investigation. One animal was killed at each time interval of 9, 14, 21, and 28 days after surgery. One animal was killed at each time interval, and a bone block consisting of the cuspid teeth and their surrounding bone and soft tissues was harvested, formalin fixed, and paraffin embedded. Samples were sectioned serially and stained with hematoxylin-eosin. Specimens were evaluated using a microscope with magnification ranging from ×10 to ×400 by a histopathologist. Four indices were used for histologic evaluation. At day 9 after surgery, a visible groove was seen in the marginal tissues of both perpendicular and beveled incisions. At day 9, both of the histologic sections showed less organized connective tissue and capillary networks with no significant difference in inflammation. In the 14-day samples, a depression was still present at the perpendicular incision sites, but not in the beveled incision group, where the groove was not visualized at all. In the 21- and 28-day samples, irregular capillary arrangements were seen in the connective tissue of the perpendicular incision groups with completely healed epithelium. There were no statistically significant differences noted histologically between the beveled and perpendicular incision groups noted at 9, 14, 21, or 28 days (P >.05). Based on these findings, it appears that clinical and histologic healing of beveled or perpendicular releasing incisions are similar 28 days after surgery. [ABSTRACT FROM AUTHOR]
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- 2021
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217. Health Care Providers' Experiences of the Non-Pharmacological Pain and Anxiety Management and Its Barriers in the Pediatric Intensive Care Units.
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Sabeti, Fahimeh, Mohammadpour, Masoud, Pouraboli, Batool, Tahmasebi, Mamak, and Hasanpour, Marzieh
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Children in the intensive care unit experience a high level of pain and anxiety. This study aimed to reveal the health care providers experience of non-pharmacological pain and anxiety management and its barriers in the pediatric intensive care unit. This qualitative-descriptive study was conducted with thirteen nurses and five physicians in the pediatric intensive care unit in Iran. Individual, in-depth and semi-structured interviews were conducted, which were analyzed by conventional content analysis. Five main categories were identified from data analysis: 1) The importance of parents' presence, 2) Disturbance in the presence of parents and communication during the COVID-19 pandemic, 3) Choosing non-pharmacological approaches according to the child's interests and conditions, 4) Building trust in the child through non-pharmacological interventions 5) Barriers to non-pharmacological pain and anxiety management in the pediatric intensive care unit. Health care providers implement some non-pharmacological methods to manage pain and anxiety in the pediatric intensive care unit. Facilitating the open presence of parents, using innovative methods to communicate with children, and training and psychological support for nurses and parents, especially during the COVID-19 pandemic are recommended. [ABSTRACT FROM AUTHOR]
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- 2021
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218. IDENTIFICATION AND PRIORITIZATION OF SEISMIC RISKS IN URBAN WORN-OUT TEXTURES USING FUZZY DELPHI METHOD.
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Sadeghi, Jalal, Oghabi, Mohsen, Sarvari, Hadi, Sabeti, Mohammad-Sediegh, Kashefi, Hamidreza, and Chan, Daniel
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Earthquake is a random natural phenomenon, which can occur at any time and location in a given seismic zone with any magnitude. The earthquake vulnerability in buildings and urban infrastructures is a key issue for crisis management. Therefore, an assessment model should be developed to identify and prioritize the significant seismic risks involved. In risk management, several numerical and descriptive phrases are used for risk identification and assessment. These phrases are estimative by nature and the accuracy of the estimations is vital in future decision-making in risk management. Fuzzy sets are a reliable tool in solving such problems and result in high level of accuracy through creating multiple-value logical models. The purpose of this study is to identify and prioritize the major risks associated with earthquakes in urban worn-out textures through the Delphi survey technique and fuzzy sets approach. The experts' opinions were collected using a fuzzy Delphi questionnaire with a five-point Likert scale of measurement method. Participants in the Delphi panel consist of 15 experts in the field of engineering. Important risks were determined and prioritized in the two phases of fuzzy Delphi method. According to the results, among the 19 identified major risks, road blockage and flood with defuzzification values of 0.917 and 0.583, respectively, have the highest and lowest risk potential respectively in Jalili Neighborhood's worn-out textures. It is expected that, because of the simplicity and the high accuracy for identification of the most vulnerable parts, this study provides scientific and useful guidance to urban managers and planners in decision-making and adopting the most appropriate strategies for mitigating damages and potential risks of earthquakes in urban worn-out textures. [ABSTRACT FROM AUTHOR]
- Published
- 2021
219. Detect and destroy: CRISPR-based technologies for the response against viruses.
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Freije, Catherine A. and Sabeti, Pardis C.
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Despite numerous viral outbreaks in the last decade, including a devastating global pandemic, diagnostic and therapeutic technologies remain severely lacking. CRISPR-Cas systems have the potential to address these critical needs in the response against infectious disease. Initially discovered as the bacterial adaptive immune system, these systems provide a unique opportunity to create programmable, sequence-specific technologies for detection of viral nucleic acids and inhibition of viral replication. This review summarizes how CRISPR-Cas systems—in particular the recently discovered DNA-targeting Cas12 and RNA-targeting Cas13, both possessing a unique trans -cleavage activity—are being harnessed for viral diagnostics and therapies. We further highlight the numerous technologies whose development has accelerated in response to the COVID-19 pandemic. In this review, Freije et al. describe the ways CRISPR-Cas systems have been harnessed for the detection and inhibition of mammalian viruses. They focus on Cas12- and Cas13-based detection technologies, including those developed in response to the COVID-19 pandemic and studies of Cas9 and Cas13's antiviral activity. [ABSTRACT FROM AUTHOR]
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- 2021
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220. Regeneration of Pulp-Dentin Complex in a Tooth with Symptomatic Irreversible Pulpitis and Open Apex Using Regenerative Endodontic Procedures.
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Sabeti, Mohammad, Golchert, Kory, and Torabinejad, Mahmoud
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PULPITIS ,REGENERATION (Biology) ,DENTAL pulp capping ,ENDODONTICS ,TEETH ,ROOT development ,INCISORS - Abstract
Regenerative endodontic procedures are undertaken on permanent teeth with necrotic pulps and open apices in an attempt to resolve symptoms, to allow the continued development of the root(s), and to reestablish vitality. The available histologic analysis of these teeth has, in the majority of studies, shown that true regeneration of the pulp-dentin complex is not achieved. A recent investigation using an animal model outlined a procedure wherein pulpal amputation a few millimeters short of the apex followed by evoked bleeding allowed the complete regeneration of the normal pulp-dentin complex in immature vital teeth of ferrets. By implementation of this procedure, we report successful pulp regeneration outcome evidenced by continued root development and a positive response to pulp vitality tests in a maxillary central incisor with an open apex diagnosed with symptomatic irreversible pulpitis. [ABSTRACT FROM AUTHOR]
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- 2021
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221. LB1609 The evolutionary trajectory of primate skin appendage traits
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Kamberov, Y., primary, Guhan, S., additional, DeMarchis, A., additional, Jiang, J., additional, Wright, S., additional, Morgan, B., additional, Sabeti, P., additional, Tabin, C., additional, and Lieberman, D., additional
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- 2018
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222. Clinical and Radiographic Failure of Nonsurgical Endodontic Treatment and Retreatment Using Single-cone Technique With Calcium Silicate-based Sealers: A Systematic Review and Meta-analysis.
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Sabeti, Mohammad A., Karimpourtalebi, Negah, Shahravan, Arash, and Dianat, Omid
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PIT & fissure sealants (Dentistry) ,ROOT canal treatment ,ENDODONTICS ,PERIAPICAL periodontitis ,COMBINED ratio ,PERIAPICAL diseases ,PERIODONTITIS - Abstract
This systematic review and meta-analysis aimed to evaluate the clinical and radiographic failure of nonsurgical endodontic treatment and retreatment for mature permanent teeth with or without apical periodontitis using the single-cone (SC) obturation technique with calcium silicate-based bio-ceramic (CSBC) sealers and to compare these failure rates to other sealer materials and obturation techniques. A comprehensive search was conducted using MEDLINE (PubMed), Embase, Cochrane Library, Scopus, Web of Science, and gray literature up to March 2023. Two reviewers assessed the eligibility of the included studies. Eligible studies were critically appraised for risk of bias and quality of evidence. Subsequently, a meta-analysis of pooled data was conducted utilizing the RevMan software (P <.05) to evaluate the failure rate of non-surgical root canal therapy using CSBC sealers and SC obturation procedures. Separately, another analysis was conducted to compare those results with the outcome of nonsurgical root canal therapy using alternative obturation materials and methods. Five studies were included. The pooled failure rate for nonsurgical endodontic treatment and retreatment combined using CSBC sealers and SC obturation technique was 6.8% [95% confidence interval (CI) = (3%–12%), I
2 = 46%]. A second analysis was conducted on the 3 included clinical trials to compare the outcomes of the intervention (CSBC sealers and SC obturation technique) and control groups (other sealers and other obturation techniques). This analysis found no significant difference between the 2 groups regarding clinical and radiographic failure of endodontic treatment and retreatment [Risk ratio = 0.71, 95% CI = (0.33, 1.51), I2 = 0]. This difference was also not statistically significant when the failure rate of primary root canal treatment and retreatment were separately analyzed [Combined Risk ratio of primary root canal treatment = 0.94, 95% CI = (0.46, 1.93), I2 = 0%; Combined Risk ratio of retreatment = 0.21, 95% CI = (0.001, 75.46), I2 = 0%]. The overall results of this systematic review and meta-analysis demonstrate that the SC obturation technique with CSBC sealer provides similar results compared to other obturation materials and techniques in facilitating the healing of apical periodontitis. [ABSTRACT FROM AUTHOR]- Published
- 2024
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223. Challenges of paediatric palliative care in the intensive care unit during the COVID-19 pandemic
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Hasanpour, Marzieh, Pouraboli, Batool, Mohammadpour, Masoud, Tahmasebi, Mamak, and Sabeti, Fahimeh
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Background:The integration of paediatric palliative care into the Iranian health system is essential.Aims:The aim of this study was to identify the challenges of palliative care in the paediatric intensive care unit during COVID-19 through the experiences of healthcare providers.Methods:A qualitative study with content analysis approach was conducted. Fifteen physicians and nurses were selected by purposeful sampling. The semi-structured, in-depth interviews were applied in the data collection.Findings:Ten main categories were extracted from data analysis, including ‘caring in COVID-19’, ‘communication and family centre care’, ‘breaking bad news’, palliative care training’, ‘pain and symptom management’, ‘support of the child, family and clinical team’, ‘physical environment’, ‘guidelines’, ‘specialised staff’ and ‘home based palliative care’.Conclusion:Palliative care in the PICU faces several challenges, especially during COVID-19, but the clinical team are making every attempt to improve the comprehensive care of children and their families. Telehealth is important in COVID-19, and education is also a key component to improve palliative care in the PICU in Iran.
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- 2021
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224. Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic
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Dudas, G, Carvalho, LM, Bedford, T, Tatem, A, Baele, G, Faria, N, Park, D, Ladner, J, Arias, A, Asogun, D, Bielejec, F, Caddy, S, Cotten, M, Dambrozio, J, Dellicour, S, Di Caro, A, Diclaro, J, Duraffour, S, Elmore, M, Fakoli, L, Gilbert, M, Gevao, S, Gire, S, Gladden-Young, A, Gnirke, A, Goba, A, Grant, D, Haagmans, B, Hiscox, J, Jah, U, Kargbo, B, Kugelman, J, Liu, D, Lu, J, Malboeuf, C, Mate, S, Matthews, D, Matranga, C, Meredith, L, Qu, J, Quick, J, Pas, S, Phan, MVT, Poliakis, G, Reusken, C, Sanchez-Lockhart, M, Schaffner, S, Schieffelin, J, Sealfon, R, Simon-Loriere, E, Smits, S, Stoecker, K, Thorne, L, Tobin, E, Vandi, M, Watson, S, West, K, Whitmer, S, Wiley, M, Winnicki, S, Wohl, S, Wölfel, R, Yozwiak, N, Andersen, K, Blyden, S, Bolay, F, Carroll, M, Dahn, B, Diallo, B, Formenty, P, Fraser, C, Gao, G, Garry, R, Goodfellow, I, Günther, S, Happi, C, Holmes, E, Kellam, P, Koopmans, MPG, Loman, N, Magassouba, N, Naidoo, D, Nichol, S, Nyenswah, T, Palacios, G, Pybus, O, Sabeti, P, Sall, A, Sakoba, K, Ströeher, U, Wurie, I, Suchard, M, Lemey, P, Rambaut, A, and Wellcome Trust
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viruses - Abstract
Summary The 2013-2016 epidemic of Ebola virus disease in West Africa was of unprecedented magnitude, duration and impact. Extensive collaborative sequencing projects have produced a large collection of over 1600 Ebola virus genomes, representing over 5% of known cases, unmatched for any single human epidemic. In this comprehensive analysis of this entire dataset, we reconstruct in detail the history of migration, proliferation and decline of Ebola virus throughout the region. We test the association of geography, climate, administrative boundaries, demography and culture with viral movement among 56 administrative regions. Our results show that during the outbreak viral lineages moved according to a classic ‘gravity’ model, with more intense migration between larger and more proximate population centers. Notably, we find that despite a strong attenuation of international dispersal after border closures, localized cross-border transmission beforehand had already set the seeds for an international epidemic, rendering these measures relatively ineffective in curbing the epidemic. We use this empirical evidence to address why the epidemic did not spread into neighboring countries, showing that although these regions were susceptible to developing significant outbreaks, they were also at lower risk of viral introductions. Finally, viral genome sequence data uniquely reveals this large epidemic to be a heterogeneous and spatially dissociated collection of transmission clusters of varying size, duration and connectivity. These insights will help inform approaches to intervention in such epidemics in the future.
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- 2016
225. A second generation human haplotype map of over 3.1 million SNPs
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Frazer, KA, Ballinger, DG, Cox, DR, Hinds, DA, Stuve, LL, Gibbs, RA, Belmont, JW, Boudreau, A, Hardenbol, P, Leal, SM, Pasternak, S, Wheeler, DA, Willis, TD, Yu, F, Yang, H, Zeng, C, Gao, Y, Hu, H, Hu, W, Li, C, Lin, W, Liu, S, Pan, H, Tang, X, Wang, J, Wang, W, Yu, J, Zhang, B, Zhang, Q, Zhao, H, Zhou, J, Gabriel, SB, Barry, R, Blumenstiel, B, Camargo, A, Defelice, M, Faggart, M, Goyette, M, Gupta, S, Moore, J, Nguyen, H, Onofrio, RC, Parkin, M, Roy, J, Stahl, E, Winchester, E, Ziaugra, L, Altshuler, D, Shen, Y, Yao, Z, Huang, W, Chu, X, He, Y, Jin, L, Liu, Y, Sun, W, Wang, H, Wang, Y, Xiong, X, Xu, L, Waye, MM, Tsui, SK, Xue, H, Wong, JT, Galver, LM, Fan, JB, Gunderson, K, Murray, SS, Oliphant, AR, Chee, MS, Montpetit, A, Chagnon, F, Ferretti, V, Leboeuf, M, Olivier, JF, Phillips, MS, Roumy, S, Sallée, C, Verner, A, Hudson, TJ, Kwok, PY, Cai, D, Koboldt, DC, Miller, RD, Pawlikowska, L, Taillon-Miller, P, Xiao, M, Tsui, LC, Mak, W, Song, YQ, Tam, PK, Nakamura, Y, Kawaguchi, T, Kitamoto, T, Morizono, T, Nagashima, A, Ohnishi, Y, Sekine, A, Tanaka, T, Tsunoda, T, Deloukas, P, Bird, CP, Delgado, M, Dermitzakis, ET, Gwilliam, R, Hunt, S, Morrison, J, Powell, D, Stranger, BE, Whittaker, P, Bentley, DR, Daly, MJ, de Bakker, PI, Barrett, J, Chretien, YR, Maller, J, McCarroll, S, Patterson, N, Pe'er, I, Price, A, Purcell, S, Richter, DJ, Sabeti, P, Saxena, R, Schaffner, SF, Sham, PC, Varilly, P, Stein, LD, Krishnan, L, Smith, AV, Tello-Ruiz, MK, Thorisson, GA, Chakravarti, A, Chen, PE, Cutler, DJ, Kashuk, CS, Lin, S, Abecasis, GR, Guan, W, Li, Y, Munro, HM, Qin, ZS, Thomas, DJ, McVean, G, Auton, A, Bottolo, L, Cardin, N, Eyheramendy, S, Freeman, C, Marchini, J, Myers, S, Spencer, C, Stephens, M, Donnelly, P, Cardon, LR, Clarke, G, Evans, DM, Morris, AP, Weir, BS, Mullikin, JC, Sherry, ST, Feolo, M, Skol, A, Zhang, H, Matsuda, I, Fukushima, Y, Macer, DR, Suda, E, Rotimi, CN, Adebamowo, CA, Ajayi, I, Aniagwu, T, Marshall, PA, Nkwodimmah, C, Royal, CD, Leppert, MF, Dixon, M, Peiffer, A, Qiu, R, Kent, A, Kato, K, Niikawa, N, Adewole, IF, Knoppers, BM, Foster, MW, Clayton, EW, Watkin, J, Muzny, D, Nazareth, L, Sodergren, E, Weinstock, GM, Yakub, I, Birren, BW, Wilson, RK, Fulton, LL, Rogers, J, Burton, J, Carter, NP, Clee, CM, Griffiths, M, Jones, MC, McLay, K, Plumb, RW, Ross, MT, Sims, SK, Willey, DL, Chen, Z, Han, H, Kang, L, Godbout, M, Wallenburg, JC, L'Archevêque, P, Bellemare, G, Saeki, K, An, D, Fu, H, Li, Q, Wang, Z, Wang, R, Holden, AL, Brooks, LD, McEwen, JE, Guyer, MS, Wang, VO, Peterson, JL, Shi, M, Spiegel, J, Sung, LM, Zacharia, LF, Collins, FS, Kennedy, K, Jamieson, R, and Stewart, J
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Male ,Recombination, Genetic ,Genetics ,Linkage disequilibrium ,education.field_of_study ,Multidisciplinary ,Homozygote ,Racial Groups ,Haplotype ,Population ,Single-nucleotide polymorphism ,Tag SNP ,Biology ,Polymorphism, Single Nucleotide ,Linkage Disequilibrium ,Article ,Haplotypes ,Humans ,Female ,Selection, Genetic ,International HapMap Project ,education ,Imputation (genetics) ,Genetic association - Abstract
We describe the Phase II HapMap, which characterizes over 3.1 million human single nucleotide polymorphisms (SNPs) genotyped in 270 individuals from four geographically diverse populations and includes 25-35% of common SNP variation in the populations surveyed. The map is estimated to capture untyped common variation with an average maximum r 2 of between 0.9 and 0.96 depending on population. We demonstrate that the current generation of commercial genome-wide genotyping products captures common Phase II SNPs with an average maximum r 2 of up to 0.8 in African and up to 0.95 in non-African populations, and that potential gains in power in association studies can be obtained through imputation. These data also reveal novel aspects of the structure of linkage disequilibrium. We show that 10-30% of pairs of individuals within a population share at least one region of extended genetic identity arising from recent ancestry and that up to 1% of all common variants are untaggable, primarily because they lie within recombination hotspots. We show that recombination rates vary systematically around genes and between genes of different function. Finally, we demonstrate increased differentiation at non-synonymous, compared to synonymous, SNPs, resulting from systematic differences in the strength or efficacy of natural selection between populations. ©2007 Nature Publishing Group., link_to_OA_fulltext
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- 2016
226. Synthetic DNA spike-ins (SDSIs) enable sample tracking and detection of inter-sample contamination in SARS-CoV-2 sequencing workflows
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Lagerborg, Kim A, Normandin, Erica, Bauer, Matthew, Adams, Gordon, Figueroa, Katherine, Loreth, Christine, Gladden-Young, Adrianne, Shaw, Bennett, Pearlman, Leah, Berenzy, Daniel, Dewey, Hannah, Kales, Susan, Dobbins, Sabrina, Seiguer Shenoy, Erica, Hooper, David, Pierce, Virginia, Zachary, Kimon, Park, Daniel, Macinnis, Bronwyn, Tewhey, Ryan, Lemieux, Jacob, Sabeti, Pardis, Reilly, Steven, and Siddle, Katherine
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Cell Biology ,Microbiology (medical) ,Genetics ,Applied Microbiology and Biotechnology ,Immunology ,Microbiology - Abstract
SDSI+AmpSeq: A DNA spike-in tool to track samples and detect key modes of error in SARS-CoV-2 genomic data Kim A. Lagerborg☨,1,2, Erica Normandin*,☨,1,3, Matthew R. Bauer☨,1,2, Gordon Adams1, Katherine Figueroa1, Christine Loreth1, Adrianne Gladden-Young1, Bennett Shaw1,4, Leah R. Pearlman1, Daniel Berenzy5, Hannah H Dewey5, Susan Kales5, Sabrina T. Dobbins1, Erica S. Shenoy4, David Hooper4, Virginia M. Pierce6,7,8, Kimon C. Zachary4,9,10, Daniel J. Park1, Bronwyn L. MacInnis1,11,12, Ryan Tewhey5,13,14, Jacob E. Lemieux1,4, Pardis C. Sabeti ⟊,1,3,11,12,15, Steven K Reilly *,⟊,1,3, Katherine J. Siddle⟊,1,3. ☨,⟊ denote equal contribution. *denotes corresponding author., The global spread and continued evolution of SARS-CoV-2 has driven an unprecedented surge in viral genomic surveillance. Amplicon-based sequencing methods provide a sensitive, low-cost and rapid approach but suffer a high potential for contamination, which can undermine laboratory processes and results. This challenge will only increase with expanding global production of sequences by diverse laboratories for epidemiological and clinical interpretation, as well in genomic surveillance in future outbreaks. We present SDSI+AmpSeq, an approach which uses synthetic DNA spike-ins (SDSIs) to track samples and detect inter-sample contamination through the sequencing workflow. Applying SDSIs to the ARTIC Consortium’s amplicon design, we demonstrate their utility and efficiency in a real-time investigation of a suspected hospital cluster of SARS-CoV-2 cases and across thousands of diagnostic samples at multiple laboratories. We establish that SDSI+AmpSeq provides increased confidence in genomic data by detecting and in some cases correcting for relatively common, yet previously unobserved modes of error without impacting genome recovery., Author's Original
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- 2021
227. Seizure incidence among neuromyelitis optica spectrum disorder patients
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Etemadifar, M., Sabeti, F., Khorvash, R., Mirbagheri, M., Nouri, H., and Salari, M.
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Neuromyelitis optica spectrum disorders (NMOSDs) are a group of neuroinflammatory diseases, which mainly affect the optic nerve and spinal cord. NMOSD is an astrocytic channelopathy involving the aquaporin-4 (AQP4) water channels in the central nervous system. Patients can present with seizure attacks as a first manifestation or relapse. However, compared with multiple sclerosis (MS) or myelin oligodendrocyte glycoprotein encephalomyelitis (MOG-EM), seizure attacks are less frequent in NMOSD.
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- 2021
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228. Cone Beam Computed Tomography and Radiographs for Endodontics: A Pictorial Illustration of the AAE-AAOMR Position Statement
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Ganguly, Rumpa and Sabeti, Mike
- Abstract
ABSTRACTBackground:Cone beam computed tomography (CBCT) has become an integral part of more challenging and complex endodontic treatments. CBCT may be considered in the presence of specific signs and symptoms when clinical questions are not addressed by conventional 2D radiographic imaging.Results:This article provides pictorial illustrations of endodontic cases where CBCT, imaging, when performed with appropriate imaging protocol, may lead to informed decision-making regarding treatment approaches of the more challenging endodontic cases. The illustrations are based on recommendations made by the AAE-AAOMR position statement.Practical implications:This pictorial essay elaborates the recommendations in the joint position statement of the AAE-AAOMR through illustrated case scenarios to help clinicians understand the impact of CBCT on diagnosis and treatment planning.
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- 2021
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229. Integrating common and rare genetic variation in diverse human populations
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Altshuler, D, Gibbs, R, Peltonen, L, Dermitzakis, E, Schaffner, S, Yu, F, Bonnen, P, de Bakker, P, Deloukas, P, Gabriel, S, Gwilliam, R, Hunt, S, Inouye, M, Jia, X, Palotie, A, Parkin, M, Whittaker, P, Chang, K, Hawes, A, Lewis, L, Ren, Y, Wheeler, D, Muzny, D, Barnes, C, Darvishi, K, Hurles, M, Korn, J, Kristiansson, K, Lee, C, McCarrol, SA, Nemesh, J, Keinan, A, Montgomery, S, Pollack, S, Price, A, Soranzo, N, Gonzaga-Jauregui, C, Anttila, V, Brodeur, W, Daly, M, Leslie, S, McVean, G, Moutsianas, L, Nguyen, H, Zhang, Q, Ghori, M, McGinnis, R, McLaren, W, Takeuchi, F, Grossman, SR, Shlyakhter, I, Hostetter, E, Sabeti, P, Adebamowo, C, Foster, M, Gordon, DR, Licinio, J, Manca, M, Marshall, P, Matsuda, I, Ngare, D, Wang, V, Reddy, D, Rotimi, C, Royal, C, Sharp, R, Zeng, C, Brooks, L, McEwen, J, Dermitzakis, Emmanouil, and Montgomery, Stephen
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DNA Copy Number Variations ,Single-nucleotide polymorphism ,Genome-wide association study ,Human genetic variation ,Biology ,Polymorphism, Single Nucleotide ,Article ,03 medical and health sciences ,Genome, Human ,0302 clinical medicine ,Population Groups ,Population Groups/*genetics ,Human Genome Project ,Humans ,ddc:576.5 ,Copy-number variation ,International HapMap Project ,030304 developmental biology ,Genetics ,0303 health sciences ,Multidisciplinary ,SNP genotyping ,Minor allele frequency ,030217 neurology & neurosurgery ,Imputation (genetics) - Abstract
Despite great progress in identifying genetic variants that influence human disease, most inherited risk remains unexplained. A more complete understanding requires genome-wide studies that fully examine less common alleles in populations with a wide range of ancestry. To inform the design and interpretation of such studies, we genotyped 1.6 million common single nucleotide polymorphisms (SNPs) in 1,184 reference individuals from 11 global populations, and sequenced ten 100-kilobase regions in 692 of these individuals. This integrated data set of common and rare alleles, called 'HapMap 3', includes both SNPs and copy number polymorphisms (CNPs). We characterized population-specific differences among low-frequency variants, measured the improvement in imputation accuracy afforded by the larger reference panel, especially in imputing SNPs with a minor allele frequency of
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- 2010
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230. Learning complex texture discrimination
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Maddess, T., Coy, D., Herrington, J. C., Carle, C. F., Sabeti, F., and Barbosa, M. S.
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Higher-order spatial correlations contribute strongly to visual structure and salience, and are common in the natural environment. One method for studying this structure has been through the use of highly controlled texture patterns whose obvious structure is defined entirely by third- and higher-order correlations. Here we examine the effects that longer-term training has on discrimination of 17 such texture types. Training took place in 14 sessions over 42 days. Discrimination performance increased at different rates for different textures. The time required to complete a visit reduced by 25.4% (p=0.0004). Factor analysis was applied to data from the learning and experienced phases of the experiment. This indicated that the gain in speed was accompanied by an increase in the number of mechanisms contributing to discrimination. Learning was not affected by sleep quality but was affected by extreme tiredness (p<0.01). The improved discrimination and speed were retained for 2.5 months. Overall, the effects were consistent with perceptual learning. The observed learning is likely related to the adaptation of innate mechanisms that underlie our ability to identify nonredundant, visually salient structure in natural images. It may involve cortical V2 and appears to involve increased strength, speed, and breadth of connections within our internal representation of this complex perceptual space.
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- 2021
231. Development of a qualitative real-time RT-PCR assay for the detection of SARS-CoV-2: a guide and case study in setting up an emergency-use, laboratory-developed molecular microbiological assay
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Anahtar, Melis N, Shaw, Bennett M, Slater, Damien, Byrne, Elizabeth H, Botti-Lodovico, Yolanda, Adams, Gordon, Schaffner, Stephen F, Eversley, Jacqueline, McGrath, Graham E G, Gogakos, Tasos, Lennerz, Jochen, Marble, Hetal Desai, Ritterhouse, Lauren L, Batten, Julie M, Georgantas, N Zeke, Pellerin, Rebecca, Signorelli, Sylvia, Thierauf, Julia, Kemball, Molly, Happi, Christian, Grant, Donald S, Ndiaye, Daouda, Siddle, Katherine J, Mehta, Samar B, Harris, Jason B, Ryan, Edward T, Pierce, Virginia M, LaRocque, Regina C, Lemieux, Jacob E, Sabeti, Pardis C, Rosenberg, Eric S, Branda, John A, and Turbett, Sarah E
- Abstract
Developing and deploying new diagnostic tests are difficult, but the need to do so in response to a rapidly emerging pandemic such as COVID-19 is crucially important. During a pandemic, laboratories play a key role in helping healthcare providers and public health authorities detect active infection, a task most commonly achieved using nucleic acid-based assays. While the landscape of diagnostics is rapidly evolving, PCR remains the gold-standard of nucleic acid-based diagnostic assays, in part due to its reliability, flexibility and wide deployment. To address a critical local shortage of testing capacity persisting during the COVID-19 outbreak, our hospital set up a molecular-based laboratory developed test (LDT) to accurately and safely diagnose SARS-CoV-2. We describe here the process of developing an emergency-use LDT, in the hope that our experience will be useful to other laboratories in future outbreaks and will help to lower barriers to establishing fast and accurate diagnostic testing in crisis conditions.
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- 2021
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232. Management of corneal melt in patients with Boston Keratoprosthesis Type 1: Repair versus repeat
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Daoud, Roy, Sabeti, Saama, and Harissi-Dagher, Mona
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To evaluate outcomes of Boston keratoprosthesis (KPro) repair versus repeat KPro as treatment for corneal melt in KPro patients.
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- 2020
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233. Deep multi-task learning structure for segmentation and classification of supratentorial brain tumors in MR images
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Kordnoori, Shirin, Sabeti, Maliheh, Shakoor, Mohammad Hossein, and Moradi, Ehsan
- Abstract
Identification of brain tumors border and determination of their possible pathology in MR images is an important step in pre-operation analyzing of this serious medical condition. Manual segmentation and classification of brain tumors could be challenge full in neurosurgical practice because of vast differences between brain tumors characteristic such as shape, border irregularity, consistency and etc. as well as interobserver variations. To solve this problem, some automatic methods have been proposed for brain tumors segmentation or classification during recent years, but an intelligence-based method for simultaneous identification of tumor type and tumor border in MR images has not proposed till now. Here, we have planned a unique automatic model includes a common encoder for feature representation, one decoder for segmentation and a multi-layer perceptron for classification of three common primary brain tumors (meningiomas, gliomas and pituitary adenomas) in brain MR images. The proposed model was examined on a brain tumor images dataset and the output were evaluated in both multi-task and single-task learning model. The multi-task learning model gains significant improvement in simultaneous classification and segmentation of brain tumors with promising accuracy of 97% for each task. So, this model could serve as a primary screening tool for early diagnosis of common primary brain tumors in general practice with a high success rate.
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- 2024
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234. Image processing and machine learning for diagnosis and screening of craniosynostosis in children
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Sabeti, Maliheh, Boostani, Reza, Taheri, Behnam, and Moradi, Ehsan
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craniosynostosis (CSO) is a congenital disorder resulting from early closure of cranial sutures in newborns, while could cause significant cosmetic and neurodevelopmental problems. As a standard method, different craniometric indices are measured directly from child head or from their 3D CT scan of skull for diagnosis or in post-operative follow-up period. We propose a novel telehealth-compatible deep learning neural network-based method for identifying different craniometric indices in non-syndromic CSO patients 2D photographic data.
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- 2024
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235. Investigation of ambient BTEX concentrations along a bus rapid transit route in Tabriz: Spatio-temporal variations and health risk assessment.
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Hosseinpour, Neda, Sabeti, Zahra, Aslani, Hassan, Benis, Khaled Zoroufchi, Shakerkhatibi, Mohammad, Najaflou, Arash, Malekzadeh, Masoumeh, and Tayefeh Rahimian, Raana
- Abstract
Urgent actions are imperative to assess ambient BTEX concentration in urban areas and increase awareness of the significant health risks linked to exposure to these volatile compounds. This study examines the spatiotemporal variations of BTEX concentration in BRT stations and provides a health risk assessment in Tabriz, located in the northwest of Iran. We collected samples repeatedly from four BRT stations and three areas between stations (N = 86). The mixture BTEX compounds had average concentrations ranging from 6.7 to 52.9 μg/m
3 , with the highest concentration belonging to o-xylene. Additionally, the average ratios of toluene/benzene, m-xylene/benzene, and o-xylene/benzene were 2.4, 2.3, and 3.0, respectively. Total BTEX concentrations were significantly higher in BRT stations than areas between stations. Furthermore, the concentration of total BTEX doubled in the evening compared to the morning. Although the maximum concentrations of BTEX were recorded in winter, there were no significant seasonal differences. The lifetime cancer risk (LCR) of benzene exposure was 1.07 × 10−7 and 1.52 × 10−5 for passengers and residents located in the vicinity of the BRT lane, respectively. In conclusion, this study suggests that emissions from BRT buses are one of the main contributors to BTEX in Tabriz. • BTEX concentrations were significantly higher in BRT stations than in-between stations. • Total BTEX concentration doubled in the evening compared to the morning. • Total BTEX levels were only marginally higher in winter than summer. • The LCR for individuals located near the BRT lane exceeded the EPA-recommended value. [ABSTRACT FROM AUTHOR]- Published
- 2024
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236. Anti-HSV-2 antibody in patients with MS and NMO.
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Etemadifar, Masoud, Izadi, Arefeh, Sabeti, Fatemeh, and Noorshargh, Pegah
- Abstract
Highlights • We found no associations between patients' mean anti-HSV2 antibody index and the diagnosis of NMO or MS. • There was no significant difference in mean anti-HSV2 antibody O.D./index between control group and MS or NMO group. • We found no associations between NMO and MS patients' demographic and clinical features and their mean anti-HSV2 antibody index/O.D. Abstract Background Multiple sclerosis (MS) and neuromyelitis optica (NMO) are demyelinating disorders of the central nervous system. There is growing evidence that viruses may play a causal role in these diseases. Human herpes viruses have been of special attention since their DNA have been detected in many of MS patients' samples. Human herpes simplex virus 2 (HSV-2) is a member of this family which has not been investigated thoroughly in MS and NMO. Methods We took blood samples from 90 subjects including 30 RRMS patients, 30 NMO patients and 30 healthy controls. After serum isolation, all serum samples were frozen at −70°C to be used for enzyme linked immunosorbent assay (ELISA) for detection of specific antibodies against HSV-2. Presence or absence of antibodies against HSV-2 was determined based on the cut-off calibrator and index values were then determined. A value of <0.9: negative, between 0.9 and 1.1: equivocal and <1.1: positive. Results Mean age of all subjects was 33.36 and female to male ratio was 4.3/1. None of the subjects were seropositive for anti-HSV-2 antibody. Analysis indicated no significant differences (P -value >0.05) among antibody levels between MS (0.19 ± 0.08), NMO (0.22 ±0.16) and control (0.21 ±0.09) groups. There were also no correlations between mean antibody index or O.D. and subjects' sex, family history, blood group, smoking history, age and presence of visual-motor-sensory or other forms of disability in any of the three MS, NMO and control groups (P -value >0.05). Conclusion We found no associations between patients' diagnosis of MS or NMO and mean anti-HSV-2 antibody index and O.D. levels. [ABSTRACT FROM AUTHOR]
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- 2019
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237. Sleep, hippocampal volume, and cognition in adults over 90 years old.
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Sabeti, Sara, Al-Darsani, Zeinah, Mander, Bryce Anthony, Corrada, Maria M., and Kawas, Claudia H.
- Abstract
Background: Several lines of research support associations between sleep and cognition in older adults. However, there is a paucity of data regarding sleep and cognition in nonagenarians and centenarians.Aims: The current study examined self-reported sleep quantity and sleep quality in relation to hippocampal volume and cognition in adults aged 90 and older.Methods: A total of 144 participants of The 90+ Study completed The Medical Outcomes Study sleep questionnaire. Participants reported subjective sleep duration in hours and three sleep quality factors: sleep problems, adequacy, and somnolence. Neuropsychological assessments of memory, global cognition, language, and executive function were completed, on average, 61 days from the questionnaire. Hippocampal volume on 3 T MRI, adjusted for intracranial volume, was obtained in 82 participants. We performed multiple linear regressions, controlling for age, sex, education, sleep medication, and depression, to examine sleep characteristics in relation to hippocampal volume and cognitive performance in all the subjects and then stratified by cognition.Results: Sleep duration > 8 h was associated with lower scores in tests of global cognition, memory, and executive function compared to sleep duration of 7-8 h when collapsing across cognitive status, but only with memory in cognitively impaired subjects, and not in cognitively normal subjects.Conclusions and discussion: Long-sleep duration is associated with poorer global cognition, memory, and executive function in the oldest-old, and is only associated with memory in cognitively impaired oldest-old. Additional research is necessary to determine if sleep duration is a risk factor or a result of poor cognition in advanced age. [ABSTRACT FROM AUTHOR]
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- 2018
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238. Impact of Access Cavity Design and Root Canal Taper on Fracture Resistance of Endodontically Treated Teeth: An Ex Vivo Investigation.
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Sabeti, Mohammad, Kazem, Majid, Dianat, Omid, Bahrololumi, Nazanin, Beglou, Amirreza, Rahimipour, Kasra, and Dehnavi, Farshad
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TEETH injury treatment ,ROOT canal treatment ,DENTAL cavity preparation ,MOLARS ,MINIMALLY invasive dentistry ,WOUNDS & injuries - Abstract
Introduction The susceptibility of endodontically treated teeth (ETT) to fracture is mainly associated with the loss of tooth structure. This study evaluated the effect of the access cavity design and taper preparation of root canals on ETT fracture resistance of maxillary molars. Methods For tapering assessment, 30 sound distobuccal roots of maxillary molars were randomly assigned to 1 of 3 groups ( n = 10): a .04 taper, a .06 taper, or a .08 taper. Endodontic canal preparations were performed using the Twisted Files rotary system (Kerr Co, Glendora, CA). In addition, 48 intact maxillary first and second molars were randomly assigned to 1 of 3 groups ( n = 16) for cavity preparation approaches: intact teeth, traditional access cavity (TAC), or conservative access cavity (CAC). Fracture resistance was tested using a universal testing machine. For statistical analysis, the level of significance was P ≤ .05. Results The .04 taper instrumentation had the highest fracture resistance (259.61 ± 52.06), and the .08 taper had the lowest (168.43 ± 59.63). The .04 and .06 groups did not differ significantly ( P > .05); however, these groups differed significantly from the .08 group ( P ≤ .05). Regarding the cavity preparation approaches, the 3 groups of intact teeth, CAC, and TAC showed fracture resistance mean values of 2118.85 ± 336.97, 1705.69 ± 591.51, and 1471.11 ± 435.34, respectively, with no significant difference between the CAC and TAC groups ( P > .05). Conclusions Increasing the taper of the root canal preparation can reduce fracture resistance. Moreover, access cavity preparation can reduce resistance; however, CAC in comparison with TAC had no significant impact. [ABSTRACT FROM AUTHOR]
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- 2018
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239. Eye care utilization and its determinants in Canada.
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Aljied, Rumaisa, Aubin, Marie-Josée, Buhrmann, Ralf, Sabeti, Saama, and Freeman, Ellen E.
- Abstract
Copyright of Canadian Journal of Ophthalmology is the property of Elsevier B.V. and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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- 2018
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240. Prevalence and determinants of visual impairment in Canada: cross-sectional data from the Canadian Longitudinal Study on Aging.
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Aljied, Rumaisa, Aubin, Marie-Josée, Buhrmann, Ralf, Sabeti, Saama, and Freeman, Ellen E.
- Abstract
Copyright of Canadian Journal of Ophthalmology is the property of Elsevier B.V. and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
- Published
- 2018
- Full Text
- View/download PDF
241. Negative Selection by Spiral Inertial Microfluidics Improves Viral Recovery and Sequencing from Blood.
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Choi, Kyungyong, Ryu, Hyunryul, Siddle, Katherine J., Piantadosi, Anne, Freimark, Lisa, Park, Daniel J., Sabeti, Pardis, and Han, Jongyoon
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- 2018
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242. The higher prevalence of multiple sclerosis among Iranian Georgians; new clues to the role of genetic factors
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Etemadifar, M., Ghourchian, S., Sabeti, F., Akbari, M., Etemadifar, F., and Salari, M.
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Multiple sclerosis (MS) is a demyelinating disease of the central nervous system (CNS) with varied prevalence rates among populations with different ethnic backgrounds. Therefore, studies done on minorities have shed more light on the risk factors.
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- 2020
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243. Arts & Ethnography in a Contemporary World: From Learning to Social Participation, Ligia Ferro and David Poveda (eds) (2019)
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Sabeti, Shari
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Review of: Arts & Ethnography in a Contemporary World: From Learning to Social Participation, Ligia Ferro and David Poveda (eds) (2019)London: Tufnell Press, 176 pp.,ISBN 978-1-87276-779-6, p/bk, £14.95
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- 2019
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244. Circulating and Tissue microRNAs as Biomarkers for Ovarian Cancer Prognosis
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Parizadeh, Seyed M., Jafarzadeh-Esfehani, Reza, Ghandehari, Maryam, Hasanzadeh, Malihe, Parizadeh, Seyed M. R., Hassanian, Seyed Mahdi, Rezaei-Kalat, Afsaneh, Aghabozorgi, Amirsaeed Sabeti, Rahimi-Kakhki, Rana, Zargaran, Bita, Ferns, Gordon A, and Avan, Amir
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Ovarian cancer (OC) is one of the most common cancers globally with a high rate of cancer- associated mortality. OC may be classified into epithelial cell neoplasms, germ cell neoplasms and stromal cell neoplasms. The five-year survival in the early and advanced stages of disease is approximately 90% and 15%, respectively. microRNAs are short, single-stranded, non-coding ribonucleic acid (RNA). miRNAs play critical roles in post transcriptionally regulations of gene expression. miRNAs are found in different tissues and body fluids. In carcinogenesis the expression of miRNAs are altered. Recent studies have revealed that there is a relationship between alteration of miRNAs expression and the prognosis of patients with OC. The aim of this review was to summarize the findings of recent studies that have investigated the expression of circulating and tissue miRNAs as novel biomarkers in the prognosis of OC.
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- 2019
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245. ECG-Based Personal Identification Using Empirical Mode Decomposition and Hilbert Transform
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Boostani, R., Sabeti, M., Omranian, S., and Kouchaki, S.
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It is evident that biological signals of each subject (e.g., electrocardiogram signal) carry his/her unique signature; consequently, several attempts have been made to extract subject-dependent features from these signals with application to human verification. Despite numerous efforts to characterize electrocardiogram (ECG) signals and provide promising results for low population of subjects, the performance of state-of-the-art methods mostly fail in the presence of noise or arrhythmia. This paper presented an efficient and fast-to-compute ECG feature by applying empirical mode decomposition (EMD) to ECG signals, and then, instantaneous frequency, instantaneous phase, amplitude, and entropy features were extracted from the analytical form of the last EMD component. Finally, the k-nearest neighbor (kNN) classifier was utilized to classify the individuals’ features. The proposed method was compared to the conventional features such as fiducial points, correlation, wavelet coefficients, and principal component analysis (PCA). These methods were all applied to ECG signals of 34 healthy subjects derived from the Physikalisch-Technische Bundesanstalt (PTB) database. The results implied the effectiveness of the proposed method, providing 95% verification accuracy, which was not the best among the competitors but provided much lower dimensional feature space compared to the top-rank counterparts.
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- 2019
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246. Cerebellopontine angle meningioma originating from choroid plexus of the foramen of Luschka: An extremely rare entity and overlook of literature.
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Ebrahimzadeh, Kaveh, Eraghi, Mohammad Mirahmadi, Tavassol, Hesameddin Hoseini, Sabeti, Shahram, Hallajnejad, Mohammad, and Bangash, Ali Haider
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Meningiomas without dural attachments are quite a novelty, with such meningiomas in the posterior fossa being even more far and few between. The authors describe an extremely rare cerebellopontine angle (CPA) meningioma lacking a dural attachment arising from the choroid plexus of the foramen of Luschka (CPFOL). A 35-year-old male presented to our center complaining of a generalized and progressive headache for 10 months. A 3 cm × 4 cm well-defined lesion in the left CPA, hypointense in T1 and hyperintense in T2-weighted magnetic resonance imaging (MRI), was noted with no evident dural base or dural attachment. CPFOL was appreciated right at the point where the tumoral base was detected, which implied that the tumor originated from CPFOL. A gross total resection (GTR) was achieved, with the postoperative period remaining uneventful. The histopathologic investigation confirmed a transitional meningioma World Health Organization (WHO) grade I with no atypical features. Meningioma without dural attachment remains a rare phenomenon, with few available in English literature, and such pathology in the posterior fossa is even more unusual. Discriminating between CPFOL and another kind of CPA meningioma is mandatory when dealing with intracranial meningioma surgeries. While managing a space-occupying lesion around CPA, although extremely rare, a meningioma originating from CPFOL is suggested to be included in the differentials with necessary imaging analysis and advised to be imperatively pursued before proceeding for surgical intervention. • Meningiomas arising from the choroid plexus of the foramen of Luschka and located in the CPA without dural attachment is an infrequent entity. • The CPA-located tumors possess specific differential diagnosis, which, in turn, demands an exceptional therapeutic plan. • Cerebellopontine angle meningioma originating from choroid plexus of the foramen of Luschka without dural base or dural attachment remains an extremely rare entity. [ABSTRACT FROM AUTHOR]
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- 2023
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247. The HLA-II immunopeptidome of SARS-CoV-2
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Weingarten-Gabbay, Shira, Chen, Da-Yuan, Sarkizova, Siranush, Taylor, Hannah B., Gentili, Matteo, Hernandez, Gabrielle M., Pearlman, Leah R., Bauer, Matthew R., Rice, Charles M., Clauser, Karl R., Hacohen, Nir, Carr, Steven A., Abelin, Jennifer G., Saeed, Mohsan, and Sabeti, Pardis C.
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Targeted synthetic vaccines have the potential to transform our response to viral outbreaks, yet the design of these vaccines requires a comprehensive knowledge of viral immunogens. Here, we report severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) peptides that are naturally processed and loaded onto human leukocyte antigen-II (HLA-II) complexes in infected cells. We identify over 500 unique viral peptides from canonical proteins as well as from overlapping internal open reading frames. Most HLA-II peptides colocalize with known CD4+T cell epitopes in coronavirus disease 2019 patients, including 2 reported immunodominant regions in the SARS-CoV-2 membrane protein. Overall, our analyses show that HLA-I and HLA-II pathways target distinct viral proteins, with the structural proteins accounting for most of the HLA-II peptidome and nonstructural and noncanonical proteins accounting for the majority of the HLA-I peptidome. These findings highlight the need for a vaccine design that incorporates multiple viral elements harboring CD4+and CD8+T cell epitopes to maximize vaccine effectiveness.
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- 2024
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248. Author Correction: Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants
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Welch, Nicole L., Zhu, Meilin, Hua, Catherine, Weller, Juliane, Mirhashemi, Marzieh Ezzaty, Nguyen, Tien G., Mantena, Sreekar, Bauer, Matthew R., Shaw, Bennett M., Ackerman, Cheri M., Thakku, Sri Gowtham, Tse, Megan W., Kehe, Jared, Uwera, Marie-Martine, Eversley, Jacqueline S., Bielwaski, Derek A., McGrath, Graham, Braidt, Joseph, Johnson, Jeremy, Cerrato, Felecia, Moreno, Gage K., Krasilnikova, Lydia A., Petros, Brittany A., Gionet, Gabrielle L., King, Ewa, Huard, Richard C., Jalbert, Samantha K., Cleary, Michael L., Fitzgerald, Nicholas A., Gabriel, Stacey B., Gallagher, Glen R., Smole, Sandra C., Madoff, Lawrence C., Brown, Catherine M., Keller, Matthew W., Wilson, Malania M., Kirby, Marie K., Barnes, John R., Park, Daniel J., Siddle, Katherine J., Happi, Christian T., Hung, Deborah T., Springer, Michael, MacInnis, Bronwyn L., Lemieux, Jacob E., Rosenberg, Eric, Branda, John A., Blainey, Paul C., Sabeti, Pardis C., and Myhrvold, Cameron
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- 2024
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249. Source Localization and Spectrum Analyzing of EEG in Stuttering State upon Dysfluent Utterances
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Bayat, Masoumeh, Boostani, Reza, Sabeti, Malihe, Yadegari, Fariba, Pirmoradi, Mohammadreza, Rao, KS, and Nami, Mohammad
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Purpose:The present study which addressed adults who stutter (AWS) attempted to investigate power spectral dynamics in the stuttering state by answering the questions using quantitative electroencephalography (qEEG). Method:A 64-channel electroencephalography (EEG) setup was used for data acquisition at 20 AWS. Since the speech, especially stuttering, causes significant noise in the EEG, 2 conditions of speech preparation (SP) and imagined speech (IS) were considered. EEG signals were decomposed into 6 bands. The corresponding sources were localized using the standard low-resolution electromagnetic tomography (sLORETA) tool in both fluent and dysfluent states. Results:Significant differences were noted after analyzing the time-locked EEG signals in fluent and dysfluent utterances. Consistent with previous studies, poor alpha and beta suppression in SP and IS conditions were localized in the left frontotemporal areas in a dysfluent state. This was partly true for the right frontal regions. In the theta range, disfluency was concurrence with increased activation in the left and right motor areas. Increased delta power in the left and right motor areas as well as increased beta2 power over left parietal regions was notable EEG features upon fluent speech. Conclusion:Based on the present findings and those of earlier studies, explaining the neural circuitries involved in stuttering probably requires an examination of the entire frequency spectrum involved in speech.
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- 2024
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250. Genome-wide detection and characterization of positive selection in human populations
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Sabeti, PC, Varilly, P, Fry, B, Lohmueller, J, Hostetter, E, Cotsapas, C, Xie, X, Byrne, EH, McCarroll, SA, Gaudet, R, Schaffner, SF, Lander, ES, Frazer, KA, Ballinger, DG, Cox, DR, Hinds, DA, Stuve, LL, Gibbs, RA, Belmont, JW, Boudreau, A, Hardenbol, P, Leal, SM, Pasternak, S, Wheeler, DA, Willis, TD, Yu, F, Yang, H, Zeng, C, Gao, Y, Hu, H, Hu, W, Li, C, Lin, W, Liu, S, Pan, H, Tang, X, Wang, J, Wang, W, Yu, J, Zhang, B, Zhang, Q, Zhao, H, Zhou, J, Gabriel, SB, Barry, R, Blumenstiel, B, Camargo, A, Defelice, M, Faggart, M, Goyette, M, Gupta, S, Moore, J, Nguyen, H, Onofrio, RC, Parkin, M, Roy, J, Stahl, E, Winchester, E, Ziaugra, L, Altshuler, D, Shen, Y, Yao, Z, Huang, W, Chu, X, He, Y, Jin, L, Liu, Y, Sun, W, Wang, H, Wang, Y, Xiong, X, Xu, L, Waye, MM, Tsui, SK, Xue, H, Wong, JT, Galver, LM, Fan, JB, Gunderson, K, Murray, SS, Oliphant, AR, Chee, MS, Montpetit, A, Chagnon, F, Ferretti, V, Leboeuf, M, Olivier, JF, Phillips, MS, Roumy, S, Sallée, C, Verner, A, Hudson, TJ, Kwok, PY, Cai, D, Koboldt, DC, Miller, RD, Pawlikowska, L, Taillon-Miller, P, Xiao, M, Tsui, LC, Mak, W, Song, YQ, Tam, PK, Nakamura, Y, Kawaguchi, T, Kitamoto, T, Morizono, T, Nagashima, A, Ohnishi, Y, Sekine, A, Tanaka, T, Tsunoda, T, Deloukas, P, Bird, CP, Delgado, M, Dermitzakis, ET, Gwilliam, R, Hunt, S, Morrison, J, Powell, D, Stranger, BE, Whittaker, P, Bentley, DR, Daly, MJ, de Bakker, PI, Barrett, J, Chretien, YR, Maller, J, McCarroll, S, Patterson, N, Pe'er, I, Price, A, Purcell, S, Richter, DJ, Sabeti, P, Saxena, R, Sham, PC, Stein, LD, Krishnan, L, Smith, AV, Tello-Ruiz, MK, Thorisson, GA, Chakravarti, A, Chen, PE, Cutler, DJ, Kashuk, CS, Lin, S, Abecasis, GR, Guan, W, Li, Y, Munro, HM, Qin, ZS, Thomas, DJ, McVean, G, Auton, A, Bottolo, L, Cardin, N, Eyheramendy, S, Freeman, C, Marchini, J, Myers, S, Spencer, C, Stephens, M, Donnelly, P, Cardon, LR, Clarke, G, Evans, DM, Morris, AP, Weir, BS, Johnson, TA, Mullikin, JC, Sherry, ST, Feolo, M, Skol, A, Zhang, H, Matsuda, I, Fukushima, Y, Macer, DR, Suda, E, Rotimi, CN, Adebamowo, CA, Ajayi, I, Aniagwu, T, Marshall, PA, Nkwodimmah, C, Royal, CD, Leppert, MF, Dixon, M, Peiffer, A, Qiu, R, Kent, A, Kato, K, Niikawa, N, Adewole, IF, Knoppers, BM, Foster, MW, Clayton, EW, Watkin, J, Muzny, D, Nazareth, L, Sodergren, E, Weinstock, GM, Yakub, I, Birren, BW, Wilson, RK, Fulton, LL, Rogers, J, Burton, J, Carter, NP, Clee, CM, Griffiths, M, Jones, MC, McLay, K, Plumb, RW, Ross, MT, Sims, SK, Willey, DL, Chen, Z, Han, H, Kang, L, Godbout, M, Wallenburg, JC, L'Archevêque, P, Bellemare, G, Saeki, K, An, D, Fu, H, Li, Q, Wang, Z, Wang, R, Holden, AL, Brooks, LD, McEwen, JE, Guyer, MS, Wang, VO, Peterson, JL, Shi, M, Spiegel, J, Sung, LM, Zacharia, LF, Collins, FS, Kennedy, K, Jamieson, R, and Stewart, J
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Models, Molecular ,Population ,Single-nucleotide polymorphism ,Human genetic variation ,Biology ,Polymorphism, Single Nucleotide ,Article ,Antiporters ,Gene Frequency ,Humans ,International HapMap Project ,Selection, Genetic ,education ,Selection (genetic algorithm) ,Genetics ,education.field_of_study ,Multidisciplinary ,Natural selection ,Geography ,Edar Receptor ,Genome, Human ,Haplotype ,Regional Index: Eurasia ,Protein Structure, Tertiary ,Europe ,Genetics, Population ,Haplotypes ,Human genome - Abstract
With the advent of dense maps of human genetic variation, it is now possible to detect positive natural selection across the human genome. Here we report an analysis of over 3 million polymorphisms from the International HapMap Project Phase 2 (HapMap2). We used 'long-range haplotype' methods, which were developed to identify alleles segregating in a population that have undergone recent selection, and we also developed new methods that are based on cross-population comparisons to discover alleles that have swept to near-fixation within a population. The analysis reveals more than 300 strong candidate regions. Focusing on the strongest 22 regions, we develop a heuristic for scrutinizing these regions to identify candidate targets of selection. In a complementary analysis, we identify 26 non-synonymous, coding, single nucleotide polymorphisms showing regional evidence of positive selection. Examination of these candidates highlights three cases in which two genes in a common biological process have apparently undergone positive selection in the same population:LARGE and DMD, both related to infection by the Lassa virus, in West Africa;SLC24A5 and SLC45A2, both involved in skin pigmentation, in Europe; and EDAR and EDA2R, both involved in development of hair follicles, in Asia. ©2007 Nature Publishing Group., link_to_OA_fulltext
- Published
- 2007
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