WHOLE GENOME SEQUENCING OF SARS‐CoV‐2: COMPARISON OF TARGET CAPTURE AND AMPLICON SINGLE MOLECULAR REAL TIME SEQUENCING PROTOCOLS

alexandrossfakianakis shared this article with you from Inoreader WHOLE GENOME SEQUENCING OF SARS‐CoV‐2: COMPARISON OF TARGET CAPTURE AND AMPLICON SINGLE MOLECULAR REAL TIME SEQUENCING PROTOCOLS via Journal of Medical Virology ABSTRACT Fast, accurate sequencing methods are needed to identify new variants and genetic mutations of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome. Single Molecular Real Time (SMRT) Pacific Biosciences (PacBio) provides long, highly accurate sequences by circular consensus reads. This study compares the performance of a target capture SMRT Pacbio protocol for whole genome sequencing (WGS) of SARS-CoV-2 to that of an amplicon Pacbio SMRT sequencing protocol. The median genome coverage was higher (p<0.05) with the target capture protocol (99.3% [IQR: 96.3-99.5]) than with the amplicon protocol (99.3% [IQR :69.9-99.3]). The clades of 65 samples determined with both protocols were 100% concordant. After adjusting for Ct values, S gene coverage was higher with the target capture protocol than with the amplicon protocol. After stratification on Ct values, higher S gene coverage with the target capture protocol was observed only for samples w ith Ct>17 (p<0.01). Pacbio SMRT sequencing protocols appears to be suitable for WGS, genotyping and detecting mutations of SARS-CoV-2. This article is protected by copyright. All rights reserved. View on Web

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Translucency, color stability, and biaxial flexural strength of advanced lithium disilicate ceramic after coffee thermocycling

alexandrossfakianakis shared this article with you from Inoreader Translucency, color stability, and biaxial flexural strength of advanced lithium disilicate ceramic after coffee thermocycling via Journal of Esthetic and Restorative Dentistry Abstract Objective To compare the color stability, translucency, and biaxial flexural strength (BFS) of differently glazed advanced lithium disilicate (ALDS) with those of lithium disilicate (LDS) and zirconia-reinforced lithium silicate (ZLS) after coffee thermocycling. Materials and methods Forty disk-shaped specimens were prepared from three lithium silicate based materials (CEREC Tessera, ALDS; IPS e.max CAD, LDS; Vita Suprinity, ZLS). ALDS specimens were divided into two subgroups according to glazing procedures (reduced glaze duration, ALDS-S and normal glaze duration, ALDS-N), while LDS and ZLS specimens were crystallized and glazed. Color coordinate measurements were performed before and after coffee thermocycling. Color differences (ΔE 00) and relative translucency parameters (RTP) were calculated. Specimens were then subjected to BFS test. Statistical analysis was performed by using 1- (ΔE 00 and BFS) and 2-way (RTP) ANOVA tests (α = 0.05). Results ΔE 00 values of tested materials were similar (df = 3, F = 0.150, p = 0.929). Two-way ANOVA showed the significant effect of material type, coffee thermocycling, and the interaction between these parameters on RTP values (p < 0.001). Both before and after thermocycling, LDS had the highest (p ≤ 0.001) and ZLS had the lowest (p < 0.001) RTP values, while ALDS-N had higher RTP than ALDS-S (p ≤ 0.001). Among tested materials, only LDS had similar RTP values before and after thermocycling (p = 0.865) as the other materials had lower RTP values after thermocycling (p < 0.001). ALDS-N had higher BFS values than ALDS-S (p = 0.005), while LDS had similar values to ALDS specimens (p ≥ 0.201). ZLS had the highest BFS (p ≤ 0.007). Conclusions ALDS had comparable values to those of other materials. However, reduced glazing duration resulted in decreased translucency and BFS of ALDS. Clinical significance ALDS may be an appropriate restorative material for those patients with increased coffee consumption considering its color stability and ability to maintain translucency, particularly when glazed by using a conventional porcelain furnace. View on Web

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Helicobacter pylori and cardiovascular risk: Only a dead Helicobacter is a good Helicobacter?

alexandrossfakianakis shared this article with you from Inoreader Helicobacter pylori and cardiovascular risk: Only a dead Helicobacter is a good Helicobacter? via Helicobacter Abstract Objectives Helicobacter pylori (H. pylori) and cardiovascular (CV) disease share common symptoms and underlie many general medical complaints. Preliminary studies suggest an association between H. pylori positivity and CV risk, and gastroenterological guidelines recommend eradication of H. pylori in patients with manifest atherosclerosis. Therefore, the aim of this study was to examine the reciprocal association of H. pylori positivity and CV risk for their independence of shared risk factors. Methods We included 3284 asymptomatic participants of a colorectal cancer screening cohort who were offered and underwent upper gastrointestinal endoscopy. We calculated the 10-year risk for a CV event using the novel SCORE2 for each patient. We evaluated the association between H. pylori positivity and CV risk assessed by SCORE2 using both multilevel logistic and linear regression. We adjusted for age, sex and the concomitant diagnosis of metabolic syndrome. Lastly, we assessed the association between H. pylori status and mortality using proportional hazard Cox regression. Results In total, 2659 patients were H. pylori negative and 625 H. pylori positive. Helicobacter pylori positivity was associated with SCORE2 and remained so (r = .33; 95% CI 0.09–0.57; p = .006) after adjustment for age, sex, and the diagnosis of metabolic syndrome. Also, SCORE2 was associated with higher odds for H. pylori positivity (aOR 1.03 95% CI 1.01–1.05; p = .02) even after multivariable adjustment. Helicobacter pylori positivity was associated with neither CV (HR 0.60 95% CI 0.14–2.63; p = .50) nor all-cause (HR 1.20 95% CI 0.77–1.87; p = .43) mortality during a median follow-up of 9 years. Conclusions In our study, H. pylori positivity and CV risk were independently associated. This did not translate into a dissimilar CV mortality between H. pylori positive and H. pylori negative patients. However, the overwhelming majority of our patients underwent H. pylori eradication. We, therefore, think that H. pylori eradication is at least safe from a cardiovascular perspective and warranted from gastrointestinal standpoint. View on Web

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Temperature-Controlled Radiofrequency Device Treatment of the Nasal Valve for Nasal Airway Obstruction

alexandrossfakianakis shared this article with you from Inoreader Temperature-Controlled Radiofrequency Device Treatment of the Nasal Valve for Nasal Airway Obstruction via JAMA Otolaryngology–Head & Neck Surgery Online First This follow-up of a cohort of a randomized clinical trial assesses if nasal valve treatment with a temperature-controlled radiofrequency device is associated with improvement in symptoms of nasal airway obstruction through 12 months. View on Web

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Diagnostic test accuracy of sentinel lymph node biopsy in squamous cell carcinoma of the oropharynx, larynx, and hypopharynx: A systematic review and meta‐analysis

alexandrossfakianakis shared this article with you from Inoreader Diagnostic test accuracy of sentinel lymph node biopsy in squamous cell carcinoma of the oropharynx, larynx, and hypopharynx: A systematic review and meta‐analysis via Head & Neck Abstract The aim of this meta-analysis was to determine the diagnostic test accuracy of sentinel lymph node biopsy (SLNB) in patients with oropharyngeal, laryngeal, and hypopharyngeal squamous cell carcinoma (SCC). For this purpose, MEDLINE, EMBASE, and Web of Science were searched from inception to March 8, 2022. Included were studies evaluating diagnostic test accuracy of SLNB to identify cervical lymph node metastases with elective neck dissection or follow-up as reference. A bivariate generalized linear mixed model approach was used for the meta-analysis. Nineteen studies were eligible, evaluating 377 cases in total. The pooled estimates of sensitivity and negative predictive value were 0.93 (95% CI: 0.86–0.96) and 0.97 (95% CI: 0.94–0.98), respectively. The excellent accuracy of SLNB justifies a place in the diagnostic workup of patients with larynx and pharynx SCC. Randomized trials are required to demonstrate oncologic safety and benefits on treatment related morbidity and quali ty of life when omitting elective neck treatment based on SLNB. View on Web

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Climate Change and the Epidemiology of Infectious Diseases

alexandrossfakianakis shared this article with you from Inoreader Climate Change and the Epidemiology of Infectious Diseases in the United States via Clinical Infectious Diseases Advance Access ABSTRACT The earth is rapidly warming, driven by increasing atmospheric carbon dioxide and other gases resulting primarily from fossil fuel combustion. In addition to causing arctic ice melting and extreme weather events, climatologic factors are linked strongly to the transmission of many infectious diseases. Changes in the prevalence of infectious diseases not only reflect the impacts of temperature, humidity, and other weather-related phenomena on pathogens, vectors, and animal hosts, but is also part of a complex of social and environmental factors which will be affected by climate change, including land use, migration, and vector control. Vector- and water-borne diseases and coccidioidomycosis are all likely to be affected by a warming planet; there is also potential for climate-driven impacts on emerging infectious diseases and antimicrobial resistance. Additional resources for surveillance and public health activities are urgently needed, as well a s systematic education of clinicians on the health impacts of climate change. View on Web

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Disease Burden, Risk Factors, and Trends of Primary Central Nervous System (CNS) Cancer: a global study of registries data

alexandrossfakianakis shared this article with you from Inoreader Disease Burden, Risk Factors, and Trends of Primary Central Nervous System (CNS) Cancer: a global study of registries data via Neuro-Oncology Advance Access Abstract Background This study aimed to evaluate the global incidence, mortality, associated risk factors, and temporal trends of central nervous system (CNS) cancer by sex, age, and country. Methods We extracted incidence and mortality of CNS cancer from the GLOBOCAN (2020), Cancer Incidence in Five Continents series I-X, WHO mortality database, the Nordic Cancer Registries, and the Surveillance, Epidemiology, and End Results Program. We searched the Global Health data exchanges for the prevalence of its associated risk factors. We tested the trends by Average Annual Percentage Change (AAPC) from Joinpoint regression analysis with 95% confidence intervals in different age groups. Results The age-standardized rates (ASRs) of CNS cancer incidence and mortality were 3.5 and 2.8 per 100,000 globally. Southern Europe (ASR=6.0) and Western Asia (ASR=4.2) had the highest incidence and mortality, respectively. The incidence was associated with Human Development Index, Gross Domestics Products per capita, prevalence of traumatic brain injuries, occupational carcinogens exposure, and mobile phone use at the country level. There was an overall stable and mixed trend in the CNS cancer burden. However, increasing incidence was observed in younger male population from five countries, with Slovakia (AAPC=5.40; 95% CI=1.88, 9.04; p=0.007) reporting the largest increase. Conclusions While the overall global trends of cancer have been largely stable, significant increasing trends were found in the younger male population. The presence of some higher-HDI countries with increasing mortality suggested an ample scope for further research and exploration of the reasons behind these epidemiological trends. View on Web

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