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1.
J Prev Alzheimers Dis ; 11(4): 802-813, 2024.
Article in English | MEDLINE | ID: mdl-39044488

ABSTRACT

BACKGROUND: Converging evidence suggests that markers of Alzheimer's disease (AD) pathology in cognitively unimpaired older individuals are associated with high risk of cognitive decline and progression to functional impairment. The Anti-Amyloid Treatment in Asymptomatic Alzheimer's disease (A4) and Longitudinal Evaluation of Amyloid and Neurodegeneration Risk (LEARN) Studies enrolled a large cohort of cognitively normal older individuals across a range of baseline amyloid PET levels. Recent advances in AD blood-based biomarkers further enable the comparison of baseline markers in the prediction of longitudinal clinical outcomes. OBJECTIVES: We sought to evaluate whether biomarker indicators of higher levels of AD pathology at baseline predicted greater cognitive and functional decline, and to compare the relative predictive power of amyloid PET imaging, tau PET imaging, and a plasma P-tau217 assay. DESIGN: All participants underwent baseline amyloid PET scan, plasma P-tau217; longitudinal cognitive testing with the Primary Alzheimer Cognitive Composite (PACC) every 6 months; and annual functional assessments with the clinical dementia rating (CDR), cognitive functional index (CFI), and activities of daily living (ADL) scales. Baseline tau PET scans were obtained in a subset of participants. Participants with elevated amyloid (Aß+) on screening PET who met inclusion/exclusion criteria were randomized to receive placebo or solanezumab in a double-blind phase of the A4 Study over 240+ weeks. Participants who did not have elevated amyloid (Aß-) but were otherwise eligible for the A4 Study were referred to the companion observational LEARN Study with the same outcome assessments over 240+ weeks. SETTING: The A4 and LEARN Studies were conducted at 67 clinical trial sites in the United States, Canada, Japan and Australia. PARTICIPANTS: Older participants (ages 65-85) who were cognitively unimpaired at baseline (CDR-GS=0, MMSE 25-30 with educational adjustment, and Logical Memory scores within the normal range LMIIa 6-18) were eligible to continue in screening. Aß+ participants were randomized to either placebo (n=583) or solanezumab (n=564) in the A4 Study. A subset of Aß+ underwent tau PET imaging in A4 (n=350). Aß- were enrolled into the LEARN Study (n=553). MEASUREMENTS: Baseline 18-F Florbetapir amyloid PET, 18-F Flortaucipir tau PET in a subset and plasma P-tau217 with an electrochemiluminescence (ECL) immunoassay were evaluated as predictors of cognitive (PACC), and functional (CDR, CFI and ADL) change. Models were evaluated to explore the impact of baseline tertiles of amyloid PET and tertiles of plasma P-tau217 on cognitive and functional outcomes in the A4 Study compared to LEARN. Multivariable models were used to evaluate the unique and common variance explained in longitudinal outcomes based on baseline predictors, including effects for age, gender, education, race/ethnic group, APOEε4 carrier status, baseline PACC performance and treatment assignment in A4 participants (solanezumab vs placebo). RESULTS: Higher baseline amyloid PET CL and P-tau217 levels were associated with faster rates of PACC decline, and increased likelihood of progression to functional impairment (CDR 0.5 or higher on two consecutive measurements), both across LEARN Aß- and A4 Aß+ (solanezumab and placebo arms). In analyses considering all baseline predictor variables, P-tau217 was the strongest predictor of PACC decline. Among participants in the highest tertiles of amyloid PET or P-tau217, >50% progressed to CDR 0.5 or greater. In the tau PET substudy, neocortical tau was the strongest predictor of PACC decline, but plasma P-tau217 contributed additional independent predictive variance in commonality variance models. CONCLUSIONS: In a large cohort of cognitively unimpaired individuals enrolled in a Phase 3 clinical trial and companion observational study, these findings confirm that higher baseline levels of amyloid and tau markers are associated with increased rates of cognitive decline and progression to functional impairment. Interestingly, plasma P-tau217 was the best predictor of decline in the overall sample, superior to baseline amyloid PET. Neocortical tau was the strongest predictor of cognitive decline in the subgroup with tau PET, suggesting that tau deposition is most closely linked to clinical decline. These findings indicate that biomarkers of AD pathology are useful to predict decline in an older asymptomatic population and may prove valuable in the selection of individuals for disease-modifying treatments.


Subject(s)
Biomarkers , Cognitive Dysfunction , Positron-Emission Tomography , tau Proteins , Humans , Female , Aged , Male , tau Proteins/blood , Longitudinal Studies , Biomarkers/blood , Alzheimer Disease/blood , Alzheimer Disease/diagnostic imaging , Alzheimer Disease/drug therapy , Activities of Daily Living , Antibodies, Monoclonal, Humanized/therapeutic use , Amyloid beta-Peptides/blood , Amyloid beta-Peptides/metabolism , Aged, 80 and over , Disease Progression , Aniline Compounds
2.
J Prev Alzheimers Dis ; 11(4): 823-830, 2024.
Article in English | MEDLINE | ID: mdl-39044490

ABSTRACT

BACKGROUND: Blood-based AD biomarkers such as plasma P-tau217 are increasingly used in clinical trials as a screening tool. OBJECTIVES: To assess the utility of an electrochemiluminescence (ECL) immunoassay in predicting brain amyloid PET status in cognitively unimpaired individuals. SETTING: Plasma samples collected at baseline, week 12, and week 240 or endpoint originated from the Anti-Amyloid Treatment in Asymptomatic Alzheimer's Disease (A4) trial and the companion Longitudinal Evaluation of Amyloid Risk and Neurodegeneration (LEARN) study. PARTICIPANTS: Both A4 and LEARN enrolled eligible cognitively unimpaired persons 65 to 85 years. Individuals with elevated brain amyloid PET levels were eligible for the A4 Study, while those without elevated brain amyloid PET levels were eligible for the LEARN Study. INTERVENTION: Participants in the A4 Study received intravenous solanezumab (up to 1600 mg) or placebo every 4 weeks. The LEARN Study is an observational study without intervention. MEASUREMENTS: Plasma P-tau217 concentration levels from A4 Study participants were measured using an ECL immunoassay. Receiver Operating Characteristic (ROC) curve analysis was performed for each biomarker against amyloid positivity, defined by ≥22 CL and ≥ 33 CL. RESULTS: Receiver operating characteristic curve (ROC) analysis indicates high diagnostic value of P-tau217 in individuals with amyloid PET ≥ 20 (Area under the ROC (AUROC): 0.87) and ≥ 33 CL (AUROC: 0.89). Repeated testing with the placebo group taken 12 weeks apart (range: 68 to 143 days) and the LEARN participants taken between 1.4 and 1.75 years resulted in a strong positive correlation (Corr. 0.91 (0.90 to 0.92)). CONCLUSION: An ECL immunoassay testing plasma P-tau217 accurately predicts amyloid PET positivity in cognitively unimpaired individuals. Our future analyses aim to determine if use of this assay may reduce the screening burden of preclinical individuals into anti-amyloid clinical trials.


Subject(s)
Alzheimer Disease , Biomarkers , Positron-Emission Tomography , tau Proteins , Humans , Alzheimer Disease/diagnostic imaging , Alzheimer Disease/blood , Alzheimer Disease/diagnosis , Aged , tau Proteins/blood , Male , Female , Biomarkers/blood , Aged, 80 and over , Longitudinal Studies , Antibodies, Monoclonal, Humanized/therapeutic use , Brain/diagnostic imaging , Brain/metabolism , Amyloid beta-Peptides/blood , Amyloid beta-Peptides/metabolism
3.
J Prev Alzheimers Dis ; 11(4): 831-837, 2024.
Article in English | MEDLINE | ID: mdl-39044491

ABSTRACT

BACKGROUND: Individuals from diverse racial and ethnic groups are severely underrepresented in Alzheimer's disease trials in part due to disproportionate biomarker ineligibility. Evidence from recent studies support plasma phosphorylated tau 217 (P-tau217) as an early marker for brain Aß pathology and a reliable marker in predicting elevated brain amyloid PET in cognitively unimpaired adults. OBJECTIVES: To examine whether the relationship between P-tau217 and 18-F florbetapir PET standard uptake value ratios (SUVR) is influenced by race and ethnicity in the Anti-Amyloid treatment in Asymptomatic Alzheimer's disease (A4) preclinical AD studies. DESIGN: We conducted a retrospective analysis of A4 clinical trial and the LEARN natural history companion study data to evaluate the relationship between baseline P-tau217 and PET SUVR concentration levels by race and ethnicity. SETTING: The analysis was conducted on samples from participants enrolled across 65 study sites in the United States and Canada. PARTICIPANTS: Cognitively unimpaired adults aged 65-85 enrolled at North American sites in the A4 preclinical AD trial, pre-dose, (N=1018), and the LEARN (N=480) study. Participants were grouped into 2 categories, racial and ethnic underrepresented group (RE-URG) and non-RE-URG (nRE-URG) based on self-identification. MEASUREMENTS: A mixed-effects regression model was fit to determine differences in the relationship between P-tau217 and PET SUVR by race and ethnicity, adjusting for age, and APOE ε4 carrier status. RESULTS: Results from the linear mixed-effects model support that there was no statistically significant effect of race and ethnicity on the relationship between P-tau217 and PET SUVR. CONCLUSION: These findings suggest that the relationship between plasma P-tau217 and PET SUVR is the same across race and ethnicity. Future analyses should corroborate these findings in a larger sample and examine whether plasma P-tau217 reflects the differential amyloid prevalence previously reported for other biomarkers of amyloid.


Subject(s)
Alzheimer Disease , Positron-Emission Tomography , tau Proteins , Humans , Aged , Female , Male , tau Proteins/metabolism , tau Proteins/blood , Alzheimer Disease/blood , Alzheimer Disease/metabolism , Alzheimer Disease/diagnostic imaging , Aged, 80 and over , Retrospective Studies , Aniline Compounds , Ethnicity , Biomarkers/blood , Biomarkers/metabolism , Brain/diagnostic imaging , Brain/metabolism , Racial Groups , United States , Canada , Ethylene Glycols , Amyloid beta-Peptides/metabolism , Amyloid beta-Peptides/blood , Phosphorylation
4.
Breast Cancer Res Treat ; 206(1): 155-162, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38689173

ABSTRACT

PURPOSE: There has been a UK national directive to ensure that patients are offered reconstructive surgical options. We aimed to assess any change in oncoplastic practice over a 10-year period. METHODS: The surgical management of 7019 breast cancers was retrospectively assessed at Nightingale Breast Centre, Manchester University UK, from 2010 to 2019. The procedures were categorised into breast conservative surgery (BCS) and mastectomy ± immediate reconstruction. The data were analysed using inclusion and exclusion criteria. RESULTS: The overall rates of BCS and mastectomy were 60.1% and 39.9% respectively. No statistically significant change in the overall rates of BCS or mastectomy was observed over the last decade (p = 0.08). The rate of simple wide local excision (WLE) decreased from 98.7% to 89.3% (p < 0.001), whilst the rate of therapeutic mammoplasty (TM) increased from 1.3% to 8% (p < 0.01). The rate of chest wall perforator flaps (CWPF) changed from zero to account for 2.7% of all BCS by 2019. The overall rate of immediate breast reconstruction (IBR) did not significantly change over the study period, but it consistently remained above the national average of 27%. The rate of implant-based IBR increased from 61.3% to 76.5% (p = 0.012), whilst the rate of Latissimus Dorsi (LD) reconstruction decreased from 26.7% to 5.1% (p < 0.05). Additionally, the rate of nipple-sparing mastectomy significantly increased from 5.2% to 24%. CONCLUSION: No significant changes in the overall rates of BCS was observed, the rates of advanced breast conservation techniques, nipple-sparing mastectomy, and implant-based IBR all have increased, whilst the use of LD reconstruction decreased.


Subject(s)
Breast Neoplasms , Mammaplasty , Mastectomy , Humans , Female , Mammaplasty/trends , Mammaplasty/methods , Mammaplasty/statistics & numerical data , Breast Neoplasms/surgery , Breast Neoplasms/pathology , Breast Neoplasms/epidemiology , Retrospective Studies , Middle Aged , Mastectomy/methods , Mastectomy/statistics & numerical data , Mastectomy/trends , Adult , Aged , Mastectomy, Segmental/methods , Mastectomy, Segmental/statistics & numerical data , United Kingdom/epidemiology
5.
Environ Sci Process Impacts ; 26(5): 928-941, 2024 May 22.
Article in English | MEDLINE | ID: mdl-38635247

ABSTRACT

Motor vehicles are among the major sources of pollutants and greenhouse gases in urban areas and a transition to "zero emission vehicles" is underway worldwide. However, emissions associated with brake and tire wear will remain. We show here that previously unrecognized volatile and semi-volatile organic compounds, which have a similarity to biomass burning emissions are emitted during braking. These include greenhouse gases or, these classified as Hazardous Air Pollutants, as well as nitrogen-containing organics, nitrogen oxides and ammonia. The distribution and reactivity of these gaseous emissions are such that they can react in air to form ozone and other secondary pollutants with adverse health and climate consequences. Some of the compounds may prove to be unique markers of brake emissions. At higher temperatures, nucleation and growth of nanoparticles is also observed. Regions with high traffic, which are often disadvantaged communities, as well as commuters can be impacted by these emissions even after combustion-powered vehicles are phased out.


Subject(s)
Air Pollutants , Environmental Monitoring , Vehicle Emissions , Volatile Organic Compounds , Volatile Organic Compounds/analysis , Air Pollutants/analysis , Vehicle Emissions/analysis , Environmental Monitoring/methods , Air Pollution/statistics & numerical data , Motor Vehicles
6.
J Chem Phys ; 160(11)2024 Mar 21.
Article in English | MEDLINE | ID: mdl-38497471

ABSTRACT

We present QuTree, a C++ library for tree tensor network approaches. QuTree provides class structures for tensors, tensor trees, and related linear algebra functions that facilitate the fast development of tree tensor network approaches such as the multilayer multiconfigurational time-dependent Hartree approach or the density matrix renormalization group approach and its various extensions. We investigate the efficiency of relevant tensor and tensor network operations and show that the overhead for managing the network structure is negligible, even in cases with a million leaves and small tensors. QuTree focuses on providing simple, high-level routines while retaining easy access to the backend to facilitate novel developments. We demonstrate the capabilities of the package by computing the eigenstates of coupled harmonic oscillator Hamiltonians and performing random circuit simulations on a virtual quantum computer.

8.
JAR Life ; 13: 1-21, 2024.
Article in English | MEDLINE | ID: mdl-38204926

ABSTRACT

Background: Emerging evidence suggests that a number of factors can influence blood-based biomarker levels for Alzheimer's disease (AD) and Alzheimer's related dementias (ADRD). We examined the associations that demographic and clinical characteristics have with AD/ADRD blood-based biomarker levels in an observational continuation of a clinical trial cohort of older individuals with type 2 diabetes and overweight or obesity. Methods: Participants aged 45-76 years were randomized to a 10-year Intensive Lifestyle Intervention (ILI) or a diabetes support and education (DSE) condition. Stored baseline and end of intervention (8-13 years later) plasma samples were analyzed with the Quanterix Simoa HD-X Analyzer. Changes in Aß42, Aß40, Aß42/Aß40, ptau181, neurofilament light chain (NfL), and glial fibrillary acidic protein (GFAP) were evaluated in relation to randomization status, demographic, and clinical characteristics. Results: In a sample of 779 participants from the Look AHEAD cohort, we found significant associations between blood-based biomarkers for AD/ADRD and 15 of 18 demographic (age, gender, race and ethnicity, education) and clinical characteristics (APOE, depression, alcohol use, smoking, body mass index, HbA1c, diabetes duration, diabetes treatment, estimated glomerular filtration rate, hypertension, and history of cardiovascular disease) . Conclusions: Blood-based biomarkers of AD/ADRD are influenced by common demographic and clinical characteristics. These factors should be considered carefully when interpreting these AD/ADRD blood biomarker values for clinical or research purposes.

9.
Intensive Care Med ; 50(4): 610-611, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38294524
10.
J Community Health ; 49(3): 385-393, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38032459

ABSTRACT

OBJECTIVE: This study utilizes geospatial analytic techniques to examine HIV hotspots in Alabama leveraging Medicaid utilization data. METHODS: This cross-sectional study leveraged Medicaid utilization data from Alabama's 67 counties, averaging 9,861 Medicaid recipients aged > 18 years old per county. We used Alabama Medicaid administrative claims data from January 1, 2016, to December 31, 2020, to identify individuals with HIV. Using Microsoft SQL Server, we obtained the average annual count of HIV Medicaid claims in each of the 67 Alabama counties (numerator) and the number of adult Medicaid recipients in each county (denominator), and standardized with a multiplier of 100,000. We also examined several other area-level summary variables (e.g., non-high school completion, income greater than four times the federal poverty level, social associations, urbanicity/rurality) as social and structural determinants of health. County-boundary choropleth maps were created representing the geographic distribution of HIV rates per 100,000 adult Medicaid recipients in Alabama. Leveraging ESRI ArcGIS and local indicators of spatial association (LISA), results were examined using local Moran's I to identify geographic hotspots. RESULTS: Eleven counties had HIV rates higher than 100 per 100,000. Three were hotspots. Being an HIV hotspot was significantly associated with relatively low educational attainment and less severe poverty than other areas in the state. CONCLUSIONS: Findings suggesting that the HIV clusters in Alabama were categorized by significantly less severe poverty and lower educational attainment can aid ongoing efforts to strategically target resources and end the HIV epidemic in U.S.' Deep South.


Subject(s)
HIV Infections , Social Determinants of Health , Adult , United States/epidemiology , Humans , Adolescent , Alabama/epidemiology , Prevalence , Cross-Sectional Studies , Medicaid , HIV Infections/epidemiology
11.
BMC Microbiol ; 23(1): 306, 2023 10 26.
Article in English | MEDLINE | ID: mdl-37880584

ABSTRACT

BACKGROUND: Salmonella spp. and pathogenic strains of Escherichia coli are among the major foodborne zoonotic pathogens. These bacterial pathogens cause human illnesses characterized by hemorrhagic colitis, vomiting, nausea, and other agent-related symptoms. The increasing occurrence of antimicrobial resistance in these pathogens is also a serious public health concern globally. Regular surveillance of phenotypes and genotypes of Salmonella spp. and Escherichia coli from animal-derived foods is necessary for effective reduction and control of these foodborne pathogens. This study was conducted to assess the occurrence, antimicrobial resistance, virulence genes and genetic diversity of Salmonella spp. and E. coli isolates from fresh Nile tilapia obtained from retail markets in Nairobi, Kenya. METHODS: A total of 68 fresh Nile tilapia fish samples were collected from retail markets and used for isolation of Salmonella spp. and E. coli. Antimicrobial susceptibilities of the isolates weretested by Kirby-Bauer agar disc diffusion method. According to the antimicrobial resistance profiles, the multi-drug resistant isolates were identified by 16 S rRNA sequencing and phylogenetic analysis using the Bayesian inference method. The MDR Salmonella spp. and E. coli isolates were subjected to PCR-based screening for the detection virulence and antibiotic resistance genes. RESULTS: The prevalence of contamination of the fish samples with Salmonella spp. and E.coli was 26.47% and 35.29% respectively. Overall phenotypic resistance among the Salmonella spp. ranged from 5.5% for ceftazidime, chloramphenicol, meropenem, nitrofurantoin and streptomycin and 22.2% for penicillin-G. For E. coli phenotypic resistance ranged from 4.2% for ceftazidime and chloramphenicol and 25% for rifampicin. Multi-drug resistance was observed in three Salmonella spp. and two E. coli isolates. Results of 16 S rRNA sequences, sequence alignment and phylogenic trees confirmed the identified MDR isolates as S. typhymurium WES-09, S. typhymurium MAK-22, S. typhimurium EMB-32 and E. coli MAK-26 and E. coli LAN-35. The presence of antibiotic-resistance genes belonging to ß-lactamases, tetracycline, sulfonamide, trimethoprim and aminoglycosides-resistant genes were detected in all the identified MDR isolates. CONCLUSIONS: The findings from this study indicate that Nile tilapia (Oreochromis niloticus) sold in retail markets can acts as reservoirs of Salmonella spp. and E. coli pathogens linked to human disease, some of which were multidrug resistance to critically important antimicrobials. Both microorganisms are of zoonotic significance and represent a significant public health risk to the society.


Subject(s)
Anti-Bacterial Agents , Cichlids , Animals , Humans , Anti-Bacterial Agents/pharmacology , Escherichia coli , Ceftazidime/pharmacology , Phylogeny , Bayes Theorem , Drug Resistance, Bacterial , Kenya , Salmonella , Chloramphenicol/pharmacology
12.
Front Pediatr ; 11: 1189722, 2023.
Article in English | MEDLINE | ID: mdl-37492608

ABSTRACT

Introduction: Foreign body aspiration is a common cause of respiratory distress in pediatrics, but the diagnosis can be challenging given aspirated objects are mostly radiolucent on chest radiographs and there is often no witnessed choking event. We present a case of a patient who was initially managed as severe status asthmaticus, requiring veno-arterial extracorporeal membrane oxygenation (VA-ECMO) for refractory hypercarbia and hypoxemia, but was later found to have bilateral bronchial foreign body aspiration. This case is unique in its severity of illness, diagnostic dilemma with findings suggesting a more common diagnosis of asthma, and use of ECMO as a bridge to diagnosis and recovery. Patient case: A previously healthy 2-year-old boy presented during peak viral season with a 3-day history of fever, cough, coryza, and increased work of breathing over the prior 24 h. There was no reported history of choking or aspiration. He was diagnosed with asthma and treated with bronchodilator therapy. Physical examination revealed pulsus paradoxus, severe work of breathing with bilateral wheeze, and at times a silent chest. Chest radiographs showed bilateral lung hyperinflation. Following a brief period of stability on maximum bronchodilator therapies and bilevel positive pressure support, the patient had a rapid deterioration requiring endotracheal intubation, with subsequent cannulation to VA-ECMO. A diagnostic flexible bronchoscopy was performed and demonstrated bilateral foreign bodies, peanuts, in the right bronchus intermedius and the left mainstem bronchus. Removal of the foreign bodies was done by rigid bronchoscopy facilitating rapid wean from VA-ECMO and decannulation within 24 h of foreign body removal. Conclusion: Foreign body aspiration should be suspected in all patients presenting with atypical history and physical examination findings, or in patients with suspected common diagnoses who do not progress as expected or deteriorate after a period of stability. Extracorporeal life support can be used as a bridge to diagnosis and recovery in patients with hemodynamic or respiratory instability.

13.
Trends Mol Med ; 29(9): 765-776, 2023 09.
Article in English | MEDLINE | ID: mdl-37474378

ABSTRACT

Electronic health records (EHRs) have become increasingly relied upon as a source for biomedical research. One important research application of EHRs is the identification of biomarkers associated with specific patient states, especially within complex conditions. However, using EHRs for biomarker identification can be challenging because the EHR was not designed with research as the primary focus. Despite this challenge, the EHR offers huge potential for biomarker discovery research to transform our understanding of disease etiology and treatment and generate biological insights informing precision medicine initiatives. This review paper provides an in-depth analysis of how EHR data is currently used for phenotyping and identifying molecular biomarkers, current challenges and limitations, and strategies we can take to mitigate challenges going forward.


Subject(s)
Biomedical Research , Electronic Health Records , Humans , Precision Medicine , Biomarkers
14.
mBio ; 14(4): e0104623, 2023 08 31.
Article in English | MEDLINE | ID: mdl-37389439

ABSTRACT

High error rates of viral RNA-dependent RNA polymerases lead to diverse intra-host viral populations during infection. Errors made during replication that are not strongly deleterious to the virus can lead to the generation of minority variants. However, accurate detection of minority variants in viral sequence data is complicated by errors introduced during sample preparation and data analysis. We used synthetic RNA controls and simulated data to test seven variant-calling tools across a range of allele frequencies and simulated coverages. We show that choice of variant caller and use of replicate sequencing have the most significant impact on single-nucleotide variant (SNV) discovery and demonstrate how both allele frequency and coverage thresholds impact both false discovery and false-negative rates. When replicates are not available, using a combination of multiple callers with more stringent cutoffs is recommended. We use these parameters to find minority variants in sequencing data from SARS-CoV-2 clinical specimens and provide guidance for studies of intra-host viral diversity using either single replicate data or data from technical replicates. Our study provides a framework for rigorous assessment of technical factors that impact SNV identification in viral samples and establishes heuristics that will inform and improve future studies of intra-host variation, viral diversity, and viral evolution. IMPORTANCE When viruses replicate inside a host cell, the virus replication machinery makes mistakes. Over time, these mistakes create mutations that result in a diverse population of viruses inside the host. Mutations that are neither lethal to the virus nor strongly beneficial can lead to minority variants that are minor members of the virus population. However, preparing samples for sequencing can also introduce errors that resemble minority variants, resulting in the inclusion of false-positive data if not filtered correctly. In this study, we aimed to determine the best methods for identification and quantification of these minority variants by testing the performance of seven commonly used variant-calling tools. We used simulated and synthetic data to test their performance against a true set of variants and then used these studies to inform variant identification in data from SARS-CoV-2 clinical specimens. Together, analyses of our data provide extensive guidance for future studies of viral diversity and evolution.


Subject(s)
COVID-19 , Orthomyxoviridae , Viruses , Humans , SARS-CoV-2/genetics , Mutation , High-Throughput Nucleotide Sequencing/methods
15.
Article in English | MEDLINE | ID: mdl-37236876

ABSTRACT

OBJECTIVE: This study measured effective (E) and equivalent doses from adult and child 3-dimensional (3D) and 2D posterior bitewing (PBW) examinations using the PORTRAY stationary-intraoral tomosynthesis radiography system. STUDY DESIGN: Adult and child phantoms and optically stimulated luminescent dosimeters were used to measure doses for adult-4 and child-2 projection PBW examinations acquired without (W/O) and with (W) a direct digital sensor in the beam path. Child doses without and with thyroid shielding were measured. RESULTS: Three-dimensional examination E values (µSv) W/O and W were 16.7 and 7.3 for adult, 9.2 and 3.5 for child, and 8.7 and 3.0 with thyroid shielding, respectively. Two-dimensional examination E values W/O and W were 4.3 and 1.5 for adult, 2.1 and 0.6 for child, and 2.0 and 0.5 with shielding, respectively. Sensor presence reduced E for all adult and child examinations (P = .0001). Child E was reduced compared with adult E for both sensor conditions in 3D (P < .0001) and 2D (P ≤ .0043) imaging. Adult and child 3D W/O and W equivalent thyroid doses did not differ (P ≥ .9996). However, child 2D W/O and W doses were lower (P ≤ .0002). Shielding produced no reduction (P ≥ .1128) for either 3D condition or 2D with the sensor (P = .6615) but reduced child 2D dose without the sensor. CONCLUSIONS: Inclusion of a sensor yielded significant reductions in adult and child E. Sensor presence impacted thyroid dose reduction more than shielding.


Subject(s)
Radiography, Bitewing , Adult , Humans , Radiation Dosage , Radiography , Phantoms, Imaging
16.
J Dent Child (Chic) ; 90(1): 3-10, 2023 Jan 15.
Article in English | MEDLINE | ID: mdl-37106534

ABSTRACT

Purpose: To compare the effective dose (E) of the Tru-Image® rectangular collimator and the universal round collimator of a Planmeca® wall-mounted radiograph unit for two bitewing radiographs (right and left) on a pediatric phantom.
Methods: Absorbed doses utilizing the Tru-Image ®rectangular collimator and universal round collimator were acquired using an anthropomorphic 10-year-old child phantom. Each set of 24 dosimeters was exposed to two bitewing exposures with the manufacturer's child settings. Fifty clinical exposures were completed for each set and three sets were exposed for each collimator. The average E per exposure was calculated.
Results: The overall E for the Tru-Image ®rectangular collimator and the universal round collimator were 6.3 microsieverts (µSv) and 25.3 µSv, respectively. This difference was statistically significant (P <0.001). The highest equivalent dose for both collimators was delivered to the oral mucosa. When compared to the universal round collimator, the Tru-Image ® rectangular collimator had significant dose reduction at all locations (P <0.05). When normalized and adjusted to the same source-to-end distance, there was an overall 65 percent dose reduction with the rectangular collimator.
Conclusion: The average effective dose was significantly reduced with the use of the Tru-Image ®rectangular collimator. Clinical use of this rectangular collimator should be considered in the pediatric population.


Subject(s)
Protective Devices , Radiometry , Child , Humans , Radiation Dosage , Radiography , Phantoms, Imaging
17.
AIMS Microbiol ; 9(1): 55-74, 2023.
Article in English | MEDLINE | ID: mdl-36891530

ABSTRACT

Microalgae biomasses are excellent sources of diverse bioactive compounds such as lipids, polysaccharides, carotenoids, vitamins, phenolics and phycobiliproteins. Large-scale production of these bioactive substances would require microalgae cultivation either in open-culture systems or closed-culture systems. Some of these bioactive compounds (such as polysaccharides, phycobiliproteins and lipids) are produced during their active growth phase. They appear to have antibacterial, antifungal, antiviral, antioxidative, anticancer, neuroprotective and chemo-preventive activities. These properties confer on microalgae the potential for use in the treatment and/or management of several neurologic and cell dysfunction-related disease conditions, including Alzheimer's disease (AD), AIDS and COVID-19, as shown in this review. Although several health benefits have been highlighted, there appears to be a consensus in the literature that the field of microalgae is still fledgling, and more research needs to be carried out to ascertain the mechanisms of action that underpin the effectiveness of microalgal compounds. In this review, two biosynthetic pathways were modeled to help elucidate the mode of action of the bioactive compounds from microalgae and their products. These are carotenoid and phycobilin proteins biosynthetic pathways. The education of the public on the importance of microalgae backed with empirical scientific evidence will go a long way to ensure that the benefits from research investigations are quickly rolled out. The potential application of these microalgae to some human disease conditions was highlighted.

18.
Women Birth ; 36(1): e118-e124, 2023 Feb.
Article in English | MEDLINE | ID: mdl-35568665

ABSTRACT

BACKGROUND: Many high-income countries have seen an increase in severe perineal trauma. Teaching strategies and conditions for learning during the active second stage of labour are scarcely described. AIM: To describe midwifery preceptors and midwifery students' experiences' of teaching and learning how to manage the second stage of labour, with the specific aim of preventing severe perineal trauma. METHODS: A qualitative study with focus group discussions and individual in depth-interviews with preceptor midwives (n = 23) and student midwives (n = 10). Data were analysed by qualitative content analysis. RESULTS: "A complex and demanding situation with mutual need for feedback, reflection and safety" was the overall theme describing the conditions. Three sub-themes were identified. "Adapting to a unique situation" refers to the difficulty of teaching and learning the aspects needed to prevent severe perineal trauma, and to provide care during this stage. "Hindering and limiting circumstances" describes teaching strategies that were perceived negatively, and how midwifery students tried to adapt to the preceptors rather than the birthing women. "A trustful and communicative relationship" describes the importance of the relationship between the student and the preceptor, where communication was a central, but not obvious part. CONCLUSION: An increased awareness among preceptors is needed to optimize teaching strategies, enabling the students to focus on learning the art of the second stage of labour; supporting the woman, preventing severe perineal trauma and ensuring the safety of the unborn baby. Future research should address how existing prevention models can include training to increase preceptors' confidence in teaching.


Subject(s)
Midwifery , Students, Nursing , Pregnancy , Humans , Female , Midwifery/education , Learning , Parturition , Qualitative Research , Teaching
19.
Adv Physiol Educ ; 47(1): 117-123, 2023 Mar 01.
Article in English | MEDLINE | ID: mdl-36546847

ABSTRACT

During the course of undergraduate studies, physiology (and related STEM) majors should acquire a both broad and in-depth foundation in physiological knowledge along with a distinct range of transferable (professional) skills (e.g., critical thinking, communication skills, data analysis). Previously, through a consultative and iterative process with physiology educators, the Professional Skills Committee of the Physiology Majors Interest Group (PMIG) defined and refined a consensus list of professional skills that physiology majors should acquire during their program of study. Here we describe the development and beta testing of a convenient tool to enable physiology and physiology-related program educators to map these professional skills across their curricula. The tool, referred to as PS-MAP, uses the Qualtrics platform and allows programs to collect and organize data about whether students are provided the opportunity to learn and develop the defined professional skills during their undergraduate experience. The authors have made the PS-MAP tool freely available to educators and provide practical tips for its implementation. Use of the PS-MAP tool and the data collected can help programs identify curricular strengths and gaps as well as facilitate curricular discussions among educators within the program.NEW & NOTEWORTHY In addition to foundational physiology knowledge, undergraduate physiology and related STEM majors should develop a range of transferable professional skills. However, evidence of this curricular goal has been lacking. Therefore, the Professional Skills Committee of the Physiology Majors Interest Group (PMIG) developed the freely available and convenient Physiology Professional Skills Curriculum Mapping Tool (PS-MAP) to assist educators in mapping these professional skills throughout their programs.


Subject(s)
Curriculum , Learning , Humans , Students , Thinking
20.
Osteoarthritis Cartilage ; 31(2): 199-212, 2023 02.
Article in English | MEDLINE | ID: mdl-36354073

ABSTRACT

OBJECTIVE: Transcriptomic changes in joint tissues during the development of osteoarthritis (OA) are of interest for the discovery of biomarkers and mechanisms of disease. The objective of this study was to use the rat medial meniscus transection (MMT) model to discover stage and tissue-specific transcriptomic changes. DESIGN: Sham or MMT surgeries were performed in mature rats. Cartilage, menisci and synovium were scored for histopathological changes at 2, 4 and 6 weeks post-surgery and processed for RNA-sequencing. Differentially expressed genes (DEG) were used to identify pathways and mechanisms. Published transcriptomic datasets from animal models and human OA were used to confirm and extend present findings. RESULTS: The total number of DEGs was already high at 2 weeks (723 in meniscus), followed by cartilage (259) and synovium (42) and declined to varying degrees in meniscus and synovium but increased in cartilage at 6 weeks. The most upregulated genes included tenascins. The 'response to mechanical stimulus' and extracellular matrix-related pathways were enriched in both cartilage and meniscus. Pathways that were enriched in synovium at 4 weeks indicate processes related to synovial hyperplasia and fibrosis. Synovium also showed upregulation of IL-11 and several MMPs. The mechanical stimulus pathway included upregulation of the mechanoreceptors PIEZO1, PIEZO2 and TRPV4 and nerve growth factor. Analysis of data from prior RNA-sequencing studies of animal models and human OA support these findings. CONCLUSION: These results indicate several shared pathways that are affected during OA in cartilage and meniscus and support the role of mechanotransduction and other pathways in OA pathogenesis.


Subject(s)
Cartilage, Articular , Osteoarthritis , Humans , Rats , Animals , Transcriptome , Mechanotransduction, Cellular , Cartilage, Articular/pathology , Osteoarthritis/metabolism , Synovial Membrane/metabolism , Extracellular Matrix/metabolism , RNA/metabolism , Disease Models, Animal , Ion Channels/metabolism , TRPV Cation Channels/metabolism
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