The accurate identification of SARS-CoV-2 (SC2) variants and estimation of their abundance in mixed population samples (
, air or wastewater) is imperative for successful surveillance of community ...level trends. Assessing the performance of SC2 variant composition estimators (VCEs) should improve our confidence in public health decision making. Here, we introduce a linear regression based VCE and compare its performance to four other VCEs: two re-purposed DNA sequence read classifiers (Kallisto and Kraken2), a maximum-likelihood based method (Lineage deComposition for Sars-Cov-2 pooled samples (LCS)), and a regression based method (Freyja).
We simulated DNA sequence datasets of known variant composition from both Illumina and Oxford Nanopore Technologies (ONT) platforms and assessed the performance of each VCE. We also evaluated VCEs performance using publicly available empirical wastewater samples collected for SC2 surveillance efforts. Bioinformatic analyses were performed with a custom NextFlow workflow (C-WAP, CFSAN Wastewater Analysis Pipeline). Relative root mean squared error (RRMSE) was used as a measure of performance with respect to the known abundance and concordance correlation coefficient (CCC) was used to measure agreement between pairs of estimators.
Based on our results from simulated data, Kallisto was the most accurate estimator as it had the lowest RRMSE, followed by Freyja. Kallisto and Freyja had the most similar predictions, reflected by the highest CCC metrics. We also found that accuracy was platform and amplicon panel dependent. For example, the accuracy of Freyja was significantly higher with Illumina data compared to ONT data; performance of Kallisto was best with ARTICv4. However, when analyzing empirical data there was poor agreement among methods and variations in the number of variants detected (
, Freyja ARTICv4 had a mean of 2.2 variants while Kallisto ARTICv4 had a mean of 10.1 variants).
This work provides an understanding of the differences in performance of a number of VCEs and how accurate they are in capturing the relative abundance of SC2 variants within a mixed sample (
, wastewater). Such information should help officials gauge the confidence they can have in such data for informing public health decisions.
Wastewater surveillance has emerged as a crucial public health tool for population-level pathogen surveillance. Supported by funding from the American Rescue Plan Act of 2021, the FDA's genomic ...epidemiology program, GenomeTrakr, was leveraged to sequence SARS-CoV-2 from wastewater sites across the United States. This initiative required the evaluation, optimization, development, and publication of new methods and analytical tools spanning sample collection through variant analyses. Version-controlled protocols for each step of the process were developed and published on protocols.io. A custom data analysis tool and a publicly accessible dashboard were built to facilitate real-time visualization of the collected data, focusing on the relative abundance of SARS-CoV-2 variants and sub-lineages across different samples and sites throughout the project. From September 2021 through June 2023, a total of 3,389 wastewater samples were collected, with 2,517 undergoing sequencing and submission to NCBI under the umbrella BioProject, PRJNA757291. Sequence data were released with explicit quality control (QC) tags on all sequence records, communicating our confidence in the quality of data. Variant analysis revealed wide circulation of Delta in the fall of 2021 and captured the sweep of Omicron and subsequent diversification of this lineage through the end of the sampling period. This project successfully achieved two important goals for the FDA's GenomeTrakr program: first, contributing timely genomic data for the SARS-CoV-2 pandemic response, and second, establishing both capacity and best practices for culture-independent, population-level environmental surveillance for other pathogens of interest to the FDA.
This paper serves two primary objectives. First, it summarizes the genomic and contextual data collected during a Covid-19 pandemic response project, which utilized the FDA's laboratory network, traditionally employed for sequencing foodborne pathogens, for sequencing SARS-CoV-2 from wastewater samples. Second, it outlines best practices for gathering and organizing population-level next generation sequencing (NGS) data collected for culture-free, surveillance of pathogens sourced from environmental samples.
A clinical trial assessed the efficacy of three treatments, all involving metformin, on glycemic control in youth-onset type 2 diabetes. This follow-up study shows that the risk of complications ...increased steadily over time, and complications developed in most participants by young adulthood.
The lecture timetabling problem is known to be a highly constrained combinatorial optimization problem. There have been many attempts to address this problem using integer programming, graph coloring ...and several heuristic search methods. However, since each university has its own timetable setting requirements, it is difficult to develop a general solution method. Thus, the work is generally done manually. This paper attempts to solve the lecture timetabling problem of the University of Asmara using a customized memetic algorithm that we have called ALTUMA. It is a hybrid of genetic algorithms with hill-climbing operators. The performance of ALTUMA was evaluated using data obtained from the University. Empirical results show that ALTUMA is capable of producing good results in a reasonable amount of time. Besides, the results demonstrate that incorporating local search operators with a probabilistic scheme and delta method of fitness evaluation into the memetic algorithm significantly improves the search capabilities of the algorithm.
Introduction
On-treatment excursions of liver laboratory test values in clinical trials involving subjects with underlying liver disease are relevant for the efficacy and safety assessment of drug ...products and biologics. Existing visualization and analysis tools do not efficiently provide an integrated view of these excursions when baseline liver tests are abnormal.
Objective
The aim of this study was to develop a composite plot that enables visualization of on-treatment changes in liver test results both as multiples of the upper limit of normal defined by each laboratory’s reference population (×ULN) and multiples of the subjects’ baseline (×BLN) values.
Methods
The composite plot approach combines biochemical evaluation for drug-induced severe hepatotoxicity (eDISH) plots sequentially applied to subjects’ baseline and peak on-treatment liver test results normalized by ULN and integrates them into a four-panel shift plot of peak on-treatment values normalized by BLN.
Results
The composite plot enabled efficient assessment of improvement in liver test values during treatment compared with pretreatment in subjects treated with the investigational drug (or the natural history of placebo-treated subjects) and identified outlier subjects for potential drug-induced liver injury.
Conclusion
For studies in subjects with abnormal baseline values, the composite plot has potential application in the assessment of beneficial and concerning on-treatment modifications in liver test values in reference to the individual subject’s baseline and population threshold values.
To describe the longitudinal effects of sex, race-ethnicity, and metabolic factors on the risk of developing diabetic kidney disease (DKD) in the Treatment Options for Type 2 Diabetes in Adolescents ...and Youth (TODAY) cohort.
Urine albumin-to-creatinine ratio (UACR) and estimated glomerular filtration rate (eGFR) by serum creatinine and cystatin C were assessed annually for up to 15 years after study entry. Markers of DKD included micro- and macroalbuminuria (UACR ≥30 mg/g and ≥300 mg/g, respectively), hyperfiltration (eGFR ≥135 mL/min/1.73 m
), and rapid eGFR annual decline (>3 mL/min/1.73 m
and/or ≥3.3%). The relationships between risk factors and DKD were evaluated longitudinally using time-to-event models.
Data were available on 677 participants, average age at baseline 14 years, with a mean ± SD follow-up of 10.2 ± 4.5 years. Each 1% increment in HbA
conferred higher risk of microalbuminuria (hazard ratio 1.24 95% CI 1.18, 1.30), macroalbuminuria (1.22, 1.11, 1.34), hyperfiltration (1.11, 1.05, 1.17), and rapid eGFR decline (1.12, 1.04, 1.20). Higher systolic blood pressure and baseline serum uric acid, and lower indices of β-cell function (C-peptide index and oral disposition index oDI), increased the risk of microalbuminuria, while higher triglycerides increased risk of micro- and macroalbuminuria. Lower oDI levels, female sex, and Hispanic ethnicity were associated with higher risk of hyperfiltration.
Elevated HbA
was a shared risk factor among all phenotypes of DKD in this longitudinal cohort of adolescents and young adults with youth-onset type 2 diabetes. Other risk factors included elevated blood pressure, triglycerides, serum uric acid, and β-cell dysfunction.
To report the prevalence of depression, eating disorder symptoms, and impaired health-related quality of life (HRQOL) and examine their longitudinal associations with glycemia and diabetes ...complications in young adults with youth-onset type 2 diabetes.
Participants recruited over a 4-year period were enrolled at 15 clinical diabetes centers in the follow-up observational Treatment Options for type 2 Diabetes in Adolescents and Youth (TODAY2) study. From 2014-2020, prevalence of symptoms of depression, eating disorders, and HRQOL by sex, race/ethnicity, and baseline family income were assessed annually. Longitudinal relationships between assessments of glycemia and complications with psychiatric symptoms and HRQOL were evaluated in adjusted models.
Participants (n = 514) were 21.7 ± 2.5 years old with a diabetes duration of 8.6 ± 1.5 years in year 1 of TODAY 2 (2014). Symptoms of depression and impaired HRQOL were common and increased significantly over 6 years (14.0% to 19.2%, P = 0.003; and 13.1% to 16.7%, P = 0.009, respectively). Depression and impaired HRQOL were more common in women and those with lower baseline family income but did not differ by race/ethnicity. Rates of binge eating were stable over time; self-reported purging increased. Over time, symptoms of depression were associated with higher HbA1c, hypertension, and retinopathy progression; impaired HRQOL was associated with higher BMI, systolic blood pressure, hypertension, and retinopathy progression; and symptoms of eating disorders were associated with higher BMI.
Significant psychiatric symptoms and impaired HRQOL are common among emerging adults with youth-onset type 2 diabetes and are positively associated with glycemia, hypertension, and retinopathy progression in this group that is at ongoing risk for medical morbidity.
Salmonella enterica is well known for its ability to survive and persist in low-moisture environments. Previous studies have indicated a link between the initial cell level and the population of ...Salmonella that survives after desiccation and subsequent storage; however, how the initial cell concentration affects survival is unknown. This study was conducted to examine this phenomenon and to determine whether it occurs in other microorganisms, specifically Shiga toxigenic Escherichia coli (STEC) and Enterococcus faecium. Salmonella, STEC, and E. faecium were grown as sessile cells on Trypticase soy agar with yeast extract (TSAYE) and harvested in buffered peptone water (BPW). To determine recovery at different initial cell levels, cultures were diluted to 9, 7, and 5 log CFU/mL and applied to filters. Filters were dried for 24 h and then stored for 28 days at 25°C and 33% relative humidity. During storage, cells were recovered from filters with BPW and cultivated on TSAYE. Recovery of both Salmonella and E. coli, but not E. faecium, was nonproportional. Lower initial populations were less viable after 24 h of desiccation; ≥10 log CFU/mL was recovered when 11 log CFU/mL was desiccated, but <3 log CFU/mL was recovered when 5 log CFU/mL was desiccated. Once dried, persistence did not appear affected by initial cell concentration. When inactivated (heat-treated) cells were added to the diluent, recovery of Salmonella was proportional with respect to the initial cell level. To further examine the response to desiccation, Salmonella was diluted in BPW containing 1 of 11 test cell components related to quorum sensing or known to affect desiccation resistance to assess recovery and persistence. Of the 11 additions, only cell debris fractions, cell-free extract, and peptidoglycan improved recovery of Salmonella. Desiccation survival appears related to cell wall components; however, the exact mechanism affecting survival remains unknown.
To assess pregnancy outcomes in young women with youth-onset type 2 diabetes followed in the Treatment Options for Type 2 Diabetes in Adolescents and Youth (TODAY) study.
Pregnancy information ...(outcome and any maternal or fetal complications) was obtained from the female participants by self-report. Additionally, medical records for the pregnancy and the child's neonatal course were obtained with data abstracted into standardized forms.
Over a maximum of 15 years, 260 pregnancies were reported by 141 women (aged 21.5 ± 3.2 years, BMI 35.6 ± 7.2 kg/m
, and diabetes duration 8.1 ± 3.2 years). Contraception use prior to pregnancy was reported by 13.5% of the women. Complications were reported by 65% of the women during their pregnancy. Pregnancy loss was observed in 25.3% and preterm birth in 32.6% of pregnancies. HbA
≥8% was observed in 31.9% of the pregnancies, and 35% of the pregnancies were complicated by chronic hypertension. Nephropathy prior to pregnancy was observed in 25% of the women. In the offspring, 7.8% were classified as small for gestational age, 26.8% large for gestational age, and 17.9% in the macrosomic range.
Based on observations from the TODAY cohort, young women with pregestational, youth-onset type 2 diabetes had very high rates of maternal complications stemming from significant socioeconomic disadvantage. The substantial maternal and infant complications seen in these young moms could potentially be avoided with improved contraception rates and reproductive planning.
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