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The possible dietary influences on in vivo antipyrine and aminopyrine kinetics with reference to energy (1500, 1800, 3000 kcal) and protein (5, 10, 15, 20% protein energy-PE) intake were studied in a carefully controlled metabolic experiment in young healthy adult male volunteers aged between 25-34 years. Antipyrine and aminopyrine were used to evaluate drug metabolism. On 1500 kcal intake with 10% PE, the metabolism of both aminopyrine and antipyrine were significantly reduced whereas on 1800 kcal with 10% PE intake, only aminopyrine metabolism decreased significantly as compared to 3000 kcal with 10% PE. Antipyrine clearance on 1800 kcal with 10% PE however had not decreased to the same extent as on 1500 kcal with 10% PE. The results indicate that on low calorie intake with 10% PE, the drug metabolism is decreased. When the protein intake on 1500 kcal was doubled (20% PE) there was a significant stimulation of both aminopyrine and antipyrine metabolism. Aminopyrine and antipyrine clearances on 3000 kcal with 5% PE were significantly reduced as compared to 3000 kcal with 10% and 15% PE indicating that unlike proteins, carbohydrate and/or fat calories per se do not significantly stimulate drug metabolism. When the protein energy in the diet was increased from 5% to 10% or 15% at 3000 kcal, there was a stimulation of both antipyrine and aminopyrine metabolism. Significant differences between 10% and 15% of protein energy were not observed when the energy was adequate (3000 kcal). Therefore it is necessary to consider both proteins and energy as important variables affecting drug clearances from plasma in malnourished conditions. [ABSTRACT FROM AUTHOR]

The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics. Here, we describe reference call sets obtained from paired tumor-normal genomic DNA (gDNA) samples derived from a breast cancer cell line-which is highly heterogeneous, with an aneuploid genome, and enriched in somatic alterations-and a matched lymphoblastoid cell line. We partially validated both somatic mutations and germline variants in these call sets via whole-exome sequencing (WES) with different sequencing platforms and targeted sequencing with >2,000-fold coverage, spanning 82% of genomic regions with high confidence. Although the gDNA reference samples are not representative of primary cancer cells from a clinical sample, when setting up a sequencing pipeline, they not only minimize potential biases from technologies, assays and informatics but also provide a unique resource for benchmarking 'tumor-only' or 'matched tumor-normal' analyses., (© 2021. This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply.)

Clinical applications of precision oncology require accurate tests that can distinguish true cancer-specific mutations from errors introduced at each step of next-generation sequencing (NGS). To date, no bulk sequencing study has addressed the effects of cross-site reproducibility, nor the biological, technical and computational factors that influence variant identification. Here we report a systematic interrogation of somatic mutations in paired tumor-normal cell lines to identify factors affecting detection reproducibility and accuracy at six different centers. Using whole-genome sequencing (WGS) and whole-exome sequencing (WES), we evaluated the reproducibility of different sample types with varying input amount and tumor purity, and multiple library construction protocols, followed by processing with nine bioinformatics pipelines. We found that read coverage and callers affected both WGS and WES reproducibility, but WES performance was influenced by insert fragment size, genomic copy content and the global imbalance score (GIV; G > T/C > A). Finally, taking into account library preparation protocol, tumor content, read coverage and bioinformatics processes concomitantly, we recommend actionable practices to improve the reproducibility and accuracy of NGS experiments for cancer mutation detection., (© 2021. This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply.)

Introduction: The Blueprint Programmed Death Ligand 1 (PD-L1) Immunohistochemistry (IHC) Assay Comparison Project is an industrial-academic collaborative partnership to provide information on the analytical and clinical comparability of four PD-L1 IHC assays used in clinical trials., Methods: A total of 39 NSCLC tumors were stained with four PD-L1 IHC assays (22C3, 28-8, SP142, and SP263), as used in the clinical trials. Three experts in interpreting their respective assays independently evaluated the percentages of tumor and immune cells staining positive at any intensity. Clinical diagnostic performance was assessed through comparisons of patient classification above and below a selected expression cutoff and by agreement using various combinations of assays and cutoffs., Results: Analytical comparison demonstrated that the percentage of PD-L1-stained tumor cells was comparable when the 22C3, 28-8, and SP263 assays were used, whereas the SP142 assay exhibited fewer stained tumor cells overall. The variability of immune cell staining across the four assays appears to be higher than for tumor cell staining. Of the 38 cases, 19 (50.0%) were classified above and five (13%) were classified below the selected cutoffs of all assays. For 14 of the 38 cases (37%), a different PD-L1 classification would be made depending on which assay/scoring system was used., Conclusions: The Blueprint PD-L1 IHC Assay Comparison Project revealed that three of the four assays were closely aligned on tumor cell staining whereas the fourth showed consistently fewer tumor cells stained. All of the assays demonstrated immune cell staining, but with greater variability than with tumor cell staining. By comparing assays and cutoffs, the study indicated that despite similar analytical performance of PD-L1 expression for three assays, interchanging assays and cutoffs would lead to "misclassification" of PD-L1 status for some patients. More data are required to inform on the use of alternative staining assays upon which to read different specific therapy-related PD-L1 cutoffs., (Copyright © 2017 International Association for the Study of Lung Cancer. Published by Elsevier Inc. All rights reserved.)

Objective: To explore the association between maternal rectovaginal colonization with group B Streptococcus (GBS) and the outcome of preeclampsia, and to identify other factors such as maternal chocolate consumption that may be associated with preeclampsia on the Texas-Mexico border., Study Design: A case-control study was conducted among 330 women who delivered at a teaching hospital in El Paso, Texas, during the time period April 2010 to April 2012. Preeclamptic cases (n = 165) and controls free of preeclampsia (n = 165) were matched by gestational age and date of delivery. Conditional logistic regression (with multiple imputation for missing data) was used to calculate odds ratios (ORs) and 95% confidence intervals (CIs) that were adjusted for maternal age and other factors., Results: Cases (94.6%) and controls (97.0%) were predominantly Hispanic. GBS colonization was not associated with preeclampsia: adjusted OR = 1.73 (95% CI 0.63-4.74, p = 0.29). Maternal consumption of chocolate desserts once daily or more frequently as compared to < 7 times weekly was associated with a 76% reduction in the odds of preeclampsia: adjusted OR = 0.24 (95% CI 0.09-0.63, p = 0.004)., Conclusion: Our study did not confirm the protective association between GBS and preeclampsia that was found in 2 existing state hospital datasets. Chocolate consumption during pregnancy was inversely associated with preeclampsia.

This study investigated the prevalence of gestational dysglycemia in a largely Hispanic population in a U.S.-Mexico border city and the influence of single plasma glucose (PG) result on the identification of gestational carbohydrate intolerance. Gestational dysglycemia was studied in a largely Mexican-American population using retrospective data. Gestational diabetes (GDM), gestational impaired fasting glucose (GIFG), and gestational impaired glucose tolerance (GIGT) were identified with Carpenter-Coustan thresholds. Glucose challenge test result was abnormal in 32.7% of 18307 women screened; 47% of them had one or more dysglycemic results in the confirmatory oral glucose tolerance test (OGTT). The prevalence of GDM, GIFG, and GIGT in these women was 8.7, 2.2, and 4.5%, respectively. Fasting, 1-hour, 2-hour, and 3-hour PGs were elevated in 20.5, 28.5, 25.0, and 15.0% of OGTT, respectively (GIFG: 6.0%; 1-hour GIGT: 6.5%; 2-hour GIGT: 4.4%; and 3-hour GIGT: 3.1%). Twelve percent of OGTTs showed dysglycemia at 1 hour with normal 2-hour PG. Isolated dysglycemia, similar to GDM, is prevalent in Mexican-American women. The minimal impact of 3-hour PG supports a 2-hour OGTT. But our results question the use of an "OGTT protocol without a first-hour specimen.", (© Thieme Medical Publishers.)

Purpose: To present multiple imputation (MI) as an appropriate method to address missing values for a laboratory parameter (serum albumin) in an epidemiologic study., Methods: A data set of patients who were hospitalized for invasive group A streptococcal infections was accessed. Age was the exposure of interest. The outcome was hospital mortality. Several variables, including serum albumin, were considered to be potential confounders. Of the 201 records, 91 had missing values for serum albumin. The MI procedure in SAS was used to perform 20 imputations of serum albumin by using a Markov chain Monte Carlo approach. Logistic regression was then performed on each of the 20 filled-in data sets, and the results were appropriately combined by using the MIANALYZE procedure., Results: Age (> or = 55 years vs. 0-54 years) was not a risk factor for hospital mortality in the complete-case analysis (n = 110): adjusted odds ratio (OR) = 2.43 (95% confidence interval [CI]: 0.79-7.53). Age was a significant risk factor in the imputed data set (n = 201): adjusted OR = 3.08 (95% CI: 1.22-7.78)., Conclusions: Epidemiologists frequently encounter data sets that contain missing values. Traditional missing data techniques such as the complete-subject analysis may lead to biased results. We have demonstrated the use of a novel technique, MI, to account for missing data.

The Drosophila testis and ovary are major genetically tractable systems for studying stem cells and their regulation. This has resulted in a deep understanding of germline stem cell regulation by the microenvironment, or niche. The male and female germline niches differ. Since sex is determined through different mechanisms in the soma than in the germline, genetic or physical manipulations can be used to experimentally mismatch somatic and germline sexual identities. The phenotypic consequences of these mismatches have striking similarities to those resulting from manipulations of signals within the niche. A critical role of the germline sex determination pathway may therefore be to ensure the proper receipt and processing of signals from the niche.

Vulval morphogenesis in Caenorhabditis elegans generates a stack of toroidal cells enclosing a tubular lumen. Mutation of egl-26 is associated with malformation of vulF, the most dorsal toroid in the stack, resulting in a blocked lumen and an egg-laying defect. Here we present evidence that vulF retains the expected gene expression pattern, functions in signaling to the uterus and retains proper polarity when egl-26 is mutated, all suggesting that mutation of egl-26 specifically results in aberrant morphogenesis as opposed to abnormal fate specification. Recent computational analysis indicates that EGL-26, which was previously characterized as novel, belongs to the LRAT (lecithin retinol acyltransferase) subfamily of the NlpC/P60 superfamily of catalytic proteins. Via site-directed mutagenesis, we demonstrate a requirement of the putative catalytic residues for EGL-26 function in vivo. We also show that mutation of conserved serine 275 perturbs the apical membrane localization and the function of the EGL-26 protein. Additional mutagenesis of this residue suggests that EGL-26 attains its membrane localization via a mechanism distinct from that of LRAT.

Retroposition is increasingly recognized as an important mechanism for the acquisition of new genes. We show that a glycogen synthase kinase-3 gene, shaggy (sgg), retroposed at least 50 MYA in the Drosophila genus to generate a new gene, mojoless (mjl). We have extensively analyzed the function of mjl and examined its functional divergence from the parental gene sgg in Drosophila melanogaster. Unlike Sgg, which is expressed in many tissues of both sexes, Mjl is expressed specifically in the male germ line, where it is required for male germ line survival. Our analysis indicates that mjl has acquired a specific function in the maintenance of male germ line viability. However, it has not completely lost its ancestral biochemical function and can partially compensate for loss of the parental gene sgg when ectopically expressed in somatic cells. We postulate that mjl has undergone functional diversification and is now under stabilizing selection in the Drosophila genus.

In a previous communication, we proposed that N-methyl-N'-nitro-N-nitrosoguanidine (MNNG)-induced cytotoxicity in an O6-methylguanine (O6-MeG)-DNA methyltransferase-deficient (MT-) HeLa cell mutant was mainly the consequence of DNA strand breaks resulting from the failure to remove O6-MeG lesions. If MNNG-induced cytotoxicity, DNA strand breaks and O6-MeG lesions are related, there should be a corresponding relationship of these properties in MNNG-resistant clones derived from the MT- strain. A study of such revertants indicated that they were a heterogeneous group with increased repair of DNA strand breaks and O6-MeG lesions and increased resistance to the cytotoxic effects of MNNG. These observations support the hypothesis relating O6-MeG, DNA strand breaks and cytotoxicity. The relationship of these 'revertants' to the MT- and wild-type strains is discussed.

Experimental studies and epidemiologic data both indicate that high-fat diets increase the risk of cancer at sites such as breast, colon, and pancreas. Dietary polyunsaturated vegetable oils promote tumorigenesis in animals whereas saturated fats and polyunsaturated fish oils either have little effect or are inhibitory. A blend of fats typical of the American diet enhanced mammary tumorigenesis effectively when fed as 40% of calories. After 9 to 10 weeks on this diet, reducing the fat to 10% of calories inhibited subsequent tumor development. Although dietary fat appears to act as a promoter, the exact mechanisms are still unknown. Cancer mortality in humans correlates better with total dietary fat than with degree of unsaturation, perhaps because most diets contain more than the amount of polyunsaturated fatty acids required for maximum effect on tumorigenesis in animals. A reduction in total dietary fat is recommended to reduce the current high cancer mortality.

The physiological significance of low levels of vitamin B12 in serum in late pregnancy was assessed by a functional test viz. urinary excretion of methylmalonic acid (MMA) after a valine load. This was normal in all but one subject despite low levels of vitamin B12 in serum in many of these subjects. Assay of serum vitamin B12 levels in pregnant women and control subjects by two different techniques viz. radio isotope dilution and microbiological methods gave essentially similar results for both groups, although the absolute values in both the groups were over-estimated by the former technique. The data presented indicate that there is no evidence of functional inadequacy in pregnant women with low levels of vitamin B12 in serum.

The influence of the nutritional status of the individual on the hepatic drug metabolising enzymes in human wedge-biopsy liver samples was investigated. The aryl hydrocarbon hydroxylase (AHH) was found to be elevated although there was no change in the cytochrome P-450 levels in the undernourished groups. Conjugating enzymes viz. UDP glucuronyl transferase (UDPGT) and glutathione-S-transferase (GST) were not found to be different. The increase in AHH activity as compared to UDPGT and GST activities suggests that the activation processes may possibly be increased in the undernourished segment of the population.

A syndrome of ataxic myelopathy with optic atrophy and perceptive deafness has been described. This is essentially similar to the Nigerian ataxic myelopathy which has been ascribed to chronic cyanide intoxication through dietary means. The results of biochemical investigations and bone marrow examination indicate that neither vitamin B12 deficiency nor cyanide intoxication are likely factors in the detiology of our cases. It is possible that the disease may be due to an unrecognized toxic for factor which may or may not be of dietary origin.

Female Sprague-Dawley rats were given 7,12-dimethylbenz(a)anthracene at 50 days of age to induce mammary tumors, and beginning one week later were fed a high-fat, semipurified diet containing 20% sunflowerseed oil to promote tumor development. After another 7 weeks, when one third of the rats had palpable mammary tumors, the rats were randomly assigned to five groups of 31 animals each, with the same number of tumor-bearers in each group. One group was continued on the high-fat diet, another was given a fat-free diet, and the three remaining groups were fed diets containing 10% lard, butter, or coconut oil, respectively. During the next 29 weeks, rats fed the diets containing 0% or 10% fat developed significantly fewer tumors than those continued on the 20% fat diet. The diets containing 10% fat suppressed tumorigenesis at least as effectively as the fat-free diet. Rats fed the 10% butter and 10% lard diets had growth rates comparable to those fed the 20% sunflowerseed-oil diet throughout, and evidence of essential fatty acid deficiency was seen only in rats on the fat-free diet. These results provide additional evidence that high-fat diets promote development of mammary cancer and suggest that reducing the level of dietary fat might help to prevent the development and recurrence of breast cancer in humans.

We have isolated an isogenic O6-methylguanine (O6-MeG)-DNA methyltransferase-defective mutant from a HeLa cell line. This mutant exhibits excess DNA strand breaks and considerable cytotoxicity after N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) treatment. The increased frequency of strand breaks after MNNG treatment was not abolished by DNA synthesis inhibitors. We propose that the presence of unrepaired O6-MeG lesions leads to excess strand breaks and these, in turn, are mainly responsible for the cytotoxicity.