The Updated Mouse Universal Genotyping Array Bioinformatic Pipeline Improves Genetic QC in Laboratory Mice.

The MiniMUGA genotyping array is a popular tool for genetic QC of laboratory mice and genotyping of samples from most types of experimental crosses involving laboratory strains, particularly for reduced complexity crosses. The content of the production version of the MiniMUGA array is fixed; however, there is the opportunity to improve array's performance and the associated report's usefulness by leveraging thousands of samples genotyped since the initial description of MiniMUGA in 2020. Here we report our efforts to update and improve marker annotation, increase the number and the reliability of the consensus genotypes for inbred strains and increase the number of constructs that can reliably be detected with MiniMUGA. In addition, we have implemented key changes in the informatics pipeline to identify and quantify the contribution of specific genetic backgrounds to the makeup of a given sample, remove arbitrary thresholds, include the Y Chromosome and mitochondrial genome in the ideogram, and improve robust detection of the presence of commercially available substrains based on diagnostic alleles. Finally, we have made changes to the layout of the report, to simplify the interpretation and completeness of the analysis and added a table summarizing the ideogram. We believe that these changes will be of general interest to the mouse research community and will be instrumental in our goal of improving the rigor and reproducibility of mouse-based biomedical research.

Artificial Intelligence-Generated Scientific Literature: A Critical Appraisal.

BACKGROUND: Review articles play a critical role in informing medical decisions and identifying avenues for future research. With the introduction of artificial intelligence (AI), there has been a growing interest in the potential of this technology to transform the synthesis of medical literature. Open AI's Generative Pre-trained Transformer (GPT-4) (Open AI Inc, San Francisco, CA) tool provides access to advanced AI that is able to quickly produce medical literature following only simple prompts. The accuracy of the generated articles requires review, especially in subspecialty fields like Allergy/Immunology. OBJECTIVE: To critically appraise AI-synthesized allergy-focused minireviews. METHODS: We tasked the GPT-4 Chatbot with generating 2 1,000-word reviews on the topics of hereditary angioedema and eosinophilic esophagitis. Authors critically appraised these articles using the Joanna Briggs Institute (JBI) tool for text and opinion and additionally evaluated domains of interest such as language, reference quality, and accuracy of the content. RESULTS: The language of the AI-generated minireviews was carefully articulated and logically focused on the topic of interest; however, reviewers of the AI-generated articles indicated that the AI-generated content lacked depth, did not appear to be the result of an analytical process, missed critical information, and contained inaccurate information. Despite being provided instruction to utilize scientific references, the AI chatbot relied mainly on freely available resources, and the AI chatbot fabricated references. CONCLUSIONS: The AI holds the potential to change the landscape of synthesizing medical literature; however, apparent inaccurate and fabricated information calls for rigorous evaluation and validation of AI tools in generating medical literature, especially on subjects associated with limited resources.

Diagnosis of eosinophilic esophagitis in patients with dysphagia during the Coronavirus Disease 2019 (COVID-19) pandemic.

Background: The coronavirus disease 2019 (COVID-19) pandemic posed restrictions to many standard practices. Dysphagia is a common presentation of eosinophilic esophagitis (EoE) in adults, and biopsy via esophagogastroduodenoscopy (EGD) is required for diagnosis. We hypothesized that a diagnosis of EoE has declined during the pandemic. Objective: To investigate whether the COVID-19 pandemic influenced the likelihood of an EGD and an EoE diagnosis in patients with dysphagia. Methods: In this retrospective matched cohort study, we used the TriNetX US Collaborative Network to identify adult patients who presented with dysphagia to the emergency department (ED) during the year of and the year preceding the pandemic. Patients with a previous EoE diagnosis were excluded. The two cohorts were balanced for demographics, gastroesophageal reflux disease (GERD) diagnosis, obesity, H2 blockers and proton-pump inhibitors use, anemia, smoking, and alcohol use. The proportion of patients who received an EGD, and an EoE and a GERD diagnosis were contrasted up to 90 days from ED evaluation. Results: We identified 16,942 adult patients during the pandemic, and 16,942 adult patients the year preceding the pandemic who presented to the ED with a concern of dysphagia. During the 30-day follow-up period, no significant difference was observed in the proportion of patients who received an EGD during the pandemic versus the prepandemic period at 1, 7, and 30 days from ED evaluation. The proportion of patients who received an EoE diagnosis was not different, but slightly more patients received a GERD diagnosis during the pandemic versus prepandemic that was evident by day 30 (31.2% versus 30%; p ≤ 0.05). Conclusion: Our results revealed that the COVID-19 pandemic did not significantly impact diagnostic EGD and an EoE diagnosis.

Comparison of Two Estrogen Chemically Activated Luciferase Expression Cell Bioassays to Liquid Chromatography-Mass Spectrometry for Quantifying Estrone in Water Samples.

Chemically activated luciferase expression (CALUX) cell bioassays are popular tools for assessing endocrine activity of chemicals such as certain environmental contaminants. Although activity equivalents can be obtained from CALUX analysis, directly comparing these equivalents to those obtained from analytical chemistry methods can be problematic because of the complexity of endocrine active pathways. We explored the suitability of two estrogen CALUX bioassays (the Organisation for Economic Co-operation and Development-approved VM7Luc4E2 cell bioassay and the VM7LucERßc9 cell bioassay) for quantitation of estrogen. Quadrupole-time of flight ultraperformance liquid chromatography-mass spectrometry (LC/MS) was selected as a comparative method. Regression analysis of measured estrone (E1) calibration samples showed all three methods to be highly predictive of nominal concentrations (p ≤ 7.5 × 10-51 ). Extracts of water sampled from laboratory dilutor tanks containing E1 at 0, 20, and 200 ng/L alone and in combination with atrazine were selected to test the quantitative capabilities of the CALUX assays. Process controls (0 and 100 ng E1/L) and a separate E1 standard (10 ng/ml, used to prepare the E1 process control) were also tested. Levels of E1 determined by LC/MS analysis and bioanalytical equivalents (ng E1/L) determined by CALUX analyses were comparable except in certain instances where the samples required dilution prior to CALUX analyses (e.g., the E1 process control and E1 standard). In those instances, measurements by CALUX were slightly but significantly decreased relative to LC/MS. Atrazine had no effect on the ability of either LC/MS or the CALUX bioassays to quantify E1. The present study illustrates the CALUX bioassays as successful in quantifying an estrogen in simple water samples and further characterizes their utility for screening. Environ Toxicol Chem 2023;42:333-339. Published 2022. This article is a U.S. Government work and is in the public domain in the USA.

Sample-efficient identification of high-dimensional antibiotic synergy with a normalized diagonal sampling design.

Antibiotic resistance is an important public health problem. One potential solution is the development of synergistic antibiotic combinations, in which the combination is more effective than the component drugs. However, experimental progress in this direction is severely limited by the number of samples required to exhaustively test for synergy, which grows exponentially with the number of drugs combined. We introduce a new metric for antibiotic synergy, motivated by the popular Fractional Inhibitory Concentration Index and the Highest Single Agent model. We also propose a new experimental design that samples along all appropriately normalized diagonals in concentration space, and prove that this design identifies all synergies among a set of drugs while only sampling a small fraction of the possible combinations. We applied our method to screen two- through eight-way combinations of eight antibiotics at 10 concentrations each, which requires sampling only 2,560 unique combinations of antibiotic concentrations.

Current ecotoxicity testing needs among selected U.S. federal agencies.

U.S. regulatory and research agencies use ecotoxicity test data to assess the hazards associated with substances that may be released into the environment, including but not limited to industrial chemicals, pharmaceuticals, pesticides, food additives, and color additives. These data are used to conduct hazard assessments and evaluate potential risks to aquatic life (e.g., invertebrates, fish), birds, wildlife species, or the environment. To identify opportunities for regulatory uses of non-animal replacements for ecotoxicity tests, the needs and uses for data from tests utilizing animals must first be clarified. Accordingly, the objective of this review was to identify the ecotoxicity test data relied upon by U.S. federal agencies. The standards, test guidelines, guidance documents, and/or endpoints that are used to address each of the agencies' regulatory and research needs regarding ecotoxicity testing are described in the context of their application to decision-making. Testing and information use, needs, and/or requirements relevant to the regulatory or programmatic mandates of the agencies taking part in the Interagency Coordinating Committee on the Validation of Alternative Methods Ecotoxicology Workgroup are captured. This information will be useful for coordinating efforts to develop and implement alternative test methods to reduce, refine, or replace animal use in chemical safety evaluations.

Content and Performance of the MiniMUGA Genotyping Array: A New Tool To Improve Rigor and Reproducibility in Mouse Research.

The laboratory mouse is the most widely used animal model for biomedical research, due in part to its well-annotated genome, wealth of genetic resources, and the ability to precisely manipulate its genome. Despite the importance of genetics for mouse research, genetic quality control (QC) is not standardized, in part due to the lack of cost-effective, informative, and robust platforms. Genotyping arrays are standard tools for mouse research and remain an attractive alternative even in the era of high-throughput whole-genome sequencing. Here, we describe the content and performance of a new iteration of the Mouse Universal Genotyping Array (MUGA), MiniMUGA, an array-based genetic QC platform with over 11,000 probes. In addition to robust discrimination between most classical and wild-derived laboratory strains, MiniMUGA was designed to contain features not available in other platforms: (1) chromosomal sex determination, (2) discrimination between substrains from multiple commercial vendors, (3) diagnostic SNPs for popular laboratory strains, (4) detection of constructs used in genetically engineered mice, and (5) an easy-to-interpret report summarizing these results. In-depth annotation of all probes should facilitate custom analyses by individual researchers. To determine the performance of MiniMUGA, we genotyped 6899 samples from a wide variety of genetic backgrounds. The performance of MiniMUGA compares favorably with three previous iterations of the MUGA family of arrays, both in discrimination capabilities and robustness. We have generated publicly available consensus genotypes for 241 inbred strains including classical, wild-derived, and recombinant inbred lines. Here, we also report the detection of a substantial number of XO and XXY individuals across a variety of sample types, new markers that expand the utility of reduced complexity crosses to genetic backgrounds other than C57BL/6, and the robust detection of 17 genetic constructs. We provide preliminary evidence that the array can be used to identify both partial sex chromosome duplication and mosaicism, and that diagnostic SNPs can be used to determine how long inbred mice have been bred independently from the relevant main stock. We conclude that MiniMUGA is a valuable platform for genetic QC, and an important new tool to increase the rigor and reproducibility of mouse research.

Biological Effects of Hydrocarbon Degradation Intermediates: Is the Total Petroleum Hydrocarbon Analytical Method Adequate for Risk Assessment?

In crude oil contaminant plumes, the dissolved organic carbon (DOC) is mainly hydrocarbon degradation intermediates only partly quantified by the diesel range total petroleum hydrocarbon (TPHd) method. To understand potential biological effects of degradation intermediates, we tested three fractions of DOC: (1) solid-phase extract (HLB); (2) dichloromethane (DCM-total) extract used in TPHd; and (3) DCM extract with hydrocarbons isolated by silica gel cleanup (DCM-SGC). Bioactivity of extracts from five wells spanning a range of DOC was tested using an in vitro multiplex reporter system that evaluates modulation of the activity of 46 transcription factors; extracts were evaluated at concentrations equivalent to the well water samples. The aryl hydrocarbon receptor (AhR) and pregnane X receptor (PXR) transcription factors showed the greatest upregulation, with HLB exceeding DCM-total, and no upregulation in the hydrocarbon fraction (DCM-SGC). The HLB extracts were further studied with HepG2 chemically activated luciferase expression (CALUX) in vitro assays at nine concentrations ranging from 40 to 0.01 times the well water concentrations. Responses decreased with distance from the source but were still present at two wells without detectable hydrocarbons. Thus, our in vitro assay results indicate that risks associated with degradation intermediates of hydrocarbons in groundwater will be underestimated when protocols that remove these chemicals are employed.

Factors Affecting Sampling Strategies for Design of an Effects-Directed Analysis for Endocrine-Active Chemicals.

Effects-directed analysis (EDA) is an important tool for identifying unknown bioactive components in a complex mixture. Such an analysis of endocrine-active chemicals (EACs) from water sources has promising regulatory implications but also unique logistical challenges. We propose a conceptual EDA (framework) based on a critical review of EDA literature and concentrations of common EACs in waste and surface waters. Required water volumes for identification of EACs under this EDA framework were estimated based on bioassay performance (in vitro and in vivo bioassays), limits of quantification by mass spectrometry (MS), and EAC water concentrations. Sample volumes for EDA across the EACs showed high variation in the bioassay detectors, with genistein, bisphenol A, and androstenedione requiring very high sample volumes and ethinylestradiol and 17ß-trenbolone requiring low sample volumes. Sample volume based on the MS detector was far less variable across the EACs. The EDA framework equation was rearranged to calculate detector "thresholds," and these thresholds were compared with the literature EAC water concentrations to evaluate the feasibility of the EDA framework. In the majority of instances, feasibility of the EDA was limited by the bioassay, not MS detection. Mixed model analysis showed that the volumes required for a successful EDA were affected by the potentially responsible EAC, detection methods, and the water source type, with detection method having the greatest effect on the EDA of estrogens and androgens. The EDA framework, equation, and model we present provide a valuable tool for designing a successful EDA. Environ Toxicol Chem 2020;39:1309-1324. © 2020 SETAC.

Development of a dual luciferase activity and fluorescamine protein assay adapted to a 384 micro-well plate format: Reducing variability in human luciferase transactivation cell lines aimed at endocrine active substances.

There is a need to adapt cell bioassays to 384-well and 1536-well formats instead of the traditional 96-well format as high-throughput screening (HTS) demands increase. However, the sensitivity and performance of the bioassay must be re-verified in these higher micro-well plates, and verification of cell health must also be HT (high-throughput). We have adapted two commonly used human breast luciferase transactivation cell bioassays, the recently re-named estrogen agonist/antagonist screening VM7Luc4E2 cell bioassay (previously designated BG1Luc4E2) and the androgen/glucocorticoid screening MDA-kb2 cell bioassay, to 384-well formats for HTS of endocrine-active substances (EASs). This cost-saving adaptation includes a fast, accurate, and easy measurement of protein amount in each well via the fluorescamine assay with which to normalize luciferase activity of cell lysates without requiring any transfer of the cell lysates. Here we demonstrate that by accounting for protein amount in the cell lysates, antagonistic agents can easily be distinguished from cytotoxic agents in the MDA-kb2 and VM7Luc4E2 cell bioassays. Additionally, we demonstrate via the fluorescamine assay improved interpretation of luciferase activity in wells along the edge of the plate (the so-called "edge effect"), thereby increasing usable wells to the entire plate, not just interior wells.

Development of a recombinant human ovarian (BG1) cell line containing estrogen receptor α and ß for improved detection of estrogenic/antiestrogenic chemicals.

Estrogenic endocrine-disrupting chemicals are found in environmental and biological samples, commercial and consumer products, food, and numerous other sources. Given their ubiquitous nature and potential for adverse effects, a critical need exists for rapidly detecting these chemicals. The authors developed an estrogen-responsive recombinant human ovarian (BG1Luc4E2) cell line recently accepted by the US Environmental Protection Agency (USEPA) and Organisation for Economic Co-operation and Development (OECD) as a bioanalytical method to detect estrogen receptor (ER) agonists/antagonists. Unfortunately, these cells appear to contain only 1 of the 2 known ER isoforms, ERα but not ERß, and the differential ligand selectivity of these ERs indicates that the currently accepted screening method only detects a subset of total estrogenic chemicals. To improve the estrogen screening bioassay, BG1Luc4E2 cells were stably transfected with an ERß expression plasmid and positive clones identified using ERß-selective ligands (genistein and Br-ERß-041). A highly responsive clone (BG1LucERßc9) was identified that exhibited greater sensitivity and responsiveness to ERß-selective ligands than BG1Luc4E2 cells, and quantitative reverse-transcription polymerase chain reaction confirmed the presence of ERß expression in these cells. Screening of pesticides and industrial chemicals identified chemicals that preferentially stimulated ERß-dependent reporter gene expression. Together, these results not only demonstrate the utility of this dual-ER recombinant cell line for detecting a broader range of estrogenic chemicals than the current BG1Luc4E2 cell line, but screening with both cell lines allows identification of ERα- and ERß-selective chemicals.

The Mouse Universal Genotyping Array: From Substrains to Subspecies.

Genotyping microarrays are an important resource for genetic mapping, population genetics, and monitoring of the genetic integrity of laboratory stocks. We have developed the third generation of the Mouse Universal Genotyping Array (MUGA) series, GigaMUGA, a 143,259-probe Illumina Infinium II array for the house mouse (Mus musculus). The bulk of the content of GigaMUGA is optimized for genetic mapping in the Collaborative Cross and Diversity Outbred populations, and for substrain-level identification of laboratory mice. In addition to 141,090 single nucleotide polymorphism probes, GigaMUGA contains 2006 probes for copy number concentrated in structurally polymorphic regions of the mouse genome. The performance of the array is characterized in a set of 500 high-quality reference samples spanning laboratory inbred strains, recombinant inbred lines, outbred stocks, and wild-caught mice. GigaMUGA is highly informative across a wide range of genetically diverse samples, from laboratory substrains to other Mus species. In addition to describing the content and performance of the array, we provide detailed probe-level annotation and recommendations for quality control.

Development of Species-Specific Ah Receptor-Responsive Third Generation CALUX Cell Lines with Enhanced Responsiveness and Improved Detection Limits.

The Ah receptor (AhR)-responsive CALUX (chemically activated luciferase expression) cell bioassay is commonly used for rapid screening of samples for the presence of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD, dioxin), dioxin-like compounds, and AhR agonists/antagonists. By increasing the number of AhR DNA recognition sites (dioxin responsive elements), we previously generated a novel third generation (G3) recombinant AhR-responsive mouse CALUX cell line (H1L7.5c3) with a significantly enhanced response to DLCs compared to existing AhR-CALUX cell bioassays. However, the elevated background luciferase activity of these cells and the absence of comparable G3 cell lines derived from other species have limited their utility for screening purposes. Here, we describe the development and characterization of species-specific G3 recombinant AhR-responsive CALUX cell lines (rat, human, and guinea pig) that exhibit significantly improved limit of detection and dramatically increased TCDD induction response. The low background luciferase activity, low minimal detection limit (0.1 pM TCDD) and enhanced induction response of the rat G3 cell line (H4L7.5c2) over the H1L7.5c3 mouse G3 cells, identifies them as a more optimal cell line for screening purposes. The utility of the new G3 CALUX cell lines were demonstrated by screening sediment extracts and a small chemical compound library for the presence of AhR agonists. The improved limit of detection and increased response of these new G3 CALUX cell lines will facilitate species-specific analysis of DLCs and AhR agonists in samples with low levels of contamination and/or in small sample volumes.

2,3-cis-2R,3R-(-)-epiafzelechin-3-O-p-coumarate, a novel flavan-3-ol isolated from Fallopia convolvulus seed, is an estrogen receptor agonist in human cell lines.

BACKGROUND: The plant genus Fallopia is well-known in Chinese traditional medicine and includes many species that contain bioactive compounds, namely phytoestrogens. Consumption of phytoestrogens may be linked to decreased incidence of breast and prostate cancers therefore discovery of novel phytoestrogens and novel sources of phytoestrogens is of interest. Although phytoestrogen content has been analyzed in the rhizomes of various Fallopia sp., seeds of a Fallopia sp. have never been examined for phytoestrogen presence. METHODS: Analytical chemistry techniques were used with guidance from an in vitro estrogen receptor bioassay (a stably transfected human ovarian carcinoma cell line) to isolate and identify estrogenic components from seeds of Fallopia convolvulus. A transiently transfected human breast carcinoma cell line was used to characterize the biological activity of the isolated compounds on estrogen receptors (ER) α and ß. RESULTS: Two compounds, emodin and the novel flavan-3-ol, (-)-epiafzelechin-3-O-p-coumarate (rhodoeosein), were identified to be responsible for estrogenic activity of F. convolvulus seed extract. Absolute stereochemistry of rhodoeosein was determined by 1 and 2D NMR, optical rotation and circular dichroism. Emodin was identified by HPLC/DAD, LC/MS/MS, and FT/ICR-MS. When characterizing the ER specificity in biological activity of rhodoeosein and emodin, rhodoeosein was able to exhibit a four-fold greater relative estrogenic potency (REP) in breast cells transiently-transfected with ERß as compared to those transfected with ERα, and emodin exhibited a six-fold greater REP in ERß-transfected breast cells. Cell type-specific differences were observed with rhodoeosein but not emodin; rhodoeosein produced superinduction of reporter gene activity in the human ovarian cell line (> 400% of maximum estradiol [E2] induction) but not in the breast cell line. CONCLUSION: This study is the first to characterize the novel flavan-3-ol compound, rhodoeosein, and its ability to induce estrogenic activity in human cell lines. Rhodoeosein and emodin may have potential therapeutic applications as natural products activating ERß, and further characterization of rhodoeosein is necessary to evaluate its selectivity as a cell type-specific ER agonist.

ARID1a-DNA interactions are required for promoter occupancy by SWI/SNF.

Every known SWI/SNF chromatin-remodeling complex incorporates an ARID DNA binding domain-containing subunit. Despite being a ubiquitous component of the complex, physiological roles for this domain remain undefined. Here, we show that disruption of ARID1a-DNA binding in mice results in embryonic lethality, with mutant embryos manifesting prominent defects in the heart and extraembryonic vasculature. The DNA binding-defective mutant ARID1a subunit is stably expressed and capable of assembling into a SWI/SNF complex with core catalytic properties, but nucleosome substrate binding and promoter occupancy by ARID1a-containing SWI/SNF complexes (BAF-A) are impaired. Depletion of ARID domain-dependent, BAF-A associations at THROMBOSPONDIN 1 (THBS1) led to the concomitant upregulation of this SWI/SNF target gene. Using a THBS1 promoter-reporter gene, we further show that BAF-A directly regulates THBS1 promoter activity in an ARID domain-dependent manner. Our data not only demonstrate that ARID1a-DNA interactions are physiologically relevant in higher eukaryotes but also indicate that these interactions facilitate SWI/SNF binding to target sites in vivo. These findings support the model wherein cooperative interactions among intrinsic subunit-chromatin interaction domains and sequence-specific transcription factors drive SWI/SNF recruitment.

Trust in primary care providers and antiretroviral adherence in an urban HIV clinic.

Interpersonal trust is an integral component of the patient-provider relationship and has been associated with patient adherence to medications. Studies suggest African Americans may have lower levels of trust in their health care providers than non-Hispanic Whites. This study examines the association between trust in one's primary care provider (PCP) and antiretroviral (ARV) adherence among 175 patients at an urban HIV clinic. Interviews elicited participants' level of trust in their current PCP using a multiple-item trust scale and assessed ARV adherence with a seven-day recall questionnaire. Logistic regression was used to ascertain the effect of trust in PCP on ARV adherence. High trust in PCP was significantly associated with increased odds of ARV adherence compared with low trust (adjusted odds ratio, 2.67; 95% confidence interval, 1.24 to 5.76; p=.01). Enhancing trust in PCPs may be a good target for interventions to improve ARV adherence, particularly among African American patients.

Role of isotope selection in long-term outcomes in patients with intermediate-risk prostate cancer treated with a combination of external beam radiotherapy and low-dose-rate interstitial brachytherapy.

OBJECTIVE: To examine the rates of long-term biochemical recurrence-free survival (BRFS) with respect to isotope in intermediate-risk prostate cancer treated with external beam radiotherapy (EBRT) and brachytherapy. METHODS: A total of 242 consecutive patients with intermediate-risk prostate cancer were treated with iodine-125 ((125)I) or palladium-103 ((103)Pd) implants after EBRT (range 45.0-50.4 Gy) from 1996 to 2002. Of the 242 patients, 119 (49.2%) were treated with (125)I and 123 (50.8%) with (103)Pd. Multivariate Cox regression analysis was used to analyze BRFS, defined according to the Phoenix definition (prostate-specific antigen nadir plus 2 ng/mL) with respect to Gleason score, stage, pretreatment prostate-specific antigen level, and source selection. Late genitourinary/gastrointestinal toxicities were assessed using the Radiation Therapy Oncology Group/European Organization for Research and Treatment of Cancer scale. RESULTS: At a median follow-up of 10 years, the BRFS rate was 77.3%. A statistically significant difference was found in the 10-year BRFS rate between the (125)I- and (103)Pd-treated groups (82.7% and 70.6%, respectively; P = .001). The addition of hormonal therapy did not improve the 10-year BRFS rate (77.6%) compared with RT alone (77.1%; P = .22). However, a statistically significant difference in the BRFS rate was found with the addition of hormonal therapy to (103)Pd, improving the 10-year BRFS rate for (73.8%) compared with (103)Pd alone (69.1%; P = .008). On multivariate analysis, isotope type ((103)Pd vs (125)I), pretreatment prostate-specific antigen level >10 ng/mL, and greater tumor stage increased the risk of recurrence by 2.6-fold (P = .007), 5.9-fold (P < .0001), and 1.7-fold (P = .14), respectively. CONCLUSION: (125)I renders a superior rate of BRFS compared with (103)Pd when used with EBRT. Hormonal therapy does not provide additional benefit in patients with intermediate-risk prostate cancer treated with a combination of EBRT and brachytherapy, except for the addition of hormonal therapy to (103)Pd.

Regression and data mining methods for analyses of multiple rare variants in the Genetic Analysis Workshop 17 mini-exome data.

Group 14 of Genetic Analysis Workshop 17 examined several issues related to analysis of complex traits using DNA sequence data. These issues included novel methods for analyzing rare genetic variants in an aggregated manner (often termed collapsing rare variants), evaluation of various study designs to increase power to detect effects of rare variants, and the use of machine learning approaches to model highly complex heterogeneous traits. Various published and novel methods for analyzing traits with extreme locus and allelic heterogeneity were applied to the simulated quantitative and disease phenotypes. Overall, we conclude that power is (as expected) dependent on locus-specific heritability or contribution to disease risk, large samples will be required to detect rare causal variants with small effect sizes, extreme phenotype sampling designs may increase power for smaller laboratory costs, methods that allow joint analysis of multiple variants per gene or pathway are more powerful in general than analyses of individual rare variants, population-specific analyses can be optimal when different subpopulations harbor private causal mutations, and machine learning methods may be useful for selecting subsets of predictors for follow-up in the presence of extreme locus heterogeneity and large numbers of potential predictors.

Bare platinum vs matrix detachable coils for the endovascular treatment of intracranial aneurysms: a multivariate logistic regression analysis and review of the literature.

BACKGROUND: Despite increasing acceptance of endovascular coiling for treating intracranial aneurysms, incomplete occlusion remains a limitation. Attempts to reduce recanalization have prompted creation of polyglycolic/polylactic acid-coated (Matrix) coils shown to improve neointima formation; however, previous publications demonstrate conflicting results regarding their efficacy. Few studies account for factors influencing recurrence, and only 4 studies include bare platinum (BP) coil control groups. OBJECTIVE: To compare initial and short- and mid-term occlusion as well as retreatment rates using Matrix compared with BP coils. METHODS: Retrospective review of patients undergoing coiling of cerebral aneurysms from 2001 to 2005 was performed. Analysis included a multivariate logistic regression model designed to detect a 35% absolute difference in initial occlusion between coil treatment groups with 80% power. RESULTS: Complete initial occlusion was achieved in 64% of BP (n = 45) and 63% of Matrix (n = 56) cases (P = 1.0). Follow-up occlusion rates in the short term and mid term were 52% and 60%, respectively, for BP cases and 42% and 67%, respectively, for Matrix cases (P = .24 and P = .38, respectively). After adjusting for size, morphology, volumetric packing density, location, rupture, and balloon remodeling, no difference in initial and subsequent occlusion or retreatment rates for BP coils versus Matrix coils was appreciated. CONCLUSION: After controlling for factors influencing recanalization, this investigation failed to show a significant difference between coil groups.

A LASSO-based approach to analyzing rare variants in genetic association studies.

Genetic markers with rare variants are spread out in the genome, making it necessary and difficult to consider them in genetic association studies. Consequently, wisely combining rare variants into "composite" markers may facilitate meaningful analyses. In this paper, we propose a novel approach of analyzing rare variant data by incorporating the least absolute shrinkage and selection operator technique. We applied this method to the Genetic Analysis Workshop 17 data, and our results suggest that this new approach is promising. In addition, we took advantage of having 200 phenotype replications and assessed the performance of our approach by means of repeated classification tree analyses. Our method and analyses were performed without knowledge of the underlying simulating model. Our method identified 38 markers (in 65 genes) that are significantly associated with the phenotype Affected and correctly identified two causal genes, SIRT1 and PDGFD.