Use of Contraception Among Hispanic Women and Men: A Qualitative Study.

Introduction: Nationally, low-income women of Hispanic ethnicity have a significantly higher rate of unintended pregnancy than their White counterparts. This disparity leads to an increased risk for poor maternal and child outcomes that have long and short-term sequelae for health and well-being. A quantitative report in Washtenaw County, Michigan in 2017 found that both men and women were at high risk for unintended pregnancy with many women reporting no contraception use, despite not desiring a pregnancy. Methods: We used semistructured interviews to assess the opinions and experiences regarding the use of contraception among 21 Hispanic women and men of reproductive age in a Midwestern county. Results: Our study found that the use of contraception to prevent unwanted pregnancy was important to our sample of Hispanic women and men. However, concerns about side effects, limited knowledge on reproductive health, the influence of partners, and financial barriers played a role in the use of contraception. Conclusion: Our findings provide insight into the influences and barriers to contraception use among Hispanic women and men and can inform future research.

TopPICR: A Companion R Package for Top-Down Proteomics Data Analysis.

Top-down proteomics is the analysis of proteins in their intact form without proteolysis, thus preserving valuable information about post-translational modifications, isoforms, and proteolytic processing. However, it is still a developing field due to limitations in the instrumentation, difficulties with the interpretation of complex mass spectra, and a lack of well-established quantification approaches. TopPIC is one of the popular tools for proteoform identification. We extended its capabilities into label-free proteoform quantification by developing a companion R package (TopPICR). Key steps in the TopPICR pipeline include filtering identifications, inferring a minimal set of protein accessions explaining the observed sequences, aligning retention times, recalibrating measured masses, clustering features across data sets, and finally compiling feature intensities using the match-between-runs approach. The output of the pipeline is an MSnSet object which makes downstream data analysis seamlessly compatible with packages from the Bioconductor project. It also provides the capability for visualizing proteoforms within the context of the parent protein sequence. The functionality of TopPICR is demonstrated on top-down LC-MS/MS data sets of 10 human-in-mouse xenografts of luminal and basal breast tumor samples.

pmartR 2.0: A Quality Control, Visualization, and Statistics Pipeline for Multiple Omics Datatypes.

The pmartR (https://github.com/pmartR/pmartR) package was designed for the quality control (QC) and analysis of mass spectrometry data, tailored to specific characteristics of proteomic (isobaric or labeled), metabolomic, and lipidomic data sets. Since its initial release, the tool has been expanded to address the needs of its growing userbase and now includes QC and statistics for nuclear magnetic resonance metabolomic data, and leverages the DESeq2, edgeR, and limma-voom R packages for transcriptomic data analyses. These improvements have made progress toward a unified omics processing pipeline for ease of reporting and streamlined statistical purposes. The package's statistics and visualization capabilities have also been expanded by adding support for paired data and by integrating pmartR with the trelliscopejs R package for the quick creation of trellis displays (https://github.com/hafen/trelliscopejs). Here, we present relevant examples of each of these enhancements to pmartR and highlight how each new feature benefits the omics community.

MRPC: An R Package for Inference of Causal Graphs.

Understanding the causal relationships between variables is a central goal of many scientific inquiries. Causal relationships may be represented by directed edges in a graph (or equivalently, a network). In biology, for example, gene regulatory networks may be viewed as a type of causal networks, where X→Y represents gene X regulating (i.e., being causal to) gene Y. However, existing general-purpose graph inference methods often result in a high number of false edges, whereas current causal inference methods developed for observational data in genomics can handle only limited types of causal relationships. We present MRPC (a PC algorithm with the principle of Mendelian Randomization), an R package that learns causal graphs with improved accuracy over existing methods. Our algorithm builds on the powerful PC algorithm (named after its developers Peter Spirtes and Clark Glymour), a canonical algorithm in computer science for learning directed acyclic graphs. The improvements in MRPC result in increased accuracy in identifying v-structures (i.e., X→Y←Z), and robustness to how the nodes are arranged in the input data. In the special case of genomic data that contain genotypes and phenotypes (e.g., gene expression) at the individual level, MRPC incorporates the principle of Mendelian randomization as constraints on edge direction to help orient the edges. MRPC allows for inference of causal graphs not only for general purposes, but also for biomedical data where multiple types of data may be input to provide evidence for causality. The R package is available on CRAN and is a free open-source software package under a GPL (≥2) license.

The yeast scavenger decapping enzyme DcpS and its application for in vitro RNA recapping.

Eukaryotic mRNAs are modified at their 5' end early during transcription by the addition of N7-methylguanosine (m7G), which forms the "cap" on the first 5' nucleotide. Identification of the 5' nucleotide on mRNA is necessary for determination of the Transcription Start Site (TSS). We explored the effect of various reaction conditions on the activity of the yeast scavenger mRNA decapping enzyme DcpS and examined decapping of 30 chemically distinct cap structures varying the state of methylation, sugar, phosphate linkage, and base composition on 25mer RNA oligonucleotides. Contrary to the generally accepted belief that DcpS enzymes only decap short oligonucleotides, we found that the yeast scavenger decapping enzyme decaps RNA transcripts as long as 1400 nucleotides. Further, we validated the application of yDcpS for enriching capped RNA using a strategy of specifically tagging the 5' end of capped RNA by first decapping and then recapping it with an affinity-tagged guanosine nucleotide.

The Early Pliocene extinction of the mega-toothed shark Otodus megalodon: a view from the eastern North Pacific.

The extinct giant shark Otodus megalodon is the last member of the predatory megatoothed lineage and is reported from Neogene sediments from nearly all continents. The timing of the extinction of Otodus megalodon is thought to be Pliocene, although reports of Pleistocene teeth fuel speculation that Otodus megalodon may still be extant. The longevity of the Otodus lineage (Paleocene to Pliocene) and its conspicuous absence in the modern fauna begs the question: when and why did this giant shark become extinct? Addressing this question requires a densely sampled marine vertebrate fossil record in concert with a robust geochronologic framework. Many historically important basins with stacked Otodus-bearing Neogene marine vertebrate fossil assemblages lack well-sampled and well-dated lower and upper Pliocene strata (e.g., Atlantic Coastal Plain). The fossil record of California, USA, and Baja California, Mexico, provides such an ideal sequence of assemblages preserved within well-dated lithostratigraphic sequences. This study reviews all records of Otodus megalodon from post-Messinian marine strata from western North America and evaluates their reliability. All post-Zanclean Otodus megalodon occurrences from the eastern North Pacific exhibit clear evidence of reworking or lack reliable provenance; the youngest reliable records of Otodus megalodon are early Pliocene, suggesting an extinction at the early-late Pliocene boundary (∼3.6 Ma), corresponding with youngest occurrences of Otodus megalodon in Japan, the North Atlantic, and Mediterranean. This study also reevaluates a published dataset, thoroughly vetting each occurrence and justifying the geochronologic age of each, as well as excluding several dubious records. Reanalysis of the dataset using optimal linear estimation resulted in a median extinction date of 3.51 Ma, somewhat older than a previously proposed Pliocene-Pleistocene extinction date (2.6 Ma). Post-middle Miocene oceanographic changes and cooling sea surface temperature may have resulted in range fragmentation, while alongside competition with the newly evolved great white shark (Carcharodon carcharias) during the Pliocene may have led to the demise of the megatoothed shark. Alternatively, these findings may also suggest a globally asynchronous extinction of Otodus megalodon.

Understanding type 2 diabetes mellitus screening practices among primary care physicians: a qualitative chart-stimulated recall study.

BACKGROUND: Early diagnosis and treatment of prediabetes and type 2 diabetes mellitus (T2DM) can prevent future health problems, yet many individuals with these conditions are undiagnosed. This could be due, in part, to primary care physicians' (PCP) screening practices, about which little is known. The objectives of this study were to identify factors that influence PCPs' decisions to screen patients for T2DM and to characterize their interpretation and communication of screening test results to patients. METHODS: We conducted semi-structured chart-stimulated recall interviews with 20 University of Michigan Health System (UMHS) primary care physicians. PCPs were asked about their recent decisions to screen or not screen 134 purposively sampled non-diabetic patients who met American Diabetes Association criteria for screening for T2DM. Interviews were audio-recorded, transcribed, and analyzed using qualitative directed content analysis. Data on patient demographic characteristics and comorbidities were abstracted from the electronic health record. RESULTS: The most common reasons PCPs gave for not screening 63 patients for T2DM were knowledge of a previously normal screening test (49%) and a visit for reasons other than a health maintenance examination (48%). The most common reasons PCPs gave for screening 71 patients for T2DM were knowledge of a previously abnormal screening test (49%), and patients' weight (42%) and age (38%). PCPs correctly interpreted 89% of screening test results and communicated 95% of test results to patients. Among 24 patients found to have prediabetes, PCPs usually (58%) recommended weight loss and increased physical activity but never recommended participation in a Diabetes Prevention Program or use of metformin. CONCLUSIONS: Previous screening test results, visit types, and patients' weight and age influenced PCPs' decisions to screen for T2DM. When patients were screened, test results were generally correctly interpreted and consistently communicated. Recommendations to patients with prediabetes could better reflect evidence-based strategies to prevent T2DM.

Self care and health-seeking behavior of migrant farmworkers.

There are an estimated three million migrant and seasonal farmworkers (MSFW) in the United States. In addition to the inherent dangers of farm work, numerous factors place MSFW at even greater risk for work-related injuries. Little is known about how MSFW care for work-related injuries, and how the decision to seek professional care is made. A prospective survey using face-to-face structured interviews was used to explore the type and frequency of occupational injuries as well as self-care and health-care seeking practices of MSFW. Musculoskeletal injuries were the most commonly reported injuries, followed by injuries of the skin and chemical exposure. Self care with over-the-counter remedies was the predominant method of dealing with injuries, and, with the exception of chemical exposure, was found to be for the most part, appropriate. The reported use of alternative medicine or herbal remedies was low. Future research efforts should focus on ergonomic modifications and farmworker education to reduce or prevent musculoskeletal injuries. The number of reported chemical exposures and inappropriate treatment draw attention to the need for continued efforts for both primary prevention of exposure and optimal treatment once exposure occurs.