Teaching transposon classification as a means to crowd source the curation of repeat annotation - a tardigrade perspective.

BACKGROUND: The advancement of sequencing technologies results in the rapid release of hundreds of new genome assemblies a year providing unprecedented resources for the study of genome evolution. Within this context, the significance of in-depth analyses of repetitive elements, transposable elements (TEs) in particular, is increasingly recognized in understanding genome evolution. Despite the plethora of available bioinformatic tools for identifying and annotating TEs, the phylogenetic distance of the target species from a curated and classified database of repetitive element sequences constrains any automated annotation effort. Moreover, manual curation of raw repeat libraries is deemed essential due to the frequent incompleteness of automatically generated consensus sequences. RESULTS: Here, we present an example of a crowd-sourcing effort aimed at curating and annotating TE libraries of two non-model species built around a collaborative, peer-reviewed teaching process. Manual curation and classification are time-consuming processes that offer limited short-term academic rewards and are typically confined to a few research groups where methods are taught through hands-on experience. Crowd-sourcing efforts could therefore offer a significant opportunity to bridge the gap between learning the methods of curation effectively and empowering the scientific community with high-quality, reusable repeat libraries. CONCLUSIONS: The collaborative manual curation of TEs from two tardigrade species, for which there were no TE libraries available, resulted in the successful characterization of hundreds of new and diverse TEs in a reasonable time frame. Our crowd-sourcing setting can be used as a teaching reference guide for similar projects: A hidden treasure awaits discovery within non-model organisms.

Determination of total folates in infant formula and adult nutritionals by trienzyme extraction and UPLC-MS/MS Quantitation: First Action 2011.06.

The method for "Determination of Total Folates in Infant Formula and Adult Nutritionals by Trienzyme Extraction and UPLC-MS/MS Quantitation" was submitted to the Folate Working Group for consideration for adoption as Official First Action by AOAC INTERNATIONAL. This method uses ultra performance liquid chromatography/tandem mass spectrometry (UPLC-MS/MS) to determine the total folates in infant formulas and adult nutritionals after trienzyme digestion. Deconjugation of the various folate polyglutamates to folate monoglutamates is achieved by using rat plasma conjugase after the sample digestion with protease and a-amylase during the trienzyme digestion process. This method shows linearity of folate concentrations in the range of 10-19 100 microg/100 g. Extension of the range to cover folate concentrations of 5-2 000 000 microg/100 g can be achieved with appropriate adjustment of the sample weight and SPE cleanup loading volume. The recoveries ranged from 94.10 to 101.34%.

Dropping diversity of products of large US firms: Models and measures.

It is widely assumed that in our lifetimes the products available in the global economy have become more diverse. This assumption is difficult to investigate directly, however, because it is difficult to collect the necessary data about every product in an economy each year. We solve this problem by mining publicly available textual descriptions of the products of every large US firms each year from 1997 to 2017. Although many aspects of economic productivity have been steadily rising during this period, our text-based measurements show that the diversity of the products of at least large US firms has steadily declined. This downward trend is visible using a variety of product diversity metrics, including some that depend on a measurement of the similarity of the products of every single pair of firms. The current state of the art in comprehensive and detailed firm-similarity measurements is a Boolean word vector model due to Hoberg and Phillips. We measure diversity using firm-similarities from this Boolean model and two more sophisticated variants, and we consistently observe a significant dropping trend in product diversity. These results make it possible to frame and start to test specific hypotheses for explaining the dropping product diversity trend.

Ulnohumeral arthroplasty.

Seven patients underwent 9 ulnohumeral arthroplasties for degenerative arthritis of the elbow. At mean follow-up of 26 months, 5 elbows were pain free; two continued to cause mild pain and one to cause moderate pain. Extension improved from 22 degrees+/-8 degrees preoperatively to 12 degrees+/-9 degrees postoperatively (p=0.02); the average correction was 10 degrees+/-10 degrees. Flexion improved from 122 degrees+/-8 degrees to 133 degrees +/- 8 degrees (p=0.02); the average correction was 11 degrees+/-11 degrees. One patient had a late supracondylar humerus fracture which healed well with open reduction and internal fixation. Overall, we believe that ulnohumeral arthroplasty is relatively safe and easy to perform. Our patients did have modest improvements in range of motion, but complete relief of pain occurred in only about two thirds of the patients.

Analyzing vitamin D in foods and supplements: methodologic challenges.

This report briefly reviews existing methods for analyzing the vitamin D content of fortified and unfortified foods. The existing chemical methods are similar; all are time consuming, require experienced technicians, and have only been validated for a few materials (eg, dairy products or animal feed materials). This report also describes the lack of standard reference materials with certified values for vitamin D that laboratories need to guarantee the accuracy of existing analytic methods. Recently, the US Department of Agriculture, as part of a project to update the vitamin D values in the National Nutrient Database of Standard Reference, established an analytic methods committee to compare several existing vitamin D methods and to characterize 5 control materials (skim milk, processed cheese, cereal, orange juice, and salmon). Initial relative SDs for the 5 materials ranged from 35% to 50%. Elimination of systematic biases related to the methods and the standards yielded much more satisfactory relative SDs of 7% to 12%. This research has shown that existing methods for analyzing the vitamin D content in foods can produce accurate results. A new, simpler, and faster method, however, would greatly benefit the field. To guarantee accuracy, we need certified reference materials for foods.