Compact and evenly distributed k-mer binning for genomic sequences

Motivation The processing of k-mers (subsequences of length k) is at the foundation of many sequence processing algorithms in bioinformatics, including k-mer counting for genome size estimation, genome assembly, and taxonomic classification for metagenomics. Minimizers—ordered m-mers where m < k—are often used to group k-mers into bins as a first step in such processing. However, minimizers are known to generate bins of very different sizes, which can pose challenges for distributed and parallel processing, as well as generally increase memory requirements. Furthermore, although various minimizer orderings have been proposed, their practical value for improving tool efficiency has not yet been fully explored. Results We present Discount, a distributed k-mer counting tool based on Apache Spark, which we use to investigate the behaviour of various minimizer orderings in practice when applied to metagenomics data. Using this tool, we then introduce the universal frequency ordering, a new combination of frequency-sampled minimizers and universal k-mer hitting sets, which yields both evenly distributed binning and small bin sizes. We show that this ordering allows Discount to perform distributed k-mer counting on a large dataset in as little as 1/8 of the memory of comparable approaches, making it the most efficient out-of-core distributed k-mer counting method available. Availability and implementation Discount is GPL licensed and available at https://github.com/jtnystrom/discount. The data underlying this article are available in the article and in its online supplementary material. Supplementary information Supplementary data are available at Bioinformatics online.

Language Learning Difficulties Reported by Beginner-Level Learners of Arabic Using Online Tools

This study examined how two classes used online supplementary material to learn Arabic and the difficulties they reported in the process of their learning. The two classes have a total of 33 students who completed the course. The data from their weekly journal entries and log information from the site where the material was housed are used to describe the extent and the ways in which students used the material and issues they faced learning Arabic. Results show that students in both classes spent roughly 265 hours practicing Arabic with an average of 8 hours per student throughout the semester and that vocabulary recall and pronunciation were key struggles in their learning. Furthermore, this paper discusses some of the themes that emerged of students’ journal entries about their learning Arabic. Further implications are provided and discussed.

D. A. Ọbasa (1879–1945): a Yoruba poet, culture activist and local intellectual in colonial Nigeria

This article examines the works of one of the earliest Yoruba poets, Denrele Adetimikan Ọbasa (1879–1945), a member of the local intelligentsia in colonial Nigeria. In my assessment of the poet as a culture activist and local intellectual, I draw on biographical information, extensive archival research and relevant textual illustration. The central argument of the article is that Ọbasa exploits Yoruba communal oral resources for ideas, themes and other linguistic influences in his poetry. Therefore, the essay explores the creative ability of Ọbasa to preserve different forms of oral literary material in his poetic composition and how he uses the folkloric materials as instruments for raising the social consciousness of his readers. At this level, the article argues, Ọbasa transforms oral traditions into metaphorical and symbolic language that best articulates his political or philosophical positions. Thus, orality is not static, but dynamic, flexible and adaptable to change. The main article offers translations of excerpts from Ọbasa's poetry, while the online supplementary material offers more complete samples of Ọbasa's poems.

Cement plug technique for the management of disc-associated cervical spondylopathy in 52 Dobermann Pinscher dogs

SummaryObjectives: To report the radiographic and clinical outcome of an intervertebral bone cement plug technique for the management of disc-associated cervical spondylopathy in Dobermann Pinscher dogs.Methods: Retrospective study of 52 Dobermann Pinscher dogs.Results: A variable degree of cement plug subsidence with loss of vertebral distraction was evident in all dogs (n = 40) that were radiographed >6 weeks postoperatively. In no case was there definitive evidence of vertebral body fusion. Eight dogs had a sudden deterioration in neurological status, cervical hyperaesthesia, or both between three days and 12 weeks following surgery that was considered to be implant-associated; six of these dogs were euthanatized. Following surgery, 43/52 dogs were considered to be neurologically normal or to have improved, however, nine of 43 subsequently deteriorated due to adjacent segment disease. At the long-term follow-up, 34 dogs were considered to be neurologically normal or to have improved. Twenty-nine dogs were dead by the end of the study period.Clinical significance: Intervertebral bone cement plug surgery results in an initial improvement in clinical signs in the majority of Dobermann Pinschers with disc-associated cervical spondylopathy. However, it fails to maintain vertebral distraction or achieve vertebral body fusion, and is associated with acute implant complications, additional cervical disc protrusions or mortality in a significant proportion of cases.Online Supplementary Material: Please note that online supplementary material for this paper is available at: http://dx.doi.org/10.3415/VCOT-15-09-0160.

Arthrodesis of the equine centro distal and tarsometatarsal joints using a single modified kerf-cut cylinder

Summary Objectives: To describe a technique for surgical placement of a modified kerf-cut cylinder for the purpose of arthrodesis across the equine centrodistal and tarsometatarsal joints. Methods: Each horse (n = 4) underwent unilateral placement of a single kerf-cut cylinder spanning the centrodistal and tarsometatarsal joints with the placement of an autologous cancellous bone graft. Horses were evaluated via lameness examination and radiography postoperatively and euthanatization of each horse was performed at four different time points up to 12 weeks post-surgery to evaluate for lameness, implant stability and success with integration in the surrounding bone. Results: Implants were placed successfully in three of four horses. In one horse, due to technical error, the implant was misaligned with the joint spaces. Although the horse exhibited minimal pain, it was euthanatized at the two week follow-up. Implant placement in the remaining three horses was successfully achieved. At eight weeks, radiographically there was evidence of osseous union across the joint spaces. No change in lameness was detected at any point after surgery. At 12 weeks post-surgery, histologically the implants were filled with mineralized osteoid and demonstrated integration with the surrounding tissue. Clinical significance: The surgical approach and placement of modified kerf-cut cylinders for arthrodesis of the centrodistal and tarsometatarsal joints were successfully achieved with minimal signs of postoperative pain and a short rehabilitation time period in normal horses.Online Supplementary Material: Please note that online supplementary material for this paper is available at: http://dx.doi.org/10.3415/VCOT-15-10-0167

Modeling Caries Experience: Advantages of the Use of the Hurdle Model

In dental epidemiology, the decayed (D), missing (M), and filled (F) teeth or surfaces index (DFM index) is a frequently used measure. The DMF index is characterized by a strongly positive skewed distribution with a large stack of zero counts for those individuals without caries experience. Therefore, standard generalized linear models often lead to a poor fit. The hurdle regression model is a highly suitable class to model a DMF index, but its use is subordinated. We aim to overcome the gap between the suitability of the hurdle model to fit DMF indices and the frequency of its use in caries research. A theoretical introduction to the hurdle model is provided, and an extensive comparison with the zero-inflated model is given. Using an illustrative data example, both types of models are compared, with a special focus on interpretation of their parameters. Accompanying R code and example data are provided as online supplementary material.