Syringe irrigation in confluent canals: A sequential computational fluid dynamics assessment.

This study aims to assess the influence of root canal preparation, irrigation needle design and its placement depth in the irrigation flow of confluent canals during syringe irrigation. A mandibular molar presenting two confluent canals in its mesial root was sequentially prepared and scanned by micro-computed tomography after mechanical preparation up to ProTaper Next system sizes X2 (25/.06v), X3 (30/.07v) and X4 (40/.06v). In each of the root canal preparation models, a side-vented and an open-ended needle at 5, 3 and 2 mm from the working length were included, and irrigation flow was assessed by a validated computational fluid dynamics model. The results revealed that the irrigant flowed out of the confluent canals mainly through the canal that did not have the needle. Apical penetration and renewal of the irrigant were most efficiently achieved with the use of a 30G open-ended needle and a 30/.07v preparation.

Trimming and Validation of Illumina Short Reads Using Trimmomatic, Trinity Assembly, and Assessment of RNA-Seq Data.

Next-generation sequencing (NGS) technologies can generate billions of reads in a single sequencing run. However, with such high-throughput comes quality issues which have to be addressed before undertaking downstream analysis. Quality control on short reads is usually performed at default settings due to a lack of in-depth understanding of a particular software's parameters and their effect if changed on the output. Here we demonstrate how to optimize read trimming using Trimmomatic. We highlight the benefits of trimming by comparing the quality of transcripts assembled using trimmed and untrimmed reads.

Assessment of Yam mild mosaic virus coat protein gene sequence diversity reveals the prevalence of cosmopolitan and African group of isolates in Ghana and Nigeria.

This study analyzed the genetic diversity of 18 Yam mild mosaic virus (YMMV, genus Potyvirus) isolates collected from field surveys in Ghana (N = 8) and Nigeria (N = 10) in 2012-13. The full coat protein (CP) encoding region of the virus genome was sequenced and used for comparison and phylogenetic analysis of the YMMV isolates available in the NCBI nucleotide database. The mean nucleotide (nt) diversity was 13.4% among the 18 isolates (17 from D. alata and one from D. rotundata), 11.4% within the isolates of Ghana and 7.4% within the isolates of Nigeria. The phylogenetic clustering of the 18 YMMV isolates did not show correlation with the country of origin, and they aligned with the reference sequences of four of the 11 YMMV monophyletic groups representing the cosmopolitan group and the African group of YMMV isolates. High sequence homology of 99% between the YMMV sequence from Nigeria (CP12-DaN6-1) and a previously reported sequence from Togo (GenBank Accession Number AF548514) suggests a prevalence of seed-borne virus spread within the region. Understanding YMMV sequence diversity in West Africa aid in the improvement of diagnostic assays necessary for virus indexing and seed certification.