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DNBSEQ-T7 is a new whole-genome sequencer developed by Complete Genomics and MGI using DNA nanoball and combinatorial probe anchor synthesis technologies to generate short reads at a very large scale-up to 60 human genomes per day. However, it has not been objectively and systematically compared against Illumina short-read sequencers.
By using the same KOREF sample, the Korean Reference Genome, we have compared 7 sequencing platforms including BGISEQ-500, DNBSEQ-T7, HiSeq2000, HiSeq2500, HiSeq4000, HiSeqX10, and NovaSeq6000. We measured sequencing quality by comparing sequencing statistics (base quality, duplication rate, and random error rate), mapping statistics (mapping rate, depth distribution, and percent GC coverage), and variant statistics (transition/transversion ratio, dbSNP annotation rate, and concordance rate with single-nucleotide polymorphism [SNP] genotyping chip) across the 7 sequencing platforms. We found that MGI platforms showed a higher concordance rate for SNP genotyping than HiSeq2000 and HiSeq4000. The similarity matrix of variant calls confirmed that the 2 MGI platforms have the most similar characteristics to the HiSeq2500 platform.
Overall, MGI and Illumina sequencing platforms showed comparable levels of sequencing quality, uniformity of coverage, percent GC coverage, and variant accuracy; thus we conclude that the MGI platforms can be used for a wide range of genomics research fields at a lower cost than the Illumina platforms.
Overall, MGI and Illumina sequencing platforms showed comparable levels of sequencing quality, uniformity of coverage, percent GC coverage, and variant accuracy; thus we conclude that the MGI platforms can be used for a wide range of genomics research fields at a lower cost than the Illumina platforms.
Digitaria exilis, white fonio, is a minor but vital crop of West Africa that is valued for its resilience in hot, dry, and low-fertility environments and for the exceptional quality of its grain for human nutrition. Its success is hindered, however, by a low degree of plant breeding and improvement.
We sequenced the fonio genome with long-read SMRT-cell technology, yielding a ∼761 Mb assembly in 3,329 contigs (N50, 1.73 Mb; L50, 126). The assembly approaches a high level of completion, with a BUSCO score of >99%. The fonio genome was found to be a tetraploid, with most of the genome retained as homoeologous duplications that differ overall by ∼4.3%, neglecting indels. The 2 genomes within fonio were found to have begun their independent divergence ∼3.1 million years ago. The repeat content (>49%) is fairly standard for a grass genome of this size, but the ratio of Gypsy to Copia long terminal repeat retrotransposons (∼6.7) was found to be exceptionally high. Several genes related to future improvement of the crop were identified including shattering, plant height, and grain size. selleck Analysis of fonio population genetics, primarily in Mali, indicated that the crop has extensive genetic diversity that is largely partitioned across a north-south gradient coinciding with the Sahel and Sudan grassland domains.
We provide a high-quality assembly, annotation, and diversity analysis for a vital African crop. The availability of this information should empower future research into further domestication and improvement of fonio.
We provide a high-quality assembly, annotation, and diversity analysis for a vital African crop. The availability of this information should empower future research into further domestication and improvement of fonio.To enhance reproducibility in scientific research, more and more datasets are becoming publicly available so that researchers can perform secondary analyses to investigate questions the original scientists had not posited. This increases the return on investment for the NIH and other funding bodies. These datasets, however, are not perfect, and a better understanding of the assumptions that shaped them is required. The 2020 Junior Research Parasite Award recognized our work that showed that the signal-to-noise ratio in a particular dataset had not been investigated, leading to an erroneous conclusion in the original research. In this commentary, I share the process that led to the identification of the problem and hopefully provide useful lessons for other research parasites.Some authors have recommended that implant-supported single crowns should only contact during heavy clenching. However, a lack of occlusal contact with moderate clenching may cause supra-eruption of antagonist natural teeth. The main objective of this study was to assess changes in the occlusal contacts of posterior implant-supported single crowns with natural antagonist teeth two years after placement. The occlusal schemes of 14 patients who received 16 implant-supported single crowns in molar and premolar regions were assessed in this prospective study. Just after crown placement, at 6 months and after 2 years a silicone maxillomandibular relationship and T-scan records were obtained during the intercuspal position with light and heavy clenching, determined using near half of the maximum force and maximum force respectively. Occlusal contacts were assessed quantitatively and qualitatively in the implant-supported single crowns, contralateral tooth and adjacent tooth; the latter two were used as controls. After six months and two years, no significant variations were observed in any region of the occlusal scheme in any assessments, including silicone record or T-Scan, using light or heavy clenching, and qualitative or quantitative occlusal contact assessment. In this preliminary study, the occlusal scheme did not vary at the intercuspal position two years after placing posterior implant-supported single crowns.This study establishes a rapid and accurate method to identify aflatoxin contamination in peanut oil. Attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy, combined with either partial least squares discriminant analysis (PLS-DA) or a support vector machine (SVM) algorithm, were used to construct discriminative models for distinguishing between uncontaminated and aflatoxin-contaminated peanut oil. Peanut oil samples containing various concentrations of aflatoxin B1 (AFB1) were subjected to spectroscopic examination using an ATR-FTIR spectrometer. Preprocessed spectral data were input to PLS-DA and SVM algorithms to construct discriminative models for aflatoxin contamination in peanut oil. link2 SVM penalty and kernel function parameters were optimized using grid search, a genetic algorithm, and particle swarm optimization. Results demonstrated that with the PLS-DA model established using spectral data, with an accuracy of 94.64%, exhibited better discriminative capacities than models established based on preprocessed data. The SVM model established after data normalization and grid search optimization with a penalty parameter of 16 and kernel function parameter of 0.0359 displayed the best discriminative capacity, with 98.2143% accuracy. The discriminative models for aflatoxin contamination in peanut oil established by combining ATR-FTIR spectral data and nonlinear SVM algorithm were superior to the linear PLS-DA models.Although guided implant surgery is widely practiced, clinical studies examining the differences in accuracy between implanting systems that use the same surgical guide are currently lacking. This study aimed to evaluate and compare the effects of different dental implanting systems on positioning accuracy using a uniform type of stereolithographic surgical guide to account for cumulative errors in guide production. link3 One hundred BEGO Semados® S implants (Group A) and ninety-one NobelActive® implants (Group B) were inserted into patients using the same type of guide. The accuracy was assessed by matching the preoperative and postoperative cone-beam computed tomography (CBCT). The implant shoulder, tip, depth and angular deviation were registered. Statistically significant differences between groups were determined using student's t-test, bivariate correlation test and generalized estimating equation. The angular deviation was 3.16±1.74° in Group A and 2.58±1.41° in Group B (P=0.013 ); the depth deviation was 0.44±0.23mm in GroupA and 0.51±0.22mm in Group B (P=0.032). In terms of vertical accuracy, the Bego implant system is superior to the Nobel implant system using the same type of surgical guide, while the angle accuracy is opposite. Therefore, it is important to control the depth when using the template guided surgery in Nobel implant system. Similarly, angle control should be emphasized in Bego implant system. Measurements of the deviations provide the basis for a clinical reference that will be useful in preoperative analysis for improvement of the safety and accuracy of guided implant surgical procedures.
To identify how refractory disease (or relevant terminology variations) in Rheumatoid Arthritis (RA) and Polyarticular Juvenile Idiopathic Arthritis (PolyJIA) is defined and establish the key components of such definitions.
Searches were undertaken of English language articles within six medical databases, including manual searching, from January 1998 to March 2020 (PROSPERO CRD42019127142). Articles were included if they incorporated a definition of refractory disease, or non-response, in RA/PolyJIA, with clear components to the description. Qualitative content analysis was undertaken to describe refractory disease in RA/PolyJIA and classify each component within each definition.
Of 6,251 studies screened, 646 studies met inclusion criteria; 581 of these applied non-response criteria whilst 65 provided refractory disease definitions/descriptions. From the non-response studies, 39 different components included various disease activity measures, emphasising persistent disease activity and symptoms, despiity, including contributing factors. A clear unifying definition needs implementing as the plethora of different definitions makes study comparisons and appropriate identification of patients difficult.Norathyriol is an aglycone of a xanthonoid C-glycoside mangiferin that possesses different bioactive properties useful for humans compared to mangiferin. Mangiferin is more readily available in nature than norathyriol; thus, efficient mangiferin conversion into norathyriol is desirable. There are a few reports regarding mangiferin C-deglycosylation because of the C-C bond resistance toward acid, alkaline, and enzyme hydrolysis. In this study, we isolated a mangiferin-deglycosylating bacterium strain KM7-1 from the mouse intestine. 16S rDNA sequencing indicated that KM7-1 belongs to the Bacillus genus. Compared to the taxonomically similar bacteria, the growth characteristic of facultative anaerobic and thermophilic resembled, yet only Bacillus sp. KM7-1 was able to convert mangiferin into norathyriol. Resting cells of Bacillus sp. KM7-1 obtained from aerobic cultivation at 50 °C showed high norathyriol formation from 1 m m of mangiferin. Norathyriol formation can be conducted either under aerobic or anaerobic conditions, and the reaction depended on time and bacterial amount.
To examine the association between β-blocker prescription and first primary-care consultation for knee osteoarthritis (OA), hip OA, knee pain and hip pain.
Data source Clinical Practice Research Datalink. Participants aged ≥40 years in receipt of new oral β-blocker prescriptions were propensity score (PS) matched to an unexposed control. Cox proportional hazard ratios (HRs) and 95% confidence intervals (CI) were calculated, and adjusted for non-osteoporotic fractures, number of primary-care consultations for knee or hip injury, and, the number of primary-care consultations, out-patient referrals and hospitalizations in the 12-months preceding cohort entry. Analysis was stratified according to β-blocker class and for commonly prescribed drugs. p< 0.05 was statistically significant. .
111 718 β-blocker exposed participants were 11 PS matched to unexposed controls. β-blocker prescription was associated with reduced cumulative risk of knee OA, knee pain, and hip pain consultations with aHR(95%CI) 0.90(0.
Website: https://www.selleckchem.com/products/jq1.html
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