Correlation between Short-Form 36 Scores and Neck Disability Index in Patients Undergoing Anterior Cervical Discectomy and Fusion

Study Design Case control study. Purpose To determine how the Neck Disability Index (NDI), a cervical spine-specific outcome, reflects health-related quality-of-life, and if NDI is correlated to the 36-item Short-Form Health Survey (SF-36) scores. Overview of Literature NDI is a useful tool for assessing health-related quality of life in patients with neck pain. Methods We used the Pearson product-moment correlation coefficient to assess the validity of all items under NDI and SF-36, and the Pearson’s correlation coefficient to assess the correlation between NDI and total SF-36 scores. The primary outcome measures were spine-specific health status- and general health status-measures after spine surgery, and these were evaluated every year for 2 years, using both NDI and SF-36 scores. Results NDI had a strong linear correlation with SF-36 and its two scales, the Physical Component Score (PCS) and the Mental Component Score (MCS), attesting to the validity of these two instruments. Among the eight subscales of SF-36, there was a strong linear correlation between NDI and PCS-physical functioning, PCS-bodily pain, and MCS-role emotional. Further, a moderate linear correlation was observed between NDI and subscales of PCS-role physical, PCS-general health, and MCS-social functioning, and between NDI and MCS-vitality and MCS-mental health. Conclusions Our findings suggest that the NDI adequately reflects the patient’s physical and mental quality of life, implying that the use of NDI to assess functional outcomes can also be ultimately used to evaluate the patient’s quality of life

GMASS: a novel measure for genome assembly structural similarity

Abstract Background Thanks to the recent advancements in next-generation sequencing (NGS) technologies, large amount of genomic data, which are short DNA sequences known as reads, has been accumulating. Diverse assemblers have been developed to generate high quality de novo assemblies using the NGS reads, but their output is very different because of algorithmic differences. However, there are not properly structured measures to show the similarity or difference in assemblies. Results We developed a new measure, called the GMASS score, for comparing two genome assemblies in terms of their structure. The GMASS score was developed based on the distribution pattern of the number and coverage of similar regions between a pair of assemblies. The new measure was able to show structural similarity between assemblies when evaluated by simulated assembly datasets. The application of the GMASS score to compare assemblies in recently published benchmark datasets showed the divergent performance of current assemblers as well as its ability to compare assemblies. Conclusion The GMASS score is a novel measure for representing structural similarity between two assemblies. It will contribute to the understanding of assembly output and developing de novo assemblers

Study on the Design of an Underwater Chain Trencher via a Genetic Algorithm

In this study, a genetic algorithm (GA) with an analytic model is adopted to conduct multi-objective optimization for design of an underwater chain trencher. The optimization problem is defined as minimizing a product of the chain power and weight subject to the uniaxial compressive strength, coefficient of traction, bar length (L), nose radius (R) and ratio of the chipping depth over the spacing (l/S), of which the ranges are determined based on the specifications of commercial trenchers satisfying established performance requirements and previous parametric studies. It is found that an optimal design of the GA was obtained with L and l/S close to their low bound and R far from its low bound while that of a simple parametric analysis was acquired with the three parameters close to their low bounds. Moreover, in the most severe soft rock and traction conditions, the power and weight in the optimal design obtained by the GA are turn to be within the feasible ranges of targeted commercial trenchers

mySyntenyPortal: an application package to construct websites for synteny block analysis

Abstract Background Advances in sequencing technologies have facilitated large-scale comparative genomics based on whole genome sequencing. Constructing and investigating conserved genomic regions among multiple species (called synteny blocks) are essential in the comparative genomics. However, they require significant amounts of computational resources and time in addition to bioinformatics skills. Many web interfaces have been developed to make such tasks easier. However, these web interfaces cannot be customized for users who want to use their own set of genome sequences or definition of synteny blocks. Results To resolve this limitation, we present mySyntenyPortal, a stand-alone application package to construct websites for synteny block analyses by using users’ own genome data. mySyntenyPortal provides both command line and web-based interfaces to build and manage websites for large-scale comparative genomic analyses. The websites can be also easily published and accessed by other users. To demonstrate the usability of mySyntenyPortal, we present an example study for building websites to compare genomes of three mammalian species (human, mouse, and cow) and show how they can be easily utilized to identify potential genes affected by genome rearrangements. Conclusions mySyntenyPortal will contribute for extended comparative genomic analyses based on large-scale whole genome sequences by providing unique functionality to support the easy creation of interactive websites for synteny block analyses from user’s own genome data

Reference-based read clustering improves the de novo genome assembly of microbial strains

Constructing accurate microbial genome assemblies is necessary to understand genetic diversity in microbial genomes and its functional consequences. However, it still remains as a challenging task especially when only short-read sequencing technologies are used. Here, we present a new read-clustering algorithm, called RBRC, for improving de novo microbial genome assembly, by accurately estimating read proximity using multiple reference genomes. The performance of RBRC was confirmed by simulation-based evaluation in terms of assembly contiguity and the number of misassemblies, and was successfully applied to existing fungal and bacterial genomes by improving the quality of the assemblies without using additional sequencing data. RBRC is a very useful read-clustering algorithm that can be used (i) for generating high-quality genome assemblies of microbial strains when genome assemblies of related strains are available, and (ii) for upgrading existing microbial genome assemblies when the generation of additional sequencing data, such as long reads, is difficult

A chromosome-level genome assembly of the Korean crossbred pig Nanchukmacdon (Sus scrofa)

Abstract As plentiful high-quality genome assemblies have been accumulated, reference-guided genome assembly can be a good approach to reconstruct a high-quality assembly. Here, we present a chromosome-level genome assembly of the Korean crossbred pig called Nanchukmacdon (the NCMD assembly) using the reference-guided assembly approach with short and long reads. The NCMD assembly contains 20 chromosome-level scaffolds with a total size of 2.38 Gbp (N50: 138.77 Mbp). Its BUSCO score is 93.1%, which is comparable to the pig reference assembly, and a total of 20,588 protein-coding genes, 8,651 non-coding genes, and 996.14 Mbp of repetitive elements are annotated. The NCMD assembly was also used to close many gaps in the pig reference assembly. This NCMD assembly and annotation provide foundational resources for the genomic analyses of pig and related species

Integrative Meta-Assembly Pipeline (IMAP): Chromosome-level genome assembler combining multiple de novo assemblies.

BackgroundGenomic data have become major resources to understand complex mechanisms at fine-scale temporal and spatial resolution in functional and evolutionary genetic studies, including human diseases, such as cancers. Recently, a large number of whole genomes of evolving populations of yeast (Saccharomyces cerevisiae W303 strain) were sequenced in a time-dependent manner to identify temporal evolutionary patterns. For this type of study, a chromosome-level sequence assembly of the strain or population at time zero is required to compare with the genomes derived later. However, there is no fully automated computational approach in experimental evolution studies to establish the chromosome-level genome assembly using unique features of sequencing data.Methods and resultsIn this study, we developed a new software pipeline, the integrative meta-assembly pipeline (IMAP), to build chromosome-level genome sequence assemblies by generating and combining multiple initial assemblies using three de novo assemblers from short-read sequencing data. We significantly improved the continuity and accuracy of the genome assembly using a large collection of sequencing data and hybrid assembly approaches. We validated our pipeline by generating chromosome-level assemblies of yeast strains W303 and SK1, and compared our results with assemblies built using long-read sequencing and various assembly evaluation metrics. We also constructed chromosome-level sequence assemblies of S. cerevisiae strain Sigma1278b, and three commonly used fungal strains: Aspergillus nidulans A713, Neurospora crassa 73, and Thielavia terrestris CBS 492.74, for which long-read sequencing data are not yet available. Finally, we examined the effect of IMAP parameters, such as reference and resolution, on the quality of the final assembly of the yeast strains W303 and SK1.ConclusionsWe developed a cost-effective pipeline to generate chromosome-level sequence assemblies using only short-read sequencing data. Our pipeline combines the strengths of reference-guided and meta-assembly approaches. Our pipeline is available online at http://github.com/jkimlab/IMAP including a Docker image, as well as a Perl script, to help users install the IMAP package, including several prerequisite programs. Users can use IMAP to easily build the chromosome-level assembly for the genome of their interest

The Effectiveness of the Use of Regdanvimab (CT-P59) in Addition to Remdesivir in Patients with Severe COVID-19: A Single Center Retrospective Study

Introduction: Coronavirus disease 2019 (COVID-19) still has a high mortality rate when it is severe. Regdanvimab (CT-P59), a neutralizing monoclonal antibody that has been proven effective against mild to moderate COVID-19, may be effective against severe COVID-19. This study was conducted to determine the effectiveness of the combined use of remdesivir and regdanvimab in patients with severe COVID-19. Methods: From March to early May 2021, 124 patients with severe COVID-19 were admitted to Ulsan University Hospital (Ulsan, Korea) and received oxygen therapy and remdesivir. Among them, 25 were also administered regdanvimab before remdesivir. We retrospectively compared the clinical outcomes between the remdesivir alone group [n = 99 (79.8%)] and the regdanvimab/remdesivir group [n = 25 (20.2%)]. Results: The oxygen-free days on day 28 (primary outcome) were significantly higher in the regdanvimab/remdesivir group [mean ± SD: 19.36 ± 7.87 vs. 22.72 ± 3.66, p = 0.003]. The oxygen-free days was also independently associated with use of regdanvimab in the multivariate analysis, after adjusting for initial pulse oximetric saturation (SpO2)/fraction of inspired oxygen (FiO2) ratio (severity index). Further, in the regdanvimab/remdesivir group, the lowest SpO2/FiO2 ratio during treatment was significantly higher (mean ± SD: 237.05 ± 89.68 vs. 295.63 ± 72.74, p = 0.003), and the Kaplan-Meier estimates of oxygen supplementation days in surviving patients (on day 28) were significantly shorter [mean ± SD: 8.24 ± 7.43 vs. 5.28 ± 3.66, p = 0.024]. Conclusions: In patients with severe COVID-19, clinical outcomes can be improved by administering regdanvimab, in addition to remdesivir

Comparative Study of Triboelectric Nanogenerators with Differently Woven Cotton Textiles for Wearable Electronics

International audienceA comparative study of the electrical performance of triboelectric nanogenerators (TENGs) with plain-and 2/1 twill-woven cotton textiles was conducted. Furthermore, the microstructures of the cotton fiber surfaces were examined to understand the fundamental mechanical interaction among the cotton fibers in the TENGs. The TENG with 2/1 twill-woven cotton textiles exhibited higher output voltages compared to that with plain-woven cotton textiles. The difference in the output voltage between the two types of TENGs resulted from the difference in triboelectric charge generation between the constituent cotton textiles. The higher output voltage of the TENG with 2/1 twill-woven cotton textiles was attributed to the higher density in triboelectric interactions among the cotton fiber molecules