Intuitive Staging Correlates With King's Clinical Stage.

BACKGROUND: Clinical stage in amyotrophic lateral sclerosis (ALS) can be assigned using King's staging with a simple protocol based on the number of CNS regions involved and the presence of significant nutritional or respiratory failure. It is important that the assigned clinical stage matches expectations, and generally corresponds with how a health care professional would intuitively stage the patient. We therefore investigated the relationship between King's clinical ALS stage and ALS stage as intuitively assigned by health care professionals. METHODS: We wrote 17 case vignettes describing people with ALS at different disease stages from very early limited disease involvement through to severe, multi-domain disease. During two workshops, we asked health care professionals to intuitively stage the vignettes and compared the answers with the actual King's clinical ALS stage. RESULTS: There was a good correlation between King's clinical ALS stage and intuitively assigned stage, with a Spearman's Rank correlation coefficient of 0.64 (p < 0.001). There was no difference in the intuitive stages assigned by practitioners of different types or at different levels of experience. CONCLUSIONS: Across a spectrum of ALS scenarios, King's clinical ALS stage corresponds to intuitive ALS stage as assigned by a range of health care professionals

DNAscan2: a versatile, scalable, and user-friendly analysis pipeline for human next-generation sequencing data

SUMMARY: The current widespread adoption of next-generation sequencing (NGS) in all branches of basic research and clinical genetics fields means that users with highly variable informatics skills, computing facilities and application purposes need to process, analyse, and interpret NGS data. In this landscape, versatility, scalability, and user-friendliness are key characteristics for an NGS analysis software. We developed DNAscan2, a highly flexible, end-to-end pipeline for the analysis of NGS data, which (i) can be used for the detection of multiple variant types, including SNVs, small indels, transposable elements, short tandem repeats, and other large structural variants; (ii) covers all standard steps of NGS analysis, from quality control of raw data and genome alignment to variant calling, annotation, and generation of reports for the interpretation and prioritization of results; (iii) is highly adaptable as it can be deployed and run via either a graphic user interface for non-bioinformaticians and a command line tool for personal computer usage; (iv) is scalable as it can be executed in parallel as a Snakemake workflow, and; (v) is computationally efficient by minimizing RAM and CPU time requirements. AVAILABILITY AND IMPLEMENTATION: DNAscan2 is implemented in Python3 and is available at https://github.com/KHP-Informatics/DNAscanv2

A standard operating procedure for King's ALS clinical staging

OBJECTIVE: Clinical stages in amyotrophic lateral sclerosis (ALS) can be measured using a simple system based on the number of CNS regions involved and requirement for gastrostomy or noninvasive ventilation (NIV). We aimed to design a standard operating procedure (SOP) to define the standardized use and application of the King's staging system. // METHODS: We designed a SOP for the King's staging system. We wrote case vignettes representative of ALS patients at different disease stages. During two workshops, we taught health care professionals how to use the SOP, then asked them to stage the vignettes using the SOP. We measured the extent to which SOP staging corresponded with correct clinical stage. // RESULTS: The reliability of staging using the SOP was excellent, with a Spearman's Rank coefficient of 0.95 (p < 0.001), and was high for different groups of health care professionals, and for those with different levels of experience in ALS. The limits of agreement between SOP staging and actual clinical stage lie within a single stage, confirming that there is a clinically acceptable level of agreement between staging using the SOP and actual King's clinical stage. There were also no systematic biases of the SOP over the range of stages, either for over-staging or under-staging. // CONCLUSIONS: We have demonstrated that the staging SOP provides a reliable method of calculating clinical stages in ALS patients and can be used prospectively by a range of health care professionals with different levels of experience, as for example may be the case in multicentre clinical trials

DNAscan: personal computer compatible NGS analysis, annotation and visualisation.

BACKGROUND: Next Generation Sequencing (NGS) is a commonly used technology for studying the genetic basis of biological processes and it underpins the aspirations of precision medicine. However, there are significant challenges when dealing with NGS data. Firstly, a huge number of bioinformatics tools for a wide range of uses exist, therefore it is challenging to design an analysis pipeline. Secondly, NGS analysis is computationally intensive, requiring expensive infrastructure, and many medical and research centres do not have adequate high performance computing facilities and cloud computing is not always an option due to privacy and ownership issues. Finally, the interpretation of the results is not trivial and most available pipelines lack the utilities to favour this crucial step. RESULTS: We have therefore developed a fast and efficient bioinformatics pipeline that allows for the analysis of DNA sequencing data, while requiring little computational effort and memory usage. DNAscan can analyse a whole exome sequencing sample in 1 h and a 40x whole genome sequencing sample in 13 h, on a midrange computer. The pipeline can look for single nucleotide variants, small indels, structural variants, repeat expansions and viral genetic material (or any other organism). Its results are annotated using a customisable variety of databases and are available for an on-the-fly visualisation with a local deployment of the gene.iobio platform. DNAscan is implemented in Python. Its code and documentation are available on GitHub: https://github.com/KHP-Informatics/DNAscan . Instructions for an easy and fast deployment with Docker and Singularity are also provided on GitHub. CONCLUSIONS: DNAscan is an extremely fast and computationally efficient pipeline for analysis, visualization and interpretation of NGS data. It is designed to provide a powerful and easy-to-use tool for applications in biomedical research and diagnostic medicine, at minimal computational cost. Its comprehensive approach will maximise the potential audience of users, bringing such analyses within the reach of non-specialist laboratories, and those from centres with limited funding available

Biomechanics of the clean and jerk in weightlifting national Jordanian team

Seven elite national Jordanian weightlifters were videoed at 50 fields per second from the sagittal plane during the execution of the clean and jerk (C&J) on an AMTI force platform with 3 weights of submaximal lifts; low medium and high weights (35%, 65%, 85%) of their maximum. Linear and angular kinematics of the barbell with the ground reaction forces histories of the lower body were analysed using Kinova & APAS. A significant decrease was found in the maximum vertical velocity of the barbell during the second pull of the heaviest lift (p < 0.05). Maximum extension velocity of the hip joint significantly increased during the first pull of the heaviest lift (p < 0.05). Vertical velocity and maximum bar height decreased during the second pull, especially at 85%. Angle-angle diagrams of the knee and hip profile showed major differences among participants, especially at the 85% lift of their maximum

Characterisation of retrotransposon insertion polymorphisms in whole genome sequencing data from individuals with amyotrophic lateral sclerosis

The genetics of an individual is a crucial factor in understanding the risk of developing the neurodegenerative disease amyotrophic lateral sclerosis (ALS). There is still a large proportion of the heritability of ALS, particularly in sporadic cases, to be understood. Among others, active transposable elements drive inter-individual variability, and in humans long interspersed element 1 (LINE1, L1), Alu and SINE-VNTR-Alu (SVA) retrotransposons are a source of polymorphic insertions in the population. We undertook a pilot study to characterise the landscape of non-reference retrotransposon insertion polymorphisms (non-ref RIPs) in 15 control and 15 ALS individuals’ whole genomes from Project MinE, an international project to identify potential genetic causes of ALS. The combination of two bioinformatics tools (mobile element locator tool (MELT) and TEBreak) identified on average 1250 Alu, 232 L1 and 77 SVA non-ref RIPs per genome across the 30 analysed. Further PCR validation of individual polymorphic retrotransposon insertions showed a similar level of accuracy for MELT and TEBreak. Our preliminary study did not identify a specific RIP or a significant difference in the total number of non-ref RIPs in ALS compared to control genomes. The use of multiple bioinformatic tools improved the accuracy of non-ref RIP detection and our study highlights the potential importance of studying these elements further in ALS

Antibacterial synergy of Tritirachium oryzae-produced silver nanoparticles with different antibiotics and essential oils derived from Cupressus sempervirens and Asteriscus graveolens (Forssk)

Purpose: To carry out eco-friendly biosynthesis of fungi-derived silver nanoparticles (AgNPs) and investigate their antibacterial synergies with essential oils (EOs) of Asteriscus graveolens (Forssk.) Less. and Cupressus sempervirens. Methods: Biosynthesis of AgNPs was carried out using a cell-free filtrate of Tritirachium oryzae. The biosynthesized AgNPs characteristics were assessed using different methods, including ultravioletvisible spectrophotometry (UV), Fourier-transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM) with energy-dispersive x-ray spectroscopy (EDS) and transmission electron microscopy (TEM). Results: Obvious synergistic effects were observed between AgNPs and chloramphenicol, vancomycin, nitrofurantoin or tetracycline with Pseudomonas aeruginosa, through increases in fold area of inhibition (IFAs) within the range of 2.4 to 9.0. Synergistic interactions were also seen between AgNPs and the antibiotics used, depending on the strain. Increase in IFA ranged from 1- to 3-fold for S. aureus, E. coli and P. aeruginosa. Similarly, combinations of AgNPs, EO of A. graveolens and cefotaxime, nitrofurantoin or amoxicillin against P. aeruginosa led to 10-, 3- and 10-fold synergy, respectively. In contrast, the use of AgNPs and trimethoprim, tetracycline or amoxicillin against E. coli led to 1 to 6-fold synergy. The best synergistic capacity resulted from AgNPs and the EO of C. sempervirens and trimethoprim against S. epidermidis, which yielded 29-fold increase in IFA. The use of combination of AgNPs and vancomycin against P. aeruginosa led to 16.4-fold enhancement of IFA. Conclusion: The findings can potentially lead to the development of a new perception of antibacterial agents (innovative medications) involving the incorporation of nanoparticles (NPs) or new materials that potentially synergize with antibiotics, NPs and the EOs of different plants

<i>C9orf72 </i>Repeat Expansion Discordance in 6 Multigenerational Kindreds

Background and Objectives:A hexanucleotide repeat expansion in the noncoding region of the C9orf72 gene is the most common genetically identifiable cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia in populations of European ancestry. Pedigrees associated with this expansion exhibit phenotypic heterogeneity and incomplete disease penetrance, the basis of which is poorly understood. Relatives of those carrying the C9orf72 repeat expansion exhibit a characteristic cognitive endophenotype independent of carrier status. To examine whether additional shared genetic or environmental risks within kindreds could compel this observation, we have conducted a detailed cross-sectional study of the inheritance within multigenerational Irish kindreds carrying the C9orf72 repeat expansion.Methods:One hundred thirty-one familial ALS pedigrees, 59 of which carried the C9orf72 repeat expansion (45.0% [95% CI 36.7–53.5]), were identified through the Irish population-based ALS register. C9orf72 genotyping was performed using repeat-primed PCR with amplicon fragment length analysis. Pedigrees were further investigated using SNP, targeted sequencing data, whole-exome sequencing, and whole-genome sequencing.Results:We identified 21 kindreds where at least 1 family member with ALS carried the C9orf72 repeat expansion and from whom DNA was available from multiple affected family members. Of these, 6 kindreds (28.6% [95% CI 11.8–48.3]) exhibited discordant segregation. The C9orf72 haplotype was studied in 2 families and was found to segregate with the C9orf72-positive affected relative but not the C9orf72-negative affected relative. No other ALS pathogenic variants were identified within these discordant kindreds.Discussion:Family members of kindreds associated with the C9orf72 repeat expansion may carry an increased risk of developing ALS independent of their observed carrier status. This has implications for assessment and counseling of asymptomatic individuals regarding their genetic risk