Advances in Methods for tRNA Sequencing and Quantification

In the past decade tRNA sequencing (tRNA-seq) has attracted considerable attention as an important tool for the development of novel approaches to quantify highly modified tRNA species and to propel tRNA research aimed at understanding the cellular physiology and disease and development of tRNA-based therapeutics. Many methods are available to quantify tRNA abundance while accounting for modifications and tRNA charging/acylation. Advances in both library preparation methods and bioinformatic workflows have enabled developments in next-generation sequencing (NGS) workflows. Other approaches forgo NGS applications in favor of hybridization-based approaches. In this review we provide a brief comparative overview of various tRNA quantification approaches, focusing on the advantages and disadvantages of these methods, which together facilitate reliable tRNA quantification

Cost-utility of transcatheter aortic valve implantation for inoperable patients with severe aortic stenosis treated by medical management: a UK cost-utility analysis based on patient-level data from the ADVANCE study.

OBJECTIVE: To use patient-level data from the ADVANCE study to evaluate the cost-effectiveness of transcatheter aortic valve implantation (TAVI) compared to medical management (MM) in patients with severe aortic stenosis from the perspective of the UK NHS. METHODS: A published decision-analytic model was adapted to include information on TAVI from the ADVANCE study. Patient-level data informed the choice as well as the form of mathematical functions that were used to model all-cause mortality, health-related quality of life and hospitalisations. TAVI-related resource use protocols were based on the ADVANCE study. MM was modelled on publicly available information from the PARTNER-B study. The outcome measures were incremental cost-effectiveness ratios (ICERs) estimated at a range of time horizons with benefits expressed as quality-adjusted life-years (QALY). Extensive sensitivity/subgroup analyses were undertaken to explore the impact of uncertainty in key clinical areas. RESULTS: Using a 5-year time horizon, the ICER for the comparison of all ADVANCE to all PARTNER-B patients was £13 943 per QALY gained. For the subset of ADVANCE patients classified as high risk (Logistic EuroSCORE >20%) the ICER was £17 718 per QALY gained). The ICER was below £30 000 per QALY gained in all sensitivity analyses relating to choice of MM data source and alternative modelling approaches for key parameters. When the time horizon was extended to 10 years, all ICERs generated in all analyses were below £20 000 per QALY gained. CONCLUSION: TAVI is highly likely to be a cost-effective treatment for patients with severe aortic stenosis

Analysis of 3.5 Million SARS-CoV-2 Sequences Reveals Unique Mutational Trends with Consistent Nucleotide and Codon Frequencies

Background: Since the onset of the SARS-CoV-2 pandemic, bioinformatic analyses have been performed to understand the nucleotide and synonymous codon usage features and mutational patterns of the virus. However, comparatively few have attempted to perform such analyses on a considerably large cohort of viral genomes while organizing the plethora of available sequence data for a month-by-month analysis to observe changes over time. Here, we aimed to perform sequence composition and mutation analysis of SARS-CoV-2, separating sequences by gene, clade, and timepoints, and contrast the mutational profile of SARS-CoV-2 to other comparable RNA viruses.Methods: Using a cleaned, filtered, and pre-aligned dataset of over 3.5 million sequences downloaded from the GISAID database, we computed nucleotide and codon usage statistics, including calculation of relative synonymous codon usage values. We then calculated codon adaptation index (CAI) changes and a nonsynonymous/synonymous mutation ratio (dN/dS) over time for our dataset. Finally, we compiled information on the types of mutations occurring for SARS-CoV-2 and other comparable RNA viruses, and generated heatmaps showing codon and nucleotide composition at high entropy positions along the Spike sequence.Results: We show that nucleotide and codon usage metrics remain relatively consistent over the 32-month span, though there are significant differences between clades within each gene at various timepoints. CAI and dN/dS values vary substantially between different timepoints and different genes, with Spike gene on average showing both the highest CAI and dN/dS values. Mutational analysis showed that SARS-CoV-2 Spike has a higher proportion of nonsynonymous mutations than analogous genes in other RNA viruses, with nonsynonymous mutations outnumbering synonymous ones by up to 20:1. However, at several specific positions, synonymous mutations were overwhelmingly predominant.Conclusions: Our multifaceted analysis covering both the composition and mutation signature of SARS-CoV-2 gives valuable insight into the nucleotide frequency and codon usage heterogeneity of SARS-CoV-2 over time, and its unique mutational profile compared to other RNA viruses

Supersonic shear wave elastography of human tendons is associated with in vivo tendon stiffness over small strains

Supersonic shear wave (SW) elastography has emerged as a useful imaging modality offering researchers and clinicians a fast, non-invasive, quantitative assessment of tendon biomechanics. However, the exact relationship between SW speed and in vivo tendon stiffness is not intuitively obvious and needs to be verified. This study aimed to explore the validity of supersonic SW elastography against a gold standard method to measure the Achilles tendon's in vivo tensile stiffness by combining conventional ultrasound imaging with dynamometry. Twelve healthy participants performed maximal voluntary isometric plantarflexion contractions (MVC) on a dynamometer with simultaneous ultrasonographic recording of the medial gastrocnemius musculotendinous junction for dynamometry-based measurement of stiffness. The tendon's force–elongation relationship and stress–strain behaviour were assessed. Tendon stiffness at different levels of tension was calculated as the slope of the stress–strain graph. SW speed was measured at the midportion of the free tendon and tendon Young's modulus was estimated. A correlation analysis between the two techniques revealed a statistically significant correlation for small strains (r(10) = 0.604, p =.038). SW-based assessments of in vivo tendon stiffness were not correlated to the gold standard method for strains in the tendon>10 % of the maximum strain during MVC. The absolute values of SW-based Young's modulus estimations were approximately-three orders of magnitude lower than dynamometry-based measurements. Supersonic SW elastography should be only used to assess SW speed for the detection and study of differences between tissue regions, differences between people or groups of people or changes over time in tendon initial stiffness (i.e., stiffness for small strains)

Plantar pressure of clipless and toe-clipped pedals in cyclists - A pilot study.

To determine the effect of clipless and toe-clipped pedals on plantar foot pressure while cycling. Seven bikers and 11 healthy volunteers were tested on a Giant ATX Team mountain bike, Tekscan Clinical 5.24 F-scan® system with an inner sole pressure sensor, a Tacx Cycle force One Turbo Trainer and a Cateye Mity 8 computerized speedometer were used. The subjects wore Shimano M037 shoes and used a standard clipless and toe-clipped pedal. The seat height was set at 100% of subject's trochanteric height. Plantar pressures were recorded over 12 consecutive crank cycles at a constant speed for each of the power outputs. The videos were analysed to record the pressure exerted at 12 positions on the foot for each variable. Whether there is any dominance of any of the metatarsals, and any difference in plantar pressures between clipped and clipless pedal. There was a significant difference in the pressure at many positions of the foot, but the sites were different for each individual. General regression analysis indicated that pedal type had a statistically significant effect on plantar pressure at the sites of 1(st) metatarsal (p=0.042), 3(rd) metatarsal (p<0.001), 5(th) metatarsal (<0.001), 2(nd) (p=0.018) and 5(th) toe (p<0.001), lateral midfoot (p<0.001) and central heel (p<0.001) areas. Clipless pedals produce higher pressures which are more spread across the foot than toe-clipped pedals. This may have implications for their use in the prevention and/or management of overuse injuries in the knee and foot

Systematic review and recommendations for intracompartmental pressure monitoring in diagnosing chronic exertional compartment syndrome of the leg.

OBJECTIVE: Although all intracompartmental pressure (ICP) measurement, magnetic resonance imaging, and near-infrared spectroscopy seem to be useful in confirming the diagnosis of chronic exertional compartment syndrome (CECS), no standard diagnostic procedure is currently universally accepted. We reviewed systematically the relevant published evidence on diagnostic criteria commonly in use for CECS to address 3 main questions: (1) Is there a standard diagnostic method available? (2) What ICP threshold criteria should be used for diagnosing CECS? (3) What are the criteria and options for surgical management? Finally, we made statements on the strength of each diagnostic criterion of ICP based on a rigorous standardized process. DATA SOURCES: We searched for studies that investigated ICP measurements in diagnosing CECS in the leg of human subjects, using PubMed, Score, PEDRO, Cochrane, Scopus, SportDiscus, Web of Knowledge, and Google Scholar. Initial searches were performed using the phrase, "chronic exertional compartment syndrome." The phrase "compartment syndrome" was then combined, using Boolean connectors ("OR" and "AND") with the words "diagnosis," "parameters," "levels," "localisation," or "measurement." Data extracted from each study included study design, number of subjects, number of controls, ICP instrument used, compartments measured, limb position during measurements, catheter position, exercise protocol, timing of measurements, mean resting compartment pressures, mean maximal compartment pressures, mean postexercise compartment pressures, diagnostic criteria used, and whether a reference diagnostic standard was used. The quality of studies was assessed based on the approach used by the American Academy of Orthopaedic Surgeons in judging the quality of diagnostic studies, and recommendations were made regarding each ICP diagnostic criteria in the literature by taking into account the quality and quantity of the available studies proposing each criterion. MAIN RESULTS: In the review, 32 studies were included. The studies varied in the ICP measurement techniques used; the most commonly measured compartment was the anterior muscle compartment, and the exercise protocol varied between running, walking, and ankle plantarflexion and dorsiflexion exercises. Preexercise, mean values ranged from 7.4 to 50.8 mm Hg for CECS patients, and 5.7 to 12 mm Hg in controls; measurements during exercise showed mean pressure readings ranging from 42 to 150 mm Hg in patients and 28 to 141 mm Hg in controls. No overlap between subjects and controls in mean ICP measurements was found at the 1-minute postexercise timing interval only showing values ranging from 34 to 55.4 mm Hg and 9 to 19 mm Hg in CECS patients and controls, respectively. The quality of the studies was generally not high, and we found the evidence for commonly used ICP criteria in diagnosing CECS to be weak. CONCLUSIONS: Studies in which an independent, blinded comparison is made with a valid reference standard among consecutive patients are yet to be undertaken. There should also be an agreed ICP test protocol for diagnosing CECS because the variability here contributes to the large differences in ICP measurements and hence diagnostic thresholds between studies. Current ICP pressure criteria for CECS diagnosis are therefore unreliable, and emphasis should remain on good history. However, clinicians may consider measurements taken at 1 minute after exercise because mean levels at this timing interval only did not overlap between subjects and controls in the studies we analyzed. Levels above the highest reported value for controls here (27.5 mm Hg) along with a good history, should be regarded as highly suggestive of CECS. It is evident that to achieve an objective recommendation for ICP threshold there is a need to set up a multi-center study group to reach an agreed testing protocol and modify the preliminary recommendations we have made