Republication of "A Biomechanical Comparison of Limited Open Versus Krackow Repair for Achilles Tendon Rupture"

Background

Soft tissue complications after Achilles tendon repair has led to increased interest in less invasive techniques. Various limited open techniques have gained popularity as an alternative to open operative repair. The purpose of this study was to biomechanically compare an open Krackow and limited open repair for Achilles tendon rupture. We hypothesized that there would be no statistical difference in load to failure, work to failure, and initial linear stiffness.

Methods

A simulated Achilles tendon rupture was created 4 cm proximal to its insertion in 18 fresh-frozen cadaveric below-knee lower limbs. Specimens were randomized to open or limited open PARS Achilles Jig System repair. Repairs were loaded to failure at a rate of 25.4 mm/s to reflect loading during normal ankle range of motion. Load to failure, work to failure, and initial linear stiffness were compared between the 2 repair types.

Results

The average load to failure (353.8 ± 88.8 N vs 313.3 ± 99.9 N; P = .38) and work to failure (6.4 ± 2.3 J vs 6.3 ± 3.5 J; P = .904) were not statistically different for Krackow and PARS repair, respectively. Mean initial linear stiffness of the Krackow repair (17.8 ± 5.4 N/mm) was significantly greater than PARS repair (11.8 ± 2.5 N/mm) (P = .011).

Conclusion

No significant difference in repair strength was seen, but higher initial linear stiffness for Krackow repair suggests superior resistance to gap formation, which may occur during postoperative rehabilitation. With equal repair strength, but less soft tissue devitalization, the PARS may be a favorable option for patients with risk factors for soft tissue complications.

Rapid High-Resolution Mosaic Acquisition for Photoacoustic Remote Sensing

Mechanical stages are routinely used to scan large expanses of biological specimens in photoacoustic imaging. This is primarily due to the limited field of view (FOV) provided by optical scanning. However, stage scanning becomes impractical at higher scanning speeds, or potentially unfeasible with heavier samples. Also, the slow scan-rate of the stages makes high resolution scanning a time-consuming process. Some clinical applications such as microsurgery require submicron resolution in a reflection-mode configuration necessitating a method that can acquire large field of views with a small raster scanning step size. In this study, we describe a method that combines mechanical stages with optical scanning for the rapid acquisition of high-resolution large FOVs. Optical scanning is used to acquire small frames in a two-dimensional grid formed by the mechanical stages. These frames are captured with specific overlap for effective image registration. Using a step size of 200 nm, we demonstrate mosaics of carbon fiber networks with FOVs of 0.8 × 0.8 mm² captured in under 70 s with 1.2 µm image resolution. Larger mosaics yielding an imaging area of 3 × 3 mm² are also shown. The method is validated by imaging a 1 × 1 mm² section of unstained histopathological human tissue.

Discerning Post Anesthesia Readiness for Transition (DPART): A Measurement Tool

PURPOSE

To develop a valid reliable measurement tool that accurately quantifies postanesthesia recuperation in adult and pediatric patients.

DESIGN

A descriptive factor-isolating design guided by measurement theory.

METHODS

Instrument development was based on collaborative discussions of professional evidence. A five-person expert panel was consulted for content and face validity. Reliability testing took place in the adult and pediatric postanesthesia care units.

FINDINGS

The expert panel's final review yielded a kappa statistic of 1 and scale content validity index based on universal agreement between raters of 1, suggesting high content validity. Reliability testing yielded a kappa statistic of 1, demonstrating complete agreement for all items.

CONCLUSIONS

The Discerning Post Anesthesia Readiness for Transition measurement tool is a valid and reliable instrument that can be used in practice or future research to assess postanesthesia recuperation in pediatric and adult patients.

dStruct: identifying differentially reactive regions from RNA structurome profiling data

RNA biology is revolutionized by recent developments of diverse high-throughput technologies for transcriptome-wide profiling of molecular RNA structures. RNA structurome profiling data can be used to identify differentially structured regions between groups of samples. Existing methods are limited in scope to specific technologies and/or do not account for biological variation. Here, we present dStruct which is the first broadly applicable method for differential analysis accounting for biological variation in structurome profiling data. dStruct is compatible with diverse profiling technologies, is validated with experimental data and simulations, and outperforms existing methods.

PATTERNA: transcriptome-wide search for functional RNA elements via structural data signatures

Establishing a link between RNA structure and function remains a great challenge in RNA biology. The emergence of high-throughput structure profiling experiments is revolutionizing our ability to decipher structure, yet principled approaches for extracting information on structural elements directly from these data sets are lacking. We present PATTERNA, an unsupervised pattern recognition algorithm that rapidly mines RNA structure motifs from profiling data. We demonstrate that PATTERNA detects motifs with an accuracy comparable to commonly used thermodynamic models and highlight its utility in automating data-directed structure modeling from large data sets. PATTERNA is versatile and compatible with diverse profiling techniques and experimental conditions.

RNA secondary structure profiling in zebrafish reveals unique regulatory features

Background

RNA is known to play diverse roles in gene regulation. The clues for this regulatory function of RNA are embedded in its ability to fold into intricate secondary and tertiary structure.

Results

We report the transcriptome-wide RNA secondary structure in zebrafish at single nucleotide resolution using Parallel Analysis of RNA Structure (PARS). This study provides the secondary structure map of zebrafish coding and non-coding RNAs. The single nucleotide pairing probabilities of 54,083 distinct transcripts in the zebrafish genome were documented. We identified RNA secondary structural features embedded in functional units of zebrafish mRNAs. Translation start and stop sites were demarcated by weak structural signals. The coding regions were characterized by the three-nucleotide periodicity of secondary structure and display a codon base specific structural constrain. The splice sites of transcripts were also delineated by distinct signature signals. Relatively higher structural signals were observed at 3’ Untranslated Regions (UTRs) compared to Coding DNA Sequence (CDS) and 5’ UTRs. The 3′ ends of transcripts were also marked by unique structure signals. Secondary structural signals in long non-coding RNAs were also explored to better understand their molecular function.

Conclusions

Our study presents the first PARS-enabled transcriptome-wide secondary structure map of zebrafish, which documents pairing probability of RNA at single nucleotide precision. Our findings open avenues for exploring structural features in zebrafish RNAs and their influence on gene expression.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4497-0) contains supplementary material, which is available to authorized users.

Acute Achilles Rupture Percutaneous Repair: Approach, Materials, Techniques

Closed traumatic Achilles tendon rupture is a common injury, especially in the aging athlete. Traditionally open repair has been recognized to offer a lower rerupture rate compared with nonoperative methods but with a higher complication rate. Percutaneous repair has been described to offer the benefits of open repair while avoiding the complications. The sural nerve is potentially susceptible to injury, and specialized instrumentation has been developed to avoid this event. This article discusses several techniques of minimally invasive Achilles tendon repair. Many authors have evaluated these techniques and the results are discussed here.

Physical activity on prescription schemes (PARS): do programme characteristics influence effectiveness? Results of a systematic review and meta-analyses

BACKGROUND

Physical activity on prescription schemes (PARS) are health promotion programmes that have been implemented in various countries. The aim of this study was to outline the differences in the design of PARS in different countries. This study also explored the differences in the adherence rate to PARS and the self-reported level of physical activity between PARS users in different countries.

METHOD

A systematic literature review and meta-analyses were conducted. We searched PubMed and EBASCO in July 2015 and updated our search in September 2015. Studies that reported adherence to the programme and self-reported level of physical activity, published in the English language in a peer-reviewed journal since 2000, were included. The difference in the pooled adherence rate after finishing the PARS programme and the adherence rate before or during the PARS programme was 17% (95% CI 9% to 24%). The difference in the pooled physical activity was 0.93 unit score (95 CI -3.57 to 1.71). For the adherence rate, a meta-regression was conducted.

RESULTS

In total, 37 studies conducted in 11 different countries met the inclusion criteria. Among them, 31 reported the adherence rate, while the level of physical activity was reported in 17 studies. Results from meta-analyses show that PARS had an effect on the adherence rate of physical activity, while the results from the meta-regressions show that programme characteristics such as type of chronic disease and the follow-up period influenced the adherence rate.

CONCLUSIONS

The effects of PARS on adherence and self-reported physical activity were influenced by programme characteristics and also by the design of the study. Future studies on the effectiveness of PARS should use a prospective longitudinal design and combine quantitative and qualitative data. Furthermore, future evaluation studies should distinguish between evaluating the adherence rate and the self-reported physical activity among participants with different chronic diseases.

Evaluation of RNA Blood Biomarkers in Individuals at Risk of Parkinson's Disease

BACKGROUND

Substantial progress has been made in the discovery of blood biomarkers for Parkinson's disease (PD), a progressive neurodegenerative disease that affects more than 4 million worldwide. Olfactory dysfunction and dopamine deficits usually precede motor symptoms years before the onset of PD. A readily accessible biomarker useful for identifying patients at risk of PD is expected to accelerate clinical trials.

OBJECTIVE

To evaluate previously identified PD blood RNA biomarkers in a cohort of asymptomatic individuals at risk of PD.

METHODS

Here we tested 16 previously identified PD RNA biomarkers using quantitative PCR assays in a total of 269 blood samples at baseline from hyposmic and normosmic participants enrolled in the Parkinson's Associated Risk Syndrome study.

RESULTS

Expression levels of four biomarkers, SOD2, PKM2, ZNF134, and ZNF160 were negatively correlated with the total Unified Parkinson's Disease Rating Scale, thus suggesting these biomarkers may be useful to stratify patients prior to the onset of motor symptoms. Levels of SOD2 were upregulated in hyposmic males compared to females, whereas levels of PKM2 were upregulated in hyposmic males compared to normosmic males and hyposmic females. Further, levels of SOD2 were upregulated in males with abnormal dopamine transporter (DAT) scans compared to females with abnormal DAT scans.

CONCLUSIONS

These results suggest that some of these biomarkers may be useful for stratification of individuals at risk for PD and that there may be sex differences in the expression of some biomarkers. Future studies in larger longitudinal studies will be key to assessing the validity of these findings.

The PARS sequence increase the efficiency of stable Pichia pastoris transformation

The methylotrophic yeast Pichia pastoris is a popular host for recombinant expression of proteins. Plasmids containing the Pichia autonomously replicating sequence (PARS) transform P. pastoris with higher efficiency than linear DNA equipped with termini designed for homologous recombination. Moreover, PARS containing constructs provide higher protein yields. Unfortunately, these autonomous plasmids are inherently unstable and the preferred method of P. pastoris transformation is therefore stable integration in the genome by homologous recombination. In the present study we report that a novel combination of PARS and linearization of plasmids for P. pastoris transformation serves to significantly increase the transformation efficiency. Moreover, it is demonstrated that the constructs do not re-circularize but integrate stably into the P. pastoris genome.

Parallel computation of genome-scale RNA secondary structure to detect structural constraints on human genome

Background

RNA secondary structure around splice sites is known to assist normal splicing by promoting spliceosome recognition. However, analyzing the structural properties of entire intronic regions or pre-mRNA sequences has been difficult hitherto, owing to serious experimental and computational limitations, such as low read coverage and numerical problems.

Results

Our novel software, “ParasoR”, is designed to run on a computer cluster and enables the exact computation of various structural features of long RNA sequences under the constraint of maximal base-pairing distance. ParasoR divides dynamic programming (DP) matrices into smaller pieces, such that each piece can be computed by a separate computer node without losing the connectivity information between the pieces. ParasoR directly computes the ratios of DP variables to avoid the reduction of numerical precision caused by the cancellation of a large number of Boltzmann factors. The structural preferences of mRNAs computed by ParasoR shows a high concordance with those determined by high-throughput sequencing analyses.

Using ParasoR, we investigated the global structural preferences of transcribed regions in the human genome. A genome-wide folding simulation indicated that transcribed regions are significantly more structural than intergenic regions after removing repeat sequences and k-mer frequency bias. In particular, we observed a highly significant preference for base pairing over entire intronic regions as compared to their antisense sequences, as well as to intergenic regions. A comparison between pre-mRNAs and mRNAs showed that coding regions become more accessible after splicing, indicating constraints for translational efficiency. Such changes are correlated with gene expression levels, as well as GC content, and are enriched among genes associated with cytoskeleton and kinase functions.

Conclusions

We have shown that ParasoR is very useful for analyzing the structural properties of long RNA sequences such as mRNAs, pre-mRNAs, and long non-coding RNAs whose lengths can be more than a million bases in the human genome. In our analyses, transcribed regions including introns are indicated to be subject to various types of structural constraints that cannot be explained from simple sequence composition biases. ParasoR is freely available at https://github.com/carushi/ParasoR.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-016-1067-9) contains supplementary material, which is available to authorized users.

Probing-directed identification of novel structured RNAs

Transcripts often harbor RNA elements, which regulate cell processes co- or post-transcriptionally. The functions of many regulatory RNA elements depend on their structure, thus it is important to determine the structure as well as to scan genomes for structured elements. State of the art ab initio approaches to predict structured RNAs rely on DNA sequence analysis. They use 2 major types of information inferred from a sequence: thermodynamic stability of an RNA structure and evolutionary footprints of base-pair interactions. In recent years, chemical probing of RNA has arisen as an alternative source of structural information. RNA probing experiments detect positions accessible to specific types of chemicals or enzymes indicating their propensity to be in a paired or unpaired state. There exist several strategies to integrate probing data into RNA secondary structure prediction algorithms that substantially improve the prediction quality. However, whether and how probing data could contribute to detection of structured RNAs remains an open question. We previously developed the energy-based approach RNASurface to detect locally optimal structured RNA elements. Here, we integrate probing data into the RNASurface energy model using a general framework. We show that the use of experimental data allows for better discrimination of ncRNAs from other transcripts. Application of RNASurface to genome-wide analysis of the human transcriptome with PARS data identifies previously undetectable segments, with evidence of functionality for some of them.

Genome-Wide Approaches for RNA Structure Probing

RNA molecules of all types fold into complex secondary and tertiary structures that are important for their function and regulation. Structural and catalytic RNAs such as ribosomal RNA (rRNA) and transfer RNA (tRNA) are central players in protein synthesis, and only function through their proper folding into intricate three-dimensional structures. Studies of messenger RNA (mRNA) regulation have also revealed that structural elements embedded within these RNA species are important for the proper regulation of their total level in the transcriptome. More recently, the discovery of microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) has shed light on the importance of RNA structure to genome, transcriptome, and proteome regulation. Due to the relatively small number, high conservation, and importance of structural and catalytic RNAs to all life, much early work in RNA structure analysis mapped out a detailed view of these molecules. Computational and physical methods were used in concert with enzymatic and chemical structure probing to create high-resolution models of these fundamental biological molecules. However, the recent expansion in our knowledge of the importance of RNA structure to coding and regulatory RNAs has left the field in need of faster and scalable methods for high-throughput structural analysis. To address this, nuclease and chemical RNA structure probing methodologies have been adapted for genome-wide analysis. These methods have been deployed to globally characterize thousands of RNA structures in a single experiment. Here, we review these experimental methodologies for high-throughput RNA structure determination and discuss the insights gained from each approach.

Clinical Outcomes and Complications of Percutaneous Achilles Repair System Versus Open Technique for Acute Achilles Tendon Ruptures

BACKGROUND

Limited incision techniques for acute Achilles tendon ruptures have been developed in recent years to improve recovery and reduce postoperative complications compared with traditional open repair. The purpose of this retrospective cohort study was to analyze the clinical outcomes and postoperative complications between acute Achilles tendon ruptures treated using a percutaneous Achilles repair system (PARS [Arthrex, Inc, Naples, FL]) versus open repair and evaluate the overall outcomes for operatively treated Achilles ruptures.

METHODS

Between 2005 and 2014, 270 consecutive cases of operatively treated acute Achilles tendon ruptures were reviewed (101 PARS, 169 open). Patients with Achilles tendinopathy, insertional ruptures, chronic tears, or less than 3-month follow-up were excluded. Operative treatment consisted of a percutaneous technique (PARS) using a 2-cm transverse incision with FiberWire (Arthrex, Inc, Naples, FL) sutures or open repair using a 5- to 8-cm posteromedial incision with FiberWire in a Krackow fashion reinforced with absorbable sutures. Patient demographics were recorded along with medical comorbidities, activity at injury, time from injury to surgery, length of follow-up, return to baseline activities by 5 months, and postoperative complications.

RESULTS

The most common activity during injury for both groups was basketball (PARS: 39%, open: 47%). A greater number of patients treated with PARS were able to return to baseline physical activities by 5 months compared with the open group (PARS: 98%, open: 82%; P = .0001). There were no significant differences (P > .05) between groups in rates of rerupture (P = 1.0), sural neuritis (P = .16), wound dehiscence (P = .74), superficial (P = .29) and/or deep infection (P = .29), or reoperation (P = .13). There were no deep vein thromboses (DVTs) or reruptures in either group. In the PARS group, there were no cases of sural neuritis, 3 cases (3%) of superficial wound dehiscence, and 2 reoperations (2%) for superficial foreign-body reaction to FiberWire. In the open group, there were 5 cases (3%) of sural neuritis, 7 cases (4%) of superficial wound dehiscence, 3 cases (2%) of superficial infection, and 3 reoperations (2%) for deep infection.

CONCLUSION

The present study reports the largest single-center series of acute Achilles tendon ruptures in the literature with lower complication rates for operatively treated Achilles ruptures compared with previous reports. The overall complication rate for all operatively treated Achilles ruptures was 8.5% with no reruptures, and most patients (88%) were able to return to baseline activities by 5 months after surgery. There were no significant differences in rates of postoperative complications between PARS and open repair for acute Achilles tendon ruptures.

LEVEL OF EVIDENCE

Level III, retrospective cohort study.

Clinical Outcomes and Complications of Percutaneous Achilles Repair System Versus Open Technique for Acute Achilles Tendon Ruptures

BACKGROUND

Limited incision techniques for acute Achilles tendon ruptures have been developed in recent years to improve recovery and reduce postoperative complications compared with traditional open repair. The purpose of this retrospective cohort study was to analyze the clinical outcomes and postoperative complications between acute Achilles tendon ruptures treated using a percutaneous Achilles repair system (PARS [Arthrex, Inc, Naples, FL]) versus open repair and evaluate the overall outcomes for operatively treated Achilles ruptures.

METHODS

Between 2005 and 2014, 270 consecutive cases of operatively treated acute Achilles tendon ruptures were reviewed (101 PARS, 169 open). Patients with Achilles tendinopathy, insertional ruptures, chronic tears, or less than 3-month follow-up were excluded. Operative treatment consisted of a percutaneous technique (PARS) using a 2-cm transverse incision with FiberWire (Arthrex, Inc, Naples, FL) sutures or open repair using a 5- to 8-cm posteromedial incision with FiberWire in a Krackow fashion reinforced with absorbable sutures. Patient demographics were recorded along with medical comorbidities, activity at injury, time from injury to surgery, length of follow-up, return to baseline activities by 5 months, and postoperative complications.

RESULTS

The most common activity during injury for both groups was basketball (PARS: 39%, open: 47%). A greater number of patients treated with PARS were able to return to baseline physical activities by 5 months compared with the open group (PARS: 98%, open: 82%; P = .0001). There were no significant differences (P > .05) between groups in rates of rerupture (P = 1.0), sural neuritis (P = .16), wound dehiscence (P = .74), superficial (P = .29) and/or deep infection (P = .29), or reoperation (P = .13). There were no deep vein thromboses (DVTs) or reruptures in either group. In the PARS group, there were no cases of sural neuritis, 3 cases (3%) of superficial wound dehiscence, and 2 reoperations (2%) for superficial foreign-body reaction to FiberWire. In the open group, there were 5 cases (3%) of sural neuritis, 7 cases (4%) of superficial wound dehiscence, 3 cases (2%) of superficial infection, and 3 reoperations (2%) for deep infection.

CONCLUSION

The present study reports the largest single-center series of acute Achilles tendon ruptures in the literature with lower complication rates for operatively treated Achilles ruptures compared with previous reports. The overall complication rate for all operatively treated Achilles ruptures was 8.5% with no reruptures, and most patients (88%) were able to return to baseline activities by 5 months after surgery. There were no significant differences in rates of postoperative complications between PARS and open repair for acute Achilles tendon ruptures.

LEVEL OF EVIDENCE

Level III, retrospective cohort study.

Meta-analysis: aerobic exercise for the treatment of anxiety disorders

BACKGROUND

This meta-analysis investigates the efficacy of exercise as a treatment for DSM-IV diagnosed anxiety disorders.

METHODS

We searched PubMED and PsycINFO for randomized, controlled trials comparing the anxiolytic effects of aerobic exercise to other treatment conditions for DSM-IV defined anxiety disorders. Seven trials were included in the final analysis, totaling 407 subjects. The control conditions included non-aerobic exercise, waitlist/placebo, cognitive-behavioral therapy, psychoeducation and meditation. A fixed-effects model was used to calculate the standardized mean difference of change in anxiety rating scale scores of aerobic exercise compared to control conditions. Subgroup analyses were performed to examine the effects of (1) comparison condition; (2) whether comparison condition controlled for time spent exercising and (3) diagnostic indication.

RESULTS

Aerobic exercise demonstrated no significant effect for the treatment of anxiety disorders (SMD=0.02 (95%CI: -0.20-0.24), z = 0.2, p = 0.85). There was significant heterogeneity between trials (χ(2) test for heterogeneity = 22.7, df = 6, p = 0.001). The reported effect size of aerobic exercise was highly influenced by the type of control condition. Trials utilizing waitlist/placebo controls and trials that did not control for exercise time reported large effects of aerobic exercise while other trials report no effect of aerobic exercise.

CONCLUSIONS

Current evidence does not support the use of aerobic exercise as an effective treatment for anxiety disorders as compared to the control conditions. This remains true when controlling for length of exercise sessions and type of anxiety disorder. Future studies evaluating the efficacy of aerobic exercise should employ larger sample sizes and utilize comparison interventions that control for exercise time.