RNAslider: a faster engine for consecutive windows folding and its application to the analysis of genomic folding asymmetry

<p>Abstract</p> <p>Background</p> <p>Scanning large genomes with a sliding window in search of locally stable RNA structures is a well motivated problem in bioinformatics. Given a predefined window size L and an RNA sequence S of size N (L < N), the consecutive windows folding problem is to compute the minimal free energy (MFE) for the folding of each of the L-sized substrings of S. The consecutive windows folding problem can be naively solved in O(NL³) by applying any of the classical cubic-time RNA folding algorithms to each of the N-L windows of size L. Recently an O(NL²) solution for this problem has been described.</p> <p>Results</p> <p>Here, we describe and implement an O(NLψ(L)) engine for the consecutive windows folding problem, where ψ(L) is shown to converge to O(1) under the assumption of a standard probabilistic polymer folding model, yielding an O(L) speedup which is experimentally confirmed. Using this tool, we note an intriguing directionality (5'-3' vs. 3'-5') folding bias, i.e. that the minimal free energy (MFE) of folding is higher in the native direction of the DNA than in the reverse direction of various genomic regions in several organisms including regions of the genomes that do not encode proteins or ncRNA. This bias largely emerges from the genomic dinucleotide bias which affects the MFE, however we see some variations in the folding bias in the different genomic regions when normalized to the dinucleotide bias. We also present results from calculating the MFE landscape of a mouse chromosome 1, characterizing the MFE of the long ncRNA molecules that reside in this chromosome.</p> <p>Conclusion</p> <p>The efficient consecutive windows folding engine described in this paper allows for genome wide scans for ncRNA molecules as well as large-scale statistics. This is implemented here as a software tool, called RNAslider, and applied to the scanning of long chromosomes, leading to the observation of features that are visible only on a large scale.</p

Arthroscopic isolated long head of biceps tenotomy in patients with degenerative rotator cuff tears:mid-term clinical results and prognostic factors

INTRODUCTION: The long head of biceps tendon is frequently involved in degenerative rotator cuff tears. Therefore, this study explored the clinical results of an isolated biceps tenotomy and identified prognostic factors for improvement in pain and function. MATERIALS AND METHODS: Between 2008 and 2017, an arthroscopic isolated biceps tenotomy was performed on 64 patients with a degenerative rotator cuff tear (> 65 years). Primary outcome was patient-perceived improvement in pain and function. Potential prognostic factors for improvement in pain and function were identified. RESULTS: A perceived improvement in pain was reported in 78% of the patients at three months after surgery and in 75% at a mean follow-up of 4.2 years (1-7 years; n = 55). A perceived improvement in function was observed in 49% of patients at three months and in 76% of patients at follow-up. Patients with a preoperatively normal acromiohumeral distance (> 10 mm) reported an improvement in pain and function significantly more often. Retraction of the supraspinatus tendon Patte 3 was significantly associated with worse functional outcome. CONCLUSIONS: A biceps tenotomy can be a reliable treatment option for patients with symptomatic degenerative cuff tears who fail conservative treatment and have a normal acromiohumeral distance (> 10 mm)

Peak incidence of distal radius fractures due to ice skating on natural ice in The Netherlands

An increase of distal radius fractures was seen in 2009 when an extended cold spell allowed natural ice skating in Amsterdam. This resulted in overload of our Emergency Departments and operating rooms. This study reports patient and fracture characteristics of these injuries. We also determined potential skating-related risk factors. All patients who sustained a distal radius fracture during natural ice skating between January 3 and January 12, 2009 were included. Patient and fracture characteristics, treatment, validated outcome (Quick DASH) at 3 months after injury were determined. Natural ice skating accounted for a 5.5-fold increase of distal radius fractures (92 fractures) compared to a similar time period without natural ice skating in 2008. Fracture types were AO-type A, n = 50, type B, n = 11 and type C, n = 31. Twenty-eight patients were casted without reduction. Fifty-four patients underwent at least one reduction before casting. The non-operative group consisted of 67 patients (68 fractures, male/female 18/49) with an average age of 55.5 years. Twenty-three patients (24 fractures) underwent internal fixation. Quick DASH for the whole group was a mean of 23.1 points (range 0–95). The mean Quick DASH for the non-operatively treated group was 19.9 points (range 0–95), for the operatively treated group 31.7 points (range 2–65). Distal radius fractures increased 5.5-fold during a period with natural ice skating. Women aged 50 and over were predominantly affected. Most fractures were extra-articular, and the vast majority was treated non-operatively. Utilization of wrist-protecting devices should be considered during future natural ice periods

Speeding up HMM algorithms for genetic linkage analysis via chain reductions of the state space

We develop an hidden Markov model (HMM)-based algorithm for computing exact parametric and non-parametric linkage scores in larger pedigrees than was possible before. The algorithm is applicable whenever there are chains of persons in the pedigree with no genetic measurements and with unknown affection status. The algorithm is based on shrinking the state space of the HMM considerably using such chains. In a two g-degree cousins pedigree the reduction drops the state space from being exponential in g to being linear in g. For a Finnish family in which two affected children suffer from a rare cold-inducing sweating syndrome, we were able to reduce the state space by more than five orders of magnitude from 250 to 232. In another pedigree of state-space size of 227, used for a study of pituitary adenoma, the state space reduced by a factor of 8.5 and consequently exact linkage scores can now be computed, rather than approximated

Psychological symptoms and the MCID of the DASH score in shoulder surgery

BACKGROUND: Psychological symptoms are frequently present in patients scheduled for shoulder surgery. The perception of functional disability, activity level and pain in the shoulder is negatively influenced by psychological symptoms, which leads to higher scores of the Disabilities of the Arm, Shoulder and Hand (DASH) questionnaire. The aim of this study was to determine the influence of psychological symptoms on the minimal clinically important difference (MCID) of the DASH score in patients after shoulder surgery. METHODS: In this prospective longitudinal cohort study, 176 patients were included. Group 1 (32 patients) had symptoms of psychological disorders before and after surgery; group 2 had no symptoms of psychological disorders (110 patients). In the remaining patients (34 patients), psychological disorders changed after surgery. Clinical outcome was measured with the change of DASH score and anchor questions for perceived improvement of pain and function after surgery. Symptoms of psychological disorders were identified with the Four-Dimensional Symptom Questionnaire. An anchor-based mean change score technique was used to determine the MCID of the DASH score. RESULTS: DASH scores before and 12 months after shoulder surgery were significantly higher in patients with symptoms of psychological disorders; change of DASH score was not different between the two groups. The MCID of the DASH score was 13.0 [SD 20.7] in the group with symptoms of psychological disorders and 12.7 [SD 17.6] in the group with no symptoms of psychological disorders. We observed no difference (p = 0.559) in the MCID between the group with and the group without symptoms of psychological disorders. CONCLUSION: Symptoms of psychological disorders had a negative effect on the DASH score but no influence on the MCID of the DASH score. The DASH score could be used in future studies to assess the influence of psychological factors on the clinical outcome of treatment

Total Hip Arthroplasty or Hemiarthroplasty for Hip Fracture.

BACKGROUND: Globally, hip fractures are among the top 10 causes of disability in adults. For displaced femoral neck fractures, there remains uncertainty regarding the effect of a total hip arthroplasty as compared with hemiarthroplasty. METHODS: We randomly assigned 1495 patients who were 50 years of age or older and had a displaced femoral neck fracture to undergo either total hip arthroplasty or hemiarthroplasty. All enrolled patients had been able to ambulate without the assistance of another person before the fracture occurred. The trial was conducted in 80 centers in 10 countries. The primary end point was a secondary hip procedure within 24 months of follow-up. Secondary end points included death, serious adverse events, hip-related complications, health-related quality of life, function, and overall health end points. RESULTS: The primary end point occurred in 57 of 718 patients (7.9%) who were randomly assigned to total hip arthroplasty and 60 of 723 patients (8.3%) who were randomly assigned to hemiarthroplasty (hazard ratio, 0.95; 95% confidence interval [CI], 0.64 to 1.40; P = 0.79). Hip instability or dislocation occurred in 34 patients (4.7%) assigned to total hip arthroplasty and 17 patients (2.4%) assigned to hemiarthroplasty (hazard ratio, 2.00; 99% CI, 0.97 to 4.09). Function, as measured with the total Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) total score, pain score, stiffness score, and function score, modestly favored total hip arthroplasty over hemiarthroplasty. Mortality was similar in the two treatment groups (14.3% among the patients assigned to total hip arthroplasty and 13.1% among those assigned to hemiarthroplasty, P = 0.48). Serious adverse events occurred in 300 patients (41.8%) assigned to total hip arthroplasty and in 265 patients (36.7%) assigned to hemiarthroplasty. CONCLUSIONS: Among independently ambulating patients with displaced femoral neck fractures, the incidence of secondary procedures did not differ significantly between patients who were randomly assigned to undergo total hip arthroplasty and those who were assigned to undergo hemiarthroplasty, and total hip arthroplasty provided a clinically unimportant improvement over hemiarthroplasty in function and quality of life over 24 months. (Funded by the Canadian Institutes of Health Research and others; ClinicalTrials.gov number, NCT00556842.)