Machine learning methods accurately predict host specificity of coronaviruses based on spike sequences alone.

Coronaviruses infect many animals, including humans, due to interspecies transmission. Three of the known human coronaviruses: MERS, SARS-CoV-1, and SARS-CoV-2, the pathogen for the COVID-19 pandemic, cause severe disease. Improved methods to predict host specificity of coronaviruses will be valuable for identifying and controlling future outbreaks. The coronavirus S protein plays a key role in host specificity by attaching the virus to receptors on the cell membrane. We analyzed 1238 spike sequences for their host specificity. Spike sequences readily segregate in t-SNE embeddings into clusters of similar hosts and/or virus species. Machine learning with SVM, Logistic Regression, Decision Tree, Random Forest gave high average accuracies, F1 scores, sensitivities and specificities of 0.95-0.99. Importantly, sites identified by Decision Tree correspond to protein regions with known biological importance. These results demonstrate that spike sequences alone can be used to predict host specificity.

Design modifications of high-flexion TKA do not improve short term clinical and radiographic outcomes.

BACKGROUND: The prosthesis of contemporary total knee arthroplasty (TKA) has been modified to provide a more familiar environment for higher flexion angle of the replaced knee. The design modifications continue based on evidence reported in the literature. However, whether these modifications of the prosthesis design lead to improvements in clinical results needs further investigation. We determined whether the prosthesis modifications based on recent evidence improve clinical and radiographic results following high flexion TKA. METHODS: 524 patients who underwent primary TKA using two different high flexion prostheses were divided to Group 1 (HF-1) using a high flexion prosthesis, group 2 (HF-2) using the more recently devised high flexion prosthesis, which claims to be adopted from evidence proposed in the literature. Clinical outcomes included ranges of motion (ROM), the Knee Society knee and function score (KSKS and KSFS), the Western Ontario and McMaster Universities Arthritis Index (WOMAC) score, radiologic evaluation, and complication related to surgery. RESULTS: No differences in terms of clinical and radiographic results were observed between the groups at the 2 year follow-up. The mean ROM was 123°and 124° in the HF-1 and HF-2 groups, respectively. KSKS were 90 and 89.1, KSFS were 76.6 and 81.8, and total WOMAC scores were 23.1 and 24.9 in the HF-1 and HF- 2 groups. No differences of the incidences of radiolucency on radiographs (1.4% in HF-1, 2.1% in HF-2) and dislocation (1 case in HF-1 only) was observed. CONCLUSIONS: Even if recent modifications in the design of high flexion TKA prosthesis were based on evidence in the literature, they did not provide meaningful improvements in short-term clinical and radiographic outcomes after TKA. Surgeons should consider our findings when choosing a prosthesis for their patients.

Reliability of a PowerPoint method for wear measurement after total hip arthroplasty: a retrieval study using 3-dimensional laser scanning.

The purpose of this study was to evaluate the reliability of the PowerPoint (PP) (2007 Version; Microsoft, Redmond, Wash) method for measuring polyethylene liner wear after total hip arthroplasty. Seventeen retrieved polyethylene liners were included in this study. Wear volumes were calculated using the PP, the Dorr and Wan, and 3-dimensional (3D) laser scanning methods. Spearman correlation coefficients for wear volume results indicated strong correlations between the PP and 3D laser scanning methods (range, 0.89-0.93). On the other hand, Spearman correlation analysis revealed only moderate correlations between the Dorr and Wan and 3D laser scanning methods (range, 0.67-0.77). The PP method can be used to monitor linear wear after total hip arthroplasty and could serve as an alternative method when computerized methods are not available.

Effect of combined sex hormone replacement on bone/cartilage turnover in a murine model of osteoarthritis.

BACKGROUND: Estrogens act on estrogen receptors distributed in articular cartilages, synovial membrane, and ligaments, which are thought to be related with degenerative changes. Meanwhile, progesterone is known to have a weak anabolic action on bone formation This study evaluates the effects of estrogen and progesterone hormone on bone/cartilage turnover in ovariectomized (OVX) rats. METHODS: Thirty-five 7-month-old female Sprague-Dawley rats were randomly divided into 5 groups and then ovariectomized bilaterally except the sham control group. The first and the second group acting as controls did not receive hormonal therapy, the third group received estrogen, the fourth group received progesterone, and the fifth group received combination of both hormones 10 weeks after surgery. Evaluations were done using the serum levels of cartilage oligomeric matrix protein (COMP) for cartilage turnover, collagen type I C-telopeptide (CTX-1) and osteocalcin (OC) for bone turnover at 11, 15, 19 weeks after OVX and histology using the Osteoarthritis Research Society International (OARSI) osteoarthritis (OA) cartilage histopathology assessment system. RESULTS: Significantly less cartilage degradation (decreased levels of COMP) was found in the combined hormone treated group in comparison with OVX group. Similarly, both hormonal treatment resulted in increased bone formation and decreased bone resorption i.e., a low overall bone turnover status (decrease in the serum OC and CTX-1 levels). CONCLUSIONS: Combined estrogen and progesterone therapy was found to be convincing in terms of reducing the severity of OA in this experimental model.

Skin-capsular Mismatch According to Knee Positions for Instrument Insertion via Arthroscopic Portals.

Damage to soft tissues, chondral surfaces, and the menisci may result from imprise or overly aggressive establishment of portals in arthroscopic knee surgeries. In this note, we address the relationship between the skin and the capsule at portal sites according to knee positions. Understanding the skin-capsular mismatch may facilitate arthroscopic procedures and indirectly reduce the operation time.