Median and small parsimony problems on RNA trees.

Motivation: Noncoding RNAs (ncRNAs) express their functions by adopting molecular structures. Specifically, RNA secondary structures serve as a relatively stable intermediate step before tertiary structures, offering a reliable signature of molecular function. Consequently, within an RNA functional family, secondary structures are generally more evolutionarily conserved than sequences.

Infrared: a declarative tree decomposition-powered framework for bioinformatics.

Motivation: Many bioinformatics problems can be approached as optimization or controlled sampling tasks, and solved exactly and efficiently using Dynamic Programming (DP). However, such exact methods are typically tailored towards specific settings, complex to develop, and hard to implement and adapt to problem variations.

Methods: We introduce the Infrared framework to overcome such hindrances for a large class of problems.

Automated design of dynamic programming schemes for RNA folding with pseudoknots.

Although RNA secondary structure prediction is a textbook application of dynamic programming (DP) and routine task in RNA structure analysis, it remains challenging whenever pseudoknots come into play. Since the prediction of pseudoknotted structures by minimizing (realistically modelled) energy is NP-hard, specialized algorithms have been proposed for restricted conformation classes that capture the most frequently observed configurations. To achieve good performance, these methods rely on specific and carefully hand-crafted DP schemes.

Bone-anchored prostheses for lower limb amputation in a French cohort with 1-15 years of follow-up: implant survival rates, mechanical complications, and reported outcomes.

Purpose: To evaluate the implant survival rate, mechanical complications, and reported patient outcomes of bone-anchored prostheses for patients with lower limb amputation in France after 1-15 years of follow-up.

Methods: This retrospective cohort study included patients who underwent surgery at a single center in France between 2007 and 2021. The primary outcomes were the implant survival rate and functional scores assessed by the Questionnaire for Transfemoral Amputees (Q-TFA).

Tree diet: reducing the treewidth to unlock FPT algorithms in RNA bioinformatics.

Hard graph problems are ubiquitous in Bioinformatics, inspiring the design of specialized Fixed-Parameter Tractable algorithms, many of which rely on a combination of tree-decomposition and dynamic programming. The time/space complexities of such approaches hinge critically on low values for the treewidth tw of the input graph. In order to extend their scope of applicability, we introduce the TREE-DIET problem, i.

Matrix-Applied Characterized Autologous Cultured Chondrocytes Versus Microfracture: Two-Year Follow-up of a Prospective Randomized Trial.

Background: Randomized controlled trials studying the efficacy and safety of matrix-applied characterized autologous cultured chondrocytes (MACI) versus microfracture (MFX) for treating cartilage defects are limited.

Purpose: To compare the clinical efficacy and safety of MACI versus MFX in the treatment of patients with symptomatic cartilage defects of the knee.

Study Design: Randomized controlled clinical trial; Level of evidence, 1.