Cohort and tag-site-specific tag-loss rates in mark–recapture studies: A southern elephant seal cautionary case

Marker-loss is a common feature of mark–recapture studies and important as it may bias parameter estimation. A slight alteration in tag-site of double tagged southern elephant seals (Mirounga leonina), marked at Marion Island from 1983 to 2005 in an ongoing mark–recapture program, had important consequences for tag-loss. We calculated age-specific tag-retention rates and cumulative tag-retention probabilities using a maximum likelihood model selection approach in the software application TAG_LOSS 3.2.0. Under the tag-loss independence assumption, double tag-loss of inner interdigital webbing tags (IIT; 17 cohorts) remained below 1% in the first 5 yr and increased monotonically as seals aged, with higher tag-loss in males. Lifetime cumulative IIT tag-loss was 11.9% for females and 18.4% for males, and equivalent for all cohorts. Changing the tag-site to the outer interdigital webbing (OIT; 6 cohorts) resulted in increased and cohort-dependent tag-loss, although the variation (mean ± 95% CI) in cumulative tag-loss probabilities never exceeded 5.3% between cohorts at similar age. Although different studies may homogenize techniques, we advocate the importance of data set-specific assessment of tag-loss rates to ensure greatest confidence in population parameters obtained from mark–recapture experiments. Permanent marking should be implemented where feasible.     

SCRAPP: A tool to assess the diversity of microbial samples from phylogenetic placements

Microbial ecology research is currently driven by the continuously decreasing cost of DNA sequencing and the improving accuracy of data analysis methods. One such analysis method is phylogenetic placement, which establishes the phylogenetic identity of the anonymous environmental sequences in a sample by means of a given phylogenetic reference tree. However, assessing the diversity of a sample remains challenging, as traditional methods do not scale well with the increasing data volumes and/or do not leverage the phylogenetic placement information. Here, we present scrapp , a highly parallel and scalable tool that uses a molecular species delimitation algorithm to quantify the diversity distribution over the reference phylogeny for a given phylogenetic placement of the sample. scrapp employs a novel approach to cluster phylogenetic placements, called placement space clustering, to efficiently perform dimensionality reduction, so as to scale on large data volumes. Furthermore, it uses the phylogeny‐aware molecular species delimitation method mPTP to quantify diversity. We evaluated scrapp using both, simulated and empirical data sets. We use simulated data to verify our approach. Tests on an empirical data set show that scrapp ‐derived metrics can classify samples by their diversity‐correlated features equally well or better than existing, commonly used approaches. scrapp is available at https://github.com/pbdas/scrapp .     

Effects of femoral component placement on the balancing of a total knee at surgery

Misalignment and soft-tissue imbalance in total knee arthroplasty (TKA) can cause discomfort, pain, inadequate motion and instability that may require revision surgery. Balancing can be defined as equal collateral ligament tensions or equal medial and lateral compartmental forces during the flexion range. Our goal was to study the effects on balancing of linear femoral component misplacements (proximal, distal, anterior, posterior); and different component rotations in mechanical alignment compared to kinematic alignment throughout the flexion path. A test rig was constructed such that the position of a standard femoral component could be adjusted to simulate the linear and rotational positions. With the knee in neutral reference values of the collateral tensions were adjusted to give anatomic contact force patterns, measured with an instrumented tibial trial. The deviations in the forces for each femoral component position were then determined. Compartmental forces were significantly influenced by 2 mm linear errors in the femoral component placement. However, the errors were least for a distal error, equivalent to undercutting the distal femur. The largest errors mainly increase the lateral condyle force, occurred for proximal and posterior component errors. There were only small contact force differences between kinematic and mechanical alignment. Based on these results, surgeons should avoid overcutting the distal femur and undercutting the posterior femur. However, the 2–3 degrees varus slope of the joint line as in kinematic alignment did not have much effect on balancing, so mechanical or kinematic alignment were equivalent.