Nestly--a framework for running software with nested parameter choices and aggregating results

The execution of a software application or pipeline using various combinations of parameters and inputs is a common task in bioinformatics. In the absence of a specialized tool to organize, streamline and formalize this process, scientists must write frequently complex scripts to perform these tasks. We present nestly, a Python package to facilitate running tools with nested combinations of parameters and inputs. nestly provides three components. First, a module to build nested directory structures corresponding to choices of parameters. Second, the nestrun script to run a given command using each set of parameter choices. Third, the nestagg script to aggregate results of the individual runs into a CSV file, as well as support for more complex aggregation. We also include a module for easily specifying nested dependencies for the SCons build tool, enabling incremental builds.

AVAILABILITY

Source, documentation and tutorial examples are available at http://github.com/fhcrc/nestly. nestly can be installed from the Python Package Index via pip; it is open source (MIT license).

Prognostic factors for bacterial cultures positive for Propionibacterium acnes and other organisms in a large series of revision shoulder arthroplasties performed for stiffness, pain, or loosening

BACKGROUND

Propionibacterium acnes has been grown on culture in half of the reported cases of chronic infection associated with shoulder arthroplasty. The presence of this organism can be overlooked because its subtle presentation may not suggest the need for culture or because, in contrast to many orthopaedic infections, multiple tissue samples and weeks of culture incubation are often necessary to recover this organism. Surgical decisions regarding implant revision and antibiotic therapy must be made before the results of intraoperative cultures are known. In the present study, we sought clinically relevant prognostic evidence that could help to guide treatment decisions.

METHODS

We statistically correlated preoperative and intraoperative observations on 193 shoulder arthroplasty revisions that were performed because of pain, loosening, or stiffness with the results of a Propionibacterium acnes-specific culture protocol. Regression models were used to identify factors predictive of a positive culture for Propionibacterium acnes.

RESULTS

One hundred and eight of the 193 revision arthroplasties were associated with positive cultures; 70% of the positive cultures demonstrated growth of Propionibacterium acnes. The rate of positive cultures per shoulder increased with the number of culture specimens obtained from each shoulder. Fifty-five percent of the positive cultures required observation for more than one week. Male sex, humeral osteolysis, and cloudy fluid were each associated with significant increases of ≥ 600% in the likelihood of obtaining a positive Propionibacterium acnes culture. Humeral loosening, glenoid wear, and membrane formation were associated with significant increases of >300% in the likelihood of obtaining a positive Propionibacterium acnes culture.

CONCLUSIONS

Preoperative and intraoperative factors can be used to help to predict the risk of a positive culture for Propionibacterium acnes. This evidence is clinically relevant to decisions regarding prosthesis removal or retention and the need for immediate antibiotic therapy at the time of revision shoulder arthroplasty before the culture results become available.

LEVEL OF EVIDENCE

Prognostic Level II. See Instructions for Authors for a complete description of levels of evidence.

Current Technique for the Ream-and-Run Arthroplasty for Glenohumeral Osteoarthritis

Introduction

The ream and run is a technically demanding shoulder arthroplasty for the management of glenohumeral arthritis that avoids the risk of failure of the glenoid component that is associated with total shoulder arthroplasty.

Step 1 Surgical Approach

After administration of prophylactic antibiotics and a thorough skin preparation, expose the glenohumeral joint through a long deltopectoral incision, incising the subscapularis tendon from its osseous insertion and the capsule from the anterior-inferior aspect of the humeral neck while carefully protecting all muscle groups and neurovascular structures.

Step 2 Humeral Preparation

Gently expose the proximal part of the humerus, resect the humeral head at 45° to the orthopaedic axis while protecting the rotator cuff, and excise all humeral osteophytes.

Step 3 Glenoid Preparation

After performing an extralabral capsular release, remove any residual cartilage, drill the glenoid centerline, and ream the glenoid to a single concavity.

Step 4 Humeral Prosthesis Selection

Select a humeral prosthesis that fits the medullary canal and that provides the desired mobility and stability of the prosthesis.

Step 5 Humeral Prosthesis Fixation

Fix the humeral component using impaction autografting.

Step 6 Soft-Tissue Balancing

After the definitive humeral prosthesis is in place, ensure the desired balance of mobility and stability. If there is excessive posterior translation, consider a rotator interval plication.

Step 7 Rehabilitation

Achieve and maintain at least 150° of flexion and good external rotation strength.

Results

In our study, comfort and function increased progressively after the ream-and-run procedure, reaching a steady state by approximately twenty months.

What to Watch For

IndicationsContraindicationsPitfalls & Challenges.

The prognosis for improvement in comfort and function after the ream-and-run arthroplasty for glenohumeral arthritis: an analysis of 176 consecutive cases

BACKGROUND

Knowledge of the factors affecting the prognosis for improvement in function and comfort with time after shoulder arthroplasty is important to clinical decision-making. This study sought to identify some of these factors in 176 consecutive patients undergoing the ream-and-run procedure.

METHODS

The time course for improvement in patient function and comfort was determined for the entire group as well as for subsets by sex, age, diagnosis, preoperative function, and surgery date. Patients having repeat surgery were analyzed in detail.

RESULTS

Shoulder comfort and function increased progressively after the ream-and-run procedure, reaching a steady state by approximately twenty months. The shoulders in 124 patients with at least two years of follow-up were improved by a minimal clinically important difference. The shoulders in sixteen patients with at least two years of follow-up were not improved by the minimal clinically important difference. Twenty-two patients had repeat procedures, but only seven had revision to a total shoulder arthroplasty. Fourteen patients did not have either a known revision arthroplasty or two years of follow-up. The best prognosis was for male patients over the age of sixty years, with primary osteoarthritis, no prior surgical procedures, a preoperative score on the simple shoulder test of ≥5 points, and surgery after 2004. Repeat surgical procedures were more common in patients who had a greater number of surgical procedures before the ream-and-run surgery.

CONCLUSIONS

This study is unique in that it characterizes the factors affecting the time course for improvement in shoulder comfort and function after a ream-and-run procedure. Improvement occurs after this procedure for at least 1.5 years. This procedure appears to be best suited for an older male patient with reasonable preoperative shoulder function without prior shoulder surgery.

LEVEL OF EVIDENCE

Prognostic Level II. See Instructions for authors for a complete description of levels of evidence.

Phylogenomic analysis reveals dynamic evolutionary history of the Drosophila heterochromatin protein 1 (HP1) gene family

Heterochromatin is the gene-poor, satellite-rich eukaryotic genome compartment that supports many essential cellular processes. The functional diversity of proteins that bind and often epigenetically define heterochromatic DNA sequence reflects the diverse functions supported by this enigmatic genome compartment. Moreover, heterogeneous signatures of selection at chromosomal proteins often mirror the heterogeneity of evolutionary forces that act on heterochromatic DNA. To identify new such surrogates for dissecting heterochromatin function and evolution, we conducted a comprehensive phylogenomic analysis of the Heterochromatin Protein 1 gene family across 40 million years of Drosophila evolution. Our study expands this gene family from 5 genes to at least 26 genes, including several uncharacterized genes in Drosophila melanogaster. The 21 newly defined HP1s introduce unprecedented structural diversity, lineage-restriction, and germline-biased expression patterns into the HP1 family. We find little evidence of positive selection at these HP1 genes in both population genetic and molecular evolution analyses. Instead, we find that dynamic evolution occurs via prolific gene gains and losses. Despite this dynamic gene turnover, the number of HP1 genes is relatively constant across species. We propose that karyotype evolution drives at least some HP1 gene turnover. For example, the loss of the male germline-restricted HP1E in the obscura group coincides with one episode of dramatic karyotypic evolution, including the gain of a neo-Y in this lineage. This expanded compendium of ovary- and testis-restricted HP1 genes revealed by our study, together with correlated gain/loss dynamics and chromosome fission/fusion events, will guide functional analyses of novel roles supported by germline chromatin.

Our genome is comprised of two compartments. The euchromatin harbors abundant genes and regulatory information, while heterochromatin harbors few genes and abundant repetitive DNA. These characteristic features of heterochromatin challenge traditional methods of sequence assembly and molecular dissection. The analysis, instead, of proteins that localize to and often functionally define heterochromatic sequence has illuminated numerous heterochromatin-dependent, essential cellular processes, including chromosome segregation, telomere stability, and gene regulation. With the aim of increasing our sample of heterochromatin-localizing proteins, we performed a comprehensive search for new members of Heterochromatin Protein 1 gene family over 40 million years of Drosophila evolution. Our report expands this family from a modest five genes to 26 genes. Unlike the founding family members, the HP1s we describe are structurally diverse, largely restricted to male reproductive tissue, and highly dynamic over evolutionary time. Despite recurrent HP1 gene birth and death, gene numbers per species are relatively constant. These gene “replacements” likely support a dynamic biological process. We propose, and present evidence for, the hypothesis that recurrent chromosomal rearrangements drive at least some HP1 gene family dynamics observed. We anticipate that these HP1 genes will help define new heterochromatin-dependent processes in the male germline.

Bacterial communities in women with bacterial vaginosis: high resolution phylogenetic analyses reveal relationships of microbiota to clinical criteria

Background

Bacterial vaginosis (BV) is a common condition that is associated with numerous adverse health outcomes and is characterized by poorly understood changes in the vaginal microbiota. We sought to describe the composition and diversity of the vaginal bacterial biota in women with BV using deep sequencing of the 16S rRNA gene coupled with species-level taxonomic identification. We investigated the associations between the presence of individual bacterial species and clinical diagnostic characteristics of BV.

Methodology/Principal Findings

Broad-range 16S rRNA gene PCR and pyrosequencing were performed on vaginal swabs from 220 women with and without BV. BV was assessed by Amsel’s clinical criteria and confirmed by Gram stain. Taxonomic classification was performed using phylogenetic placement tools that assigned 99% of query sequence reads to the species level. Women with BV had heterogeneous vaginal bacterial communities that were usually not dominated by a single taxon. In the absence of BV, vaginal bacterial communities were dominated by either Lactobacillus crispatus or Lactobacillus iners. Leptotrichia amnionii and Eggerthella sp. were the only two BV-associated bacteria (BVABs) significantly associated with each of the four Amsel’s criteria. Co-occurrence analysis revealed the presence of several sub-groups of BVABs suggesting metabolic co-dependencies. Greater abundance of several BVABs was observed in Black women without BV.

Conclusions/Significance

The human vaginal bacterial biota is heterogeneous and marked by greater species richness and diversity in women with BV; no species is universally present. Different bacterial species have different associations with the four clinical criteria, which may account for discrepancies often observed between Amsel and Nugent (Gram stain) diagnostic criteria. Several BVABs exhibited race-dependent prevalence when analyzed in separate groups by BV status which may contribute to increased incidence of BV in Black women. Tools developed in this project can be used to study microbial ecology in diverse settings at high resolution.

The phylogenetic Kantorovich-Rubinstein metric for environmental sequence samples

It is now common to survey microbial communities by sequencing nucleic acid material extracted in bulk from a given environment. Comparative methods are needed that indicate the extent to which two communities differ given data sets of this type. UniFrac, which gives a somewhat ad hoc phylogenetics-based distance between two communities, is one of the most commonly used tools for these analyses. We provide a foundation for such methods by establishing that, if we equate a metagenomic sample with its empirical distribution on a reference phylogenetic tree, then the weighted UniFrac distance between two samples is just the classical Kantorovich-Rubinstein, or earth mover's, distance between the corresponding empirical distributions. We demonstrate that this Kantorovich-Rubinstein distance and extensions incorporating uncertainty in the sample locations can be written as a readily computable integral over the tree, we develop L(p) Zolotarev-type generalizations of the metric, and we show how the p-value of the resulting natural permutation test of the null hypothesis 'no difference between two communities' can be approximated by using a Gaussian process functional. We relate the L(2)-case to an analysis-of-variance type of decomposition, finding that the distribution of its associated Gaussian functional is that of a computable linear combination of independent [Formula: see text] random variables.

Ubiquity of synonymity: almost all large binary trees are not uniquely identified by their spectra or their immanantal polynomials

Background

There are several common ways to encode a tree as a matrix, such as the adjacency matrix, the Laplacian matrix (that is, the infinitesimal generator of the natural random walk), and the matrix of pairwise distances between leaves. Such representations involve a specific labeling of the vertices or at least the leaves, and so it is natural to attempt to identify trees by some feature of the associated matrices that is invariant under relabeling. An obvious candidate is the spectrum of eigenvalues (or, equivalently, the characteristic polynomial).

Results

We show for any of these choices of matrix that the fraction of binary trees with a unique spectrum goes to zero as the number of leaves goes to infinity. We investigate the rate of convergence of the above fraction to zero using numerical methods. For the adjacency and Laplacian matrices, we show that the a priori more informative immanantal polynomials have no greater power to distinguish between trees.

Conclusion

Our results show that a generic large binary tree is highly unlikely to be identified uniquely by common spectral invariants.

Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots

BACKGROUND

Although taxonomy is often used informally to evaluate the results of phylogenetic inference and the root of phylogenetic trees, algorithmic methods to do so are lacking.

RESULTS

In this paper we formalize these procedures and develop algorithms to solve the relevant problems. In particular, we introduce a new algorithm that solves a "subcoloring" problem to express the difference between a taxonomy and a phylogeny at a given rank. This algorithm improves upon the current best algorithm in terms of asymptotic complexity for the parameter regime of interest; we also describe a branch-and-bound algorithm that saves orders of magnitude in computation on real data sets. We also develop a formalism and an algorithm for rooting phylogenetic trees according to a taxonomy.

CONCLUSIONS

The algorithms in this paper, and the associated freely-available software, will help biologists better use and understand taxonomically labeled phylogenetic trees.

A format for phylogenetic placements

We have developed a unified format for phylogenetic placements, that is, mappings of environmental sequence data (e.g., short reads) into a phylogenetic tree. We are motivated to do so by the growing number of tools for computing and post-processing phylogenetic placements, and the lack of an established standard for storing them. The format is lightweight, versatile, extensible, and is based on the JSON format, which can be parsed by most modern programming languages. Our format is already implemented in several tools for computing and post-processing parsimony- and likelihood-based phylogenetic placements and has worked well in practice. We believe that establishing a standard format for analyzing read placements at this early stage will lead to a more efficient development of powerful and portable post-analysis tools for the growing applications of phylogenetic placement.

The ability of primate lentiviruses to degrade the monocyte restriction factor SAMHD1 preceded the birth of the viral accessory protein Vpx

The human SAMHD1 protein potently restricts lentiviral infection in dendritic cells and monocyte/macrophages but is antagonized by the primate lentiviral protein Vpx, which targets SAMHD1 for degradation. However, only two of eight primate lentivirus lineages encode Vpx, whereas its paralog, Vpr, is conserved across all extant primate lentiviruses. We find that not only multiple Vpx but also some Vpr proteins are able to degrade SAMHD1, and such antagonism led to dramatic positive selection of SAMHD1 in the primate subfamily Cercopithecinae. Residues that have evolved under positive selection precisely determine sensitivity to Vpx/Vpr degradation and alter binding specificity. By overlaying these functional analyses on a phylogenetic framework of Vpr and Vpx evolution, we can decipher the chronology of acquisition of SAMHD1-degrading abilities in lentiviruses. We conclude that vpr neofunctionalized to degrade SAMHD1 even prior to the birth of a separate vpx gene, thereby initiating an evolutionary arms race with SAMHD1.

Published evidence relevant to the diagnosis of impingement syndrome of the shoulder

BACKGROUND

Acromioplasty for impingement syndrome of the shoulder is one of the most common orthopaedic surgical procedures. The rate with which this procedure is performed has increased dramatically. This investigation sought high levels of evidence in the published literature related to five hypotheses pertinent to the concept of the impingement syndrome and the rationale supporting acromioplasty in its treatment.

METHODS

We conducted a systematic review of articles relevant to the following hypotheses: (1) clinical signs and tests can reliably differentiate the so-called impingement syndrome from other conditions, (2) clinically common forms of rotator cuff abnormality are caused by contact with the coracoacromial arch, (3) contact between the coracoacromial arch and the rotator cuff does not occur in normal shoulders, (4) spurs seen on the anterior aspect of the acromion extend beyond the coracoacromial ligament and encroach on the underlying rotator cuff, and (5) successful treatment of the impingement syndrome requires surgical alteration of the acromion and/or coracoacromial arch. Three of the authors independently reviewed each article and determined the type of study, the level of evidence, and whether it supported the concept of the impingement syndrome. Articles with level-III or IV evidence were excluded from the final analysis.

RESULTS

These hypotheses were not supported by high levels of evidence.

CONCLUSIONS

The concept of impingement syndrome was originally introduced to cover the full range of rotator cuff disorders, as it was recognized that rotator cuff tendinosis, partial tears, and complete tears could not be reliably differentiated by clinical signs alone. The current availability of sonography, magnetic resonance imaging, and arthroscopy now enable these conditions to be accurately differentiated. Nonoperative and operative treatments are currently being used for the different rotator cuff abnormalities. Future clinical investigations can now focus on the indications for and the outcome of treatments for the specific rotator cuff diagnoses. It may be time to replace the nonspecific diagnosis of so-called impingement syndrome by using modern methods to differentiate tendinosis, partial tears, and complete tears of the rotator cuff.

Shoulder hemiarthroplasty with concentric glenoid reaming in patients 55 years old or less

BACKGROUND

Glenohumeral arthritis in younger individuals is challenging because of the complex pathology, need for extended durability, and high expectations of the patients. Humeral hemiarthroplasty combined with concentric glenoid reaming is a surgical option for the management of glenohumeral arthritis that avoids the risks of glenoid component failure and avoids the challenges of tissue interposition. The results of this procedure in young patients have not been previously reported.

METHODS

Sixty-five shoulders in patients who were 55 years old or less at the time of surgery underwent humeral hemiarthroplasty combined with concentric glenoid reaming and were followed for a minimum of 2 years or until the time of revision surgery. Patient self-assessments of shoulder comfort and function were compared before and after surgery. For 22 of these shoulders, standardized radiographs were available for follow-up evaluation.

RESULTS

Nine shoulders required revision surgery. These shoulders had 3 ± 3 prior surgeries, in comparison to 1 ± 1 prior surgeries for the unrevised group. For the 56 unrevised shoulders, the number of Simple Shoulder Test functions that could be performed improved from a mean of 4.1 before surgery to a mean of 9.5 at an average follow-up of 43 months (range, 24-85) (P < .001). For the 22 shoulders with radiographic follow-up, medial glenoid erosion averaged 1.1 mm (range, 0.0-6.3 mm) at an average of 44 months after the procedure.

CONCLUSION

In selected patients 55 years or younger with glenohumeral arthritis, this procedure can provide significant improvement in self-assessed shoulder comfort and function.

Risk factors for chondrolysis of the glenohumeral joint: a study of three hundred and seventy-five shoulder arthroscopic procedures in the practice of an individual community surgeon

BACKGROUND

Glenohumeral chondrolysis is a complication of arthroscopic shoulder surgery characterized by the dissolution of the articular cartilage of the glenoid and the humeral head. An analysis of 375 intra-articular shoulder arthroscopic surgical procedures by an individual community orthopaedic surgeon was performed to explore which factors or combinations of factors might be associated with glenohumeral chondrolysis.

METHODS

The occurrence of chondrolysis was correlated with several demographic and surgical variables with use of hazard ratios from Cox proportional hazards models and Kaplan-Meier survivorship curves. Sensitivity analysis was used to examine the effect of two different definitions of the date of the onset of chondrolysis.

RESULTS

In this cohort, each case of documented chondrolysis was associated with the intra-articular post-arthroscopic infusion of a local anesthetic, either Marcaine (bupivacaine) or lidocaine. In an analysis of the group that received an intra-articular postoperative infusion of a local anesthetic, the risk of chondrolysis was found to be greater for those with one or more suture anchors placed in the glenoid, for younger patients, and for those who had the surgery near the end of the ten-year study period.

CONCLUSIONS

To our knowledge, this is the first Level-II retrospective cohort study of the factors associated with the development of post-arthroscopic glenohumeral chondrolysis. In this cohort of intra-articular shoulder arthroscopic procedures, chondrolysis was observed only in cases in which either Marcaine or lidocaine had been infused into the joint during the postoperative period. Avoiding such a postoperative infusion may reduce the risk of chondrolysis.

A reproducible and practical method for documenting the position of the humeral head center relative to the scapula on standardized plain radiographs

BACKGROUND

Recent articles in this journal showed the clinical importance of the position of the humeral head center in relation to the glenoid. However, the precision, reproducibility, and sensitivity of this and other methods of documenting the head center position have not been evaluated in detail.

MATERIALS AND METHODS

We used templates to fit a coordinate system to the scapular anatomy visible on standardized radiographs. Two observers then used these templates to measure the position of the head center relative to this coordinate system on 25 normal shoulder radiographs and on 25 radiographs of shoulders with cuff tear arthropathy (CTA).

RESULTS

Head center measurements had excellent precision. Normal shoulder radiographs showed a consistent head center position (0.7 ± 1.7 mm medial and 0.6 ± 1.3 mm inferior to the coordinate origin on the anteroposterior view and 0.1 ± 1.3 mm medial and 0.0 ± 1.3 mm anterior to the coordinate origin on the axillary view). The head center of CTA shoulder radiographs was 10.18 ± 5.16 mm above the coordinate origin on the anteroposterior view, significantly different from that for the normal shoulder radiographs (P < .001).

DISCUSSION

The relative position of the humeral head center to the scapula determines the resting length and the moment arms of the scapulohumeral muscles. Correlation of shoulder function with the head center position may provide insights into both shoulder pathomechanics and the optimization of shoulder arthroplasty.

CONCLUSION

This practical technique showed a high degree of precision and reproducibility for normal and CTA shoulder radiographs as well as a high level of discrimination between these two groups.

A quantitative method for determining medial migration of the humeral head after shoulder arthroplasty: preliminary results in assessing glenoid wear at a minimum of two years after hemiarthroplasty with concentric glenoid reaming

HYPOTHESIS

Glenoid erosion and medial migration of the humeral head prosthesis have been observed after most types of shoulder arthroplasty. A method of measuring the change in humeral head position with time after shoulder prosthetic arthroplasty was applied it to 14 shoulders that underwent humeral hemiarthroplasty with concentric glenoid reaming. We hypothesized that the measurement technique would be reproducible and that the rate of wear would be small in the series of shoulders studied.

MATERIALS AND METHODS

Standardized anteroposterior and axillary radiographs were obtained after surgery. Two examiners measured the position of the humeral head center in relation to scapular reference coordinates for the anteroposterior and axillary projections and plotted these values against time after surgery. The change in position was characterized as the slope of this plot. Shoulders were included if there were at least 3 sets of postoperative films, the last being at least 2 years after surgery.

RESULTS

The slopes measured by the 2 examiners agreed within 0.5 mm/y for the anteroposterior and the axillary projections. For the series of shoulder arthroplasties, the rate of movement of the head center toward the scapula was less than 0.4 mm/y for either examiner in either projection.

DISCUSSION

Medial migration is a concern after any type of shoulder arthroplasty, whether a hemiarthroplasty, a biological interpositional arthroplasty, or a total shoulder arthroplasty. Quantifying the rate of medial migration over time after shoulder arthroplasty is an important element of clinical follow-up.

CONCLUSIONS

This is an inexpensive, practical, and reproducible method that can be used to determine the rate of medial migration of the humeral head on plain radiographs after shoulder arthroplasty. The average rate of medial migration in the shoulders in this study was small.

Thermal effects of glenoid reaming during shoulder arthroplasty in vivo

BACKGROUND

Glenoid component loosening is a common cause of failure of total shoulder arthroplasty. It has been proposed that the heat generated during glenoid preparation may reach temperatures capable of producing osteonecrosis at the bone-implant interface. We hypothesized that temperatures sufficient to induce thermal necrosis can be produced with routine drilling and reaming during glenoid preparation for shoulder arthroplasty in vivo. Furthermore, we hypothesized that irrigation of the glenoid during reaming can reduce this temperature increase.

METHODS

Real-time, high-definition, infrared thermal video imaging was used to determine the temperatures produced by drilling and reaming during glenoid preparation in ten consecutive patients undergoing total shoulder arthroplasty. The maximum temperature and the duration of temperatures greater than the established thresholds for thermal necrosis were documented. The first five arthroplasties were performed without irrigation and were compared with the second five arthroplasties, in which continuous bulb irrigation was used during drilling and reaming. A one-dimensional finite element model was developed to estimate the depth of penetration of critical temperatures into the bone of the glenoid on the basis of recorded surface temperatures.

RESULTS

Our first hypothesis was supported by the recording of maximum surface temperatures above the 56°C threshold during reaming in four of the five arthroplasties done without irrigation and during drilling in two of the five arthroplasties without irrigation. The estimated depth of penetration of the critical temperature (56°C) to produce instantaneous osteonecrosis was beyond 1 mm (range, 1.97 to 5.12 mm) in four of these patients during reaming and one of these patients during drilling, and two had estimated temperatures above 56°C at 3 mm. Our second hypothesis was supported by the observation that, in the group receiving irrigation, the temperature exceeded the critical threshold in only one specimen during reaming and in two during drilling. The estimated depth of penetration for the critical temperature (56°C) did not reach a depth of 1 mm in any of these patients (range, 0.07 to 0.19 mm).

CONCLUSIONS

Temperatures sufficient to induce thermal necrosis of glenoid bone can be generated by glenoid preparation in shoulder arthroplasty in vivo. Frequent irrigation may be effective in preventing temperatures from reaching the threshold for bone necrosis during glenoid preparation.

Glenohumeral arthritis in the young adult

Treating glenohumeral arthritis in the young adult remains a significant challenge. There are a variety of etiologies that can lead to this condition, and the diagnosis is often not straightforward. With advances in both surgical techniques and biologic options, the treatment algorithm for patients with glenohumeral arthritis is constantly evolving. When nonsurgical treatment fails, there are a variety of possible surgical options, each with potential benefits. It is helpful to review the diagnostic challenges presented by these patients and understand the palliative, reparative, restorative, and reconstructive surgical options and their associated clinical outcomes, which provide a framework for clinical and surgical decision making.

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

BACKGROUND

Likelihood-based phylogenetic inference is generally considered to be the most reliable classification method for unknown sequences. However, traditional likelihood-based phylogenetic methods cannot be applied to large volumes of short reads from next-generation sequencing due to computational complexity issues and lack of phylogenetic signal. "Phylogenetic placement," where a reference tree is fixed and the unknown query sequences are placed onto the tree via a reference alignment, is a way to bring the inferential power offered by likelihood-based approaches to large data sets.

RESULTS

This paper introduces pplacer, a software package for phylogenetic placement and subsequent visualization. The algorithm can place twenty thousand short reads on a reference tree of one thousand taxa per hour per processor, has essentially linear time and memory complexity in the number of reference taxa, and is easy to run in parallel. Pplacer features calculation of the posterior probability of a placement on an edge, which is a statistically rigorous way of quantifying uncertainty on an edge-by-edge basis. It also can inform the user of the positional uncertainty for query sequences by calculating expected distance between placement locations, which is crucial in the estimation of uncertainty with a well-sampled reference tree. The software provides visualizations using branch thickness and color to represent number of placements and their uncertainty. A simulation study using reads generated from 631 COG alignments shows a high level of accuracy for phylogenetic placement over a wide range of alignment diversity, and the power of edge uncertainty estimates to measure placement confidence.

CONCLUSIONS

Pplacer enables efficient phylogenetic placement and subsequent visualization, making likelihood-based phylogenetics methodology practical for large collections of reads; it is freely available as source code, binaries, and a web service.

A method for documenting the change in center of rotation with reverse total shoulder arthroplasty and its application to a consecutive series of 68 shoulders having reconstruction with one of two different reverse prostheses

BACKGROUND

Reverse shoulder arthroplasty changes the center of rotation (COR) of the glenohumeral joint and in doing so affects the resting tension in the deltoid and residual cuff muscles, as well as their respective moment arms. The purpose of this study was to assess the change in COR from the preoperative to postoperative state in a group of patients undergoing reverse shoulder arthroplasty.

MATERIALS AND METHODS

The position of the COR in relation to a scapular coordinate system was determined for the anteroposterior and axillary radiographs before and after reverse total shoulder arthroplasty for 68 shoulders (63 patients) receiving either a Delta prosthesis or an Encore Reverse Shoulder Prosthesis.

RESULTS

Preoperatively, the COR was superiorly displaced a mean of 9 ± 7 mm from the origin of the coordinate system. For all shoulders, the postoperative COR was inferiorly displaced by 12 mm to a position 3 ± 3 mm below the coordinate origin (P < .001) and medially displaced by 27 ± 4 mm from the coordinate origin (P < .001) in the anteroposterior projection. For the shoulders receiving the Delta prosthesis, the COR was inferiorly displaced by 2 ± 3 mm from the coordinate origin, whereas it was inferiorly displaced by 7 ± 3 mm with the Encore prosthesis (P < .001). The COR was medially displaced by 28 ± 4 mm with the Delta prosthesis and by 19 ± 3 mm with the Encore prosthesis (P < .001).

CONCLUSIONS

The position of the COR relative to the scapula is significantly altered by reverse shoulder arthroplasty and is significantly different for 2 different implant designs.

Glenohumeral chondrolysis: a systematic review of 100 cases from the English language literature

HYPOTHESIS

Chondrolysis can be a devastating complication of shoulder arthroscopy. We undertook a review of the 100 cases reported in the English language to test the hypothesis that common factors could be identified and that the identification of these factors could suggest strategies for avoiding this complication.

MATERIALS AND METHODS

We systematically reviewed the English language literature and identified 16 articles reporting 100 shoulders in which postsurgical glenohumeral chondrolysis had developed.

RESULTS

The average reported patient age was 27 +/- 11 years at the time of surgery; 35 were women. The most common indications for surgery were instability (n = 68) and superior labrum anteroposterior lesions (n = 17). In 59 cases, chondrolysis was reported to be associated with the use of intra-articular pain pumps. The infusate was known to include bupivacaine in 50 shoulders and lidocaine in 2. Radiofrequency capsulorrhaphy was performed in 2 shoulders.

DISCUSSION

Fifty-nine percent of the reported cases of glenohumeral chondrolysis occurred with the combination of arthroscopic surgery and postarthroscopy infusion of local anesthetic. The arthroscopic operations observed with chondrolysis were not limited to stabilization procedures, and the infused anesthetic was not limited to bupivacaine.

CONCLUSION

In that postoperative infusion of local anesthetic and radiofrequency may not be essential to the success of shoulder arthroscopy, surgeons may wish to consider the possible risks of their use.

Polyhedral geometry of phylogenetic rogue taxa

It is well known among phylogeneticists that adding an extra taxon (e.g. species) to a data set can alter the structure of the optimal phylogenetic tree in surprising ways. However, little is known about this "rogue taxon" effect. In this paper we characterize the behavior of balanced minimum evolution (BME) phylogenetics on data sets of this type using tools from polyhedral geometry. First we show that for any distance matrix there exist distances to a "rogue taxon" such that the BME-optimal tree for the data set with the new taxon does not contain any nontrivial splits (bipartitions) of the optimal tree for the original data. Second, we prove a theorem which restricts the topology of BME-optimal trees for data sets of this type, thus showing that a rogue taxon cannot have an arbitrary effect on the optimal tree. Third, we computationally construct polyhedral cones that give complete answers for BME rogue taxon behavior when our original data fits a tree on four, five, and six taxa. We use these cones to derive sufficient conditions for rogue taxon behavior for four taxa, and to understand the frequency of the rogue taxon effect via simulation.