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Find video protocols related to scientific articles indexed in Pubmed.
Propionibacterium persists in the skin despite standard surgical preparation.
J Bone Joint Surg Am
PUBLISHED: 09-05-2014
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Propionibacterium acnes, which normally resides in the skin, is known to play a role in surgical site infection in orthopaedic surgery. Studies have suggested a persistence of propionibacteria on the skin surface, with rates of positive cultures ranging from 7% to 29% after surgical preparation. However, as Propionibacterium organisms normally reside in the dermal layer, these studies may underestimate the true prevalence of propionibacteria after surgical skin preparation. We hypothesized that, after surgical skin preparation, viable Propionibacterium remains in the dermis at a much higher rate than previously reported.
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Phylogenetics and the Human Microbiome.
Syst. Biol.
PUBLISHED: 08-07-2014
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The human microbiome is the ensemble of genes in the microbes that live inside and on the surface of humans. Because microbial sequencing information is now much easier to come by than phenotypic information, there has been an explosion of sequencing and genetic analysis of microbiome samples. Much of the analytical work for these sequences involves phylogenetics, at least indirectly, but methodology has developed in a somewhat different direction than for other applications of phylogenetics. In this article, I review the field and its methods from the perspective of a phylogeneticist, as well as describing current challenges for phylogenetics coming from this type of work.
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Metal-Backed Glenoid Components Have a Higher Rate of Failure and Fail by Different Modes in Comparison with All-Polyethylene Components: A Systematic Review.
J Bone Joint Surg Am
PUBLISHED: 06-22-2014
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Glenoid component failure is a common and serious complication of total shoulder arthroplasty. The purpose of this study was to evaluate published evidence on whether metal backing lessens the rate of glenoid component failure.METHODS: A comprehensive systematic review yielded twenty-one studies on radiolucency, radiographic failure, and revision after arthroplasty with metal-backed glenoid components and twenty-three studies with all-polyethylene components. Our analysis included data on 1571 metal-backed and 3035 all-polyethylene components. The mean duration of follow-up was 5.8 years in the studies with metal-backed components and 7.3 years with all-polyethylene components.RESULTS: All-polyethylene components had a 42.5% rate of radiolucency compared with 34.9% for metal-backed components (p = 0.0026) and a 21.1% rate of radiographic loosening or failure compared with 16.8% for metal-backed components (p = 0.0005). However, the rate of revision was more than three times higher with metal-backed components (14.0%) than with all-polyethylene components (3.8%, p < 0.0001). Although 77% of the revisions of all-polyethylene components were for loosening, 62% of the revisions of metal-backed components were for other reasons, such as component fracture, screw breakage, component dissociation, polyethylene wear, metal wear, and rotator cuff tear (p < 0.0001).CONCLUSIONS: The published evidence indicates that metal-backed glenoid components require revision at a significantly higher rate and for different reasons in comparison with all-polyethylene components.LEVEL OF EVIDENCE: Therapeutic Level IV. See Instructions for Authors for a complete description of levels of evidence.
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Rotator Cuff Repair: Published Evidence on Factors Associated With Repair Integrity and Clinical Outcome.
Am J Sports Med
PUBLISHED: 04-23-2014
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BACKGROUND:Rotator cuff tears are common, and rotator cuff repair represents a major health care expense. While patients often benefit from rotator cuff repair, anatomic failure of the repair is not unusual. PURPOSE:To identify the published evidence on the factors associated with retears and with suboptimal clinical outcomes of rotator cuff repairs. STUDY DESIGN:Systematic review and meta-analysis of articles with evidence levels 1-4. METHODS:A total of 2383 articles on rotator cuff repairs published between 1980 and 2012 were identified. Only 108 of these articles, reporting on over 8011 shoulders, met the inclusion criteria of reporting quantitative data on both imaging and clinical outcomes after rotator cuff repair. Factors related to the patients, their shoulders, the procedures, and the results were systematically categorized and submitted for meta-analysis. RESULTS:While the number of relevant articles published per year increased dramatically over the period of the study, the clinical and anatomic results did not show improvement over this period. The weighted mean retear rate was 26.6% at a mean of 23.7 months after surgery. Retears were associated with more fatty infiltration, larger tear size, advanced age, and double-row repairs. Clinical improvement averaged 72% of the maximum possible improvement. Patient-reported outcomes were generally improved whether or not the repair restored the integrity of the rotator cuff. The inconsistent and incomplete data in the published articles limited the meta-analysis of factors affecting the outcome of rotator cuff repair. CONCLUSION:In spite of a dramatic increase in the number of publications per year, there is little evidence that the results of rotator cuff repair are improving. The information needed to guide the management of this commonly treated and costly condition is seriously deficient. To accumulate the evidence necessary to inform practice, future clinical studies on the outcome of rotator cuff repair must report important data relating to each patient's condition, the surgical technique, the outcome in terms of integrity, and the change in patient self-assessed comfort and function.
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Substantial cultures of Propionibacterium can be found in apparently aseptic shoulders revised three years or more after the index arthroplasty.
J Shoulder Elbow Surg
PUBLISHED: 02-11-2014
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Revisions of apparently "aseptic" shoulder arthroplasties are not infrequently culture positive for Propionibacterium, organisms that may be introduced at the time of the index surgery when the dermal sebaceous glands are transected. This report seeks to answer the question, Do surgeons performing revision shoulder arthroplasty years after the index procedure need to be concerned about the persistence of Propionibacterium?
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A novel bayesian method for detection of APOBEC3-mediated hypermutation and its application to zoonotic transmission of simian foamy viruses.
PLoS Comput. Biol.
PUBLISHED: 02-01-2014
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Simian Foamy Virus (SFV) can be transmitted from non-human primates (NHP) to humans. However, there are no documented cases of human to human transmission, and significant differences exist between infection in NHP and human hosts. The mechanism for these between-host differences is not completely understood. In this paper we develop a new Bayesian approach to the detection of APOBEC3-mediated hypermutation, and use it to compare SFV sequences from human and NHP hosts living in close proximity in Bangladesh. We find that human APOBEC3G can induce genetic changes that may prevent SFV replication in infected humans in vivo.
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PhyloSift: phylogenetic analysis of genomes and metagenomes.
PeerJ
PUBLISHED: 01-01-2014
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Like all organisms on the planet, environmental microbes are subject to the forces of molecular evolution. Metagenomic sequencing provides a means to access the DNA sequence of uncultured microbes. By combining DNA sequencing of microbial communities with evolutionary modeling and phylogenetic analysis we might obtain new insights into microbiology and also provide a basis for practical tools such as forensic pathogen detection. In this work we present an approach to leverage phylogenetic analysis of metagenomic sequence data to conduct several types of analysis. First, we present a method to conduct phylogeny-driven Bayesian hypothesis tests for the presence of an organism in a sample. Second, we present a means to compare community structure across a collection of many samples and develop direct associations between the abundance of certain organisms and sample metadata. Third, we apply new tools to analyze the phylogenetic diversity of microbial communities and again demonstrate how this can be associated to sample metadata. These analyses are implemented in an open source software pipeline called PhyloSift. As a pipeline, PhyloSift incorporates several other programs including LAST, HMMER, and pplacer to automate phylogenetic analysis of protein coding and RNA sequences in metagenomic datasets generated by modern sequencing platforms (e.g., Illumina, 454).
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Failure of the glenoid component in anatomic total shoulder arthroplasty: a systematic review of the english-language literature between 2006 and 2012.
J Bone Joint Surg Am
PUBLISHED: 12-20-2013
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Although glenoid component failure is one of the most common complications of anatomic total shoulder arthroplasty, substantial evidence from the recent published literature is lacking regarding the temporal trend in the rate of this complication and the risk factors for its occurrence.
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Origin of propionibacterium in surgical wounds and evidence-based approach for culturing propionibacterium from surgical sites.
J Bone Joint Surg Am
PUBLISHED: 12-06-2013
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To explore the origin of Propionibacterium in surgical wounds and to suggest an optimized strategy for culturing this organism at the time of revision surgery, we studied the presence of this organism on the skin and in the surgical wounds of patients who underwent revision arthroplasty for reasons other than apparent infection.
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Simian foamy virus infection of rhesus macaques in bangladesh: relationship of latent proviruses and transcriptionally active viruses.
J. Virol.
PUBLISHED: 10-09-2013
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Simian foamy viruses (SFV) are complex retroviruses that are ubiquitous in nonhuman primates (NHP) and are zoonotically transmitted to humans, presumably through NHP saliva, by licking, biting, and other behaviors. We have studied SFV in free-ranging rhesus macaques in Bangladesh. It has been previously shown that SFV in immunocompetent animals replicates to detectable levels only in superficial epithelial cells of the oral mucosa, although latent proviruses are found in most, if not all, tissues. In this study, we compare DNA sequences from latent SFV proviruses found in blood cells of 30 Bangladesh rhesus macaques to RNA sequences of transcriptionally active SFV from buccal swabs obtained from the same animals. Viral strains, defined by differences in SFV gag sequences, from buccal mucosal specimens overlapped with those from blood samples in 90% of animals. Thus, latent proviruses in peripheral blood mononuclear cells (PBMC) are, to a great extent, representative of viruses likely to be transmitted to other hosts. The level of SFV RNA in buccal swabs varied greatly between macaques, with increasing amounts of viral RNA in older animals. Evidence of APOBEC3-induced mutations was found in gag sequences derived from the blood and oral mucosa.
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HIV-1 superinfection occurs less frequently than initial infection in a cohort of high-risk Kenyan women.
PLoS Pathog.
PUBLISHED: 08-01-2013
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HIV superinfection (reinfection) has been reported in several settings, but no study has been designed and powered to rigorously compare its incidence to that of initial infection. Determining whether HIV infection reduces the risk of superinfection is critical to understanding whether an immune response to natural HIV infection is protective. This study compares the incidence of initial infection and superinfection in a prospective seroincident cohort of high-risk women in Mombasa, Kenya. A next-generation sequencing-based pipeline was developed to screen 129 women for superinfection. Longitudinal plasma samples at <6 months, >2 years and one intervening time after initial HIV infection were analyzed. Amplicons in three genome regions were sequenced and a median of 901 sequences obtained per gene per timepoint. Phylogenetic evidence of polyphyly, confirmed by pairwise distance analysis, defined superinfection. Superinfection timing was determined by sequencing virus from intervening timepoints. These data were combined with published data from 17 additional women in the same cohort, totaling 146 women screened. Twenty-one cases of superinfection were identified for an estimated incidence rate of 2.61 per 100 person-years (pys). The incidence rate of initial infection among 1910 women in the same cohort was 5.75 per 100 pys. Andersen-Gill proportional hazards models were used to compare incidences, adjusting for covariates known to influence HIV susceptibility in this cohort. Superinfection incidence was significantly lower than initial infection incidence, with a hazard ratio of 0.47 (CI 0.29-0.75, p?=?0.0019). This lower incidence of superinfection was only observed >6 months after initial infection. This is the first adequately powered study to report that HIV infection reduces the risk of reinfection, raising the possibility that immune responses to natural infection are partially protective. The observation that superinfection risk changes with time implies a window of protection that coincides with the maturation of HIV-specific immunity.
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The quality of upper extremity orthopedic care in liability claims filed and claims paid.
J Hand Surg Am
PUBLISHED: 07-10-2013
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To review a series of closed liability claims for upper extremity conditions to guide improvements for upper extremity care and thereby reduce the frequency of paid claims.
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Minimizing the average distance to a closest leaf in a phylogenetic tree.
Syst. Biol.
PUBLISHED: 07-10-2013
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When performing an analysis on a collection of molecular sequences, it can be convenient to reduce the number of sequences under consideration while maintaining some characteristic of a larger collection of sequences. For example, one may wish to select a subset of high-quality sequences that represent the diversity of a larger collection of sequences. One may also wish to specialize a large database of characterized "reference sequences" to a smaller subset that is as close as possible on average to a collection of "query sequences" of interest. Such a representative subset can be useful whenever one wishes to find a set of reference sequences that is appropriate to use for comparative analysis of environmentally derived sequences, such as for selecting "reference tree" sequences for phylogenetic placement of metagenomic reads. In this article, we formalize these problems in terms of the minimization of the Average Distance to the Closest Leaf (ADCL) and investigate algorithms to perform the relevant minimization. We show that the greedy algorithm is not effective, show that a variant of the Partitioning Around Medoids (PAM) heuristic gets stuck in local minima, and develop an exact dynamic programming approach. Using this exact program we note that the performance of PAM appears to be good for simulated trees, and is faster than the exact algorithm for small trees. On the other hand, the exact program gives solutions for all numbers of leaves less than or equal to the given desired number of leaves, whereas PAM only gives a solution for the prespecified number of leaves. Via application to real data, we show that the ADCL criterion chooses chimeric sequences less often than random subsets, whereas the maximization of phylogenetic diversity chooses them more often than random. These algorithms have been implemented in publicly available software.
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The mean and variance of phylogenetic diversity under rarefaction.
Methods Ecol Evol
PUBLISHED: 07-09-2013
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Phylogenetic diversity (PD) depends on sampling depth, which complicates the comparison of PD between samples of different depth. One approach to dealing with differing sample depth for a given diversity statistic is to rarefy, which means to take a random subset of a given size of the original sample. Exact analytical formulae for the mean and variance of species richness under rarefaction have existed for some time but no such solution exists for PD.We have derived exact formulae for the mean and variance of PD under rarefaction. We confirm that these formulae are correct by comparing exact solution mean and variance to that calculated by repeated random (Monte Carlo) subsampling of a dataset of stem counts of woody shrubs of Toohey Forest, Queensland, Australia. We also demonstrate the application of the method using two examples: identifying hotspots of mammalian diversity in Australasian ecoregions, and characterising the human vaginal microbiome.There is a very high degree of correspondence between the analytical and random subsampling methods for calculating mean and variance of PD under rarefaction, although the Monte Carlo method requires a large number of random draws to converge on the exact solution for the variance.Rarefaction of mammalian PD of ecoregions in Australasia to a common standard of 25 species reveals very different rank orderings of ecoregions, indicating quite different hotspots of diversity than those obtained for unrarefied PD. The application of these methods to the vaginal microbiome shows that a classical score used to quantify bacterial vaginosis is correlated with the shape of the rarefaction curve.The analytical formulae for the mean and variance of PD under rarefaction are both exact and more efficient than repeated subsampling. Rarefaction of PD allows for many applications where comparisons of samples of different depth is required.
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Axillary View: Arthritic Glenohumeral Anatomy and Changes After Ream and Run.
Clin. Orthop. Relat. Res.
PUBLISHED: 07-03-2013
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The technique and results of shoulder arthroplasty are influenced by glenohumeral pathoanatomy. Although some authors advocate a routine preoperative CT scan to define this anatomy, ordering a CT scan substantially increases the cost and the radiation exposure for the patient.
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Published evidence demonstrating the causation of glenohumeral chondrolysis by postoperative infusion of local anesthetic via a pain pump.
J Bone Joint Surg Am
PUBLISHED: 06-21-2013
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Glenohumeral chondrolysis is the irreversible destruction of previously normal articular cartilage, occurring most commonly after shoulder surgery in young individuals. The reported incidence of this complication has risen rapidly since the early 2000s. As chondrolysis cannot be reversed, its occurrence can only be prevented by establishing and avoiding its causes.
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High-throughput sequencing of B- and T-lymphocyte antigen receptors in hematology.
Blood
PUBLISHED: 05-08-2013
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Application of high-throughput DNA sequencing to the analysis of B- and T-lymphocyte antigen receptors has great potential for improving the monitoring of lymphoid malignancies, assessing immune reconstitution after hematopoietic cell transplantation, and characterizing the composition of lymphocyte repertoires. Current technology can define the number and frequency of immunoglobulin heavy, T-cell receptor (TCR)?, TCR?, or TCR? chains expressed in a population of lymphocytes; techniques for determining the number of antigen receptor heterodimers, such as TCR?? pairs, expressed in the population are under development.
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Gene loss and adaptation to hominids underlie the ancient origin of HIV-1.
Cell Host Microbe
PUBLISHED: 03-25-2013
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HIV-1 resulted from cross-species transmission of SIVcpz, a simian immunodeficiency virus that naturally infects chimpanzees. SIVcpz, in turn, is a recombinant between two SIV lineages from Old World monkeys. Lentiviral interspecies transmissions are partly driven by the evolution and capacity of viral accessory genes, such as vpx, vpr, and vif, to antagonize host antiviral factors, such as SAMHD1 and the APOBEC3 proteins. We show that vpx, which in other lentiviruses antagonizes SAMHD1, was deleted during the creation of SIVcpz. This genomic deletion resulted in the reconstruction of the overlapping vif gene by "overprinting," creating a unique vif that overlaps in its 3 end with the vpr gene and can antagonize hominid APOBEC3s. Moreover, passage of SIVs through chimpanzees facilitated the subsequent adaptation of HIV-1 to humans. Thus, HIV-1 originated through a series of gene loss and adaptation events that generated its chimpanzee precursor and lowered the species barrier to human infection.
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Demographics of disclosure of conflicts of interest at the 2011 annual meeting of the American Academy of Orthopaedic Surgeons.
J Bone Joint Surg Am
PUBLISHED: 03-08-2013
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There is growing concern regarding conflicts of interest in orthopaedic research and education. Because of their potential influence on orthopaedic practice, conflicts of interest among participants in the educational programs of the American Academy of Orthopaedic Surgeons (AAOS) are of particular interest.
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Lessons regarding the safety of orthopaedic patient care: an analysis of four hundred and sixty-four closed malpractice claims.
J Bone Joint Surg Am
PUBLISHED: 02-22-2013
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An orthopaedic malpractice claim alleges that the patient sustained a preventable iatrogenic injury. The analysis of a representative series of malpractice claims provides a unique view of alleged orthopaedic adverse events, revealing what can potentially go wrong across a spectrum of practice settings and anatomic locations. The goal of this study was to identify high-impact targets in order to institute measures to reduce claims through efforts focused on patient safety.
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Edge principal components and squash clustering: using the special structure of phylogenetic placement data for sample comparison.
PLoS ONE
PUBLISHED: 01-16-2013
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Principal components analysis (PCA) and hierarchical clustering are two of the most heavily used techniques for analyzing the differences between nucleic acid sequence samples taken from a given environment. They have led to many insights regarding the structure of microbial communities. We have developed two new complementary methods that leverage how this microbial community data sits on a phylogenetic tree. Edge principal components analysis enables the detection of important differences between samples that contain closely related taxa. Each principal component axis is a collection of signed weights on the edges of the phylogenetic tree, and these weights are easily visualized by a suitable thickening and coloring of the edges. Squash clustering outputs a (rooted) clustering tree in which each internal node corresponds to an appropriate "average" of the original samples at the leaves below the node. Moreover, the length of an edge is a suitably defined distance between the averaged samples associated with the two incident nodes, rather than the less interpretable average of distances produced by UPGMA, the most widely used hierarchical clustering method in this context. We present these methods and illustrate their use with data from the human microbiome.
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More than meets the eye: associations of vaginal bacteria with gram stain morphotypes using molecular phylogenetic analysis.
PLoS ONE
PUBLISHED: 01-01-2013
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Bacterial vaginosis (BV) is a highly prevalent condition associated with adverse health outcomes. Gram stain analysis of vaginal fluid is the standard for confirming the diagnosis of BV, wherein abundances of key bacterial morphotypes are assessed. These Lactobacillus, Gardnerella, Bacteroides, and Mobiluncus morphotypes were originally linked to particular bacterial species through cultivation studies, but no studies have systematically investigated associations between uncultivated bacteria detected by molecular methods and Gram stain findings. In this study, 16S-rRNA PCR/pyrosequencing was used to examine associations between vaginal bacteria and bacterial morphotypes in 220 women with and without BV. Species-specific quantitative PCR (qPCR) and fluorescence in Situ hybridization (FISH) methods were used to document concentrations of two bacteria with curved rod morphologies: Mobiluncus and the fastidious BV-associated bacterium-1 (BVAB1). Rank abundance of vaginal bacteria in samples with evidence of curved gram-negative rods showed that BVAB1 was dominant (26.1%), while Mobiluncus was rare (0.2% of sequence reads). BVAB1 sequence reads were associated with Mobiluncus morphotypes (p<0.001). Among women with curved rods, mean concentration of BVAB1 DNA was 2 log units greater than Mobiluncus (p<0.001) using species-specific quantitative PCR. FISH analyses revealed that mean number of BVAB1 cells was 2 log units greater than Mobiluncus cells in women with highest Nugent score (p<0.001). Prevotella and Porphyromonas spp. were significantly associated with the "Bacteroides morphotype," whereas Bacteroides species were rare. Gram-negative rods designated Mobiluncus morphotypes on Gram stain are more likely BVAB1. These findings provide a clearer picture of the bacteria associated with morphotypes on vaginal Gram stain.
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Abundance-weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampling depth.
PeerJ
PUBLISHED: 01-01-2013
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In microbial ecology studies, the most commonly used ways of investigating alpha (within-sample) diversity are either to apply non-phylogenetic measures such as Simpsons index to Operational Taxonomic Unit (OTU) groupings, or to use classical phylogenetic diversity (PD), which is not abundance-weighted. Although alpha diversity measures that use abundance information in a phylogenetic framework do exist, they are not widely used within the microbial ecology community. The performance of abundance-weighted phylogenetic diversity measures compared to classical discrete measures has not been explored, and the behavior of these measures under rarefaction (sub-sampling) is not yet clear. In this paper we compare the ability of various alpha diversity measures to distinguish between different community states in the human microbiome for three different datasets. We also present and compare a novel one-parameter family of alpha diversity measures, BWPD?, that interpolates between classical phylogenetic diversity (PD) and an abundance-weighted extension of PD. Additionally, we examine the sensitivity of these phylogenetic diversity measures to sampling, via computational experiments and by deriving a closed form solution for the expectation of phylogenetic quadratic entropy under re-sampling. On the three datasets, a phylogenetic measure always performed best, and two abundance-weighted phylogenetic diversity measures were the only measures ranking in the top four across all datasets. OTU-based measures, on the other hand, are less effective in distinguishing community types. In addition, abundance-weighted phylogenetic diversity measures are less sensitive to differing sampling intensity than their unweighted counterparts. Based on these results we encourage the use of abundance-weighted phylogenetic diversity measures, especially for cases such as microbial ecology where species delimitation is difficult.
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Rapid 16S rRNA next-generation sequencing of polymicrobial clinical samples for diagnosis of complex bacterial infections.
PLoS ONE
PUBLISHED: 01-01-2013
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Classifying individual bacterial species comprising complex, polymicrobial patient specimens remains a challenge for culture-based and molecular microbiology techniques in common clinical use. We therefore adapted practices from metagenomics research to rapidly catalog the bacterial composition of clinical specimens directly from patients, without need for prior culture. We have combined a semiconductor deep sequencing protocol that produces reads spanning 16S ribosomal RNA gene variable regions 1 and 2 (?360 bp) with a de-noising pipeline that significantly improves the fraction of error-free sequences. The resulting sequences can be used to perform accurate genus- or species-level taxonomic assignment. We explore the microbial composition of challenging, heterogeneous clinical specimens by deep sequencing, culture-based strain typing, and Sanger sequencing of bulk PCR product. We report that deep sequencing can catalog bacterial species in mixed specimens from which usable data cannot be obtained by conventional clinical methods. Deep sequencing a collection of sputum samples from cystic fibrosis (CF) patients reveals well-described CF pathogens in specimens where they were not detected by standard clinical culture methods, especially for low-prevalence or fastidious bacteria. We also found that sputa submitted for CF diagnostic workup can be divided into a limited number of groups based on the phylogenetic composition of the airway microbiota, suggesting that metagenomic profiling may prove useful as a clinical diagnostic strategy in the future. The described method is sufficiently rapid (theoretically compatible with same-day turnaround times) and inexpensive for routine clinical use.
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Published evidence relevant to the diagnosis of impingement syndrome of the shoulder.
J Bone Joint Surg Am
PUBLISHED: 10-19-2011
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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.
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Genome sequence of a novel species, Propionibacterium humerusii.
J. Bacteriol.
PUBLISHED: 05-13-2011
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As part of a larger project to sequence multiple clinical isolates of Propionibacterium acnes, we have produced a draft genome sequence of a novel Propionibacterium species that is closely related to, yet distinct (by sequence) from P. acnes. We have tentatively named this new species Propionibacterium humerusii.
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Glenohumeral arthritis in the young adult.
Instr Course Lect
PUBLISHED: 05-11-2011
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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.
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Optimization of periprosthetic culture for diagnosis of Propionibacterium acnes prosthetic joint infection.
J. Clin. Microbiol.
PUBLISHED: 05-04-2011
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Propionibacterium acnes is increasingly recognized as an important agent of prosthetic joint infection (PJI). However, the optimum culture conditions for recovery of this organism from PJI specimens have not been determined. By applying a prolonged 28-day culture incubation to all periprosthetic specimens received for bacterial culture from 198 revision arthroplasty procedures, we retrospectively determined that a 13-day culture incubation period is necessary for the recovery of P. acnes from patients with PJI. Incubation beyond this period was associated with increasing recovery of nondiagnostic isolates: 21.7% of P. acnes isolates believed to be clinically unimportant were recovered after 13 days of incubation. Importantly, a diagnosis of P. acnes PJI would have been missed in 29.4% of patients had extended culture incubation been applied only to anaerobic culture media. Although specimens from P. acnes PJIs were more commonly associated with the presence of ? 2 culture media positive for growth, acute inflammation (? 5 neutrophils/high-power field) was observed in only 40% of patients with PJIs that had more than one specimen submitted for bacterial culture. These results support the need for a minimum culture incubation period of 13 days to be applied to both aerobic and anaerobic culture media for all periprosthetic specimens. Optimal recovery of infecting organisms from PJI specimens will be an important component in generating a universal definition for PJI due to indolent agents of infection, such as P. acnes.
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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.
J Bone Joint Surg Am
PUBLISHED: 02-25-2011
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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.
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Thermal effects of glenoid reaming during shoulder arthroplasty in vivo.
J Bone Joint Surg Am
PUBLISHED: 01-07-2011
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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.
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Factors affecting acceptance of a Web-based self-referral system.
IEEE Trans Inf Technol Biomed
PUBLISHED: 10-28-2010
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With the growing availability of health information on the Web, people are becoming more knowledgeable on their health conditions and treatment options, and more patients seek specialists by themselves. To aid patients in requesting self-referrals, we have developed and evaluated a web-based self-referral system in three specialty clinics at the University of Washington. Two clinics adopted the system for routine clinical use, while the third clinic decided not to. A major difference between these two groups was in how fast online requests from patients were handled, which significantly influenced patients satisfaction. Clinics preparedness for handling the temporarily increased workload due to the introduction of a new health information system played a role as well. Also, we noticed that the physician leadership/championship made a difference in the acceptance of our system.
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constNJ: an algorithm to reconstruct sets of phylogenetic trees satisfying pairwise topological constraints.
J. Comput. Biol.
PUBLISHED: 05-27-2010
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This article introduces constNJ (constrained neighbor-joining), an algorithm for phylogenetic reconstruction of sets of trees with constrained pairwise rooted subtree-prune-regraft (rSPR) distance. We are motivated by the problem of constructing sets of trees that must fit into a recombination, hybridization, or similar network. Rather than first finding a set of trees that are optimal according to a phylogenetic criterion (e.g., likelihood or parsimony) and then attempting to fit them into a network, constNJ estimates the trees while enforcing specified rSPR distance constraints. The primary input for constNJ is a collection of distance matrices derived from sequence blocks which are assumed to have evolved in a tree-like manner, such as blocks of an alignment which do not contain any recombination breakpoints. The other input is a set of rSPR constraint inequalities for any set of pairs of trees. constNJ is consistent and a strict generalization of the neighbor-joining algorithm; it uses the new notion of maximum agreement partitions (MAPs) to assure that the resulting trees satisfy the given rSPR distance constraints.
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pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree.
BMC Bioinformatics
PUBLISHED: 03-18-2010
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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.
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Shoulder hemiarthroplasty with concentric glenoid reaming in patients 55 years old or less.
J Shoulder Elbow Surg
PUBLISHED: 03-15-2010
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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.
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A reproducible and practical method for documenting the position of the humeral head center relative to the scapula on standardized plain radiographs.
J Shoulder Elbow Surg
PUBLISHED: 03-15-2010
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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.
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Polyhedral geometry of phylogenetic rogue taxa.
Bull. Math. Biol.
PUBLISHED: 01-28-2010
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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.
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Glenohumeral chondrolysis: a systematic review of 100 cases from the English language literature.
J Shoulder Elbow Surg
PUBLISHED: 01-19-2010
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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.
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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.
J Shoulder Elbow Surg
PUBLISHED: 01-15-2010
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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.
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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.
J Shoulder Elbow Surg
PUBLISHED: 01-13-2010
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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.
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Comparison of patients undergoing primary shoulder arthroplasty before and after the age of fifty.
J Bone Joint Surg Am
PUBLISHED: 01-06-2010
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The reported outcomes of shoulder arthroplasty in patients under the age of fifty years are worse than those in patients over fifty. While there are several possible explanations for this finding, we explored the possibility that patients who had a primary shoulder arthroplasty when they were under fifty years of age differed from those who had the procedure when they were over fifty with respect to their pre-arthroplasty self-assessed comfort and function, sex distribution, and specific type of arthritis.
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A method for investigating relative timing information on phylogenetic trees.
Syst. Biol.
PUBLISHED: 06-12-2009
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In this paper, we present a new way to describe the timing of branching events in phylogenetic trees. Our description is in terms of the relative timing of diversification events between sister clades; as such it is complementary to existing methods using lineages-through-time plots which consider diversification in aggregate. The method can be applied to look for evidence of diversification happening in lineage-specific "bursts", or the opposite, where diversification between 2 clades happens in an unusually regular fashion. In order to be able to distinguish interesting events from stochasticity, we discuss 2 classes of neutral models on trees with relative timing information and develop a statistical framework for testing these models. These model classes include both the coalescent with ancestral population size variation and global rate speciation-extinction models. We end the paper with 2 example applications: first, we show that the evolution of the hepatitis C virus deviates from the coalescent with arbitrary population size. Second, we analyze a large tree of ants, demonstrating that a period of elevated diversification rates does not appear to have occurred in a bursting manner.
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Differential suture loading in an experimental rotator cuff repair.
Am J Sports Med
PUBLISHED: 04-21-2009
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Repairs of large rotator cuff tears often fail to heal. A possible factor in these failures is excessive tension in the repair sutures, causing them to pull through the tendon.
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Pronation can increase the pressure on the posterior interosseous nerve under the arcade of Frohse: a possible mechanism of palsy after two-incision repair for distal biceps rupture--clinical experience and a cadaveric investigation.
J Shoulder Elbow Surg
PUBLISHED: 04-08-2009
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Posterior interosseous nerve palsy is a recognized complication of 2-incision distal biceps tendon repair. We hypothesize that intraoperative forearm pronation can cause compression of the posterior interosseous nerve beneath the supinator and arcade of Frohse. Six human male cadaver upper extremities were dissected. Pressure on the posterior interosseous nerve beneath the arcade of Frohse and supinator was measured with a Swan-Ganz catheter connected to a pressure transducer. Pressure was significantly elevated in maximal pronation in all specimens with the elbow in both flexion and extension. Pressures at full pronation were significantly higher than pressures measured at 60 degrees of pronation (5 +/- 2 mm Hg in 60 degrees of pronation and 90 degrees of flexion, P < .0001; 7 +/- 3 mm Hg in 60 degrees of pronation and extension, P < 005). Maximal pronation can cause increased pressure on the posterior interosseous nerve. The safety of 2-incision distal biceps repair may be increased by avoiding prolonged, uninterrupted periods of hyperpronation.
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Postsurgical chondrolysis of the shoulder.
Orthopedics
PUBLISHED: 03-25-2009
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There are multiple reports in the literature of chondrolysis following arthroscopic shoulder surgery. Although the etiology of these cases is not known for certain, there has been speculation that radiofrequency devices, young patient age, instability surgery, intra-articular pain pumps, and type of anesthetic may be precipitating factors. This article describes a case of a 37-year-old law enforcement officer who injured both shoulders and ultimately underwent nearly identical bilateral procedures: arthroscopic superior labrum anteroposterior (SLAP) repair, Bankart repair, capsulorrhaphy, acromioplasty, and distal clavicle excision. Intra-articular pain catheters were placed following both procedures, but the right-sided catheter never functioned properly, as evidenced by continuous leakage outside of her body until it was removed. Subsequently she had an arthroscopic lysis of adhesions done for residual stiffness, in which the left humeral head and glenoid cavity were noted to be completely devoid of articular cartilage. Over the ensuing months, multiple cortisone injections, 5 viscosupplementation injections, physical therapy, and narcotics all failed to relieve her left shoulder pain. Radiographs showed significant left glenohumeral joint space narrowing and a normal-appearing joint space on the right. Our impression was postsurgical chondrolysis of the left shoulder. The patient has recently undergone humeral hemiarthroplasty with nonprosthetic glenoid arthroplasty. This case differs from others reported in the literature in that nearly identical bilateral procedures were performed by the same surgeon, yet chondrolysis only developed on the side that had a functioning postoperative pain catheter.
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Proximal humeral fracture as a risk factor for subsequent hip fractures.
J Bone Joint Surg Am
PUBLISHED: 03-04-2009
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With the aging of the worlds population, the social and economic implications of osteoporotic fractures are at epidemic proportions. This study was performed to test the hypothesis that a proximal humeral fracture is an independent risk factor for a subsequent hip fracture and that the risk of the subsequent hip fracture is highest within the first five years after the humeral fracture.
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Treatment of osseous defects associated with anterior shoulder instability.
J Shoulder Elbow Surg
PUBLISHED: 02-17-2009
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Bone loss of the glenoid and/or humerus is a common consequence of traumatic anterior shoulder instability and can be a cause of recurrent instability after a Bankart repair. Accurate characterization of the size and location of osseous defects associated with traumatic instability is important when planning treatment. Open or arthroscopic soft tissue repairs are usually sufficient when less than 25% of the width of the glenoid bone has been lost. Bone replacement techniques may be necessary when glenoid bone loss is greater than 25% of the glenoid width. Glenoid bone restoration techniques include the use of a tricortical iliac crest graft or the transfer of the coracoid process to the area of glenoid deficiency. Bone grafting becomes a strong consideration when soft tissue repairs have failed to restore stability. Treatment of these severe defects may be followed by osteoarthritis. The destabilizing effects of anterior glenoid bone defects are compounded by concurrent defects of the posterior-lateral humeral head, commonly known as Hill-Sachs lesions, which can engage the glenoid defect. Large humeral head defects can be treated by transhumeral bone grafting techniques or osteoarticular allograft reconstruction. Prosthetic replacement of the proximal humerus is considered for humeral head defects involving more than 40% of the articular surface. Understanding the importance of humeral and glenoid bone deficiencies may help guide the treatment of recurrent anterior glenohumeral instability.
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Charles Neer: on the giant of the shoulder.
J Shoulder Elbow Surg
PUBLISHED: 01-31-2009
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In the world of orthopedics, certain giants have become known as associated with a single subspecialty or for work on a single joint. Among these are John Charnley, for his work on total hip arthroplasty, and Amory Codman, for his work on the shoulder. But in the second half of the 20th century, the true giant of shoulder surgery was Charles Neer. His contributions to our subspecialty may not have been surpassed by any orthopedic surgeon for any subspecialty. This article explores his life and his contributions to shoulder surgery from those who knew him best.
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Fourier transform inequalities for phylogenetic trees.
IEEE/ACM Trans Comput Biol Bioinform
PUBLISHED: 01-31-2009
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Phylogenetic invariants are not the only constraints on site-pattern frequency vectors for phylogenetic trees. A mutation matrix, by its definition, is the exponential of a matrix with non-negative off-diagonal entries; this positivity requirement implies non-trivial constraints on the site-pattern frequency vectors. We call these additional constraints "edge-parameter inequalities". In this paper, we first motivate the edge-parameter inequalities by considering a pathological site-pattern frequency vector corresponding to a quartet tree with a negative internal edge. This site-pattern frequency vector nevertheless satisfies all of the constraints described up to now in the literature. We next describe two complete sets of edge-parameter inequalities for the group-based models; these constraints are square-free monomial inequalities in the Fourier transformed coordinates. These inequalities, along with the phylogenetic invariants, form a complete description of the set of site-pattern frequency vectors corresponding to bona fide trees. Said in mathematical language, this paper explicitly presents two finite lists of inequalities in Fourier coordinates of the form "monomial < or = 1", each list characterizing the phylogenetically relevant semialgebraic subsets of the phylogenetic varieties.
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Nestly--a framework for running software with nested parameter choices and aggregating results.
Bioinformatics
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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.
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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.
J Bone Joint Surg Am
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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.
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The phylogenetic Kantorovich-Rubinstein metric for environmental sequence samples.
J R Stat Soc Series B Stat Methodol
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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 movers, 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.
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The prognosis for improvement in comfort and function after the ream-and-run arthroplasty for glenohumeral arthritis: an analysis of 176 consecutive cases.
J Bone Joint Surg Am
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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.
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Phylogenomic analysis reveals dynamic evolutionary history of the Drosophila heterochromatin protein 1 (HP1) gene family.
PLoS Genet.
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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.
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Bacterial communities in women with bacterial vaginosis: high resolution phylogenetic analyses reveal relationships of microbiota to clinical criteria.
PLoS ONE
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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.
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Ubiquity of synonymity: almost all large binary trees are not uniquely identified by their spectra or their immanantal polynomials.
Algorithms Mol Biol
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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).
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Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots.
Algorithms Mol Biol
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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.
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Low-frequency nevirapine resistance at multiple sites may predict treatment failure in infants on nevirapine-based treatment.
J. Acquir. Immune Defic. Syndr.
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Resistance commonly arises in infants exposed to single-dose nevirapine (sdNVP) for prevention of mother to child transmission. Although K103N and Y181C are common following sdNVP, multiple other mutations also confer NVP resistance. It remains unclear whether specific NVP resistance mutations or combinations of mutations predict virologic failure in infants when present at low frequencies before NVP-based treatment.
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A format for phylogenetic placements.
PLoS ONE
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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.
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Intramedullary fibular and impaction allografting in revision total elbow arthroplasty with endosteal deficiency.
Tech Hand Up Extrem Surg
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One of the many reasons for failed revision elbow replacement is loss of the normally irregular shape of the endosteal surface leading to reduced ability to provide rotational control of the humeral or ulnar component within the intramedullary canal. The endosteal bone loss of the distal humerus or proximal ulna compromises the rotational stability of the stem in the intramedullary canal. In these cases, impaction cancellous allografting techniques, similar to the ones used in revision total hip arthroplasties, are commonly used to address the osseous deficiency, but these methods are not optimal for providing rotational control of the prosthetic stem. We describe a technique of restoring the irregular shape of the endosteal bone using intramedullary fibular allografting to enhance the rotational control of the prosthetic stem within the intramedullary bone canal.
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The ability of primate lentiviruses to degrade the monocyte restriction factor SAMHD1 preceded the birth of the viral accessory protein Vpx.
Cell Host Microbe
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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.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

How does it work?

We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.