Improvements to a Class of Distance Matrix Methods for Inferring Species Trees from Gene Trees

Abstract Among the methods currently available for inferring species trees from gene trees, the GLASS method of Mossel and Roch (2010), the Shallowest Divergence (SD) method of Maddison and Knowles (2006), the STEAC method of Liu et al. (2009), and a related method that we call Minimum Average Coalescence (MAC) are computationally efficient and provide branch length estimates. Further, GLASS and STEAC have been shown to be consistent estimators of tree topology under a multispecies coalescent model. However, divergence time estimates obtained with these methods are all systematically biased under the model because the pairwise interspecific gene divergence times on which they rely must be more ancient than the species divergence time. Jewett and Rosenberg (2012) derived an expression for the bias of GLASS and used it to propose an improved method that they termed iGLASS. Here, we derive the biases of SD, STEAC, and MAC, and we propose improved analogues of these methods that we call iSD, iSTEAC, and iMAC. We conduct simulations to compare the performance of these methods with their original counterparts and with GLASS and iGLASS, finding that each of them decreases the bias and mean squared error of pairwise divergence time estimates. The new methods can therefore contribute to improvements in the estimation of species trees from information on gene trees.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/98441/1/cmb%2E2012%2E0042.pd

The Comparability of Men Who Have Sex With Men Recruited From Venue-Time-Space Sampling and Facebook: A Cohort Study

Background: Recruiting valid samples of men who have sex with men (MSM) is a key component of the US human immunodeficiency virus (HIV) surveillance and of research studies seeking to improve HIV prevention for MSM. Social media, such as Facebook, may present an opportunity to reach broad samples of MSM, but the extent to which those samples are comparable with men recruited from venue-based, time-space sampling (VBTS) is unknown. Objective: The objective of this study was to assess the comparability of MSM recruited via VBTS and Facebook. Methods: HIV-negative and HIV-positive black and white MSM were recruited from June 2010 to December 2012 using VBTS and Facebook in Atlanta, GA. We compared the self-reported venue attendance, demographic characteristics, sexual and risk behaviors, history of HIV-testing, and HIV and sexually transmitted infection (STI) prevalence between Facebook- and VTBS-recruited MSM overall and by race. Multivariate logistic and negative binomial models estimated age/race adjusted ratios. The Kaplan-Meier method was used to assess 24-month retention. Results: We recruited 803 MSM, of whom 110 (34/110, 30.9% black MSM, 76/110, 69.1% white MSM) were recruited via Facebook and 693 (420/693, 60.6% black MSM, 273/693, 39.4% white MSM) were recruited through VTBS. Facebook recruits had high rates of venue attendance in the previous month (26/34, 77% among black and 71/76, 93% among white MSM; between-race P=.01). MSM recruited on Facebook were generally older, with significant age differences among black MSM (P=.02), but not white MSM (P=.14). … See full text for complete abstract

Patients' perspectives on quality of care for chronic hand eczema:a qualitative study

BACKGROUND: Hand eczema (HE) has a significant impact on quality of life and work related activities. Little is known about the patients' perspectives on quality of care for HE. OBJECTIVES: To evaluate the patient perspective of the HE care process in a tertiary referral center. METHODS: Qualitative, semi-structured focus groups were carried out and recorded, transcribed and analysed by an inductive-deductive thematic approach. RESULTS: Fifteen patients participated in four focus groups. Time and attention, together with being listened to and understood by the health care professional, were the most important aspects of care for HE mentioned by participants. Other important insights included: Diagnoses, causes and follow-up of HE were not always clear to the participant; more psychosocial support was needed; participants experienced frequent changes in doctors. Information provided by nurses was valuable, but more individualized advice was needed. CONCLUSIONS: In order to better meet the needs of patients, more explanation should be given about the causes of HE and final diagnosis. Besides focusing on the treatment, it is also important to focus on its impact on the patient and options for psychosocial and peer support should be discussed. Furthermore, the specialized nurse as part of integrated care was emphasized. This article is protected by copyright. All rights reserved

Missing the forest (plot) for the trees? A critique of the systematic review in tobacco control

<p>Abstract</p> <p>Background</p> <p>The systematic review (SR) lies at the core of evidence-based medicine. While it may appear that the SR provides a reliable summary of existing evidence, standards of SR conduct differ. The objective of this research was to examine systematic review (SR) methods used by the Cochrane Collaboration ("<it>Cochrane</it>") and the Task Force on Community Preventive Services ("the <it>Guide</it>") for evaluation of effectiveness of tobacco control interventions.</p> <p>Methods</p> <p>We searched for all reviews of tobacco control interventions published by Cochrane (4^thquarter 2008) and the <it>Guide</it>. We recorded design rigor of included studies, data synthesis method, and setting.</p> <p>Results</p> <p>About a third of the Cochrane reviews and two thirds of the Guide reviews of interventions in the community setting included uncontrolled trials. Most (74%) Cochrane reviews in the clinical setting, but few (15%) in the community setting, provided pooled estimates from RCTs. Cochrane often presented the community results narratively. The Guide did not use inferential statistical approaches to assessment of effectiveness.</p> <p>Conclusions</p> <p>Policy makers should be aware that SR methods differ, even among leading producers of SRs and among settings studied. The traditional SR approach of using pooled estimates from RCTs is employed frequently for clinical but infrequently for community-based interventions. The common lack of effect size estimates and formal tests of significance limit the contribution of some reviews to evidence-based decision making. Careful exploration of data by subgroup, and appropriate use of random effects models, may assist researchers in overcoming obstacles to pooling data.</p

Initiation of a critical pathway for pancreaticoduodenectomy at an academic institution -- the first step in multi-disciplinary team building

Objective: This study was designed to identify quantifiable parameters to track performance improvements brought about by the implementation of a critical pathway for complex alimentary tract surgery. Background: Pancreaticoduodenectomy (PD) is a complex general surgical procedure performed in varying numbers at many academic institutions. Originally associated with significant perioperative morbidity and mortality, multiple studies have now shown that this operation can be performed quite safely at high volume institutions that develop a particular expertise. Critical pathways are one of the key tools used to achieve consistently excellent outcomes as these institutions. It remains to be determined if implementation of a critical pathway at an academic institution with prior moderate experience with PD will result in performance gains and improved outcomes. Methods: Between January 1, 2004 and October 15, 2006 135 patients underwent PD, 44 before the implementation of a critical pathway on October 15, 2005, and 91 after. Perioperative and postoperative parameters were analyzed retrospectively to identify those that could be used to track performance improvement and outcomes. Key aspects of the pathway include spending the night of surgery in the intensive care unit with careful attention to fluid balance, early mobilization on post-operative day one, aggressive early removal of encumbrances such as nasogastric tubes and urinary catheters, early post-operative feeding, and targeting discharge for postoperative day 6 or 7. Results: The pre- and post-pathway implementation groups were not statistically different with regards to age, sex, race, or pathology (malignant versus benign). Perioperative mortality, operative blood loss, and number of transfused units of packed red blood cells were also similar. As compared to the pre-pathway group, the post-pathway group had a significantly shorter postoperative length of stay (13 versus 7 days, P ≤ 0.0001), operative time (435 ± 14 minutes versus 379 ± 12 minutes, P ≤ 0.0001), and in room non-operative time (95 ± 4 minutes versus 76 ± 2 minutes, P ≤ 0.0001). Total hospital charges were significantly reduced from $240,242 ±$32,490 versus $126,566 ±$4883 (P ≤ 0.0001) after pathway implementation. Postoperative complication rates remained constant (44% pre-pathway versus 37% after, P = NS). Readmission rates were not negatively affected by the reduction in length of stay, with a 7% readmission rate prior to implementation and a 7.7% rate after implementation. Conclusion: Implementation of a critical pathway for a complex procedure can be demonstrated to improve short-term outcomes at an academic institution. This improvement can be quantified and tracked and has implications for better utilization of resources (greater OR and hospital bed availability) and overall cost containment. With a very conservative estimate of 75 pancreaticoduodenectomies per year by this group, this translates to a savings of 450 hospital days and over $8,550,000 in hospital charges on an annual basis. As we enter the pay for performance era, institutions will be required to generate such data in order to retain patient volumes, attract new patients, and receive incentive payments for high quality services rendered

The Use of Virtual Reality Facilitates Dialectical Behavior Therapy® “Observing Sounds and Visuals” Mindfulness Skills Training Exercises for a Latino Patient with Severe Burns: A Case Study

Sustaining a burn injury increases an individual's risk of developing psychological problems such as generalized anxiety, negative emotions, depression, acute stress disorder, or post-traumatic stress disorder. Despite the growing use of Dialectical Behavioral Therapy® (DBT®) by clinical psychologists, to date, there are no published studies using standard DBT® or DBT® skills learning for severe burn patients. The current study explored the feasibility and clinical potential of using Immersive Virtual Reality (VR) enhanced DBT® mindfulness skills training to reduce negative emotions and increase positive emotions of a patient with severe burn injuries. The participant was a hospitalized (in house) 21-year-old Spanish speaking Latino male patient being treated for a large (&gt;35% TBSA) severe flame burn injury.Methods: The patient looked into a pair of Oculus Rift DK2 virtual reality goggles to perceive the computer-generated virtual reality illusion of floating down a river, with rocks, boulders, trees, mountains, and clouds, while listening to DBT® mindfulness training audios during 4 VR sessions over a 1 month period. Study measures were administered before and after each VR session.Results: As predicted, the patient reported increased positive emotions and decreased negative emotions. The patient also accepted the VR mindfulness treatment technique. He reported the sessions helped him become more comfortable with his emotions and he wanted to keep using mindfulness after returning home.Conclusions: Dialectical Behavioral Therapy is an empirically validated treatment approach that has proved effective with non-burn patient populations for treating many of the psychological problems experienced by severe burn patients. The current case study explored for the first time, the use of immersive virtual reality enhanced DBT® mindfulness skills training with a burn patient. The patient reported reductions in negative emotions and increases in positive emotions, after VR DBT® mindfulness skills training. Immersive Virtual Reality is becoming widely available to mainstream consumers, and thus has the potential to make this treatment available to a much wider number of patient populations, including severe burn patients. Additional development, and controlled studies are needed

Self-related consequences of death fear and death denial

This study explores self-related outcomes (e.g., esteem, self-concept clarity, existential well-being) as a function of the interaction between self-reported levels of death fear and death denial. Consistent with the idea that positive existential growth can come from individuals facing, rather than denying, their mortality (Cozzolino, 2006), the authors observed that not fearing and denying death can bolster important positive components of the self. That is, individuals low in death denial and death fear evidenced an enhanced self that is valued, clearly conceived, efficacious, and that has meaning and purpose

Multiple locus VNTR analysis highlights that geographical clustering and distribution of Dichelobacter nodosus, the causal agent of footrot in sheep, correlates with inter-country movements

Dichelobacter nodosus is a Gram-negative, anaerobic bacterium and the causal agent of footrot in sheep. Multiple locus variable number tandem repeat (VNTR) analysis (MLVA) is a portable technique that involves the identification and enumeration of polymorphic tandem repeats across the genome. The aims of this study were to develop an MLVA scheme for D. nodosus suitable for use as a molecular typing tool, and to apply it to a global collection of isolates. Seventy-seven isolates selected from regions with a long history of footrot (GB, Australia) and regions where footrot has recently been reported (India, Scandinavia), were characterised. From an initial 61 potential VNTR regions, four loci were identified as usable and in combination had the attributes required of a typing method for use in bacterial epidemiology: high discriminatory power (D > 0.95), typeability and reproducibility. Results from the analysis indicate that D. nodosus appears to have evolved via recombinational exchanges and clonal diversification. This has resulted in some clonal complexes that contain isolates from multiple countries and continents; and others that contain isolates from a single geographic location (country or region). The distribution of alleles between countries matches historical accounts of sheep movements, suggesting that the MLVA technique is sufficiently specific and sensitive for an epidemiological investigation of the global distribution of D. nodosus

The Application of Digital Pathology to Improve Accuracy in Glomerular Enumeration in Renal Biopsies.

BACKGROUND: In renal biopsy reporting, quantitative measurements, such as glomerular number and percentage of globally sclerotic glomeruli, is central to diagnostic accuracy and prognosis. The aim of this study is to determine the number of glomeruli and percent globally sclerotic in renal biopsies by means of registration of serial tissue sections and manual enumeration, compared to the numbers in pathology reports from routine light microscopic assessment. DESIGN: We reviewed 277 biopsies from the Nephrotic Syndrome Study Network (NEPTUNE) digital pathology repository, enumerating 9,379 glomeruli by means of whole slide imaging. Glomerular number and the percentage of globally sclerotic glomeruli are values routinely recorded in the official renal biopsy pathology report from the 25 participating centers. Two general trends in reporting were noted: total number per biopsy or average number per level/section. Both of these approaches were assessed for their accuracy in comparison to the analogous numbers of annotated glomeruli on WSI. RESULTS: The number of glomeruli annotated was consistently higher than those reported (p CONCLUSIONS: Although glass slides were not available for direct comparison to whole slide image annotation, this study indicates that routine manual light microscopy assessment of number of glomeruli is inaccurate, and the magnitude of this error is proportional to the total number of glomeruli