TreeViewJ: An Application for Viewing and Analyzing Phylogenetic Trees

BACKGROUND. Phylogenetic trees are widely used to visualize evolutionary relationships between different organisms or samples of the same organism. There exists a variety of both free and commercial tree visualization software available, but limitations in these programs often require researchers to use multiple programs for analysis, annotation, and the production of publication-ready images. RESULTS. We present TreeViewJ, a Java tool for visualizing, editing and analyzing phylogenetic trees. The software allows researchers to color and change the width of branches that they wish to highlight, and add names to nodes. If collection dates are available for taxa, the software can map them onto a timeline, and sort the tree in ascending or descending date order. CONCLUSION. TreeViewJ is a tool for researchers to visualize, edit, "decorate," and produce publication-ready images of phylogenetic trees. It is open-source, and released under an GPL license, and available at http://treeviewj.sourceforge.net

Benchmarking Treatment Response in Tourette’s Disorder: A Psychometric Evaluation and Signal Detection Analysis of the Parent Tic Questionnaire

This study assessed the psychometric properties of a parent-reported tic severity measure, the Parent Tic Questionnaire (PTQ), and used the scale to establish guidelines for delineating clinically significant tic treatment response. Participants were 126 children ages 9 to 17 who participated in a randomized controlled trial of Comprehensive Behavioral Intervention for Tics (CBIT). Tic severity was assessed using the Yale Global Tic Severity Scale (YGTSS), Hopkins Motor/Vocal Tic Scale (HMVTS) and PTQ; positive treatment response was defined by a score of 1 (very much improved) or 2 (much improved) on the Clinical Global Impressions – Improvement (CGI-I) scale. Cronbach’s alpha and intraclass correlations (ICC) assessed internal consistency and test-retest reliability, with correlations evaluating validity. Receiver- and Quality-Receiver Operating Characteristic analyses assessed the efficiency of percent and raw-reduction cutoffs associated with positive treatment response. The PTQ demonstrated good internal consistency (α = 0.80 to 0.86), excellent test-retest reliability (ICC = .84 to .89), good convergent validity with the YGTSS and HM/VTS, and good discriminant validity from hyperactive, obsessive-compulsive, and externalizing (i.e., aggression and rule-breaking) symptoms. A 55% reduction and 10-point decrease in PTQ Total score were optimal for defining positive treatment response. Findings help standardize tic assessment and provide clinicians with greater clarity in determining clinically meaningful tic symptom change during treatment

Investigating Habituation to Premonitory Urges in Behavior Therapy for Tic Disorders

Behavior therapy is effective for Persistent Tic Disorders (PTDs), but behavioral processes facilitating tic reduction are not well understood. One process, habituation, is thought to create tic reduction through decreases in premonitory urge severity. The current study tested whether premonitory urges decreased in youth with PTDs (N = 126) and adults with PTDs (N = 122) who participated in parallel randomized clinical trials comparing behavior therapy to psychoeducation and supportive therapy (PST). Trends in premonitory urges, tic severity, and treatment outcome were analyzed according to the predictions of a habituation model, whereby urge severity would be expected to decrease in those who responded to behavior therapy. Although adults who responded to behavior therapy showed a significant trend of declining premonitory urge severity across treatment, results failed to demonstrate that behavior therapy specifically caused changes in premonitory urge severity. In addition, reductions in premonitory urge severity in those who responded to behavior therapy were significant greater than those who did not respond to behavior therapy but no different than those who responded or did not respond to PST. Children with PTDs failed to show any significant changes in premonitory urges. Reductions in premonitory urge severity did not mediate the relationship between treatment and outcome in either adults or children. These results cast doubt on the notion that habituation is the therapeutic process underlying the effectiveness of behavior therapy, which has immediate implications for the psychoeducation and therapeutic rationale presented in clinical practice. Moreover, there may be important developmental changes in premonitory urges in PTDs, and alternative models of therapeutic change warrant investigation

Analytical and Experimental Evaluation of Aerodynamic Thrust Vectoring on an Aerospike Nozzle

Results from numerical and cold-flow experimental investigations of aerodynamic thrust vectoring on a small-scale aerospike thruster are presented. Thrust vectoring was created by the injection of a secondary fluid into the primary flow field normal to the nozzle axis. The experimental aerospike nozzle was truncated at 57% of its full theoretical length. Data derived from cold-flow thrust vectoring tests with carbon dioxide as the working fluid are presented. Injection points near the end of the truncated spike produced the highest force amplification factors. Explanations are given for this phenomenon. For secondary injection near the end of the aerospike, side force amplification factors up to approximately 1.4 and side force specific impulses up to approximately 55 s with main flow specific impulses clustering around 38 s were demonstrated. These forces crisply reproduce input pulses with a high degree of fidelity. The side force levels are approximately 2.7% of the total thrust level at maximum effectiveness. Higher side forces on the order of 4.7% of axial thrust were also achieved at reduced efficiency. The side force amplification factors were independent of operating nozzle pressure ratio for the range of chamber pressures used in this test series

Effects of Pubertal Growth Variation on Knee Mechanics During Walking in Female and Male Adolescents

Introduction: Puberty substantially alters the body\u27s mechanical properties, neuromuscular control, and sex differences therein, likely contributing to increased, sex-biased knee injury risk during adolescence. Female adolescents have higher risk for knee injuries than male adolescents of similar age engaging in similar physical activities, and much research has investigated sex differences in mechanical risk factors. However, few studies address the considerable variation in pubertal growth (timing, pace), knee mechanics, and injury susceptibility within sexes, or the impact of such growth variation on mechanical injury risk. Objectives: The present study tested for effects of variation in pubertal growth on established mechanical knee injury risk factors, examining relationships between and within sexes. Methods: Pubertal growth indices describing variation in the timing and rate of pubertal growth were developed using principal component analysis and auxological data from serial stature measurements. Linear mixed models were applied to evaluate relationships between these indices and knee mechanics during walking in a sample of adolescents. Results: Later developing female adolescents with slower pubertal growth had higher extension moments throughout stance, whereas earlier developers had higher valgus knee angles and moments. In male adolescents, faster and later growth were related to higher extension moments throughout gait. In both sexes, faster growers had higher internal rotation moments at foot-strike. Conclusions: Pubertal growth variation has important effects on mechanical knee injury risk in adolescence, affecting females and males differently. Earlier developing females exhibit greater injury risk via frontal plane factors, whereas later/faster developing males have elevated risk via sagittal plane mechanisms

Design and Implementation of Views: Isolated Perspectives of a File System

We present Views, a file system architecture that provides isolation between system components for the purposes of access control, regulatory compliance, and sandboxing. Views allows for discrete I/O entities, such as users, groups, or processes, to have a logically complete yet fully isolated perspective (view) of the file system. This ensures that each entity’s file system activities only modify that entity’s view of the file system, but in a transparent fashion that does not limit or restrict the entity’s functionality. Views can therefore be used to monitor system activity based on user accounts for access control (as required by federal regulations such as HIPAA), provide a reliable sandbox for arbitrary applications without inducing any noticeable loss in performance, and enable traditional snapshotting functionality by manipulating and transplanting views as snapshots in time. Views’ architecture is designed to be file system independent, extremely easy to use and manage, and flexible in defining isolation and sharing polices. Our implementation of Views is built on ext3cow, which additionally provides versioning capabilities to all entities. Benchmarking results show that the performance of Views is nearly identical to other traditional file systems such as ext3

Design and Implementation of Views: Isolated Perspectives of a File System for Regulatory Compliance

We present Views, a file system architecture designed to meet the role-based access control (RBAC) requirement of federal regulations, such as those in HIPAA. Views allows for discrete IO entities, such as users, groups or processes, to have a logically complete but isolated perspective of the file system. Entities may perform IO using the standard system call interface without affecting the views of other entities. Views is designed to be file system independent, extremely easy to use and manage, and flexible in defining isolation and sharing polices. Our implementation of Views is built on ext3cow, which additionally provides versioning capabilities to all entities. Preliminary results show the performance of Views is comparable with other traditional disk file systems.The Johns Hopkins Universit

Effect of Sociality and Season on Gray Wolf (Canis lupus) Foraging Behavior: Implications for Estimating Summer Kill Rate

BACKGROUND: Understanding how kill rates vary among seasons is required to understand predation by vertebrate species living in temperate climates. Unfortunately, kill rates are only rarely estimated during summer. METHODOLOGY/PRINCIPAL FINDINGS: For several wolf packs in Yellowstone National Park, we used pairs of collared wolves living in the same pack and the double-count method to estimate the probability of attendance (PA) for an individual wolf at a carcass. PA quantifies an important aspect of social foraging behavior (i.e., the cohesiveness of foraging). We used PA to estimate summer kill rates for packs containing GPS-collared wolves between 2004 and 2009. Estimated rates of daily prey acquisition (edible biomass per wolf) decreased from 8.4±0.9 kg (mean ± SE) in May to 4.1±0.4 kg in July. Failure to account for PA would have resulted in underestimating kill rate by 32%. PA was 0.72±0.05 for large ungulate prey and 0.46±0.04 for small ungulate prey. To assess seasonal differences in social foraging behavior, we also evaluated PA during winter for VHF-collared wolves between 1997 and 2009. During winter, PA was 0.95±0.01. PA was not influenced by prey size but was influenced by wolf age and pack size. CONCLUSIONS/SIGNIFICANCE: Our results demonstrate that seasonal patterns in the foraging behavior of social carnivores have important implications for understanding their social behavior and estimating kill rates. Synthesizing our findings with previous insights suggests that there is important seasonal variation in how and why social carnivores live in groups. Our findings are also important for applications of GPS collars to estimate kill rates. Specifically, because the factors affecting the PA of social carnivores likely differ between seasons, kill rates estimated through GPS collars should account for seasonal differences in social foraging behavior