STOCHASTIC OPTIMIZATION FOR TROPICAL PRINCIPAL COMPONENT ANALYSIS OVER TREE SPACES

A known challenge in the rapidly growing area of phylogenomics is the lack of tools to analyze the large volume of genome data. Genomic data includes information on the evolution, structure and mapping of genomes. Phylogenetic trees are branching diagrams that show the evolutionary history of species and their genes. Gene trees show the evolutionary history of a particular gene. To analyze evolutionary history from genomic data, we reduce the dimensionality of gene trees, overcoming high dimensional analytical challenges. Through the vectorization of pairwise distances between each combination of two leaves within a phylogenetic tree, we utilize a tropical principle component analysis: a principal component analysis (PCA) in terms of a tropical metric. We project gene trees onto a two-dimensional space using a tropical PCA, a tropical convex hull that minimizes the sum of residuals between each gene tree in the dataset and its projection onto the tropical convex hull over the tree space, which is the set of all possible gene trees. Since computing a tropical PCA for the given dataset is computationally time intensive, we implement a Markov Chain Monte Carlo Metropolis-Hastings algorithm to effectively and efficiently estimate the tropical PCA. Utilizing simulation and real-world data, we implement our tropical PCA algorithm and visualize the results in two-dimensional plots, the results of which look promising and demonstrate our algorithm's strengths.http://archive.org/details/stochasticoptimi1094562731Major, United States ArmyApproved for public release; distribution is unlimited

Adaptive Management and NEPA: How to Reconcile Predictive Assessment in the Face of Uncertainty with Natural Resource Management Flexibility and Success

For years, public lands scholars lamented the limited success that federal agencies had in applying adaptive management decisionmaking processes in pursuit of their natural resource management responsibilities. Agency duties to comply with the National Environmental Policy Act (NEPA) have played a role in creating a disconnect between the theory and application of adaptive management. NEPA was designed to force agencies to predict (and consider ways to avoid) the adverse environmental impacts of actions before committing to them. Adaptive management is built on the premise that, at least in conditions of uncertainty such as those that often characterize natural resource management, acting on the basis of one-time predictive judgments is a prescription for failure. Instead, resource managers need to continuously track the consequences of their decisions, reevaluate their management approaches based on evolving evidence, and make appropriate adjustments before starting this iterative process anew.Notwithstanding the tension between the decisionmaking approaches reflected in NEPA and adaptive management, the federal land management agencies have had to figure out how to implement their NEPA responsibilities as they have increasingly resorted to adaptive management strategies. This Article analyzes the inevitable litigation that these efforts have spurred, identifying how courts have applied various aspects of NEPA’s mandates to agency resort to adaptive management. This analysis reveals that careful attention to NEPA’s requirements makes reconciliation of the tension between NEPA and adaptive management possible. The Article gleans a series of best practices that should allow agencies to benefit from the flexibility that adaptive management affords its practitioners while satisfying NEPA’s “stop and think”mandates

Adhesion of Three Brands of Elastic Therapeutic Tape

Purpose: The purpose of this study was to compare, over a period of 5 days, the rate of adhesion of TheraBand® Kinesiology Tape (TKT) with either KT Tape® (KT) or Kinesio® Tex Gold (KTEX) under 25% elongation among healthy adults. Methods: In this study, 2 independent cohorts of 20 healthy volunteers were randomly assigned to simultaneously receive applications of 2 brands of deidentified elastic therapeutic tape (ETT) applied to their lower back at 25% elongation. Cohort 1 received TKT and KTEX tape, whereas cohort 2 received TKT and KT. Data were collected at 1 h (D1), 3 days (D3), and 5 days (D5) following the initial application of the ETT. Data collected included 3 digital photographs of the subjects’ lower back. The percentage of the tape that remained adhered (0%–100%) was assessed independently by 3 evaluators and then averaged to arrive at a percentage of tape adhesion for each brand of tape at each data collection point. Results: Repeated-measures ANOVA of cohort 1 indicated no differences (P \u3e .05) in adhesion between the TKT and KTEX at any data collection point, although post hoc analysis of the significant time effect indicated that the rate of adhesion of the KTEX brand declined from D1 (97%) to D3 (74%) to D5 (59%), whereas that of the TKT tape did not change over the duration of the study (97%, D1; 86%, D2; 70%, D3). In cohort 2, the analysis indicated a significant interaction effect with the KT brand (99%, D1; 67%, D2; 35%), declining over the course of the study and exhibiting lower rate of adhesion than the TKT (99%, D1; 83%, D2; 76%, D3) brand at D3 and D5. The rate of adhesion of the TKT tape did not significantly decline in cohort 2. Conclusions: Clinicians can use evidence from this study when choosing different ETT brands

Inappropriate prescribing in the hospitalized elderly patient: Defining the problem, evaluation tools, and possible solutions

Potentially inappropriate medication (PIM) prescribing in older adults is quite prevalent and is associated with an increased risk for adverse drug events, morbidity, and utilization of health care resources. In the acute care setting, PIM prescribing can be even more problematic due to multiple physicians and specialists who may be prescribing for a single patient as well as difficulty with medication reconciliation at transitions and limitations imposed by hospital formularies. This article highlights critical issues surrounding PIM prescribing in the acute care setting such as risk factors, screening tools, and potential strategies to minimize this significant public health problem

Black Holes Radiate Mainly on the Brane

We examine the evaporation of a small black hole on a brane in a world with large extra dimensions. Since the masses of many Kaluza-Klein modes are much smaller than the Hawking temperature of the black hole, it has been claimed that most of the energy is radiated into these modes. We show that this is incorrect. Most of the energy goes into the modes on the brane. This raises the possibility of observing Hawking radiation in future high energy colliders if there are large extra dimensions.Comment: 11 page

Models of Models: The Symbiotic Relationship between Models and Wargames

Military planning uses wargames to model the processes and decisions of an operation. As these operations become increasingly complex, the wargames similarly become more complex. Complex wargames are difficult to design and execute. As such, computer-based modeling and simulation can aid the wargame development, ensuring smooth execution. In particular, computer-based modeling and simulation can develop and validate the processes, determine initial conditions, evaluate the rules, and aid in validation. In turn, the wargame can provide useful data that can be fed into detailed models that can provide quantitative analysis to decision-makers

Community next steps for making globally unique identifiers work for biocollections data

Biodiversity data is being digitized and made available online at a rapidly increasing rate but current practices typically do not preserve linkages between these data, which impedes interoperation, provenance tracking, and assembly of larger datasets. For data associated with biocollections, the biodiversity community has long recognized that an essential part of establishing and preserving linkages is to apply globally unique identifiers at the point when data are generated in the field and to persist these identifiers downstream, but this is seldom implemented in practice. There has neither been coalescence towards one single identifier solution (as in some other domains), nor even a set of recommended best practices and standards to support multiple identifier schemes sharing consistent responses. In order to further progress towards a broader community consensus, a group of biocollections and informatics experts assembled in Stockholm in October 2014 to discuss community next steps to overcome current roadblocks. The workshop participants divided into four groups focusing on: identifier practice in current field biocollections; identifier application for legacy biocollections; identifiers as applied to biodiversity data records as they are published and made available in semantically marked-up publications; and cross-cutting identifier solutions that bridge across these domains. The main outcome was consensus on key issues, including recognition of differences between legacy and new biocollections processes, the need for identifier metadata profiles that can report information on identifier persistence missions, and the unambiguous indication of the type of object associated with the identifier. Current identifier characteristics are also summarized, and an overview of available schemes and practices is provided

Effects of Running on Femoral Articular Cartilage Thickness for Anterior Cruciate Ligament Reconstruction Patients and Non-ACLR Control Subjects

Anterior cruciate ligament reconstruction (ACLR) patients are more likely to develop posttraumatic knee osteoarthritis than non-ACLR counterparts. The effect of running on femoral articular cartilage thickness is unclear. PURPOSE: The purpose of this study was to compare how 30 minutes of running influences femoral articular cartilage thickness for ACLR patients and non-ACLR control subjects. We hypothesized that running would deform the femoral articular cartilage more for the ACLR patients than for the control subjects. METHODS: We recruited 20 individuals with primary unilateral ACLR and 20 matched non-ACLR controls. ACLR patients and control subjects were matched based upon age, gender, BMI, and weekly running mileage. The present procedures were approved by the appropriate institutional board and all subjects provided informed consent before data collection. We used ultrasound imaging to measure femoral articular cartilage thickness before and after 30 minutes of running. The ultrasound images were manually analyzed using ImageJ software by the same investigator. Total femoral articular cartilage cross-sectional area of each image was segmented into three regions: medial, lateral, and intercondylar. Deformation due to the run was compared between the ACLR patients and control subjects for each region using independent t tests (P \u3c 0.05, adjusted for multiple comparisons). RESULTS: The 30-minute run resulted in more deformation for the ACLR patients (0.03 ± 0.01 cm) than the matched controls (0.01 ± 0.01 cm) for the medial region (p \u3c 0.01) of the femoral articular cartilage. Identically, the 30-minute run resulted in more deformation for the ACLR patients (0.03 ± 0.01 cm) than the matched controls (0.01 ± 0.01 cm; p \u3c 0.01) for an average of the entire articular cartilage area (medial, lateral, and intercondylar). No significant differences existed between groups for the lateral or intercondylar regions. CONCLUSION: Thirty minutes of running deformed medial and overall femoral articular cartilage more for ACLR patients than non-ACLR control subjects

Gravitomagnetism and Relative Observer Clock Effects

The gravitomagnetic clock effect and the Sagnac effect for circularly rotating orbits in stationary axisymmetric spacetimes are studied from a relative observer point of view, clarifying their relationships and the roles played by special observer families. In particular Semer\'ak's recent characterization of extremely accelerated observers in terms of the two-clock clock effect is shown to be complemented by a similarly special property of the single-clock clock effect.Comment: 19 pages, LaTeX, IOP macros with package epsf and 1 eps figure, to appear in Classical and Quantum Gravity, slight revisio