Evaluating the performance of survey-based operational management procedures

The design and evaluation of survey-based management strategies is addressed in this article, using three case-study fisheries: North Sea herring, Bay of Biscay anchovy and North Sea cod, with a brief history and the main management issues with each fishery outlined. A range of operational management procedures for the case study stocks were designed and evaluated using trends that may be derived from survey indices (spawner biomass, year-class strength and total mortality) with an array of simple and more structured observation error regimes simulated. Model-free and model-based indicators of stock status were employed in the management procedures. On the basis of stochastic stock-specific simulations, we identified the following key determinants of successful management procedures: (i) adequate specification of the stock-recruit relationship (model structure, parameter estimates and variability), (ii) knowledge of the magnitude and structure of the variation in the survey indices, and (iii) explication of the particular management objectives, when assessing management performance. More conservative harvesting strategies are required to meet specified targets in the presence of increasing stochasticity, due to both process and observation error. It was seen that survey-based operational management procedures can perform well in the absence of commercial data, and can also inform aspects of survey design with respect to acceptable levels of error or bias in the surveys

High-Performance approaches for Phylogenetic Placement, and its application to species and diversity quantification

In den letzten Jahren haben Fortschritte in der Hochdurchsatz-Genesequenzierung, in Verbindung mit dem anhaltenden exponentiellen Wachstum und der Verfügbarkeit von Rechenressourcen, zu fundamental neuen analytischen Ansätzen in der Biologie geführt. Es ist nun möglich den genetischen Inhalt ganzer Organismengemeinschaften anhand einzelner Umweltproben umfassend zu sequenzieren. Solche Methoden sind besonders für die Mikrobiologie relevant. Die Mikrobiologie war zuvor weitgehend auf die Untersuchung jener Mikroben beschränkt, welche im Labor (d.h., in vitro) kultiviert werden konnten, was jedoch lediglich einen kleinen Teil der in der Natur vorkommenden Diversität abdeckt. Im Gegensatz dazu ermöglicht die Hochdurchsatzsequenzierung nun die direkte Erfassung der genetischen Sequenzen eines Mikrobioms, wie es in seiner natürlichen Umgebung vorkommt (d.h., in situ). Ein typisches Ziel von Mikrobiomstudien besteht in der taxonomischen Klassifizierung der in einer Probe enthaltenen Sequenzen (Querysequenzen). Üblicherweise werden phylogenetische Methoden eingesetzt, um detaillierte taxonomische Beziehungen zwischen Querysequenzen und vertrauenswürdigen Referenzsequenzen, die von bereits klassifizierten Organismen stammen, zu bestimmen. Aufgrund des hohen Volumens ($10 ^ 6$ bis $10 ^ 9$) von Querysequenzen, die aus einer Mikrobiom-Probe mittels Hochdurchsatzsequenzierung generiert werden können, ist eine akkurate phylogenetische Baumrekonstruktion rechnerisch nicht mehr möglich. Darüber hinaus erzeugen derzeit üblicherweise verwendete Sequenzierungstechnologien vergleichsweise kurze Sequenzen, die ein begrenztes phylogenetisches Signal aufweisen, was zu einer Instabilität bei der Inferenz der Phylogenien aus diesen Sequenzen führt. Ein weiteres typisches Ziel von Mikrobiomstudien besteht in der Quantifizierung der Diversität innerhalb einer Probe, bzw. zwischen mehreren Proben. Auch hierfür werden üblicherweise phylogenetische Methoden verwendet. Oftmals setzen diese Methoden die Inferenz eines phylogenetischen Baumes voraus, welcher entweder alle Sequenzen, oder eine geclusterte Teilmenge dieser Sequenzen, umfasst. Wie bei der taxonomischen Identifizierung können Analysen, die auf dieser Art von Bauminferenz basieren, zu ungenauen Ergebnissen führen und/oder rechnerisch nicht durchführbar sein. Im Gegensatz zu einer umfassenden phylogenetischen Inferenz ist die phylogenetische Platzierung eine Methode, die den phylogenetischen Kontext einer Querysequenz innerhalb eines etablierten Referenzbaumes bestimmt. Dieses Verfahren betrachtet den Referenzbaum typischerweise als unveränderlich, d.h. der Referenzbaum wird vor, während oder nach der Platzierung einer Sequenz nicht geändert. Dies erlaubt die phylogenetische Platzierung einer Sequenz in linearer Zeit in Bezug auf die Größe des Referenzbaums durchzuführen. In Kombination mit taxonomischen Informationen über die Referenzsequenzen ermöglicht die phylogenetische Platzierung somit die taxonomische Identifizierung einer Sequenz. Darüber hinaus erlaubt eine phylogenetische Platzierung die Anwendung einer Vielzahl zusätzlicher Analyseverfahren, die beispielsweise die Zuordnung der Zusammensetzungen humaner Mikrobiome zu klinisch-diagnostischen Eigenschaften ermöglicht. In dieser Dissertation präsentiere ich meine Arbeit bezüglich des Entwurfs, der Implementierung, und Verbesserung von EPA-ng, einer Hochleistungsimplementierung der phylogenetischen Platzierung anhand des Maximum-Likelihood Modells. EPA-ng wurde entwickelt um auf Milliarden von Querysequenzen zu skalieren und auf Tausenden von Kernen in Systemen mit gemeinsamem und verteiltem Speicher ausgeführt zu werden. EPA-ng beschleunigt auch die Verarbeitungsgeschwindigkeit auf einzelnen Kernen um das bis zu $30$-fache, im Vergleich zu dessen direkten Konkurrenzprogrammen. Vor kurzem haben wir eine zusätzliche Methode für EPA-ng eingeführt, welche die Platzierung in wesentlich größeren Referenzbäumen ermöglicht. Hierfür verwenden wir einen aktiven Speicherverwaltungsansatz, bei dem reduzierter Speicherverbrauch gegen größere Ausführungszeiten eingetauscht wird. Zusätzlich präsentiere ich einen massiv-parallelen Ansatz um die Diversität einer Probe zu quantifizieren, welcher auf den Ergebnissen phylogenetischer Platzierungen basiert. Diese Software, genannt \toolname{SCRAPP}, kombiniert aktuelle Methoden für die Maximum-Likelihood basierte phylogenetische Inferenz mit Methoden zur Abgrenzung molekularer Spezien. Daraus resultiert eine Verteilung der Artenanzahl auf den Kanten eines Referenzbaums für eine gegebene Probe. Darüber hinaus beschreibe ich einen neuartigen Ansatz zum Clustering von Platzierungsergebnissen, anhand dessen der Benutzer den Rechenaufwand reduzieren kann

MobilityMirror: Bias-Adjusted Transportation Datasets

We describe customized synthetic datasets for publishing mobility data. Private companies are providing new transportation modalities, and their data is of high value for integrative transportation research, policy enforcement, and public accountability. However, these companies are disincentivized from sharing data not only to protect the privacy of individuals (drivers and/or passengers), but also to protect their own competitive advantage. Moreover, demographic biases arising from how the services are delivered may be amplified if released data is used in other contexts. We describe a model and algorithm for releasing origin-destination histograms that removes selected biases in the data using causality-based methods. We compute the origin-destination histogram of the original dataset then adjust the counts to remove undesirable causal relationships that can lead to discrimination or violate contractual obligations with data owners. We evaluate the utility of the algorithm on real data from a dockless bike share program in Seattle and taxi data in New York, and show that these adjusted transportation datasets can retain utility while removing bias in the underlying data.Comment: Presented at BIDU 2018 workshop and published in Springer Communications in Computer and Information Science vol 92

Femoral anteversion and tibial torsion only explain 25% of variance in regression analysis of foot progression angle in children with diplegic cerebral palsy

Background : The relationship between torsional bony deformities and rotational gait parameters has not been sufficiently investigated. This study was to investigate the degree of contribution of torsional bony deformities to rotational gait parameters in patients with diplegic cerebral palsy (CP). Methods : Thirty three legs from 33 consecutive ambulatory patients (average age 9.5 years, SD 6.9 years; 20 males and 13 females) with diplegic CP who underwent preoperative three dimensional gait analysis, foot radiographs, and computed tomography (CT) were included. Adjusted foot progression angle (FPA) was retrieved from gait analysis by correcting pelvic rotation from conventional FPA, which represented the rotational gait deviation of the lower extremity from the tip of the femoral head to the foot. Correlations between rotational gait parameters (FPA, adjusted FPA, average pelvic rotation, average hip rotation, and average knee rotation) and radiologic measurements (acetabular version, femoral anteversion, knee torsion, tibial torsion, and anteroposteriortalo-first metatarsal angle) were analyzed. Multiple regression analysis was performed to identify significant contributing radiographic measurements to adjusted FPA. Results : Adjusted FPA was significantly correlated with FPA (r=0.837, p<0.001), contralateral FPA (r=0.492, p=0.004), pelvic rotation during gait (r=−0.489, p=0.004), knee rotation during gait (r=0.376, p=0.031), and femoral anteversion (r=0.350, p=0.046). In multiple regression analysis, femoral anteversion (p=0.026) and tibial torsion (p=0.034) were found to be the significant contributing structural deformities to the adjusted FPA (R2=0.247). Conclusions : Femoral anteversion and tibial torsion were found to be the significant structural deformities that could affect adjusted FPA in patients with diplegic CP. Femoral anteversion and tibial torsion could explain only 24.7% of adjusted FPA.This study was supported by research funding (grant no. 02-2011-045) from Seoul National University Bundang Hospital, Republic of Korea.Peer Reviewe

Aerothermodynamic Analysis of a Mars Sample Return Earth-Entry Vehicle

Because of the severe quarantine constraints that must be imposed on any returned extraterrestrial samples, the Mars sample return Earth-entry vehicle must remain intact through sample recovery. Vehicles returning on a Mars-Earth trajectory will attain velocities exceeding any that have been experienced by prior space exploration missions, with velocities approaching 14 km/s. Velocities as high as these will encounter significant heating during atmospheric re-entry to Earth. The purpose of this study has been to systematically investigate the aerothermodynamic challenges that will result from a Mars sample return, Earth-entry vehicle design. The goal was to enable efficient estimation of maximum stagnation point convective and radiative heating that will be encountered during Earth-entry over a wide range of spherically blunted cone angles, entry velocities, flight path angles, and ballistic coefficients. Assembling a robust and validated aerothermodynamic database for a potential Mars sample return Earth-entry vehicle has been accomplished by estimating peak heating over a wide range of possible designs. This goal was achieved by utilizing fundamental knowledge, along with the use of engineering analysis tools, such as POST2 (Program to Optimize Simulated Trajectories II) and LAURA (Langley Aerothermodynamic Upwind Relaxation Algorithm) computational fluid dynamics analysis. The aerothermodynamic analysis conducted in this thesis provides a catalog of heating trends to be used for optimal selection of mission design constraints such as vehicle geometry, thermal protection system, and entry trajectory, with the primary goal of returning a Mars soil and atmospheric sample for thorough analysis on Earth; this acts as a step towards safely landing humans on the Martian surface

NASA Tech Briefs, May 2012

Topics covered include: An "Inefficient Fin" Non-Dimensional Parameter to Measure Gas Temperatures Efficiently; On-Wafer Measurement of a Multi-Stage MMIC Amplifier with 10 dB of Gain at 475 GHz; Software to Control and Monitor Gas Streams; Miniaturized Laser Heterodyne Radiometer (LHR) for Measurements of Greenhouse Gases in the Atmospheric Column; Anomaly Detection in Test Equipment via Sliding Mode Observers; Absolute Position of Targets Measured Through a Chamber Window Using Lidar Metrology Systems; Goldstone Solar System Radar Waveform Generator; Fast and Adaptive Lossless Onboard Hyperspectral Data Compression System; Iridium Interfacial Stack - IrIS; Downsampling Photodetector Array with Windowing; Optical Phase Recovery and Locking in a PPM Laser Communication Link; High-Speed Edge-Detecting Line Scan Smart Camera; Optical Communications Channel Combiner; Development of Thermal Infrared Sensor to Supplement Operational Land Imager; Amplitude-Stabilized Oscillator for a Capacitance-Probe Electrometer; Automated Performance Characterization of DSN System Frequency Stability Using Spacecraft Tracking Data; Histogrammatic Method for Determining Relative Abundance of Input Gas Pulse; Predictive Sea State Estimation for Automated Ride Control and Handling - PSSEARCH; LEGION: Lightweight Expandable Group of Independently Operating Nodes; Real-Time Projection to Verify Plan Success During Execution; Automated Performance Characterization of DSN System Frequency Stability Using Spacecraft Tracking Data; Web-Based Customizable Viewer for Mars Network Overflight Opportunities; Fabrication of a Cryogenic Terahertz Emitter for Bolometer Focal Plane Calibrations; Fabrication of an Absorber-Coupled MKID Detector; Graphene Transparent Conductive Electrodes for Next- Generation Microshutter Arrays; Method of Bonding Optical Elements with Near-Zero Displacement; Free-Mass and Interface Configurations of Hammering Mechanisms; Wavefront Compensation Segmented Mirror Sensing and Control; Long-Life, Lightweight, Multi-Roller Traction Drives for Planetary Vehicle Surface Exploration; Reliable Optical Pump Architecture for Highly Coherent Lasers Used in Space Metrology Applications; Electrochemical Ultracapacitors Using Graphitic Nanostacks; Improved Whole-Blood-Staining Device; Monitoring Location and Angular Orientation of a Pill; Molecular Technique to Reduce PCR Bias for Deeper Understanding of Microbial Diversity; Laser Ablation Electrodynamic Ion Funnel for In Situ Mass Spectrometry on Mars; High-Altitude MMIC Sounding Radiometer for the Global Hawk Unmanned Aerial Vehicle; PRTs and Their Bonding for Long-Duration, Extreme-Temperature Environments; Mid- and Long-IR Broadband Quantum Well Photodetector; 3D Display Using Conjugated Multiband Bandpass Filters; Real-Time, Non-Intrusive Detection of Liquid Nitrogen in Liquid Oxygen at High Pressure and High Flow; Method to Enhance the Operation of an Optical Inspection Instrument Using Spatial Light Modulators; Dual-Compartment Inflatable Suitlock; Large-Strain Transparent Magnetoactive Polymer Nanocomposites; Thermodynamic Vent System for an On-Orbit Cryogenic Reaction Control Engine; Time Distribution Using SpaceWire in the SCaN Testbed on ISS; and Techniques for Solution- Assisted Optical Contacting