Knowledge Management: A Discovery Process

Getting strategic about how you organize and redistribute knowledge can help just about anyone achieve their goals more efficiently. We at The McKnight Foundation often find ourselves at the center of meaty, data-rich, analytic conversations. This case study summarizes our yearlong exploration and planning to consume, organize, and share knowledge better

Search for Second-Generation Leptoquarks in Proton-Antiproton Collisions

This document describes the search for second-generation leptoquarks (LQ_2) in around 114 pb^-1 of proton-antiproton collisions, recorded with the D0 detector between September 2002 and June 2003 at a centre-of-mass energy of sqrt{s} = 1.96 TeV. The predictions of the Standard Model and models including scalar leptoquark production are compared to the data for various kinematic distributions. Since no excess of data over the Standard Model prediction has been observed, a lower limit on the leptoquark mass of M(LQ_2)_{beta=1} > 200 GeV/c^2 has been calculated at 95% confidence level (C.L.), assuming a branching fraction of beta = BF(LQ_2 --> mu j) = 100% into a charged lepton and a quark. The corresponding limit for beta = 1/2 is M(LQ_2)_{beta=1/2} > 152 GeV/c^2. Finally, the results were combined with those from the search in the same channel at D0 Run I. This combination yields the exclusion limit of 222 GeV/c^2 (177 GeV/c^2) for beta=1 (1/2) at 95% C.L., which is the best exclusion limit for scalar second-generation leptoquarks (for beta=1) from a single experiment to date.In diesem Dokument wird die Suche nach Leptoquarks der zweiten Generation (LQ_2) in Proton-Antiproton-Kollisionen beschrieben, die mit dem D0-Detektor am TeVatron-Beschleuniger aufgezeichnet wurden. Im Zeitraum von September 2002 bis Juni 2003 wurde eine integrierte Luminosität von rund 114 pb^-1 bei einer Schwerpunktsenergie von sqrt{s} = 1.96 TeV gesammelt. Die Vorhersagen des Standardmodells der Teilchenphysik und darüber hinausgehender Modelle mit skalaren Leptoquarks wurden mit den Daten verglichen. Da kein Überschuss an Daten über der Standardmodellvorhersage beobachtet werden konnte, wurde unter der Annahme, dass Leptoquarks zu 100% in geladene Leptonen und Quarks zerfallen (beta = BF(LQ_2 --> mu j) = 100%), eine untere Schranke von M(LQ_2)_{beta=1} > 200 GeV/c^2 (95% C.L.) für die Masse von skalaren Leptoquarks der zweiten Generation ermittelt. Die entsprechende Ausschlussgrenze für beta=1/2 liegt bei M(LQ_2)_{beta=1/2} > 152 GeV/c^2. Schließlich wurden die Resultate mit den Ergebnissen einer Suche im gleichen Kanal bei D0 Run I kombiniert. Diese Kombination liefert die Ausschlussgrenzen M(LQ_2)_{beta=1} > 222 GeV/c^2 (177 GeV/c^2) für beta=1 (1/2) und ist somit für beta=1 das zur Zeit beste Ergebnis für skalare Leptoquarks der zweiten Generation eines einzelnen Experimentes

Relative Abundance of Sixgill Sharks (Hexanchus griseus) in Elliott Bay, Seattle, Washington

The Sixgill Shark Research Project is designed to address gaps in the body of scientific knowledge on bluntnose sixgill sharks (Hexanchus griseus) in Puget Sound. This project utilizes three interwoven techniques: (1) genetics research, (2) visual marker tagging, and (3) video analysis. Seattle Aquarium biologists monitor sixgill shark sightings reported by local divers (since 1999) and study their relative abundance in Elliott Bay under the Aquarium’s pier (since 2003). Here we report on our findings of relative abundance. Bluntnose sixgills are a species of conservation concern. Sixgills are listed as “near threatened” on the IUCN Red List. Living mainly at abyssal depths but also in the shallow waters of the Salish Sea, sixgills are thought to be long-lived and slow-growing, and appear to have established movement corridors and home ranges that remain relatively fixed over time. As apex predators they are important members of marine communities; and, owing to their life history characteristics such as a slow rate of maturity and low reproductive rates, are thought to be extremely vulnerable to exploitation. Here we present our findings of relative abundance of sixgill sharks in Elliot Bay during the two time periods that the research was conducted: 2003-2005 and 2008-2015. We present the number of individual sharks seen each night, number of sharks tagged, number of returning tagged sharks, sex ratios, estimated number of sixgills residing in Elliott Bay (using capture-mark-recapture techniques), and seasonal and long-term trends in abundance

Observations on abundance of bluntnose sixgill sharks, Hexanchus griseus, in an urban waterway in the Salish Sea, 2003-2012

The bluntnose sixgill shark, Hexanchus griseus, is a widely distributed but poorly understood large, apex predator. Anecdotal reports of diver-shark encounters in the late 1990’s and early 2000’s in the Pacific Northwest stimulated interest in the normally deep-dwelling shark and the reason for its presence in the shallow waters of the Salish Sea. Analysis of underwater video documenting sharks at the Seattle Aquarium’s sixgill research site on Seattle’s waterfront and mark-recapture techniques were used to identify individual sharks to answer simple questions about abundance and seasonality. Temporal changes in relative abundance in Puget Sound were reported from a controlled study site from 2003-2012. At the Seattle Aquarium study site, 45 sixgills were observed and tagged with modified Floy visual marker tags, along with an estimated 116 observations of untagged sharks. Mark/Recapture statistical model estimates based on video observations ranged from a high of 98 sharks observed in July of 2004 to a low of 0 sharks observed in several research events from 2008-2012. Both analyses found sixgills significantly more abundant in the summer months at the Aquarium’s research station from 2003-2005 than at any other time during the study

A mariner transposon vector adapted for mutagenesis in oral streptococci

This article describes the construction and characterization of a mariner-based transposon vector designed for use in oral streptococci, but with a potential use in other Gram-positive bacteria. The new transposon vector, termed pMN100, contains the temperature-sensitive origin of replication repATs-pWV01, a selectable kanamycin resistance gene, a Himar1 transposase gene regulated by a xylose-inducible promoter, and an erythromycin resistance gene flanked by himar inverted repeats. The pMN100 plasmid was transformed into Streptococcus mutans UA159 and transposon mutagenesis was performed via a protocol established to perform high numbers of separate transpositions despite a low frequency of transposition. The distribution of transposon inserts in 30 randomly picked mutants suggested that mariner transposon mutagenesis is unbiased in S. mutans. A generated transposon mutant library containing 5000 mutants was used in a screen to identify genes involved in the production of sucrose-dependent extracellular matrix components. Mutants with transposon inserts in genes encoding glycosyltransferases and the competence-related secretory locus were predominantly found in this screen.Published versio

A procedure to characterize geographic distributions of rare disorders in cohorts

<p>Abstract</p> <p>Background</p> <p>Individual point data can be analyzed against an entire cohort instead of only sampled controls to accurately picture the geographic distribution of populations at risk for low prevalence diseases. Analyzed as individual points, many smaller clusters with high relative risks (RR) and low empirical p values are indistinguishable from a random distribution. When points are aggregated into areal units, small clusters may result in a larger cluster with a low RR or be lost if divided into pieces included in units of larger populations that show no increased prevalence. Previous simulation studies showed lowered validity of spatial scan tests for true clusters with low RR. Using simulations, this study explored the effects of low cluster RR and areal unit size on local area clustering test (LACT) results, proposing a procedure to improve accuracy of cohort spatial analysis for rare events.</p> <p>Results</p> <p>Our simulations demonstrated the relationship of true RR to observed RR and p values with various, randomly located, cluster shapes, areal unit sizes and scanning window shapes in a diverse population distribution. Clusters with RR < 1.7 had elevated observed RRs and high p values.</p> <p>We propose a cluster identification procedure that applies parallel multiple LACTs, one on point data and three on two distinct sets of areal units created with varying population parameters that minimize the range of population sizes among units. By accepting only clusters identified by all LACTs, having a minimum population size, a minimum relative risk and a maximum p value, this procedure improves the specificity achieved by any one of these tests alone on a cohort study of low prevalence data while retaining sensitivity for small clusters. The procedure is demonstrated on two study regions, each with a five-year cohort of births and cases of a rare developmental disorder.</p> <p>Conclusion</p> <p>For truly exploratory research on a rare disorder, false positive clusters can cause costly diverted research efforts. By limiting false positives, this procedure identifies 'crude' clusters that can then be analyzed for known demographic risk factors to focus exploration for geographically-based environmental exposure on areas of otherwise unexplained raised incidence.</p

A regime view of the North Atlantic Oscillation and its response to anthropogenic forcing

The distribution of the daily wintertime North Atlantic Oscillation (NAO) index in the 40-yr ECMWF Re-Analysis (ERA-40) is significantly negatively skewed. Dynamical and statistical analyses both suggest that this skewness reflects the presence of two distinct regimes—referred to as “Greenland blocking” and “subpolar jet.” Changes in both the relative occurrence and in the structure of the regimes are shown to contribute to the long-term NAO trend over the ERA-40 period. This is contrasted with the simulation of the NAO in 100-yr control and doubled CO2 integrations of the third climate configuration of the Met Office Unified Model (HadCM3). The model has clear deficiencies in its simulation of the NAO in the control run, so its predictions of future behavior must be treated with caution. However, the subpolar jet regime does become more dominant under anthropogenic forcing and, while this change is small it is clearly statistically significant and does represent a real change in the nature of NAO variability in the model