David Moody Hopkins (1921-2001)

David M. Hopkins, a Quaternary geologist widely known for his broad-ranging studies of the Bering Land Bridge region ("Beringia"), passed away at his home in Menlo Park, California, on November 2, 2001. Dave was a longtime member of Alaskan units of the U.S. Geological Survey (USGS). In search of a deeper understanding of Beringia, he became a pioneer in interdisciplinary research and in collaborative research with Russian investigators. Following his retirement from the USGS in 1985, Dave became director of the Alaskan Quaternary Center and Professor of Quaternary Studies at the Fairbanks campus of the University of Alaska. During the 57 years of his professional career, he was a mentor, friend, and source of inspiration to several generations of Arctic scholars. ... After graduating from the University of New Hampshire with a bachelor's degree in Geology in 1942, he joined the USGS and began graduate studies at Harvard University. Dave spent his initial field seasons with the USGS in southern regions of Alaska, where he investigated strategic minerals, engineering geology, and other aspects of geology that were considered essential to the ongoing war effort. In 1944, he was inducted into the Army and assigned to carry out meteorological observations at Cold Bay, situated at the tip of the Alaska Peninsula. Following his discharge, Dave resumed graduate studies at Harvard and field work with the USGS. He obtained an M.S. degree in Geology (1948) and a Ph.D. in Quaternary Geology (1955) from Harvard University. In 1947, Dave began geological investigations on the Seward Peninsula under the permafrost program of the USGS Alaska Terrain and Permafrost Section (which later became the Branch of Alaskan Geology). ... In 1948, he initiated a productive collaboration with the botanist Robert Sigafoos. Their seminal publications on the interactions of permafrost, soil, and vegetation on the Seward Peninsula are considered classics today. Dave also began a long-term collaboration with the archeologist Louis Giddings on dating and reconstructing the paleoecology of prehistoric village sites and other early human habitations in northwestern Alaska. ... Dave's investigations of elevated and submerged gold-bearing beaches at Nome during the 1950s initiated his long-lasting interest in the sea-level history of Beringia and the paleoecology of parts of the Bering platform that are submerged today. ... Dave's broadening interests in the paleoecology of Beringia led to increasing contacts with Russian colleagues that developed into a fruitful, 40-year collaboration across the Bering Strait. ... After Dave's retirement from the USGS, he began a second career of teaching and research as Distinguished Professor of Quaternary Studies at the University of Alaska at Fairbanks (UAF). ... As a direct result of Dave's broad-ranging research on the northern Seward Peninsula, the U.S. National Park Service (NPS) set aside much of his former field area as the Bering Land Bridge National Preserve. ... Dave's scientific influence encompasses such diverse fields as bedrock geology, marine geology, paleontology, limnology, hydrology, ecology, archeology, and paleoclimatology - the topics of his more than 200 refereed papers and abstracts. Numerous awards and commendations from the USGS and other scientific organizations recognized his contributions. ... During his highly productive career, Dave always found time to advise and encourage younger colleagues and students. ... We shall all miss his warmth, his humor, and his infectious passion for Beringia, but his legacy of inspired research and interdisciplinary scholarship will be enduring. ..

Extreme endurance flights by landbirds crossing the Pacific Ocean: ecological corridor rather than barrier?

Mountain ranges, deserts, ice fields and oceans generally act as barriers to the movement of land-dependent animals, often profoundly shaping migration routes. We used satellite telemetry to track the southward flights of bar-tailed godwits (Limosa lapponica baueri), shorebirds whose breeding and non-breeding areas are separated by the vast central Pacific Ocean. Seven females with surgically implanted transmitters flew non-stop 8117–11 680 km (10 153±1043 s.d.) directly across the Pacific Ocean; two males with external transmitters flew non-stop along the same corridor for 7008–7390 km. Flight duration ranged from 6.0 to 9.4 days (7.8±1.3 s.d.) for birds with implants and 5.0 to 6.6 days for birds with externally attached transmitters. These extraordinary non-stop flights establish new extremes for avian flight performance, have profound implications for understanding the physiological capabilities of vertebrates and how birds navigate, and challenge current physiological paradigms on topics such as sleep, dehydration and phenotypic flexibility. Predicted changes in climatic systems may affect survival rates if weather conditions at their departure hub or along the migration corridor should change. We propose that this transoceanic route may function as an ecological corridor rather than a barrier, providing a wind-assisted passage relatively free of pathogens and predators

Rotation measure variations for 20 millisecond pulsars

We report on variations in the mean position angle of the 20 millisecond pulsars being observed as part of the Parkes Pulsar Timing Array (PPTA) project. It is found that the observed variations are dominated by changes in the Faraday rotation occurring in the Earth's ionosphere. Two ionospheric models are used to correct for the ionospheric contribution and it is found that one based on the International Reference Ionosphere gave the best results. Little or no significant long-term variation in interstellar RM was found with limits typically about 0.1 rad m$^{-2}$ yr$^{-1}$ in absolute value. In a few cases, apparently significant RM variations over timescales of a few 100 days or more were seen. These are unlikely to be due to localised magnetised regions crossing the line of sight since the implied magnetic fields are too high. Most probably they are statistical fluctuations due to random spatial and temporal variations in the interstellar electron density and magnetic field along the line of sight.Comment: Accepted for publication in Astrophysics & Space Scienc

Planck-scale quintessence and the physics of structure formation

In a recent paper we considered the possibility of a scalar field providing an explanation for the cosmic acceleration. Our model had the interesting properties of attractor-like behavior and having its parameters of O(1) in Planck units. Here we discuss the effect of the field on large scale structure and CMB anisotropies. We show how some versions of our model inspired by "brane" physics have novel features due to the fact that the scalar field has a significant role over a wider range of redshifts than for typical "dark energy" models. One of these features is the additional suppression of the formation of large scale structure, as compared with cosmological constant models. In light of the new pressures being placed on cosmological parameters (in particular H_0) by CMB data, this added suppression allows our "brane" models to give excellent fits to both CMB and large scale structure data.Comment: 18 pages, 12 figures, submitted to PR

Fast automated cell phenotype image classification

BACKGROUND: The genomic revolution has led to rapid growth in sequencing of genes and proteins, and attention is now turning to the function of the encoded proteins. In this respect, microscope imaging of a protein's sub-cellular localisation is proving invaluable, and recent advances in automated fluorescent microscopy allow protein localisations to be imaged in high throughput. Hence there is a need for large scale automated computational techniques to efficiently quantify, distinguish and classify sub-cellular images. While image statistics have proved highly successful in distinguishing localisation, commonly used measures suffer from being relatively slow to compute, and often require cells to be individually selected from experimental images, thus limiting both throughput and the range of potential applications. Here we introduce threshold adjacency statistics, the essence which is to threshold the image and to count the number of above threshold pixels with a given number of above threshold pixels adjacent. These novel measures are shown to distinguish and classify images of distinct sub-cellular localization with high speed and accuracy without image cropping. RESULTS: Threshold adjacency statistics are applied to classification of protein sub-cellular localization images. They are tested on two image sets (available for download), one for which fluorescently tagged proteins are endogenously expressed in 10 sub-cellular locations, and another for which proteins are transfected into 11 locations. For each image set, a support vector machine was trained and tested. Classification accuracies of 94.4% and 86.6% are obtained on the endogenous and transfected sets, respectively. Threshold adjacency statistics are found to provide comparable or higher accuracy than other commonly used statistics while being an order of magnitude faster to calculate. Further, threshold adjacency statistics in combination with Haralick measures give accuracies of 98.2% and 93.2% on the endogenous and transfected sets, respectively. CONCLUSION: Threshold adjacency statistics have the potential to greatly extend the scale and range of applications of image statistics in computational image analysis. They remove the need for cropping of individual cells from images, and are an order of magnitude faster to calculate than other commonly used statistics while providing comparable or better classification accuracy, both essential requirements for application to large-scale approaches

Hadronic final states in deep-inelastic scattering with Sherpa

We extend the multi-purpose Monte-Carlo event generator Sherpa to include processes in deeply inelastic lepton-nucleon scattering. Hadronic final states in this kinematical setting are characterised by the presence of multiple kinematical scales, which were up to now accounted for only by specific resummations in individual kinematical regions. Using an extension of the recently introduced method for merging truncated parton showers with higher-order tree-level matrix elements, it is possible to obtain predictions which are reliable in all kinematical limits. Different hadronic final states, defined by jets or individual hadrons, in deep-inelastic scattering are analysed and the corresponding results are compared to HERA data. The various sources of theoretical uncertainties of the approach are discussed and quantified. The extension to deeply inelastic processes provides the opportunity to validate the merging of matrix elements and parton showers in multi-scale kinematics inaccessible in other collider environments. It also allows to use HERA data on hadronic final states in the tuning of hadronisation models.Comment: 32 pages, 22 figure

Recent Advances in Understanding Particle Acceleration Processes in Solar Flares

We review basic theoretical concepts in particle acceleration, with particular emphasis on processes likely to occur in regions of magnetic reconnection. Several new developments are discussed, including detailed studies of reconnection in three-dimensional magnetic field configurations (e.g., current sheets, collapsing traps, separatrix regions) and stochastic acceleration in a turbulent environment. Fluid, test-particle, and particle-in-cell approaches are used and results compared. While these studies show considerable promise in accounting for the various observational manifestations of solar flares, they are limited by a number of factors, mostly relating to available computational power. Not the least of these issues is the need to explicitly incorporate the electrodynamic feedback of the accelerated particles themselves on the environment in which they are accelerated. A brief prognosis for future advancement is offered.Comment: This is a chapter in a monograph on the physics of solar flares, inspired by RHESSI observations. The individual articles are to appear in Space Science Reviews (2011

Spectroscopic examinations of hydro- and glaciovolcanic basaltic tuffs: Modes of alteration and relevance for Mars

Hydro- and glaciovolcanism are processes that have taken place on both Earth and Mars. The amount of materials produced by these processes that are present in the martian surface layer is unknown, but may be substantial. We have used Mars rover analogue analysis techniques to examine altered tuff samples collected from multiple hydrovolcanic features, tuff rings and tuff cones, in the American west and from glaciovolcanic hyaloclastite ridges in Washington state and in Iceland. Analysis methods include VNIR-SWIR reflectance, MWIR thermal emissivity, thin section petrography, XRD, XRF, and Mössbauer spectroscopy. We distinguish three main types of tuff that differ prominently in petrography and VNIR-SWIR reflectance: minimally altered sideromelane tuff, gray to brown colored smectite-bearing tuff, and highly palagonitized tuff. Differences are also observed between the tuffs associated with hydrovolcanic tuff rings and tuff cones and those forming glaciovolcanic hyaloclastite ridges. For the locations sampled, hydrovolcanic palagonite tuffs are more smectite and zeolite rich while the palagonitized hyaloclastites from the sampled sites are largely devoid of zeolites and relatively lacking in smectites as well. The gray to brown colored tuffs are only observed in the hydrovolcanic deposits and appear to represent a distinct alteration pathway, with formation of smectites without associated palagonite formation. This is attributed to lower temperatures and possibly longer time scale alteration. Altered hydro- or glaciovolcanic materials might be recognized on the surface of Mars with rover-based instrumentation based on the results of this study

Detector Description and Performance for the First Coincidence Observations between LIGO and GEO

For 17 days in August and September 2002, the LIGO and GEO interferometer gravitational wave detectors were operated in coincidence to produce their first data for scientific analysis. Although the detectors were still far from their design sensitivity levels, the data can be used to place better upper limits on the flux of gravitational waves incident on the earth than previous direct measurements. This paper describes the instruments and the data in some detail, as a companion to analysis papers based on the first data.Comment: 41 pages, 9 figures 17 Sept 03: author list amended, minor editorial change

Quantum walks: a comprehensive review

Quantum walks, the quantum mechanical counterpart of classical random walks, is an advanced tool for building quantum algorithms that has been recently shown to constitute a universal model of quantum computation. Quantum walks is now a solid field of research of quantum computation full of exciting open problems for physicists, computer scientists, mathematicians and engineers. In this paper we review theoretical advances on the foundations of both discrete- and continuous-time quantum walks, together with the role that randomness plays in quantum walks, the connections between the mathematical models of coined discrete quantum walks and continuous quantum walks, the quantumness of quantum walks, a summary of papers published on discrete quantum walks and entanglement as well as a succinct review of experimental proposals and realizations of discrete-time quantum walks. Furthermore, we have reviewed several algorithms based on both discrete- and continuous-time quantum walks as well as a most important result: the computational universality of both continuous- and discrete- time quantum walks.Comment: Paper accepted for publication in Quantum Information Processing Journa