Roy Wood Sellar's criticism of idealism

Dissertation (Ph.D.)--Boston University, 1945. This item was digitized by the Internet Archive

Observations of sound-speed fluctuations on the New Jersey continental shelf in the summer of 2006

Author Posting. © Acoustical Society of America, 2012. This article is posted here by permission of Acoustical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Acoustical Society of America 131 (2012): 1733-1748, doi:10.1121/1.3666014.Environmental sensors moored on the New Jersey continental shelf tracked constant density surfaces (isopycnals) for 35 days in the summer of 2006. Sound-speed fluctuations from internal-wave vertical isopycnal displacements and from temperature/salinity variability along isopycnals (spiciness) are analyzed using frequency spectra and vertical covariance functions. Three varieties of internal waves are studied: Diffuse broadband internal waves (akin to waves fitting the deep water Garrett/Munk spectrum), internal tides, and, to a lesser extent, nonlinear internal waves. These internal-wave contributions are approximately distinct in the frequency domain. It is found that in the main thermocline spicy thermohaline structure dominates the root mean square sound-speed variability, with smaller contributions coming from (in order) nonlinear internal waves, diffuse internal waves, and internal tides. The frequency spectra of internal-wave displacements and of spiciness have similar form, likely due to the advection of variable-spiciness water masses by horizontal internal-wave currents, although there are technical limitations to the observations at high frequency. In the low-frequency, internal-wave band the internal-wave spectrum follows frequency to the −1.81 power, whereas the spice spectrum shows a −1.73 power. Mode spectra estimated via covariance methods show that the diffuse internal-wave spectrum has a smaller mode bandwidth than Garrett/Munk and that the internal tide has significant energy in modes one through three.This work was supported by the Office of Naval Research, and Professor Colosi gratefully acknowledges his additional support from the Naval Postgraduate School’s Undersea Warfare Chair that he holds

A test of basin-scale acoustic thermometry using a large-aperture vertical array at 3250-km range in the eastern North Pacific Ocean

Author Posting. © Acoustical Society of America, 1999. This article is posted here by permission of Acoustical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Acoustical Society of America 105 (1999): 3185, doi:10.1121/1.424649.Broadband acoustic signals were transmitted during November 1994 from a 75-Hz source suspended near the depth of the sound-channel axis to a 700-m long vertical receiving array approximately 3250 km distant in the eastern North Pacific Ocean. The early part of the arrival pattern consists of raylike wave fronts that are resolvable, identifiable, and stable. The later part of the arrival pattern does not contain identifiable raylike arrivals, due to scattering from internal-wave-induced sound-speed fluctuations. The observed ray travel times differ from ray predictions based on the sound-speed field constructed using nearly concurrent temperature and salinity measurements by more than a priori variability estimates, suggesting that the equation used to compute sound speed requires refinement. The range-averaged oceansound speed can be determined with an uncertainty of about 0.05 m/s from the observed ray travel times together with the time at which the near-axial acoustic reception ends, used as a surrogate for the group delay of adiabatic mode 1. The change in temperature over six days can be estimated with an uncertainty of about 0.006 °C. The sensitivity of the travel times to ocean variability is concentrated near the ocean surface and at the corresponding conjugate depths, because all of the resolved ray arrivals have upper turning depths within a few hundred meters of the surface.This work was supported largely by the Strategic Environmental Research and Development Program through Defense Advanced Research Projects Agency ~DARPA! Grant No. MDA972-93- 1-0003. Additional support was provided at SIO by the Office of Naval Research ~ONR! through Grant No. N00014- 97-1-0258. J. Colosi wishes to acknowledge support from an ONR Young Investigator Award, from the J. Lamar Worzel Assistant Scientist Fund, and from the Penzance Endowed Fund in support of scientific staff at WHOI

An attenuated strain of Bacillus anthracis (CDC 684) has a large chromosomal inversion and altered growth kinetics

BackgroundAn isolate originally labeled Bacillus megaterium CDC 684 was found to contain both pXO1 and pXO2, was non-hemolytic, sensitive to gamma-phage, and produced both the protective antigen and the poly-D-glutamic acid capsule. These phenotypes prompted Ezzell et al., (J. Clin. Microbiol. 28:223) to reclassify this isolate to Bacillus anthracis in 1990.ResultsWe demonstrate that despite these B. anthracis features, the isolate is severely attenuated in a guinea pig model. This prompted whole genome sequencing and closure. The comparative analysis of CDC 684 to other sequenced B. anthracis isolates and further analysis reveals: a) CDC 684 is a close relative of a virulent strain, Vollum A0488; b) CDC 684 defines a new B. anthracis lineage (at least 51 SNPs) that includes 15 other isolates; c) the genome of CDC 684 contains a large chromosomal inversion that spans 3.3 Mbp; d) this inversion has caused a displacement of the usual spatial orientation of the origin of replication (ori) to the termination of replication (ter) from 180° in wild-type B. anthracis to 120° in CDC 684 and e) this isolate also has altered growth kinetics in liquid media.ConclusionsWe propose two alternative hypotheses explaining the attenuated phenotype of this isolate. Hypothesis 1 suggests that the skewed ori/ter relationship in CDC 684 has altered its DNA replication and/or transcriptome processes resulting in altered growth kinetics and virulence capacity. Hypothesis 2 suggests that one or more of the single nucleotide polymorphisms in CDC 684 has altered the expression of a regulatory element or other genes necessary for virulence

Comparing nuclear power trajectories in Germany and the UK: from ‘regimes' to ‘democracies’ in sociotechnical transitions and Discontinuities

This paper focuses on arguably the single most striking contrast in contemporary major energy politics in Europe (and even the developed world as a whole): the starkly differing civil nuclear policies of Germany and the UK. Germany is seeking entirely to phase out nuclear power by 2022. Yet the UK advocates a ‘nuclear renaissance’, promoting the most ambitious new nuclear construction programme in Western Europe.Here,this paper poses a simple yet quite fundamental question: what are the particular divergent conditions most strongly implicated in the contrasting developments in these two countries. With nuclear playing such an iconic role in historical discussions over technological continuity and transformation, answering this may assist in wider understandings of sociotechnical incumbency and discontinuity in the burgeoning field of‘sustainability transitions’. To this end, an ‘abductive’ approach is taken: deploying nine potentially relevant criteria for understanding the different directions pursued in Germany and the UK. Together constituted by 30 parameters spanning literatures related to socio-technical regimes in general as well as nuclear technology in particular, the criteria are divided into those that are ‘internal’ and ‘external’ to the ‘focal regime configuration’ of nuclear power and associated ‘challenger technologies’ like renewables. It is ‘internal’ criteria that are emphasised in conventional sociotechnical regime theory, with ‘external’ criteria relatively less well explored. Asking under each criterion whether attempted discontinuation of nuclear power would be more likely in Germany or the UK, a clear picture emerges. ‘Internal’ criteria suggest attempted nuclear discontinuation should be more likely in the UK than in Germany– the reverse of what is occurring. ‘External’ criteria are more aligned with observed dynamics –especially those relating to military nuclear commitments and broader ‘qualities of democracy’. Despite many differences of framing concerning exactly what constitutes ‘democracy’, a rich political science literature on this point is unanimous in characterising Germany more positively than the UK. Although based only on a single case,a potentially important question is nonetheless raised as to whether sociotechnical regime theory might usefully give greater attention to the general importance of various aspects of democracy in constituting conditions for significant technological discontinuities and transformations. If so, the policy implications are significant. A number of important areas are identified for future research, including the roles of diverse understandings and specific aspects of democracy and the particular relevance of military nuclear commitments– whose under-discussion in civil nuclear policy literatures raises its own questions of democratic accountability

Improving virtual screening of G protein-coupled receptors via ligand-directed modeling

G protein-coupled receptors (GPCRs) play crucial roles in cell physiology and pathophysiology. There is increasing interest in using structural information for virtual screening (VS) of libraries and for structure-based drug design to identify novel agonist or antagonist leads. However, the sparse availability of experimentally determined GPCR/ligand complex structures with diverse ligands impedes the application of structure-based drug design (SBDD) programs directed to identifying new molecules with a select pharmacology. In this study, we apply ligand-directed modeling (LDM) to available GPCR X-ray structures to improve VS performance and selectivity towards molecules of specific pharmacological profile. The described method refines a GPCR binding pocket conformation using a single known ligand for that GPCR. The LDM method is a computationally efficient, iterative workflow consisting of protein sampling and ligand docking. We developed an extensive benchmark comparing LDM-refined binding pockets to GPCR X-ray crystal structures across seven different GPCRs bound to a range of ligands of different chemotypes and pharmacological profiles. LDM-refined models showed improvement in VS performance over origin X-ray crystal structures in 21 out of 24 cases. In all cases, the LDM-refined models had superior performance in enriching for the chemotype of the refinement ligand. This likely contributes to the LDM success in all cases of inhibitor-bound to agonist-bound binding pocket refinement, a key task for GPCR SBDD programs. Indeed, agonist ligands are required for a plethora of GPCRs for therapeutic intervention, however GPCR X-ray structures are mostly restricted to their inactive inhibitor-bound state

Ecological commonalities among pelagic fishes: comparison of freshwater ciscoes and marine herring and sprat

Systematic comparisons of the ecology between functionally similar fish species from freshwater and marine aquatic systems are surprisingly rare. Here, we discuss commonalities and differences in evolutionary history, population genetics, reproduction and life history, ecological interactions, behavioural ecology and physiological ecology of temperate and Arctic freshwater coregonids (vendace and ciscoes, Coregonus spp.) and marine clupeids (herring, Clupea harengus, and sprat, Sprattus sprattus). We further elucidate potential effects of climate warming on these groups of fish based on the ecological features of coregonids and clupeids documented in the previous parts of the review. These freshwater and marine fishes share a surprisingly high number of similarities. Both groups are relatively short-lived, pelagic planktivorous fishes. The genetic differentiation of local populations is weak and seems to be in part correlated to an astonishing variability of spawning times. The discrete thermal window of each species influences habitat use, diel vertical migrations and supposedly also life history variations. Complex life cycles and preference for cool or cold water make all species vulnerable to the effects of global warming. It is suggested that future research on the functional interdependence between spawning time, life history characteristics, thermal windows and genetic differentiation may profit from a systematic comparison of the patterns found in either coregonids or clupeids

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead