The Imaging Probe Development Center and the Production of Molecular Imaging Probes

The Imaging Probe Development Center (IPDC), part of the NIH Roadmap for Medical Research Initiative (http://nihroadmap.nih.gov/) recently became fully operational at its newly refurbished laboratories in Rockville, MD. The IPDC (http://nihroadmap.nih.gov/molecularlibraries/ipdc/) is dedicated to the production of known and novel molecular imaging probes, with its services currently being used by the NIH intramural community, although in the future it is intended that the extramural community will also benefit from the IPDC’s resources. The Center has been set up with the belief that molecular imaging, and the probe chemistry that underpins it, will constitute key technologies going forward. As part of the larger molecular libraries and imaging initiative, it is planned that the IPDC will work closely with scientists from the molecular libraries effort. Probes produced at the IPDC include optical, radionuclide and magnetic resonance agents and may encompass any type of contrast agent. As IPDC is a trans-NIH resource it can serve each of the 27 Institutes and Centers that comprise NIH so its influence can be expected to impact widely different subjects and disease conditions spanning biological research. IPDC is expected to play a key part in interdisciplinary collaborative imaging projects and to support translational R&D from basic research through clinical development, for all of the imaging modalities. Examples of probes already prepared or under preparation are outlined to illustrate the breadth of the chemistries undertaken together with a reference outline of the diverse biological applications for which the various probes are intended

Molecular Dynamics Simulation of Solvent-Polymer Interdiffusion. I. Fickian diffusion

The interdiffusion of a solvent into a polymer melt has been studied using large scale molecular dynamics and Monte Carlo simulation techniques. The solvent concentration profile and weight gain by the polymer have been measured as a function of time. The weight gain is found to scale as t^{1/2}, which is expected for Fickian type of diffusion. The concentration profiles are fit very well assuming Fick's second law with a constant diffusivity. The diffusivity found from fitting Fick's second law is found to be independent of time and equal to the self diffusion constant in the dilute solvent limit. We separately calculated the diffusivity as a function of concentration using the Darken equation and found that the diffusivity is essentially constant for the concentration range relevant for interdiffusion.Comment: 17 pages and 7 figure

The black hole final state

We propose that in quantum gravity one needs to impose a final state boundary condition at black hole singularities. This resolves the apparent contradiction between string theory and semiclassical arguments over whether black hole evaporation is unitary.Comment: 17 pages, harvmac, 1 figure, v2: comment about interactions and references adde

Context Is Everything: Harmonization of Critical Food Microbiology Descriptors and Metadata for Improved Food Safety and Surveillance

Globalization of food networks increases opportunities for the spread of foodborne pathogens beyond borders and jurisdictions. High resolution whole-genome sequencing (WGS) subtyping of pathogens promises to vastly improve our ability to track and control foodborne disease, but to do so it must be combined with epidemiological, clinical, laboratory and other health care data (called “contextual data”) to be meaningfully interpreted for regulatory and health interventions, outbreak investigation, and risk assessment. However, current multi-jurisdictional pathogen surveillance and investigation efforts are complicated by time-consuming data re-entry, curation and integration of contextual information owing to a lack of interoperable standards and inconsistent reporting. A solution to these challenges is the use of ‘ontologies’ - hierarchies of well-defined and standardized vocabularies interconnected by logical relationships. Terms are specified by universal IDs enabling integration into highly regulated areas and multi-sector sharing (e.g., food and water microbiology with the veterinary sector). Institution-specific terms can be mapped to a given standard at different levels of granularity, maximizing comparability of contextual information according to jurisdictional policies. Fit-for-purpose ontologies provide contextual information with the auditability required for food safety laboratory accreditation. Our research efforts include the development of a Genomic Epidemiology Ontology (GenEpiO), and Food Ontology (FoodOn) that harmonize important laboratory, clinical and epidemiological data fields, as well as existing food resources. These efforts are supported by a global consortium of researchers and stakeholders worldwide. Since foodborne diseases do not respect international borders, uptake of such vocabularies will be crucial for multi-jurisdictional interpretation of WGS results and data sharing

Emergence: Key physical issues for deeper philosophical inquiries

A sketch of three senses of emergence and a suggestive view on the emergence of time and the direction of time is presented. After trying to identify which issues philosophers interested in emergent phenomena in physics view as important I make several observations pertaining to the concepts, methodology and mechanisms required to understand emergence and describe a platform for its investigation. I then identify some key physical issues which I feel need be better appreciated by the philosophers in this pursuit. I end with some comments on one of these issues, that of coarse-graining and persistent structures.Comment: 16 pages. Invited Talk at the Heinz von Foerster Centenary International Conference on Self-Organization and Emergence: Emergent Quantum Mechanics (EmerQuM11). Nov. 10-13, 2011, Vienna, Austria. Proceedings to appear in J. Phys. (Conf. Series

Emergence: Key physical issues for deeper philosophical inquiries

A sketch of three senses of emergence and a suggestive view on the emergence of time and the direction of time is presented. After trying to identify which issues philosophers interested in emergent phenomena in physics view as important I make several observations pertaining to the concepts, methodology and mechanisms required to understand emergence and describe a platform for its investigation. I then identify some key physical issues which I feel need be better appreciated by the philosophers in this pursuit. I end with some comments on one of these issues, that of coarse-graining and persistent structures.Comment: 16 pages. Invited Talk at the Heinz von Foerster Centenary International Conference on Self-Organization and Emergence: Emergent Quantum Mechanics (EmerQuM11). Nov. 10-13, 2011, Vienna, Austria. Proceedings to appear in J. Phys. (Conf. Series

Characterisation of a Wheat Breeders’ Array suitable for high throughput SNP genotyping of global accessions of hexaploid bread wheat (<i>Triticum aestivium</i>)

Targeted selection and inbreeding have resulted in a lack of genetic diversity in elite hexaploid bread wheat accessions. Reduced diversity can be a limiting factor in the breeding of high yielding varieties and crucially can mean reduced resilience in the face of changing climate and resource pressures. Recent technological advances have enabled the development of molecular markers for use in the assessment and utilization of genetic diversity in hexaploid wheat. Starting with a large collection of 819 571 previously characterized wheat markers, here we describe the identification of 35 143 single nucleotide polymorphism-based markers, which are highly suited to the genotyping of elite hexaploid wheat accessions. To assess their suitability, the markers have been validated using a commercial high-density Affymetrix Axiom® genotyping array (the Wheat Breeders' Array), in a high-throughput 384 microplate configuration, to characterize a diverse global collection of wheat accessions including landraces and elite lines derived from commercial breeding communities. We demonstrate that the Wheat Breeders' Array is also suitable for generating high-density genetic maps of previously uncharacterized populations and for characterizing novel genetic diversity produced by mutagenesis. To facilitate the use of the array by the wheat community, the markers, the associated sequence and the genotype information have been made available through the interactive web site 'CerealsDB'

Weak Lensing with SDSS Commissioning Data: The Galaxy-Mass Correlation Function To 1/h Mpc

(abridged) We present measurements of galaxy-galaxy lensing from early commissioning imaging data from the Sloan Digital Sky Survey (SDSS). We measure a mean tangential shear around a stacked sample of foreground galaxies in three bandpasses out to angular radii of 600'', detecting the shear signal at very high statistical significance. The shear profile is well described by a power-law. A variety of rigorous tests demonstrate the reality of the gravitational lensing signal and confirm the uncertainty estimates. We interpret our results by modeling the mass distributions of the foreground galaxies as approximately isothermal spheres characterized by a velocity dispersion and a truncation radius. The velocity dispersion is constrained to be 150-190 km/s at 95% confidence (145-195 km/s including systematic uncertainties), consistent with previous determinations but with smaller error bars. Our detection of shear at large angular radii sets a 95% confidence lower limit $s>140^{\prime\prime}$, corresponding to a physical radius of $260h^{-1}$ kpc, implying that galaxy halos extend to very large radii. However, it is likely that this is being biased high by diffuse matter in the halos of groups and clusters. We also present a preliminary determination of the galaxy-mass correlation function finding a correlation length similar to the galaxy autocorrelation function and consistency with a low matter density universe with modest bias. The full SDSS will cover an area 44 times larger and provide spectroscopic redshifts for the foreground galaxies, making it possible to greatly improve the precision of these constraints, measure additional parameters such as halo shape, and measure the properties of dark matter halos separately for many different classes of galaxies.Comment: 28 pages, 11 figures, submitted to A

A holistic and comprensive data approach validates the distribution of the critically endangered flapper skate (Dipturus intermedius)

Morphological similarities between skates of the genus Dipturus in the north-eastern Atlantic and mediterranean have resulted in longstanding confusion, misidentification and misreporting. Current evidence indicates that the common skate is best explained as two species, the flapper skate (Dipturus intermedius) and the common blue skate (D. batis). However, some management and conservation initiatives developed prior to the separation continue to refer to common skate (as ‘D. batis’). This taxonomic uncertainty can lead to errors in estimating population viability, distribution range, and impact on fisheries management and conservation status. Here, we demonstrate how a concerted taxonomic approach, using molecular data and a combination of survey, angler and fisheries data, in addition to expert witness statements, can be used to build a higher resolution picture of the current distribution of D. intermedius. Collated data indicate that flapper skate has a more constrained distribution compared to the perceived distribution of the ‘common skate’, with most observations recorded from Norway and the western and northern seaboards of Ireland and Scotland, with occasional specimens from Portugal and the Azores. Overall, the revised spatial distribution of D. intermedius has significantly reduced the extant range of the species, indicating a possibly fragmented distribution range.acceptedVersio