Proteomics FASTA Archive and Reference Resource

A FASTA file archive and reference resource has been added to ProteomeCommons.org. Motivation for this new functionality derives from two primary sources. The first is the recent FASTA standardization work done by the Human Proteome Organization's Proteomics Standards Initiative (HUPO-PSI). Second is the general lack of a uniform mechanism to properly cite FASTA files used in a study, and to publicly access such FASTA files post-publication. An extension to the Tranche data sharing network has been developed that includes web-pages, documentation, and tools for facilitating the use of FASTA files. These include conversion to the new HUPO-PSI format, and provisions for both citing and publicly archiving FASTA files. This new resource is available immediately, free of charge, and can be accessed at http://www.proteomecommons.org/data/fasta/. Source-code for related tools is also freely available under the BSD license.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/58584/1/1756_ftp.pd

Compositional Variations in the \u3cem\u3eFire Clay Coal Bed\u3c/em\u3e of Eastern Kentucky: Geochemistry, Petrography, Palynology, and Paleoecology

Bench samples of the Fire Clay coal bed, collected from 28 localities in a study area of eight 7.5-minute quadrangles in the Eastern Kentucky Coal Field, were analyzed geochemically, petrographically, and palynologically to determine any spatial or temporal trends among the studied parameters. At most sample sites the Fire Clay is split by a flint-clay parting of probable volcanic origin. The upper bench of the Fire Clay coal generally is thick, laterally continuous, low in ash yield and sulfur content, has a moderate to high calorific value, and is high in total vitrinite content. In contrast, the lower bench generally is thin, laterally discontinuous, moderate to high in ash yield and sulfur content, has a low to moderate calorific value, and has high liptinite and inertinite contents. Rider coals, present at two sample sites, are thin, laterally discontinuous, and high in both ash yield and sulfur content. Fire Clay coal extracted from underground mines typically contains roof and floor rock, which is separated by conventional coal-cleaning methods. The analytical data were grouped into categories of increasing coal purity to approximate a cleaned coal product. Results indicate that some parameters (Btu and total vitrinite content) increase along a trend from higher ash to lower ash coal. Other parameters (ash yield, total sulfur content, and several minor elements) decrease. Still others (thickness and total moisture) show no trend at all. A comparison of these data with previously accumulated data from 64 cleaned coal samples (collected from preparation plants) confirms these trends. This is significant, especially with regard to Titles III and IV of the Clean Air Act Amendments of 1990, in that many deleterious components of coal appear to be removable by conventional coal-cleaning methods prior to combustion in an industrial furnace. Examples of these undesirable constituents include pyrite, chromium, cobalt, and nickel. The Fire Clay coal was grouped into four compositional categories for paleoecological interpretation. The categories are (1) a Lycospora-dominant group with high vitrinite contents that is interpreted to have formed in areas of the Fire Clay paleomire that were kept very wet, to the point of having standing water, a majority of the time (this group probably developed in areas of the mire that were dominantly rheotrophic and planar); (2) a mixed-palynoflora group with high vitrinite contents that is defined by having a more diverse palynoflora than the first group (increased percentages of small lycopsid, fern, and calamite spores), and high percentages of vitrinite (this group is also interpreted to have formed in areas that were very wet most of the time, and were predominantly rheotrophic and planar); (3) a mixed-palynoflora group with moderate to low vitrinite contents that contains increased percentages of inertinite compared to the first two groups and a diverse palynoflora, possibly because the mire became more ombrotrophic and domed; and (4) a mixed-palynoflora group with high ash yield whose palynoflora is marked by various mixtures of lycopsids (trees and small forms), ferns (tree-like and small forms), calamites, and cordaite spores; samples defined by this group contain elevated percentages of liptinite and inertinite macerals, as well as higher ash yields. The conditions under which group 4 formed probably were rheotrophic and planar. Group 4 defines all the samples in the lower bench of the Fire Clay coal bed

ALMA Observations of the Orion Proplyds

We present ALMA observations of protoplanetary disks ("proplyds") in the Orion Nebula Cluster. We imaged 5 individual fields at 856um containing 22 HST-identified proplyds and detected 21 of them. Eight of those disks were detected for the first time at submillimeter wavelengths, including the most prominent, well-known proplyd in the entire Orion Nebula, 114-426. Thermal dust emission in excess of any free-free component was measured in all but one of the detected disks, and ranged between 1-163 mJy, with resulting disk masses of 0.3-79 Mjup. An additional 26 stars with no prior evidence of associated disks in HST observations were also imaged within the 5 fields, but only 2 were detected. The disk mass upper limits for the undetected targets, which include OB stars, theta1Ori C and theta1Ori F, range from 0.1-0.6 Mjup. Combining these ALMA data with previous SMA observations, we find a lack of massive (>3 Mjup) disks in the extreme-UV dominated region of Orion, within 0.03 pc of O-star theta1Ori C. At larger separations from theta1Ori C, in the far-UV dominated region, there is a wide range of disk masses, similar to what is found in low-mass star forming regions. Taken together, these results suggest that a rapid dissipation of disk masses likely inhibits potential planet formation in the extreme-UV dominated regions of OB associations, but leaves disks in the far-UV dominated regions relatively unaffected.Comment: ApJ, in pres

Energy efficient hopping with Hill-type muscle properties on segmented legs.

The intrinsic muscular properties of biological muscles are the main source of stabilization during locomotion, and superior biological performance is obtained with low energy costs. Man-made actuators struggle to reach the same energy efficiency seen in biological muscles. Here, we compare muscle properties within a one-dimensional and a two-segmented hopping leg. Different force-length-velocity relations (constant, linear, and Hill) were adopted for these two proposed models, and the stable maximum hopping heights from both cases were used to estimate the cost of hopping. We then performed a fine-grained analysis during landing and takeoff of the best performing cases, and concluded that the force-velocity Hill-type model is, at maximum hopping height, the most efficient for both linear and segmented models. While hopping at the same height the force-velocity Hill-type relation outperformed the linear relation as well. Finally, knee angles between 60° and 90° presented a lower energy expenditure than other morphologies for both Hill-type and constant relations during maximum hopping height. This work compares different muscular properties in terms of energy efficiency within different geometries, and these results can be applied to decrease energy costs of current actuators and robots during locomotion.RoboSoft—Coordination Action for Soft RoboticsThis is the author accepted manuscript. The final version is available from the Institute of Physics via http://dx.doi.org/10.1088/1748-3190/11/3/03600

Use of the MATRIXx Integrated Toolkit on the Microwave Anisotropy Probe Attitude Control System

Recent advances in analytical software tools allow the analysis, simulation, flight code, and documentation of an algorithm to be generated from a single source, all within one integrated analytical design package. NASA's Microwave Anisotropy Probe project has used one such package, Integrated Systems' MATRIXx suite, in the design of the spacecraft's Attitude Control System. The project's experience with the linear analysis, simulation, code generation, and documentation tools will be presented and compared with more traditional development tools. In particular, the quality of the flight software generated will be examined in detail. Finally, lessons learned on each of the tools will be shared

Features in geometric receiver shapes modelling bat-like directivity patterns

The directional properties of bat ears as receivers is a current area of interest in ultrasound research. This paper presents a new approach to analyse the relationship between morphological features and acoustical properties of the external ear of bat species. The beam pattern of Rousettus leschenaultii’s right ear is measured and compared to that of receiver structures whose design is inspired by the bat ear itself and made of appropriate geometric shapes. The regular shape of these receivers makes it possible to control the key reception parameters and thus to understand the effect on the associated beam pattern of the parameters themselves. Measurements show one receiver structure has a beam pattern very similar to that of R. leschenaultii’s ear, thus explaining the function of individual parts constituting its ear. As it is applicable to all bat species, this approach can provide a useful tool to investigate acoustics in bats, and possibly other mammals

Available Resources of the Fire Clay Coal in Part of the Eastern Kentucky Coal Field

Available resources for the Fire Clay coal were calculated for a 15-quadrangle area in the Eastern Kentucky Coal Field. Original coal resources were estimated to be 1.8 billion tons (BT). Coal mined or lost in mining was estimated at 449 million tons (MT), leaving 1.3 BT of remaining Fire Clay resources in the study area. Of the remaining resources, 400 MT is restricted from mining, primarily because the coal is less than 28 in. thick, normally considered too thin to mine underground using present technology. The total coal available for mining in the study area is 911 MT, or 52 percent of the original resource. Of the 911 MT, 14.9 percent is thicker than 42 in., and only 6.1 percent is accessible by surface-mining methods. The largest block of available coal is in the Leatherwood quadrangle, is less than 42 in. thick, and mostly occurs below drainage

Acoustic Energy and Momentum in a Moving Medium

By exploiting the mathematical analogy between the propagation of sound in a non-homogeneous potential flow and the propagation of a scalar field in a background gravitational field, various wave ``energy'' and wave ``momentum'' conservation laws are established in a systematic manner. In particular the acoustic energy conservation law due to Blokhintsev appears as the result of the conservation of a mixed co- and contravariant energy-momentum tensor, while the exchange of relative energy between the wave and the mean flow mediated by the radiation stress tensor, first noted by Longuet-Higgins and Stewart in the context of ocean waves, appears as the covariant conservation of the doubly contravariant form of the same energy-momentum tensor.Comment: 25 Pages, Late

Topology of the pore-region of a K+ channel revealed by the NMR-derived structures of scorpion toxins

AbstractThe architecture of the pore-region of a voltage-gated K+ channel, Kv1.3, was probed using four high affinity scorpion toxins as molecular calipers. We established the structural relatedness of these toxins by solving the structures of kaliotoxin and margatoxin and comparing them with the published structure of charybdotoxin; a homology model of noxiustoxin was then developed. Complementary mutagenesis of Kv1.3 and these toxins, combined with electrostatic compliance and thermodynamic mutant cycle analyses, allowed us to identify multiple toxin-challel interactions. Our analyses reveals the existence of a shallow vestibule at the external entrance to the pore. This vestibule is ∼28−32A˚wide at its outer margin, ∼28−34A˚wide at its base, and ∼4−8A˚deep. The pore is 9–14A˚wide at its external entrance and tapers to a width of 4–5A˚at a depth of ∼5−7A˚from the vestibule. This structural information should directly aid in developing topological models of the pores of related ion channels and facilitate therapeutic drug design

Generation and trapping of a mesoderm biased state of human pluripotency

We postulate that exit from pluripotency involves intermediates that retain pluripotency while simultaneously exhibiting lineage-bias. Using a MIXL1 reporter, we explore mesoderm lineage-bias within the human pluripotent stem cell compartment. We identify a substate, which at the single cell level coexpresses pluripotent and mesodermal gene expression programmes. Functionally these cells initiate stem cell cultures and exhibit mesodermal bias in differentiation assays. By promoting mesodermal identity through manipulation of WNT signalling while preventing exit from pluripotency using lysophosphatidic acid, we ‘trap’ and maintain cells in a lineage-biased stem cell state through multiple passages. These cells correspond to a normal state on the differentiation trajectory, the plasticity of which is evidenced by their reacquisition of an unbiased state upon removal of differentiation cues. The use of ‘cross-antagonistic’ signalling to trap pluripotent stem cell intermediates with different lineage-bias may have general applicability in the efficient production of cells for regenerative medicine