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PubMed2006

PET energy-based scatter estimation and image reconstruction with energy-dependent corrections.

In this paper we propose a comprehensive energy-based scatter correction approach for positron emission tomography (PET). We take advantage of the marked difference between the energy spectra of the unscattered and scattered photons, and use the detailed energy information that comes with the list-mode data for the estimation of the scattered events distribution in the data space. Also, inside the maximum-likelihood expectation maximization (ML-EM) image reconstruction algorithm, we introduce energy-dependent factors that individualize the correction terms for each event, given its position and energy information. The central piece of our approach is the two-dimensional detector energy response model represented as a linear combination of four components, each one representing a particular state a PET event can be found in: both photons unscattered, the second scattered while the first not, the first photon scattered while the second not and both photons scattered. For a set of events collected in the vicinity of a point in the projection space, the coefficient of each component is determined by applying a statistical estimator. As a result we obtain the number of scattered events that are in the given set. The model also gives us the variation of scatter fraction with the photon pair energies for that particular position in the data space. A simulation study that demonstrates the proposed methods is presented.

Algorithms↗
PubMed2005

Impact seeding and reseeding in the inner solar system.

Assuming that asteroidal and cometary impacts onto Earth can liberate material containing viable microorganisms, we studied the subsequent distribution of the escaping impact ejecta throughout the inner Solar System on time scales of 30,000 years. Our calculations of the delivery rates of this terrestrial material to Mars and Venus, as well as back to Earth, indicate that transport to great heliocentric distances may occur in just a few years and that the departure speed is significant. This material would have been efficiently and quickly dispersed throughout the Solar System. Our study considers the fate of all the ejected mass (not just the slowly moving material), and tabulates impact rates onto Venus and Mars in addition to Earth itself. Expressed as a fraction of the ejected particles, roughly 0.1% and 0.001% of the ejecta particles would have reached Venus and Mars, respectively, in 30,000 years, making the biological seeding of those planets viable if the target planet supported a receptive environment at the time. In terms of possibly safeguarding terrestrial life by allowing its survival in space while our planet cools after a major killing thermal pulse, we show via our 30,000- year integrations that efficient return to Earth continues for this duration. Our calculations indicate that roughly 1% of the launched mass returns to Earth after a major impact regardless of the impactor speed; although a larger mass is ejected following impacts at higher speeds, a smaller fraction of these ejecta is returned. Early bacterial life on Earth could have been safeguarded from any purported impact-induced extinction by temporary refuge in space.

Earth, Planet↗
PubMed2005

Lithopanspermia in star-forming clusters.

This paper considers the lithopanspermia hypothesis in star-forming groups and clusters, where the chances of biological material spreading from one solar system to another is greatly enhanced (relative to action in the field) because of the close proximity of the systems and lower relative velocities. These effects more than compensate for the reduced time spent in such crowded environments. This paper uses approximately 300,000 Monte Carlo scattering calculations to determine the cross sections for rocks to be captured by binaries and provides fitting formulae for other applications. We assess the odds of transfer as a function of the ejection speed v (eject) and number N(.) of members in the birth aggregate. The odds of any given ejected meteoroid being recaptured by another solar system are relatively low, about 1:10(3)-10(6) over the expected range of ejection speeds and cluster sizes. Because the number of ejected rocks (with mass m > 10 kg) per system can be large, N (R) approximately 10(16), virtually all solar systems are likely to share rocky ejecta with all of the other solar systems in their birth cluster. The number of ejected rocks that carry living microorganisms is much smaller and less certain, but we estimate that N (B) approximately 10(7) rocks can be ejected from a biologically active solar system. For typical birth environments, the capture of life-bearing rocks is expected to occur N (bio) asymptotically equal to 10-16,000 times (per cluster), depending on the ejection speeds. Only a small fraction (f (imp) approximately 10(4)) of the captured rocks impact the surfaces of terrestrial planets, so that N (lps) asymptotically equal to 10(3)-1.6 lithopanspermia events are expected per cluster (under favorable conditions). Finally, we discuss the question of internal versus external seeding of clusters and the possibility of Earth seeding young clusters over its biologically active lifetime.

Astronomical Phenomena↗
PubMed2005

Biologically enhanced energy and carbon cycling on Titan?

With the Cassini-Huygens Mission in orbit around Saturn, the large moon Titan, with its reducing atmosphere, rich organic chemistry, and heterogeneous surface, moves into the astrobiological spotlight. Environmental conditions on Titan and Earth were similar in many respects 4 billion years ago, the approximate time when life originated on Earth. Life may have originated on Titan during its warmer early history and then developed adaptation strategies to cope with the increasingly cold conditions. If organisms originated and persisted, metabolic strategies could exist that would provide sufficient energy for life to persist, even today. Metabolic reactions might include the catalytic hydrogenation of photochemically produced acetylene, or involve the recombination of radicals created in the atmosphere by ultraviolet radiation. Metabolic activity may even contribute to the apparent youth, smoothness, and high activity of Titan's surface via biothermal energy.

Carbon↗
PubMed2006

Microbial survival rates of Escherichia coli and Deinococcus radiodurans under low temperature, low pressure, and UV-Irradiation conditions, and their relevance to possible Martian life.

Viability rates were determined for microbial populations of Escherichia coli and Deinococcus radiodurans under the environmental stresses of low temperature (-35 degrees C), low-pressure conditions (83.3 kPa), and ultraviolet (UV) irradiation (37 W/m(2)). During the stress tests the organisms were suspended in saltwater soil and freshwater soil media, at variable burial depths, and in seawater. Microbial populations of both organisms were most susceptible to dehydration stress associated with low-pressure conditions, and to UV irradiation. However, suspension in a liquid water medium and burial at larger depths (5 cm) improved survival rates markedly. Our results indicate that planetary surfaces that possess little to no atmosphere and have low water availability do not constitute a favorable environment for terrestrial microorganisms.

Atmospheric Pressure↗
PubMed2003

Classification of protein quaternary structure with support vector machine.

MOTIVATION: Since the gap between sharply increasing known sequences and slow accumulation of known structures is becoming large, an automatic classification process based on the primary sequences and known three-dimensional structure becomes indispensable. The classification of protein quaternary structure based on the primary sequences can provide some useful information for the biologists. So a fully automatic and reliable classification system is needed. This work tries to look for the effective methods of extracting attribute and the algorithm for classifying the quaternary structure from the primary sequences. RESULTS: Both of the support vector machine (SVM) and the covariant discriminant algorithms have been first introduced to predict quaternary structure properties from the protein primary sequences. The amino acid composition and the auto-correlation functions based on the amino acid index profile of the primary sequence have been taken into account in the algorithms. We have analyzed 472 amino acid indices and selected the four amino acid indices as the examples, which have the best performance. Thus the five attribute parameter data sets (COMP, FASG, NISK, WOLS and KYTJ) were established from the protein primary sequences. The COMP attribute data set is composed of amino acid composition, and the FASG, NISK, WOLS and KYTJ attribute data sets are composed of the amino acid composition and the auto-correlation functions of the corresponding amino acid residue index. The overall accuracies of SVM are 78.5, 87.5, 83.2, 81.7 and 81.9%, respectively, for COMP, FASG, NISK, WOLS and KYTJ data sets in jackknife test, which are 19.6, 7.8, 15.5, 13.1 and 15.8%, respectively, higher than that of the covariant discriminant algorithm in the same test. The results show that SVM may be applied to discriminate between the primary sequences of homodimers and non-homodimers and the two protein sequence descriptors can reflect the quaternary structure information. Compared with previous Robert Garian's investigation, the performance of SVM is almost equal to that of the Decision tree models, and the methods of extracting feature vector from the primary sequences are superior to Robert's binning function method. AVAILABILITY: Programs are available on request from the authors.

Algorithms↗
PubMed2001

Nutritional status assessment in semiclosed environments: ground-based and space flight studies in humans.

Adequate nutrition is critical during long-term spaceflight, as is the ability to easily monitor dietary intake. A comprehensive nutritional status assessment profile was designed for use before, during and after flight. It included assessment of both dietary intake and biochemical markers of nutritional status. A spaceflight food-frequency questionnaire (FFQ) was developed to evaluate intake of key nutrients during spaceflight. The nutritional status assessment protocol was evaluated during two ground-based closed-chamber studies (60 and 91 d; n = 4/study), and was implemented for two astronauts during 4-mo stays on the Mir space station. Ground-based studies indicated that the FFQ, administered daily or weekly, adequately estimated intake of key nutrients. Chamber subjects maintained prechamber energy intake and body weight. Astronauts tended to eat 40--50% of WHO-predicted energy requirements, and lost >10% of preflight body mass. Serum ferritin levels were lower after the chamber stays, despite adequate iron intake. Red blood cell folate concentrations were increased after the chamber studies. Vitamin D stores were decreased by > 40% on chamber egress and after spaceflight. Mir crew members had decreased levels of most nutritional indices, but these are difficult to interpret given the insufficient energy intake and loss of body mass. Spaceflight food systems can provide adequate intake of macronutrients, although, as expected, micronutrient intake is a concern for any closed or semiclosed food system. These data demonstrate the utility and importance of nutritional status assessment during spaceflight and of the FFQ during extended-duration spaceflight.

Adult↗
PubMed2001

Responses of TLD-BeO:Na (UD-170A) to heavy ions and space radiation.

Responses of TLD-BeO:Na (UD-170A) to high-LET particles were examined with selected heavy ion beams (He, C, Ne, Ar, and Kr) at NIRS-HIMAC, and compared with TLD-Mg2SiO4:Tb (TLMS) and radiophotoluminescent glass (RPLG). The relative TL efficiency of UD-170A as 137Cs gamma ray equivalent arose notably with increasing LET infinity.H2O for He and C, and decreased for the heavier charged particles. In contrast, the efficiencies of TLMS and RPLG did not increase over the range of LET from 0.5 to 410 keV.micron-1. The three detectors were used for space radiation measurement in the Mir space station for 40 days at 400 km altitude and 51.65 degrees inclination. The values from each detector as gamma ray absorbed dose equivalent showed a large spatial variation by a factor 2 in the same Core module. The detector values were in the order of UD-170A > TLMS > RPLG as expected from the results obtained on the ground, although ratios of these values changed depending on positions. These results indicate that both radiation quality and dose level in a spacecraft change significantly and a measurement at one location cannot accurately represent the individual dose to an astronaut. These small detectors should be useful as supplementary personal dosemeters for astronauts.

Beryllium↗
PubMed1997

Vibrational force alters mRNA expression in osteoblasts.

Serum-deprived mouse osteoblastic (MC3T3E1) cells were subjected to a vibrational force modeled by NASA to simulate a space shuttle launch (7.83 G rms). The mRNA levels for eight genes were investigated to determine the effect of vibrational force on mRNA expression. The mRNA levels of two growth-related protooncogenes, c-fos and c-myc, were up-regulated significantly within 30 min after vibration, whereas those of osteocalcin as well as transforming growth factor-beta1 were decreased significantly within 3 h after vibration. No changes were detected in the levels of beta-actin, histone H4, or cytoplasmic phospholipase A2 after vibration. No basal levels of cyclooxygenase-2 expression were detected. In addition, the extracellular concentrations of prostaglandin E2 (PGE2), a potent autocrine/paracrine growth factor in bone, were not significantly altered after vibration most likely due to the serum deprivation state of the osteoblasts. In comparison with the gravitational launch profile, vibrational-induced changes in gene expression were greater both in magnitude and number of genes activated. Taken together, these data suggest that the changes in mRNA expression are due to a direct mechanical effect of the vibrational force on the osteoblast cells and not to changes in the local PGE2 concentrations. The finding that launch forces induce gene expression is of utmost importance since many of the biological experiments do not dampen vibrational loads on experimental samples. This lack of dampening of vibrational forces may partially explain why 1-G onboard controls sometimes do not reflect 1-G ground controls. These data may also suggest that scientists use extra ground controls that are exposed to launch forces, have these forces dampened on launched samples, or use facilities such as Biorack that provide an onboard 1-G centrufuge in order to control for space shuttle launch forces.

Animals↗
PubMed1995

Biomechanical evaluation of anterior thoracolumbar spinal instrumentation.

STUDY DESIGN: A biomechanical study was designed to assess relative construct stabilities of modern anterior thoracolumbar instrumentations in a calf spine model with an anterior and middle column defect. OBJECTIVES: The purpose is to compare the biomechanical stability of various anterior fixation devices in an unstable calf spine model. SUMMARY OF BACKGROUND DATA: Modern types of anterior thoracolumbar instrumentations evolved to either rods or plates. Biomechanical properties and comparative studies of these instrumentations are lacking. METHODS: Twenty fresh calf spines (L2-L5) were used for the biomechanical tests. L2 and L5 vertebrae were used to attach the loading and base frames, respectively. Specimens underwent nondestructive biomechanical tests performed using a three-dimensional motion measuring system. In each specimen, three different cases were tested: intact spine, anterior fixation with an interbody graft after total discectomy and endplate excision of L3-L4 disc, anterior fixation only without the graft. Four anterior fixators, University Anterior Plating System, the Kaneda device, the Z-plate, and Texas Scottish Rite Hospital system were used. Each device was tested on five specimens. A polymethylmethacrylate block was inserted into the disc space to simulate the interbody grafting, and a fixation device was implanted with axial compression. Rotational angles of the L3-L4 segment stabilized by a fixation device and graft were normalized by the corresponding angles of the intact specimen to study the overall stabilizing effects. RESULTS: With the interbody graft and fixation devices, all showed significant stabilizing effects in flexion, extension, and lateral bending. All devices restored axial rotation stability to intact specimen, but only the Kaneda device restored the torsional stability beyond the intact specimen. No statistical differences in stabilizing effects in axial rotation were found between any of the tested devices. When the graft was removed, the Kaneda device significantly decreased the motions in all directions compared with the intact motion, whereas the University plate decreased the motions in flexion, extension, and lateral bending. The Texas Scottish Rite Hospital system was found to reduce the flexion and lateral bending motions significantly, and Z-plate decreased lateral bending motions only. Stabilizing effects of the interbody graft were significant in lateral bendings for all devices. Additionally, the significant stabilizing role of the graft was noted in flexion and extension in Z-plate only. The graft did not significantly reduce the axial rotation motion in any instrumentations. CONCLUSIONS: Modern anterior instrumentations for the thoracolumbar spine, such as the Kaneda device, Texas Scottish Rite Hospital system, Z-plate, and University plate, restored the stability in all motions when an interbody graft was inserted. The stability of fixation devices revealed that the Kaneda device is the best, particularly in restoring the torsional stability. The information on the relative stability provided by different instrumentations should help the spine surgeon in choosing the appropriate instrumentation for the particular circumstance.

Analysis of Variance↗
PubMed2025

Large future genetic diversity losses are predicted even with habitat protection.

Genetic diversity within species is the basis for evolutionary adaptive capacity and has recently been included as a target for protection in the United Nations' Global Biodiversity Framework (GBF). However, we lack large-scale mathematical frameworks to quantify how much genetic diversity has already been lost, let alone to predict future losses under 21st century conservation scenarios. To fill this gap, we developed an area-based spatio-temporal predictive framework of genetic diversity calibrated with population-scale genomic data of 29 plant and animal species. To estimate present genetic diversity loss with our framework, we used species' habitat area and population sizes losses reported in the Living Planet Index, the Red List, and new GBF indicators across 13,808 species for the last 5 decades. Applying our evolutionary framework across these species, we estimate genetic diversity loss lags behind population and habitat area declines, with an estimated current 13-22% π genetic diversity loss. However, we forecast future genetic diversity losses will reach 41-76% even if populations are not further contracted. These results highlight that safeguarding existing habitats is insufficient to maintain the genetic health of species and relying solely on continuous genetic monitoring underestimates lagging long term impacts.

Genetic diversity↗
PubMed2002

Targeted transfer of solitons in continua and lattices.

We propose a robust mechanism of targeted energy transfer along a line, as well as on a surface, in the form of transport of coherent solitary-wave structures, driven by a moving, spatially localized external ac field ("arm") in a lossy medium. The efficiency and robustness of the mechanism are demonstrated analytically and numerically in terms of the nonlinear Schrödinger (NLS) equation, and broad regions of stable operation are identified in the model's parameter space. Direct simulations show that the driving arm can manipulate solitons equally well in a lattice NLS model. A salient feature, which is revealed by simulations and explained analytically, is a resonant character of the operation of the driving arm in the lattice medium, both integer and fractional resonances being identified. Numerical experiments also demonstrate that the same solitary-wave-transport mechanism works well in two-dimensional lattice media.

Journal Article↗
PubMed2003

Thermally activated processes in polymer dynamics.

Jumps between neighboring minima in the energy landscape of both homopolymeric and heteropolymeric chains are numerically investigated by determining the average escape time from different valleys. The numerical results are compared to the theoretical expression derived by Langer [J.S. Langer, Ann. Phys. (N.Y.) 54, 258 (1969)] with reference to a 2N-dimensional space. Our simulations indicate that the dynamics within the native valley is well described by a sequence of thermally activated process up to temperatures well above the folding temperature. At larger temperatures, systematic deviations from the Langer's estimate are instead observed. Several sources for such discrepancies are thoroughly discussed.

Journal Article↗
PubMed1998

Internuclear cascade-evaporation model for LET spectra of 200 MeV protons used for parts testing.

The Linear Energy Transfer (LET) spectrum produced in microelectronic components during testing with 200 MeV protons is calculated with an intemuclear cascade-evaporation code. This spectrum is compared to the natural space heavy ion environment for various earth orbits. This comparison is used to evaluate the results of proton testing in terms of determining a firm upper bound to the on-orbit heavy ion upset rate and the risk of on-orbit heavy ion failures that would not be detected with protons.

Electronics↗
PubMed1999

A molecular dynamics study of the 41-56 beta-hairpin from B1 domain of protein G.

The structural and dynamical behavior of the 41-56 beta-hairpin from the protein G B1 domain (GB1) has been studied at different temperatures using molecular dynamics (MD) simulations in an aqueous environment. The purpose of these simulations is to establish the stability of this hairpin in view of its possible role as a nucleation site for protein folding. The conformation of the peptide in the crystallographic structure of the protein GB1 (native conformation) was lost in all simulations. The new equilibrium conformations are stable for several nanoseconds at 300K (>10 ns), 350 K (>6.5 ns), and even at 450 K (up to 2.5 ns). The new structures have very similar hairpin-like conformations with properties in agreement with available experimental nuclear Overhauser effect (NOE) data. The stability of the structure in the hydrophobic core region during the simulations is consistent with the experimental data and provides further evidence for the role played by hydrophobic interactions in hairpin structures. Essential dynamics analysis shows that the dynamics of the peptide at different temperatures spans basically the same essential subspace. The main equilibrium motions in this subspace involve large fluctuations of the residues in the turn and ends regions. Of the six interchain hydrogen bonds, the inner four remain stable during the simulations. The space spanned by the first two eigenvectors, as sampled at 450 K, includes almost all of the 47 different hairpin structures found in the database. Finally, analysis of the hydration of the 300 K average conformations shows that the hydration sites observed in the native conformation are still well hydrated in the equilibrium MD ensemble.

Amino Acid Sequence↗
PubMed2005

Intraspecific differences in bacterial responses to modelled reduced gravity.

AIMS: Bacteria are important residents of water systems, including those of space stations which feature specific environmental conditions, such as lowered effects of gravity. The purpose of this study was to compare responses with modelled reduced gravity of space station, water system bacterial isolates with other isolates of the same species. METHODS AND RESULTS: Bacterial isolates, Stenotrophomonas paucimobilis and Acinetobacter radioresistens, originally recovered from the water supply aboard the International Space Station (ISS) were grown in nutrient broth under modelled reduced gravity. Their growth was compared with type strains S. paucimobilis ATCC 10829 and A. radioresistens ATCC 49000. Acinetobacter radioresistens ATCC 49000 and the two ISS isolates showed similar growth profiles under modelled reduced gravity compared with normal gravity, whereas S. paucimobilis ATCC 10829 was negatively affected by modelled reduced gravity. CONCLUSIONS: These results suggest that microgravity might have selected for bacteria that were able to thrive under this unusual condition. These responses, coupled with impacts of other features (such as radiation resistance and ability to persist under very oligotrophic conditions), may contribute to the success of these water system bacteria. SIGNIFICANCE AND IMPACT OF THE STUDY: Water quality is a significant factor in many environments including the ISS. Efforts to remove microbial contaminants are likely to be complicated by the features of these bacteria which allow them to persist under the extreme conditions of the systems.

Acinetobacter↗
PubMed2005

A novel extension of the parallel-beam projection-slice theorem to divergent fan-beam and cone-beam projections.

The general goal of this paper is to extend the parallel-beam projection-slice theorem to divergent fan-beam and cone-beam projections without rebinning the divergent fan-beam and cone-beam projections into parallel-beam projections directly. The basic idea is to establish a novel link between the local Fourier transform of the projection data and the Fourier transform of the image object. Analogous to the two- and three-dimensional parallel-beam cases, the measured projection data are backprojected along the projection direction and then a local Fourier transform is taken for the backprojected data array. However, due to the loss of the shift invariance of the image object in a single view of the divergent-beam projections, the measured projection data is weighted by a distance dependent weight w(r) before the local Fourier transform is performed. The variable r in the weighting function w(r) is the distance from the backprojected point to the x-ray source position. It is shown that a special choice of the weighting function, w(r)=1/r, will facilitate the calculations and a simple relation can be established between the Fourier transform of the image function and the local Fourier transform of the 1/r-weighted backprojection data array. Unlike the parallel-beam cases, a one-to-one correspondence does not exist for a local Fourier transform of the backprojected data array and a single line in the two-dimensional (2D) case or a single slice in the 3D case of the Fourier transform of the image function. However, the Fourier space of the image object can be built up after the local Fourier transforms of the 1/r-weighted backprojection data arrays are shifted and then summed in a laboratory frame. Thus the established relations Eq. (27) and Eq. (29) between the Fourier space of the image object and the Fourier transforms of the backprojected data arrays can be viewed as a generalized projection-slice theorem for divergent fan-beam and cone-beam projections. Once the Fourier space of the image function is built up, an inverse Fourier transform could be performed to reconstruct tomographic images from the divergent beam projections. Due to the linearity of the Fourier transform, an image reconstruction step can be performed either when the complete Fourier space is available or in parallel with the building of the Fourier space. Numerical simulations are performed to verify the generalized projection-slice theorem by using a disc phantom in the fan-beam case.

Algorithms↗