bluuebunny/crossref_metadata_2025 huggingface dataset:
Peak velocity determination using fast Fourier velocity encoding with minimal spatial encoding
Authors: Galea Daniela , Lauzon M. Louis , Drangova Maria
Published: October 2002

For quantitative peak velocity determination, a technique was developed that uses Fourier velocity encoding (FVE) for the fast acquisition of images of velocity with no spatial encoding other than slice selection. The technique produces images of velocity versus temporal frequency. In applications where the quantity of interest is the peak velocity and in‐plane spatial localization is not required, high SNR images are produced with reduced sensitivity to errors due to slice thickness and motion. The technique was validated using steady and pulsatile flow in a straight tube, and compared to both phase contrast measurements and numerical models using steady flow in a 50% and a 75% cosinusoidal stenosis phantom. Results show that for slices as large as 2 cm and/or undergoing periodic motion, FVE can accurately measure the peak velocity in cases where a distribution of velocities exist.
A dual‐energy subtraction technique for microcalcification imaging in digital mammography—A signal‐to‐noise analysis
Authors: Lemacks Michael R. , Kappadath S. Cheenu , Shaw Chris C. , Liu Xinming , Whitman Gary J.
Published: October 2002

Breast cancer may manifest as microcalcifications (μCs) in x‐ray mammography. However, the detection and visualization of μCs are often obscured by the overlapping tissue structures. The dual‐energy subtraction imaging technique offers an alternative approach for imaging and visualizing μCs. With this technique, separate high‐ and low‐energy images are acquired and their differences are used to “cancel” out the background tissue structures. However, the subtraction process could increase the statistical noise level relative to the calcification contrast. Therefore, a key issue with the dual‐energy subtraction imaging technique is to weigh the benefit of removing the cluttered background tissue structure over the drawback of reduced signal‐to‐noise ratio in the subtracted μC images. In this report, a theoretical framework for calculating the (quantum) noise in the subtraction images is developed and the numerical computations are described. We estimate the noise levels in the dual‐energy subtraction signals under various imaging conditions, including the x‐ray spectra, μC size, tissue composition, and breast thickness. The selection of imaging parameters is optimized to evaluate the feasibility of using a dual‐energy subtraction technique for the improved detection and visualization of μCs. We present the results and discuss its dependence on imaging parameters.
Using a tungsten rollbar to characterize the source spot of a megavoltage bremsstrahlung linac
Authors: Schach von Wittenau A. E. , Logan C. M. , Rikard R. D.
Published: October 2002

In photon teletherapy, the size and functional form of the photon source spot affect both the sharpness of the penumbra of treatment fields and the sharpness of portal images. Photon source spot parameters are also used in photon teletherapy dose calculation codes. A simple method for characterizing the source spot would complement the existing, more involved methods that have been described in the medical physics literature. Such a method, using a rollbar made of tungsten or other high‐Zmetal, is used in industrial radiography. We describe the use of a tungsten rollbar for characterizing the source spot edge spread function (and thereby the source spot size and shape) of a megavoltage bremsstrahlung photon source. We use Monte Carlo simulations to quantify anticipated experimental artifacts of the method, assuming typical spot sizes for circ‐function, Gaussian, and Bennett line shapes. We illustrate the use of the rollbar method by characterizing the source spot of a typical 9 MV linac used for industrial radiography. The source spot is analyzed using two approaches: (a) fitting the rollbar image with analytic functions and (b) using Abel inversion to obtain the cylindrically symmetric spot profile consistent with the measured rollbar image. Monte Carlo simulations, based on a 6 MV photon teletherapy accelerator, suggest that aspects of the method are applicable to medical bremsstrahlung sources.
A knowledge‐based cone‐beam x‐ray CT algorithm for dynamic volumetric cardiac imaging
Authors: Wang Ge , Zhao Shiying , Heuscher Dominic
Published: October 2002

With the introduction of spiral/helical multislice CT, medical x‐ray CT began a transition into cone‐beam geometry. The higher speed, thinner slice, and wider coverage with multislice/cone‐beam CT indicate a great potential for dynamic volumetric imaging, with cardiac CT studies being the primary example. Existing ECG‐gated cardiac CT algorithms have achieved encouraging results, but they do not utilize any time‐varying anatomical information of the heart, and need major improvements to meet critical clinical needs. In this paper, we develop a knowledge‐based spiral/helical multislice/cone‐beam CT approach for dynamic volumetric cardiac imaging. This approach assumes the relationship between the cardiac status and the ECG signal, such as the volume of the left ventricle as a function of the cardiac phase. Our knowledge‐based cardiac CT algorithm is evaluated in numerical simulation and patient studies. In the patient studies, the cardiac status is estimated initially from ECG data and subsequently refined with reconstructed images. Our results demonstrate significant image quality improvements in cardiac CT studies, giving clearly better clarity of the chamber boundaries and vascular structures. In conclusion, this approach seems promising for practical cardiac CT screening and diagnosis.
Resource Letter: FMMLS-1: Friction at macroscopic and microscopic length scales
Authors: Krim J.
Published: October 2002

This Resource Letter provides a guide to the literature on the fundamental origins of friction. Books, reviews, and journal articles are cited for the following topics: History of friction and tribology, the adhesion theory of macroscopic friction, first principles’ treatments of frictional energy dissipation at the atomic level, experimental methods for studying friction at the atomic-scale, stick-slip phenomena and lattice commensurability effects.
From Lorenz to Coulomb and other explicit gauge transformations
Authors: Jackson J. D.
Published: October 2002

The main purposes of this paper are (i) to illustrate explicitly by a number of examples the gauge functions χ(x,t) whose spatial and temporal derivatives transform one set of electromagnetic potentials into another equivalent set; and (ii) to show that, whatever propagation or nonpropagation characteristics are exhibited by the potentials in a particular gauge, the electric and magnetic fields are always the same and display the experimentally verified properties of causality and propagation at the speed of light. The example of the transformation from the Lorenz gauge (retarded solutions for both scalar and vector potential) to the Coulomb gauge (instantaneous, action-at-a-distance, scalar potential) is treated in detail. A transparent expression is obtained for the vector potential in the Coulomb gauge, with a finite nonlocality in time replacing the expected spatial nonlocality of the transverse current. A class of gauges (v-gauge) is described in which the scalar potential propagates at an arbitrary speed ν relative to the speed of light. The Lorenz and Coulomb gauges are special cases of the v-gauge. The last examples of gauges and explicit gauge transformation functions are the Hamiltonian or temporal gauge, the nonrelativistic Poincaré or multipolar gauge, and the relativistic Fock–Schwinger gauge.
Entangled photons, nonlocality, and Bell inequalities in the undergraduate laboratory
Authors: Dehlinger Dietrich , Mitchell M. W.
Published: October 2002

We use polarization-entangled photon pairs to demonstrate quantum nonlocality in an experiment suitable for advanced undergraduates. The photons are produced by spontaneous parametric downconversion using a violet diode laser and two nonlinear crystals. The polarization state of the photons is tunable. Using an entangled state analogous to that described in the Einstein–Podolsky–Rosen paradox, we demonstrate strong polarization correlations of the entangled photons. Bell’s idea of a hidden variable theory is presented by way of an example and compared to the quantum prediction. A test of the Clauser, Horne, Shimony, and Holt version of the Bell inequality finds S=2.307±0.035, in clear contradiction of hidden variable theories. The experiments described can be performed in an afternoon.
Planar near-field acoustical holography in a moving medium
Authors: Ruhala Richard J. , Swanson David C.
Published: October 2002

Near-field acoustical holography (NAH) is a well-established method to study acoustic radiation near a stationary sound source in a homogeneous, stationary medium. However, the current theory of NAH is not applicable to moving sound sources, such as automobiles and trains. In this paper, the inclusion of a moving medium (i.e., moving source and receiver) is introduced in the wave equation and a new set of equations for plannar NAH is developed. Equations are developed for the acoustic pressure, particle velocity, and intensity when mean flow is either parallel or perpendicular to the hologram plane. If the source and the measurement plane are moving at the same speed, the frequency Doppler effect is absent, but a wave number Doppler effect exists. This leads to errors when reconstructing the acoustic field both towards and away from the source using static NAH. To investigate these errors, a point source is studied analytically using planar NAH with flow in one direction. The effect of the medium moving parallel to the hologram plane is noted by a shift of the radiation circle in wave number space (k-space). A k-space Green’s function and a k-space filter are developed that include the effects of the moving medium.
Scattering from a ribbed finite cylindrical shell with internal axisymmetric oscillators
Authors: Tran-Van-Nhieu Michel
Published: October 2002

A theoretical formalism is elaborated to determine the acoustic field scattered from a finite cylindrical shell reinforced by a set of ribs with internal axisymmetric oscillators, the locations and properties of which can vary arbitrarily along the cylinder axis. Analytical expressions are derived for the scattered pressure and approximate expressions are proposed to calculate the backscattered field. Some applications have been carried out to investigate the problem of backscattering from a periodically ribbed finite cylindrical shell in the presence of rib aperiodicity or axisymmetric internal oscillators. The modifications of the main features associated with scattering from helical and Bloch–Floquet waves are examined and numerical results are presented with respect to the mean rib spacing and to the total mass of the internal structures.
Linear time domain model of the acoustic potential field
Authors: Lesniewski Peter J.
Published: October 2002

A new time domain formulation of the acoustic wave is developed to avoid approximating assumptions of the linearized scalar wave equation that limit its validity to low Mach particle velocity modeling or to a smooth potential field in a stationary medium. The proposed model offers precision of the moving frame while retaining the form of the widely used linearized scalar wave equation although with respect to modified coordinates. It is applicable to field calculations involving transient waves with unlimited particle velocity, propagating in inhomogenous fluids or in those with time varying density. The model is based on the exact flux continuity equation and the equation of motion, both using the moving reference frame. The resulting closed-form free space scalar wave equation employing total derivatives is converted back to the partial differential form by using modified independent variables. The modified variables are related to the common coordinates of space and time following integral expressions involving transient particle velocity representing wave radiated by each point of a stationary source. Consequently, transient field produced by complex surface velocity sources can be calculated following existing surface integrals of the radiation theory although using modified coordinates. The use of the proposed model is presented in a numerical simulation of a transient velocity source vibrating at selected magnitudes, leading to the determination of the propagating pressure and velocity wave at any point.
Comodulation masking release in consonant recognition
Authors: Kwon Bom Jun
Published: October 2002

Comodulation masking release (CMR) refers to an improvement in the detection threshold of a signal masked by noise with coherent amplitude fluctuation across frequency, as compared to noise without the envelope coherence. The present study tested whether such an advantage for signal detection would facilitate the identification of speech phonemes. Consonant identification of bandpass speech was measured under the following three masker conditions: (1) a single band of noise in the speech band (“on-frequency” masker); (2) two bands of noise, one in the on-frequency band and the other in the “flanking band,” with coherence of temporal envelope fluctuation between the two bands (comodulation); and (3) two bands of noise (on-frequency band and flanking band), without the coherence of the envelopes (noncomodulation). A pilot experiment with a small number of consonant tokens was followed by the main experiment with 12 consonants and the following masking conditions: three frequency locations of the flanking band and two masker levels. Results showed that in all conditions, the comodulation condition provided higher identification scores than the noncomodulation condition, and the difference in score was 3.5% on average. No significant difference was observed between the on-frequency only condition and the comodulation condition, i.e., an “unmasking” effect by the addition of a comodulated flaking band was not observed. The positive effect of CMR on consonant recognition found in the present study endorses a “cued-listening” theory, rather than an envelope correlation theory, as a basis of CMR in a suprathreshold task.
Rating, ranking, and understanding acoustical quality in university classrooms
Authors: Hodgson Murray
Published: October 2002

Nonoptimal classroom acoustical conditions directly affect speech perception and, thus, learning by students. Moreover, they may lead to voice problems for the instructor, who is forced to raise his/her voice when lecturing to compensate for poor acoustical conditions. The project applied previously developed simplified methods to predict speech intelligibility in occupied classrooms from measurements in unoccupied and occupied university classrooms. The methods were used to predict the speech intelligibility at various positions in 279 University of British Columbia (UBC) classrooms, when 70% occupied, and for four instructor voice levels. Classrooms were classified and rank ordered by acoustical quality, as determined by the room-average speech intelligibility. This information was used by UBC to prioritize classrooms for renovation. Here, the statistical results are reported to illustrate the range of acoustical qualities found at a typical university. Moreover, the variations of quality with relevant classroom acoustical parameters were studied to better understand the results. In particular, the factors leading to the best and worst conditions were studied. It was found that 81% of the 279 classrooms have “good,” “very good,” or “excellent” acoustical quality with a “typical” (average-male) instructor. However, 50 (18%) of the classrooms had “fair” or “poor” quality, and two had “bad” quality, due to high ventilation-noise levels. Most rooms were “very good” or “excellent” at the front, and “good” or “very good” at the back. Speech quality varied strongly with the instructor voice level. In the worst case considered, with a quiet female instructor, most of the classrooms were “bad” or “poor.” Quality also varies with occupancy, with decreased occupancy resulting in decreased quality. The research showed that a new classroom acoustical design and renovation should focus on limiting background noise. They should promote high instructor speech levels at the back of the classrooms. This involves, in part, limiting the amount of sound absorption that is introduced into classrooms to control reverberation. Speech quality is not very sensitive to changes in reverberation, so controlling it for its own sake should not be a design priority.
Buildup and breakdown of echo suppression for stimuli presented over headphones—the effects of interaural time and level differences
Authors: Krumbholz Katrin , Nobbe Andrea
Published: October 2002

The current study investigates buildup and breakdown of echo suppression for stimuli presented over headphones. The stimuli consisted of pairs of 120-μs clicks. The leading click (lead) and the lagging click (lag) in each pair were lateralized on opposite sides of the midline by means of interaural level differences (ILDs) of ±10 dB or interaural time differences (ITDs) of ±300 μs. Echo threshold was measured with an adaptive one-interval, two-alternative, forced-choice procedure with a subjective decision criterion, in which listeners had to report whether they heard a single, fused auditory event on one side of the midline, or two separate events on both sides. In the control conditions, referred to as the “single” conditions, echo threshold was measured for a single click pair, the test pair, presented in isolation. In addition to the control conditions, two kinds of test conditions were investigated, in which the test pair was preceded by 12 identical conditioning pairs: in the “same” conditions, the interaural configuration (ILDs or ITDs) of the conditioning pairs was identical to that of the test pair; in the “switch” conditions, the interaural configuration of lead and lag was reversed between the conditioning pairs and the test pair, in order to produce a switch in the lateralizations of the stimuli between the conditioning train and the test pair. No matter whether the lateralization of the clicks was produced by ILDs or by ITDs, most listeners experienced a buildup of echo suppression in the “same” conditions, manifested by a prolongation of echo threshold relative to the respective “single” conditions. However, the breakdown of echo suppression was much stronger in the ILD-switch than in the ITD-switch conditions. In five out of six listeners, the ITD switch had hardly any effect on echo threshold, although the ITDs (±300 μs) produced roughly the same degree of lateral displacement as the ILDs (±10 dB). These results suggest that the dynamic processes in echo suppression operate differentially in pathways responsible for the processing of interaural time and level differences.
Surf-generated noise signatures: A comparison of plunging and spilling breakers
Authors: Means Steven L. , Heitmeyer Richard M.
Published: October 2002

Range-time-frequency distributions of surf-generated noise were measured within the surf zone during the SandyDuck’97 experiment at Duck, NC. A 24-phone, 138-m, bottom-mounted, linear array located along a line perpendicular to the shore at a depth of 1 to 3 m recorded the surf-generated noise. Concurrent video measurements of the location, size, and time-evolution of the individual breaking waves directly above the array were made from a nearby 43-m tower. Source level spectra are obtained by using a modified fast field program to account for water column and geoacoustic propagation from the distributed source region to an individual hydrophone. The length, location, and orientation of the leading edge of breakers are tracked in time from rectified video images. It is observed that the source levels from spilling breakers are lower (∼5–10 dB) than those produced by plunging breakers that occurred during the same time period. Plunging breakers generated time-frequency signatures with a sharp onset while spilling breakers’ signatures had a gradual low-frequency precursor. Range-time signatures of plunging breakers indicate a burst of acoustic energy while spilling breakers’ signatures depict sound being generated over a longer time period with the source region moving with the breaking surface wave.
Modulation frequency and modulation level owing to vocal microtremor
Authors: Schoentgen Jean
Published: October 2002

Vocal microtremor designates a normal slow modulation of the vocal cycle lengths of speakers who do not suffer from pathological tremor of the limbs and whose voices are not perceived as tremulous. Vocal microtremor is therefore distinct from pathological vocal tremor. The objective is to report data about the modulation frequency and modulation level owing to vocal microtremor. The modulation data have been obtained for vowels [a], [i], and [u] sustained by normophonic and mildly dysphonic male and female speakers. The results are the following. First, modulation frequencies and relative modulation levels do not differ significantly for male and female speakers, normophonic and mildly dysphonic speakers, as well as for vowel timbres [a], [i], and [u]. Second, the typical interquartile intervals of the modulation frequency and modulation level are equal to 2.0–4.7 Hz and 0.4%–1.3%, respectively. Third, dissimilarities between data reported by different studies are due to different cutoff frequencies below which spectral peaks are considered not to contribute to vocal microtremor.
Auditory temporal resolution in birds: Discrimination of harmonic complexes
Authors: Dooling Robert J. , Leek Marjorie R. , Gleich Otto , Dent Micheal L.
Published: October 2002

The ability of three species of birds to discriminate among selected harmonic complexes with fundamental frequencies varying from 50 to 1000 Hz was examined in behavioral experiments. The stimuli were synthetic harmonic complexes with waveform shapes altered by component phase selection, holding spectral and intensive information constant. Birds were able to discriminate between waveforms with randomly selected component phases and those with all components in cosine phase, as well as between positive and negative Schroeder-phase waveforms with harmonic periods as short as 1–2 ms. By contrast, human listeners are unable to make these discriminations at periods less than about 3–4 ms. Electrophysiological measures, including cochlear microphonic and compound action potential measurements to the same stimuli used in behavioral tests, showed differences between birds and gerbils paralleling, but not completely accounting for, the psychophysical differences observed between birds and humans. It appears from these data that birds can hear the fine temporal structure in complex waveforms over very short periods. These data show birds are capable of more precise temporal resolution for complex sounds than is observed in humans and perhaps other mammals. Physiological data further show that at least part of the mechanisms underlying this high temporal resolving power resides at the peripheral level of the avian auditory system.
Hearing Sounds, Understanding Actions: Action Representation in Mirror Neurons
Authors: Kohler Evelyne , Keysers Christian , Umiltà M. Alessandra , Fogassi Leonardo , Gallese Vittorio , Rizzolatti Giacomo
Published: October 2002

Many object-related actions can be recognized by their sound. We found neurons in monkey premotor cortex that discharge when the animal performs a specific action and when it hears the related sound. Most of the neurons also discharge when the monkey observes the same action. These audiovisual mirror neurons code actions independently of whether these actions are performed, heard, or seen. This discovery in the monkey homolog of Broca's area might shed light on the origin of language: audiovisual mirror neurons code abstract contents—the meaning of actions—and have the auditory access typical of human language to these contents.
Sliding Density Wave in Sr
14
Cu
24
O
41
Ladder Compounds
Authors: Blumberg G. , Littlewood P. , Gozar A. , Dennis B. S. , Motoyama N. , Eisaki H. , Uchida S.
Published: October 2002

We used transport and Raman scattering measurements to identify the insulating state of self-doped spin ½ two-leg ladders of Sr
14
Cu
24
O
41
as a weakly pinned, sliding density wave with nonlinear conductivity and a giant dielectric response that persists to remarkably high temperatures.
Determination of Deforestation Rates of the World's Humid Tropical Forests
Authors: Achard Frédéric , Eva Hugh D. , Stibig Hans-Jürgen , Mayaux Philippe , Gallego Javier , Richards Timothy , Malingreau Jean-Paul
Published: October 2002

A recently completed research program (TREES) employing the global imaging capabilities of Earth-observing satellites provides updated information on the status of the world's humid tropical forest cover. Between 1990 and 1997, 5.8 ± 1.4 million hectares of humid tropical forest were lost each year, with a further 2.3 ± 0.7 million hectares of forest visibly degraded. These figures indicate that the global net rate of change in forest cover for the humid tropics is 23% lower than the generally accepted rate. This result affects the calculation of carbon fluxes in the global budget and means that the terrestrial sink is smaller than previously inferred.
A Structural Probe of the Doped Holes in Cuprate Superconductors
Authors: Abbamonte P. , Venema L. , Rusydi A. , Sawatzky G. A. , Logvenov G. , Bozovic I.
Published: October 2002

An unresolved issue concerning cuprate superconductors is whether the distribution of carriers in the CuO
2
plane is uniform or inhomogeneous. Because the carriers comprise a small fraction of the total charge density and may be rapidly fluctuating, modulations are difficult to detect directly. We demonstrate that in anomalous x-ray scattering at the oxygen K edge of the cuprates, the contribution of carriers to the scattering amplitude is selectively magnified 82 times. This enhances diffraction from the doped holes by more than 10
3
, permitting direct structural analysis of the superconducting ground state. Scattering from thin films of La
2
CuO
4+δ
(superconducting transition temperature = 39 K) at temperature = 50 ± 5 kelvin on the reciprocal space intervals (0,0,0.21) → (0,0,1.21) and (0,0,0.6) → (0.3,0,0.6) shows a rounding of the carrier density near the substrate suggestive of a depletion zone or similar effect. The structure factor for off-specular scattering was less than 3 × 10
−7
electrons, suggesting an absence of in-plane hole ordering in this material.
Stochastic Gene Expression in a Single Cell
Authors: Elowitz Michael B. , Levine Arnold J. , Siggia Eric D. , Swain Peter S.
Published: October 2002

Clonal populations of cells exhibit substantial phenotypic variation. Such heterogeneity can be essential for many biological processes and is conjectured to arise from stochasticity, or noise, in gene expression. We constructed strains of
Escherichia coli
that enable detection of noise and discrimination between the two mechanisms by which it is generated. Both stochasticity inherent in the biochemical process of gene expression (intrinsic noise) and fluctuations in other cellular components (extrinsic noise) contribute substantially to overall variation. Transcription rate, regulatory dynamics, and genetic factors control the amplitude of noise. These results establish a quantitative foundation for modeling noise in genetic networks and reveal how low intracellular copy numbers of molecules can fundamentally limit the precision of gene regulation.
Amphiphysin 2 (Bin1) and T-Tubule Biogenesis in Muscle
Authors: Lee Eunkyung , Marcucci Melissa , Daniell Laurie , Pypaert Marc , Weisz Ora A. , Ochoa Gian-Carlo , Farsad Khashayar , Wenk Markus R. , De Camilli Pietro
Published: October 2002

In striated muscle, the plasma membrane forms tubular invaginations (transverse tubules or T-tubules) that function in depolarization-contraction coupling. Caveolin-3 and amphiphysin were implicated in their biogenesis. Amphiphysin isoforms have a putative role in membrane deformation at endocytic sites. An isoform of amphiphysin 2 concentrated at T-tubules induced tubular plasma membrane invaginations when expressed in nonmuscle cells. This property required exon 10, a phosphoinositide-binding module. In developing myotubes, amphiphysin 2 and caveolin-3 segregated in tubular and vesicular portions of the T-tubule system, respectively. These findings support a role of the bilayer-deforming properties of amphiphysin at T-tubules and, more generally, a physiological role of amphiphysin in membrane deformation.
Recent Segmental Duplications in the Human Genome
Authors: Bailey Jeffrey A. , Gu Zhiping , Clark Royden A. , Reinert Knut , Samonte Rhea V. , Schwartz Stuart , Adams Mark D. , Myers Eugene W. , Li Peter W. , Eichler Evan E.
Published: October 2002

Primate-specific segmental duplications are considered important in human disease and evolution. The inability to distinguish between allelic and duplication sequence overlap has hampered their characterization as well as assembly and annotation of our genome. We developed a method whereby each public sequence is analyzed at the clone level for overrepresentation within a whole-genome shotgun sequence. This test has the ability to detect duplications larger than 15 kilobases irrespective of copy number, location, or high sequence similarity. We mapped 169 large regions flanked by highly similar duplications. Twenty-four of these hot spots of genomic instability have been associated with genetic disease. Our analysis indicates a highly nonrandom chromosomal and genic distribution of recent segmental duplications, with a likely role in expanding protein diversity.
Whole-Genome Shotgun Assembly and Analysis of the Genome of
Fugu rubripes
Authors: Aparicio Samuel , Chapman Jarrod , Stupka Elia , Putnam Nik , Chia Jer-ming , Dehal Paramvir , Christoffels Alan , Rash Sam , Hoon Shawn , Smit Arian , Gelpke Maarten D. Sollewijn , Roach Jared , Oh Tania , Ho Isaac Y. , Wong Marie , Detter Chris , Verhoef Frans , Predki Paul , Tay Alice , Lucas Susan , Richardson Paul , Smith Sarah F. , Clark Melody S. , Edwards Yvonne J. K. , Doggett Norman , Zharkikh Andrey , Tavtigian Sean V. , Pruss Dmitry , Barnstead Mary , Evans Cheryl , Baden Holly , Powell Justin , Glusman Gustavo , Rowen Lee , Hood Leroy , Tan Y. H. , Elgar Greg , Hawkins Trevor , Venkatesh Byrappa , Rokhsar Daniel , Brenner Sydney
Published: October 2002

The compact genome of
Fugu rubripes
has been sequenced to over 95% coverage, and more than 80% of the assembly is in multigene-sized scaffolds. In this 365-megabase vertebrate genome, repetitive DNA accounts for less than one-sixth of the sequence, and gene loci occupy about one-third of the genome. As with the human genome, gene loci are not evenly distributed, but are clustered into sparse and dense regions. Some “giant” genes were observed that had average coding sequence sizes but were spread over genomic lengths significantly larger than those of their human orthologs. Although three-quarters of predicted human proteins have a strong match to
Fugu
, approximately a quarter of the human proteins had highly diverged from or had no pufferfish homologs, highlighting the extent of protein evolution in the 450 million years since teleosts and mammals diverged. Conserved linkages between
Fugu
and human genes indicate the preservation of chromosomal segments from the common vertebrate ancestor, but with considerable scrambling of gene order.
Biosynthesis of the Enediyne Antitumor Antibiotic C-1027
Authors: Liu Wen , Christenson Steven D. , Standage Scott , Shen Ben
Published: October 2002

C-1027 is a potent antitumor agent with a previously undescribed molecular architecture and mode of action. Cloning and characterization of the 85-kilobase C-1027 biosynthesis gene cluster from
Streptomyces globisporus
revealed (i) an iterative type I polyketide synthase that is distinct from any bacterial polyketide synthases known to date, (ii) a general polyketide pathway for the biosynthesis of both the 9- and 10-membered enediyne antibiotics, and (iii) a convergent biosynthetic strategy for the C-1027 chromophore from four building blocks. Manipulation of genes governing C-1027 biosynthesis allowed us to produce an enediyne compound in a predicted manner.
Role of Formins in Actin Assembly: Nucleation and Barbed-End Association
Authors: Pruyne David , Evangelista Marie , Yang Changsong , Bi Erfei , Zigmond Sally , Bretscher Anthony , Boone Charles
Published: October 2002

Nucleation of branched actin filaments by the Arp2/3 complex is a conserved process in eukaryotic cells, yet the source of unbranched actin filaments has remained obscure. In yeast, formins stimulate assembly of actin cables independently of Arp2/3. Here, the conserved core of formin homology domains 1 and 2 of Bni1p (Bni1pFH1FH2) was found to nucleate unbranched actin filaments in vitro
.
Bni1pFH2 provided the minimal region sufficient for nucleation. Unique among actin nucleators, Bni1pFH1FH2 remained associated with the growing barbed ends of filaments. This combination of properties suggests a direct role for formins in regulating nucleation and polarization of unbranched filamentous actin structures.
Activation of Central Melanocortin Pathways by Fenfluramine
Authors: Heisler Lora K. , Cowley Michael A. , Tecott Laurence H. , Fan Wei , Low Malcolm J. , Smart James L. , Rubinstein Marcelo , Tatro Jeffrey B. , Marcus Jacob N. , Holstege Henne , Lee Charlotte E. , Cone Roger D. , Elmquist Joel K.
Published: October 2002

D-fenfluramine (d-FEN) was once widely prescribed and was among the most effective weight loss drugs, but was withdrawn from clinical use because of reports of cardiac complications in a subset of patients. Discerning the neurobiology underlying the anorexic action of d-FEN may facilitate the development of new drugs to prevent and treat obesity. Through a combination of functional neuroanatomy, feeding, and electrophysiology studies in rodents, we show that d-FEN–induced anorexia requires activation of central nervous system melanocortin pathways. These results provide a mechanistic explanation of d-FEN's anorexic actions and indicate that drugs targeting these downstream melanocortin pathways may prove to be effective and more selective anti-obesity treatments.
Microbial Reefs in the Black Sea Fueled by Anaerobic Oxidation of Methane
Authors: Michaelis Walter , Seifert Richard , Nauhaus Katja , Treude Tina , Thiel Volker , Blumenberg Martin , Knittel Katrin , Gieseke Armin , Peterknecht Katharina , Pape Thomas , Boetius Antje , Amann Rudolf , Jørgensen Bo Barker , Widdel Friedrich , Peckmann Jörn , Pimenov Nikolai V. , Gulin Maksim B.
Published: October 2002

Massive microbial mats covering up to 4-meter-high carbonate buildups prosper at methane seeps in anoxic waters of the northwestern Black Sea shelf. Strong
13
C depletions indicate an incorporation of methane carbon into carbonates, bulk biomass, and specific lipids. The mats mainly consist of densely aggregated archaea (phylogenetic ANME-1 cluster) and sulfate-reducing bacteria (
Desulfosarcina/Desulfococcus
group). If incubated in vitro, these mats perform anaerobic oxidation of methane coupled to sulfate reduction. Obviously, anaerobic microbial consortia can generate both carbonate precipitation and substantial biomass accumulation, which has implications for our understanding of carbon cycling during earlier periods of Earth's history.
Band Gap Fluorescence from Individual Single-Walled Carbon Nanotubes
Authors: O'Connell Michael J. , Bachilo Sergei M. , Huffman Chad B. , Moore Valerie C. , Strano Michael S. , Haroz Erik H. , Rialon Kristy L. , Boul Peter J. , Noon William H. , Kittrell Carter , Ma Jianpeng , Hauge Robert H. , Weisman R. Bruce , Smalley Richard E.
Published: October 2002

Fluorescence has been observed directly across the band gap of semiconducting carbon nanotubes. We obtained individual nanotubes, each encased in a cylindrical micelle, by ultrasonically agitating an aqueous dispersion of raw single-walled carbon nanotubes in sodium dodecyl sulfate and then centrifuging to remove tube bundles, ropes, and residual catalyst. Aggregation of nanotubes into bundles otherwise quenches the fluorescence through interactions with metallic tubes and substantially broadens the absorption spectra. At pH less than 5, the absorption and emission spectra of individual nanotubes show evidence of band gap–selective protonation of the side walls of the tube. This protonation is readily reversed by treatment with base or ultraviolet light.
Use of Ionic Liquids for π-Conjugated Polymer Electrochemical Devices
Authors: Lu Wen , Fadeev Andrei G. , Qi Baohua , Smela Elisabeth , Mattes Benjamin R. , Ding Jie , Spinks Geoffrey M. , Mazurkiewicz Jakub , Zhou Dezhi , Wallace Gordon G. , MacFarlane Douglas R. , Forsyth Stewart A. , Forsyth Maria
Published: October 2002

π-Conjugated polymers that are electrochemically cycled in ionic liquids have enhanced lifetimes without failure (up to 1 million cycles) and fast cycle switching speeds (100 ms). We report results for electrochemical mechanical actuators, electrochromic windows, and numeric displays made from three types of
π
-conjugated polymers: polyaniline, polypyrrole, and polythiophene. Experiments were performed under ambient conditions, yet the polymers showed negligible loss in electroactivity. These performance advantages were obtained by using environmentally stable, room-temperature ionic liquids composed of 1-butyl-3-methyl imidazolium cations together with anions such as tetrafluoroborate or hexafluorophosphate.
Aerial Dispersal of Pathogens on the Global and Continental Scales and Its Impact on Plant Disease
Authors: Brown James K. M. , Hovmøller Mogens S.
Published: October 2002

Some of the most striking and extreme consequences of rapid, long-distance aerial dispersal involve pathogens of crop plants. Long-distance dispersal of fungal spores by the wind can spread plant diseases across and even between continents and reestablish diseases in areas where host plants are seasonally absent. For such epidemics to occur, hosts that are susceptible to the same pathogen genotypes must be grown over wide areas, as is the case with many modern crops. The strongly stochastic nature of long-distance dispersal causes founder effects in pathogen populations, such that the genotypes that cause epidemics in new territories or on cultivars with previously effective resistance genes may be atypical. Similar but less extreme population dynamics may arise from long-distance aerial dispersal of other organisms, including plants, viruses, and fungal pathogens of humans.
Formation of Immiscible Alloy Powders with Egg-Type Microstructure
Authors: Wang C. P. , Liu X. J. , Ohnuma I. , Kainuma R. , Ishida K.
Published: October 2002

The egg-type core microstructure where one alloy encases another has previously been obtained during experiments in space. Working with copper-iron base alloys prepared by conventional gas atomization, we were able to obtain this microstructure under gravity conditions. The minor liquid phase always formed the core of the egg, and it sometimes also formed a shell layer. The origin of the formation of this core microstructure can be explained by Marangoni motion on the basis of the temperature dependence of the interfacial energy, which shows that this type of powder can be formed even if the cooling rate is very high.
Brownian Motion of DNA Confined Within a Two-Dimensional Array
Authors: Nykypanchuk Dmytro , Strey Helmut H. , Hoagland David A.
Published: October 2002

Linear DNA molecules are visualized while undergoing Brownian motion inside media patterned with molecular-sized spatial constraints. The media, prepared by colloidal templating, trap the macromolecules within a two-dimensional array of spherical cavities interconnected by circular holes. Across a broad DNA size range, diffusion does not proceed by the familiar mechanisms of reptation or sieving. Rather, because of their inherent flexibility, DNA molecules strongly localize in cavities and only sporadically “jump” through holes. Jumping closely follows Poisson statistics. By reducing DNA's configurational freedom, the holes act as molecular weight–dependent entropic barriers. Sterically constrained macromolecular diffusion underlies many separation methods and assumes an important role in intracellular and extracellular transport.
Delocalization of Protons in Liquid Water
Authors: Bakker H. J. , Nienhuys H.-K.
Published: October 2002

We find that the vibrational potential of the O-H stretch vibrations of liquid water shows extreme anharmonicity that arises from the O-H ⋯ O hydrogen bond interaction. We observe that already in the second excited state of the O-H stretch vibration, the hydrogen atom becomes delocalized between the oxygen atoms of two neighboring water molecules. The energy required for this delocalization is unexpectedly low and corresponds to less than 20% of the dissociation energy of the O-H bond of the water molecule in the gas phase.
Modulation of Postendocytic Sorting of G Protein-Coupled Receptors
Authors: Whistler Jennifer L. , Enquist Johan , Marley Aaron , Fong Jamie , Gladher Fredrik , Tsuruda Pamela , Murray Stephen R. , von Zastrow Mark
Published: October 2002

Recycling of the mu opioid receptor to the plasma membrane after endocytosis promotes rapid resensitization of signal transduction, whereas targeting of the delta opioid receptor (DOR) to lysosomes causes proteolytic down-regulation. We identified a protein that binds preferentially to the cytoplasmic tail of the DOR as a candidate heterotrimeric GTP-binding protein (G protein)–coupled receptor-associated sorting protein (GASP). Disruption of the DOR-GASP interaction through receptor mutation or overexpression of a dominant negative fragment of GASP inhibited receptor trafficking to lysosomes and promoted recycling. The GASP family of proteins may modulate lysosomal sorting and functional down-regulation of a variety of G protein–coupled receptors.
Travelers in Space and Time
Authors: Grady Monica
Published: October 2002

Meteorites
A Journey Through Space and Time. Alex Bevan and John de Laeter. Smithsonian Institution Press, Washington, DC, and University of New South Wales Press, Sydney, Australia, 2002. $35.95, £27.50, A$59.95. ISBN 1-58834-021-X.

The Cambridge Encyclopedia of Meteorites
. O. Richard Norton. Cambridge University Press, New York, 2002. 374 pp. $50. ISBN 0-521-62143-7.

Both of these profusely illustrated books review the origins, composition, structure, classification, and study of extraterrestrial rocks for nonspecialists.
Variant of SCN5A Sodium Channel Implicated in Risk of Cardiac Arrhythmia
Authors: Splawski Igor , Timothy Katherine W. , Tateyama Michihiro , Clancy Colleen E. , Malhotra Alka , Beggs Alan H. , Cappuccio Francesco P. , Sagnella Giuseppe A. , Kass Robert S. , Keating Mark T.
Published: October 2002

Every year, ∼450,000 individuals in the United States die suddenly of cardiac arrhythmia. We identified a variant of the cardiac sodium channel gene
SCN5A
that is associated with arrhythmia in African Americans (
P
= 0.000028) and linked with arrhythmia risk in an African-American family (
P
= 0.005). In transfected cells, the variant allele (Y1102) accelerated channel activation, increasing the likelihood of abnormal cardiac repolarization and arrhythmia. About 13.2% of African Americans carry the Y1102 allele. Because Y1102 has a subtle effect on risk, most carriers will never have an arrhythmia. However, Y1102 may be a useful molecular marker for the prediction of arrhythmia susceptibility in the context of additional acquired risk factors such as the use of certain medications.
Electron Solvation in Two Dimensions
Authors: Miller A. D. , Bezel I. , Gaffney K. J. , Garrett-Roe S. , Liu S. H. , Szymanski P. , Harris C. B.
Published: October 2002

Ultrafast two-photon photoemission has been used to study electron solvation at two-dimensional metal/polar-adsorbate interfaces. The molecular motion that causes the excess electron solvation is manifested as a dynamic shift in the electronic energy. Although the initially excited electron is delocalized in the plane of the interface, interactions with the adsorbate can lead to its localization. A method for determining the spatial extent of the localized electron in the plane of the interface has been developed. This spatial extent was measured to be on the order of a single adsorbate molecule.
Steering Attosecond Electron Wave Packets with Light
Authors: Kienberger R. , Hentschel M. , Uiberacker M. , Spielmann Ch. , Kitzler M. , Scrinzi A. , Wieland M. , Westerwalbesloh Th. , Kleineberg U. , Heinzmann U. , Drescher M. , Krausz F.
Published: October 2002

Photoelectrons excited by extreme ultraviolet or x-ray photons in the presence of a strong laser field generally suffer a spread of their energies due to the absorption and emission of laser photons. We demonstrate that if the emitted electron wave packet is temporally confined to a small fraction of the oscillation period of the interacting light wave, its energy spectrum can be up- or downshifted by many times the laser photon energy without substantial broadening. The light wave can accelerate or decelerate the electron's drift velocity, i.e., steer the electron wave packet like a classical particle. This capability strictly relies on a sub-femtosecond duration of the ionizing x-ray pulse and on its timing to the phase of the light wave with a similar accuracy, offering a simple and potentially single-shot diagnostic tool for attosecond pump-probe spectroscopy.
Structural Studies of Several Distinct Metastable Forms of Amorphous Ice
Authors: Tulk C. A. , Benmore C. J. , Urquidi J. , Klug D. D. , Neuefeind J. , Tomberli B. , Egelstaff P. A.
Published: October 2002

Structural changes during annealing of high-density amorphous ice were studied with both neutron and x-ray diffraction. The first diffraction peak was followed from the high- to the low-density amorphous form. Changes were observed to occur through a series of intermediate forms that appear to be metastable at each anneal temperature. Five distinct amorphous forms were studied with neutron scattering, and many more forms may be possible. Radial distribution functions indicate that the structure evolves systematically between 4 and 8 angstroms. The phase transformations in low-temperature liquid water may be much more complex than currently understood.
The Vibration-Rotation Emission Spectrum of Free BeH
2
Authors: Bernath Peter F. , Shayesteh Alireza , Tereszchuk Keith , Colin Reginald
Published: October 2002

The gaseous BeH
2
molecule has been synthesized by means of an electrical discharge inside a high-temperature furnace and identified with infrared emission spectroscopy. The antisymmetric stretching mode ν
3
has been detected near 2179 reciprocal centimeters. The BeH
2
molecule has a linear, symmetric structure with an
r
0
BeH bond length of 1.333761(2) angstroms.
How Surface Topography Relates to Materials' Properties
Authors: Assender Hazel , Bliznyuk Valery , Porfyrakis Kyriakos
Published: October 2002

The topography of a surface is known to substantially affect the bulk properties of a material. Despite the often nanoscale nature of the surface undulations, the influence they have may be observed by macroscopic measurements. This review explores many of the areas in which the effect of topography is macroscopically relevant, as well as introducing some recent developments in topographic analysis and control.