bluuebunny/crossref_metadata_2025 huggingface dataset:
Is the Kramers-Kronig relationship between ultrasonic attenuation and dispersion maintained in the presence of apparent losses due to phase cancellation?
Authors: Bauer Adam Q. , Marutyan Karen R. , Holland Mark R. , Miller James G.
Published: July 2007

Phase cancellation effects can compromise the integrity of ultrasonic measurements performed with phase sensitive receiving apertures. A lack of spatial coherence of the ultrasonic field incident on a phase sensitive receiving array can produce inaccuracies of the measured attenuation coefficient and phase velocity. The causal (Kramers-Kronig) link between these two quantities in the presence of phase distortion is investigated using two plastic polymer materials, Plexiglas™ and Lexan™, that exhibit attenuation coefficients that increase linearly with frequency, in a fashion analogous to that of soft tissue. Flat and parallel plates were machined to have a step of a thickness corresponding to an integer number of half wavelengths within the bandwidth investigated, 3 to 7MHz. Insonification of the stepped portion of each plate produces phase cancellation artifacts at the receiving aperture and, therefore, in the measured frequency dependent attenuation coefficient. Dispersion predictions using two different forms of the Kramers-Kronig relations were performed for the flat and the stepped regions of each plastic plate. Despite significant phase distortion and a detection system sensitive to these aberrations, the Kramers-Kronig link between the apparent attenuation coefficient and apparent phase velocity dispersion remains intact.
Nonlinear standing waves in a resonator with feedback control
Authors: Huang X. Y. , Nguyen N. T. , Jiao Z. J.
Published: July 2007

An experimental study is presented to demonstrate that nonlinear effect on standing waves in a resonator can be reduced by a feedback loop responding to the second harmonic. The resonator was a cylindrical tube sealed at one end and driven by a horn driver unit at another end. The feedback control loop consisted of a pressure sensor, a frequency filter, a phase shifter, and an actuator. The results show that the waveform distortions can be eliminated and large amplitude sinusoidal pressure oscillations are obtained. A simple model is proposed for a qualitative discussion on the control mechanism, which shows that the feedback loop alters the imaginary part of the complex mode frequency so as to suppress (or enhance) the second harmonic.
Vorticity dynamics and sound generation in two-dimensional fluid flow
Authors: Nagem Raymond J. , Sandri Guido , Uminsky David
Published: July 2007

An approximate solution to the two-dimensional incompressible fluid equations is constructed by expanding the vorticity field in a series of derivatives of a Gaussian vortex. The expansion is used to analyze the motion of a corotating Gaussian vortex pair, and the spatial rotation frequency of the vortex pair is derived directly from the fluid vorticity equation. The resulting rotation frequency includes the effects of finite vortex core size and viscosity and reduces, in the appropriate limit, to the rotation frequency of the Kirchhoff point vortex theory. The expansion is then used in the low Mach number Lighthill equation to derive the far-field acoustic pressure generated by the Gaussian vortex pair. This pressure amplitude is compared with that of a previous fully numerical simulation in which the Reynolds number is large and the vortex core size is significant compared to the vortex separation. The present analytic result for the far-field acoustic pressure is shown to be substantially more accurate than previous theoretical predictions. The given example suggests that the vorticity expansion is a useful tool for the prediction of sound generated by a general distributed vorticity field.
Uncertainty estimation in seismo-acoustic reflection travel time inversion
Authors: Dettmer Jan , Dosso Stan E. , Holland Charles W.
Published: July 2007

This paper develops a nonlinear Bayesian inversion for high-resolution seabed reflection travel time data including rigorous uncertainty estimation and examination of statistical assumptions. Travel time data are picked on seismo-acoustic traces and inverted for a layered sediment sound-velocity model. Particular attention is paid to picking errors which are often biased, correlated, and nonstationary. Non-Toeplitz data covariance matrices are estimated and included in the inversion along with unknown travel time offset (bias) parameters to account for these errors. Simulated experiments show that neglecting error covariances and biases can cause misleading inversion results with unrealistically high confidence. The inversion samples the posterior probability density and provides a solution in terms of one- and two-dimensional marginal probability densities, correlations, and credibility intervals. Statistical assumptions are examined through the data residuals with rigorous statistical tests. The method is applied to shallow-water data collected on the Malta Plateau during the SCARAB98 experiment.
Influence of fundamental frequency and source elevation on the vertical localization of complex tones and complex tone pairs
Authors: Cabrera Densil , Morimoto Masayuki
Published: July 2007

This study investigates the vertical localization of single complex tones (monads) and simultaneous complex tone pairs (dyads), especially as it is affected by their fundamental frequency and source elevation. Two complex tone timbres are considered: one consisting of five low-order harmonics, and the other of all odd harmonics (a square wave). Sound sources were at −15, 0, 15, and 30deg from the horizontal plane at ear height. For eight subjects, this source array was in the median plane, and for a further nine subjects, it was directly to the subject’s left (lateral plane). The subjects localized the angle of the auditory image(s) of one or two complex tones around the vertical plane containing the sound sources. Mean responses for the five-harmonic complex tones show a systematic effect (referred to as Pratt’s effect) of fundamental frequency on vertical localization—whereby high-frequency complex tones are localized to positions higher than low-frequency complex tones for equivalent source positions. For the square wave, the sound-source position dominates localization, although some effect of fundamental frequency is evident for median plane sources.
Acoustic scattering by a sphere with a hemispherically split boundary condition
Authors: Treeby Bradley E. , Pan Jie , Paurobally Roshun M.
Published: July 2007

A general analytical model is developed for the scattering of sound by a sphere with a nonuniform impedance boundary condition that is divided into two uniformly distributed hemispheres. In addition to the overall solution for the time harmonic pressure, the analytical result gives insight into the modal contributions and coupling for different cases of source incidence and boundary impedance. Modal cross coupling is shown to exist between incoming and scattered wave modes of equi-order and nonequal degree when the degrees are opposite in parity (odd-even or even-odd coupling). This cross coupling is strongest between modes of adjacent degree, and decreases as the degrees become dissimilar. The overall magnitude of the cross coupling is dependent on the extent of the impedance mismatch between the two surface hemispheres. Simulation and discussion are given for several specific cases of source incidence and impedance (each hemisphere is given a different constant impedance value). These results are consistent with expectations from the scattering of sound by a sphere with a uniformly distributed surface boundary. The broad scattering characteristics of the hemispherically divided sphere are shown to be analogous to connecting the appropriate sectors from the corresponding uniformly distributed spheres.
An improved multimodal method for sound propagation in nonuniform lined ducts
Authors: Bi WenPing , Pagneux Vincent , Lafarge Denis , Aurégan Yves
Published: July 2007

An efficient method is proposed for modeling time harmonic acoustic propagation in a nonuniform lined duct without flow. The lining impedance is axially segmented uniform, but varies circumferentially. The sound pressure is expanded in term of rigid duct modes and an additional function that carries the information about the impedance boundary. The rigid duct modes and the additional function are known a priori so that calculations of the true liner modes, which are difficult, are avoided. By matching the pressure and axial velocity at the interface between different uniform segments, scattering matrices are obtained for each individual segment; these are then combined to construct a global scattering matrix for multiple segments. The present method is an improvement of the multimodal propagation method, developed in a previous paper [Bi et al., J. Sound Vib. 289, 1091–1111 (2006)]. The radial rate of convergence is improved from O(n−2), where n is the radial mode indices, to O(n−4). It is numerically shown that using the present method, acoustic propagation in the nonuniform lined intake of an aeroengine can be calculated by a personal computer for dimensionless frequency K up to 80, approaching the third blade passing frequency of turbofan noise.
Otoacoustic emission sensitivity to low levels of noise-induced hearing loss
Authors: Sisto Renata , Chelotti Silvia , Moriconi Lido , Pellegrini Stefania , Citroni Angela , Monechi Valeria , Gaeta Rosa , Pinto Iole , Stacchini Nicola , Moleti Arturo
Published: July 2007

With the aim of investigating the capability of otoacoustic emission (OAE) in the detection of low levels of noise-induced hearing loss, audiometric and otoacoustic data of young workers (age: 18–35) exposed to different levels of industrial noise have been recorded. These subjects are participating in a long-term longitudinal study, in which audiometric, exposure (both professional and extra-professional), and OAE data (transient evoked and distortion product) will be collected for a period of several years. All measurements have been performed, during routine occupational health surveillance, with a standard clinical apparatus and acquisition procedure, which can be easily used in the occupational safety practice. The first study was focused on the correlation between transient evoked OAE signal-to-noise ratio and distortion product (DPOAE) OAE level and the audiometric threshold, investigating the causes of the rather large intersubject variability of the OAE levels. The data analysis has shown that, if both OAE data and audiometric data are averaged over a sufficiently large bandwidth, the correlation between DPOAE levels and audiometric hearing threshold is sufficient to design OAE-based diagnostic tests with good sensitivity and specificity also in a very mild hearing loss range, between 10 and 20dB.
Anisotropy of the backscatter coefficient of formalin-fixed ovine myocardium
Authors: Yang Min , Krueger Todd M. , Holland Mark R. , Miller James G.
Published: July 2007

The objective of this study was to measure the backscatter coefficient of formalin-fixed myocardial tissue as a function of angle of insonification relative to the myocardial fiber direction. Backscatter measurements were performed on eight cylindrical formalin-fixed lamb myocardial specimens and compensated for attenuation and diffraction effects to determine the backscatter coefficient. The backscatter coefficient at 5MHz was found to be maximum for insonification perpendicular to the predominant myofiber orientation and minimum for parallel insonification, with values of (17±14) and (1.2±0.7)×10−4cm−1sr−1 (mean±standard deviation), respectively.
Numerical and experimental validation of a hybrid finite element-statistical energy analysis method
Authors: Cotoni Vincent , Shorter Phil , Langley Robin
Published: July 2007

The finite element (FE) and statistical energy analysis (SEA) methods have, respectively, high and low frequency limitations and there is therefore a broad class of “mid-frequency” vibro-acoustic problems that are not suited to either FE or SEA. A hybrid method combining FE and SEA was recently presented for predicting the steady-state response of vibro-acoustic systems with uncertain properties. The subsystems with long wavelength behavior are modeled deterministically with FE, while the subsystems with short wavelength behavior are modeled statistically with SEA. The method yields the ensemble average response of the system where the uncertainty is confined in the SEA subsystems. This paper briefly summarizes the theory behind the method and presents a number of detailed numerical and experimental validation examples for structure-borne noise transmission.
Density and sound speed of two gelatinous zooplankton: Ctenophore (Mnemiopsis leidyi) and lion’s mane jellyfish (Cyanea capillata)
Authors: Warren Joseph D. , Smith Joy N.
Published: July 2007

The density and sound speed of two coastal, gelatinous zooplankton, Mnemiopsis leidyi (a ctenophore) and Cyanea capillata (lion’s mane jellyfish), were measured. These parameters are important inputs to acoustic scattering models. Two different methods were used to measure the density of individual animals: one used a balance and graduated cylinder to determine the mass and displacement volume of the animal, the other varied the density of the solution the animal was immersed in. When the same animal was measured using both methods, density values were within 1% of each other. A travel-time difference method was used to measure the sound speed within the animals. The densities of both zooplankton slightly decreased as the animals increased in length, mass, and volume. The ratio of animal density and sound speed to the surrounding seawater (g and h, respectively) are reported for both animals. For Mnemiopsis leidyi ranging in length from 1 to 5cm, the mean value (±standard deviation) of g and h were 1.009 (±0.004) and 1.007 (±0.001). For Cyanea capillata ranging in bell diameter from 2 to 11cm, the mean value (±standard deviation) of g and single value of h were 1.009 (±0.004) and 1.0004.
Tele-infrasonic studies of hard-rock mining explosions
Authors: McKenna Mihan H. , Stump Brian W. , Hayek Sylvia , McKenna Jason R. , Stanton Terry R.
Published: July 2007

The Lac-du-Bonnet infrasound station, IS-10, and the Minnesota iron mines 390km to the southeast are ideally located to assess the accuracy of atmospheric profiles needed for infrasound modeling. Infrasonic data from 2003 associated with explosions at the iron mine were analyzed for effects of explosion size and atmospheric conditions on observations with well-constrained ground truth. Noise was the determining factor for observation; high noise conditions sometimes prevented unequivocal identification of infrasound arrivals. Observed arrivals had frequencies of 0.5to5Hz, with a dominant frequency of 2Hz, and generally had durations on the order of 10s or less. There was no correlation between explosive amount and observability. Tele-infrasonic propagation distances (greater than 250km) produce thermospheric ray paths. Modeling is based upon MSIS/HWM (Mass Spectrometer Incoherent Scatter/Horizontal Wind Model) and NRL-G2S (Naval Research Laboratory Ground to Space) datasets. The NRL-G2S dataset provided more accurate travel time predictions that the MSIS/HWM dataset. PE modeling for the NRL-G2S dataset indicates energy loss at higher frequencies (around 4Hz). Additionally, applying the Sutherland/Bass model through the NRL-G2S realization of the atmosphere in InfraMAP results in predicted amplitudes too small to be observed.
Padé approximation in time-domain boundary conditions of porous surfaces
Authors: Ostashev Vladimir E. , Collier Sandra L. , Wilson D. Keith , Aldridge David F. , Symons Neill P. , Marlin David
Published: July 2007

Formulation and implementation of time-domain boundary conditions (TDBCs) at the surface of a reactive porous material are made challenging by the slow decay, complexity, or noncausal nature of many commonly used models of porous materials. In this paper, approaches are described that improve computational efficiency and enforce causality. One approach involves approximating the known TDBC for the modified Zwikker-Kosten impedance model as a summation of decaying exponential functions. A second approach, which can be applied to any impedance model, involves replacing the characteristic admittance with its Padé approximation. Then, approximating fractional derivatives with decaying exponentials, a causal and recursive TDBC is formulated
Individual differences in auditory abilities
Authors: Kidd Gary R. , Watson Charles S. , Gygi Brian
Published: July 2007

Performance on 19 auditory discrimination and identification tasks was measured for 340 listeners with normal hearing. Test stimuli included single tones, sequences of tones, amplitude-modulated and rippled noise, temporal gaps, speech, and environmental sounds. Principal components analysis and structural equation modeling of the data support the existence of a general auditory ability and four specific auditory abilities. The specific abilities are (1) loudness and duration (overall energy) discrimination; (2) sensitivity to temporal envelope variation; (3) identification of highly familiar sounds (speech and nonspeech); and (4) discrimination of unfamiliar simple and complex spectral and temporal patterns. Examination of Scholastic Aptitude Test (SAT) scores for a large subset of the population revealed little or no association between general or specific auditory abilities and general intellectual ability. The findings provide a basis for research to further specify the nature of the auditory abilities. Of particular interest are results suggestive of a familiar sound recognition (FSR) ability, apparently specialized for sound recognition on the basis of limited or distorted information. This FSR ability is independent of normal variation in both spectral-temporal acuity and of general intellectual ability.
Investigation of microphones as near-ground sensors for seismic detection of buried landmines
Authors: Larson Gregg D. , Martin James S. , Scott Waymond R.
Published: July 2007

Commercially available microphones were investigated as near-ground sensors to measure the acoustic pressure and the vertical pressure gradient of evanescent air-acoustic waves associated with audio-frequency seismic waves. Measurements in close proximity to the surface and the use of waveguides were found to improve the microphone signal’s quality, the comparison of its seismic sensitivity to its sensitivity to propagating sound (ambient acoustic noise and nonseismic reverberation). Landmine images formed using microphone data collected in a laboratory experimental model clearly locate buried inert landmines but exhibit more clutter than images of the same objects formed with seismic displacement data collected using other techniques.
Spectral properties of the interference head wave
Authors: Choi Jee Woong , Dahl Peter H.
Published: July 2007

The interference head wave propagating through a sediment with a linear sound speed gradient is studied as a function of the parameter ζ, which is itself a function of acoustic frequency f, sediment sound speed and its gradient, and range. For ζ<1 the amplitude spectrum of the interference head waves goes as ∣S(f)∣∕f, where S(f) is the source spectrum. For increasing ζ beyond unity a more complicated modulation of S(f) ensues, which is explained by a channel transfer function H1(f), constructed analytically from a summation of terms involving zeroth-order refracted waves (referred to as a ray approach). For ζ≳2 this summation compares well with a wave theory result for the interference head wave involving a fluid-fluid boundary. The amplitude spectrum of the interference head wave in the absence of sediment attenuation is ∣S(f)∣∙∣H1(f)∣ and it is essential to know these to obtain an estimate of sediment attenuation from field observations. Examples of ∣S(f)∣∙∣H1(f)∣ are presented for which H1(f) is computed directly using the ray approach and indirectly using the parabolic wave equation. A brief discussion on the application of these results towards the inversion of sediment attenuation is given.
A new definition of boundary point between early reflections and late reverberation in room impulse responses
Authors: Hidaka Takayuki , Yamada Yoshinari , Nakagawa Takehiko
Published: July 2007

The early reflections in the room impulse response are usually defined as those observed within the initial 80ms after the arrival of the direct sound, after which time the sound field is called reverberant. This number was chosen from measurements of other functions in a limited number of halls. In order to give an objective foundation to this time separation and to establish a physical indicator for it, a new method is proposed that defines a “transition time tL,” which is the time at which the energy correlation between the direct plus initial sound and the subsequent decaying sound first achieves a specified low value. For various halls this number is shown and its relevance as a new parameter is discussed.
Acoustical classification of woods for string instruments
Authors: Yoshikawa Shigeru
Published: July 2007

Two basic types of wood are used to make stringed musical instruments: woods for soundboards (top plates) and those for frame boards (back and side plates). A new way to classify the acoustical properties of woods and clearly separate these two groups is proposed in this paper. The transmission parameter (product of propagation speed and Q value of the longitudinal wave along the wood grain) and the antivibration parameter (wood density divided by the propagation speed along the wood grain) are introduced in the proposed classification scheme. Two regression lines, drawn for traditional woods, show the distinctly different functions required by soundboards and frame boards. These regression lines can serve as a reference to select the best substitute woods when traditional woods are not available. Moreover, some peculiarities of Japanese string instruments, which are made clear by comparing woods used for them with woods used for Western and Chinese instruments, are briefly discussed.
Stability and Diversity of Ecosystems
Authors: Ives Anthony R. , Carpenter Stephen R.
Published: July 2007

Understanding the relationship between diversity and stability requires a knowledge of how species interact with each other and how each is affected by the environment. The relationship is also complex, because the concept of stability is multifaceted; different types of stability describing different properties of ecosystems lead to multiple diversity-stability relationships. A growing number of empirical studies demonstrate positive diversity-stability relationships. These studies, however, have emphasized only a few types of stability, and they rarely uncover the mechanisms responsible for stability. Because anthropogenic changes often affect stability and diversity simultaneously, diversity-stability relationships cannot be understood outside the context of the environmental drivers affecting both. This shifts attention away from diversity-stability relationships toward the multiple factors, including diversity, that dictate the stability of ecosystems.
Dopamine-Mushroom Body Circuit Regulates Saliency-Based Decision-Making in
Drosophila
Authors: Zhang Ke , Guo Jian Zeng , Peng Yueqing , Xi Wang , Guo Aike
Published: July 2007

Drosophila melanogaster
can make appropriate choices among alternative flight options on the basis of the relative salience of competing visual cues. We show that this choice behavior consists of early and late phases; the former requires activation of the dopaminergic system and mushroom bodies, whereas the latter is independent of these activities. Immunohistological analysis showed that mushroom bodies are densely innervated by dopaminergic axons. Thus, the circuit from the dopamine system to mushroom bodies is crucial for choice behavior in
Drosophila.
Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization
Authors: Putnam Nicholas H. , Srivastava Mansi , Hellsten Uffe , Dirks Bill , Chapman Jarrod , Salamov Asaf , Terry Astrid , Shapiro Harris , Lindquist Erika , Kapitonov Vladimir V. , Jurka Jerzy , Genikhovich Grigory , Grigoriev Igor V. , Lucas Susan M. , Steele Robert E. , Finnerty John R. , Technau Ulrich , Martindale Mark Q. , Rokhsar Daniel S.
Published: July 2007

Sea anemones are seemingly primitive animals that, along with corals, jellyfish, and hydras, constitute the oldest eumetazoan phylum, the Cnidaria. Here, we report a comparative analysis of the draft genome of an emerging cnidarian model, the starlet sea anemone
Nematostella vectensis
. The sea anemone genome is complex, with a gene repertoire, exon-intron structure, and large-scale gene linkage more similar to vertebrates than to flies or nematodes, implying that the genome of the eumetazoan ancestor was similarly complex. Nearly one-fifth of the inferred genes of the ancestor are eumetazoan novelties, which are enriched for animal functions like cell signaling, adhesion, and synaptic transmission. Analysis of diverse pathways suggests that these gene “inventions” along the lineage leading to animals were likely already well integrated with preexisting eukaryotic genes in the eumetazoan progenitor.
Nitrite, an Electron Donor for Anoxygenic Photosynthesis
Authors: Griffin Benjamin M. , Schott Joachim , Schink Bernhard
Published: July 2007

We report a previously unknown process in which anoxygenic phototrophic bacteria use nitrite as an electron donor for photosynthesis. We isolated a purple sulfur bacterium 98% identical to Thiocapsa species that stoichiometrically oxidizes nitrite to nitrate in the light. Growth and nitrate production strictly depended on both light and nitrite. This is the first known microbial mechanism for the stoichiometric oxidation of nitrite to nitrate in the absence of oxygen and the only known photosynthetic oxidation in the nitrogen cycle. This work demonstrates nitrite as the highest-potential electron donor for anoxygenic photosynthesis known so far.
Domesticated Nature: Shaping Landscapes and Ecosystems for Human Welfare
Authors: Kareiva Peter , Watts Sean , McDonald Robert , Boucher Tim
Published: July 2007

Like all species, humans have exercised their impulse to perpetuate and propagate themselves. In doing so, we have domesticated landscapes and ecosystems in ways that enhance our food supplies, reduce exposure to predators and natural dangers, and promote commerce. On average, the net benefits to humankind of domesticated nature have been positive. We have, of course, made mistakes, causing unforeseen changes in ecosystem attributes, while leaving few, if any, truly wild places on Earth. Going into the future, scientists can help humanity to domesticate nature more wisely by quantifying the tradeoffs among ecosystem services, such as how increasing the provision of one service may decrease ecosystem resilience and the provision of other services.
Gender Disparity in Liver Cancer Due to Sex Differences in MyD88-Dependent IL-6 Production
Authors: Naugler Willscott E. , Sakurai Toshiharu , Kim Sunhwa , Maeda Shin , Kim KyoungHyun , Elsharkawy Ahmed M. , Karin Michael
Published: July 2007

Hepatocellular carcinoma (HCC), the most common liver cancer, occurs mainly in men. Similar gender disparity is seen in mice given a chemical carcinogen, diethylnitrosamine (DEN). DEN administration caused greater increases in serum interleukin-6 (IL-6) concentration in males than it did in females. Furthermore, ablation of IL-6 abolished the gender differences in hepatocarcinogenesis in mice. DEN exposure promoted production of IL-6 in Kupffer cells (KCs) in a manner dependent on the Toll-like receptor adaptor protein MyD88, ablation of which also protected male mice from DEN-induced hepatocarcinogenesis. Estrogen inhibited secretion of IL-6 from KCs exposed to necrotic hepatocytes and reduced circulating concentrations of IL-6 in DEN-treated male mice. We propose that estrogen-mediated inhibition of IL-6 production by KCs reduces liver cancer risk in females, and these findings may be used to prevent HCC in males.
Comment on "Wandering Minds: The Default Network and Stimulus-Independent Thought"
Authors: Gilbert Sam J. , Dumontheil Iroise , Simons Jon S. , Frith Chris D. , Burgess Paul W.
Published: July 2007

Mason
et al.
(Reports, 19 January 2007, p. 393) attributed activity in certain regions of the “resting” brain to the occurrence of mind-wandering. However, previous research has demonstrated the difficulty of distinguishing this type of stimulus-independent thought from stimulus-oriented thought (e.g., watchfulness). Consideration of both possibilities is required to resolve this ambiguity.
Restriction of DNA Replication to the Reductive Phase of the Metabolic Cycle Protects Genome Integrity
Authors: Chen Zheng , Odstrcil Elizabeth A. , Tu Benjamin P. , McKnight Steven L.
Published: July 2007

When prototrophic yeast cells are cultured under nutrient-limited conditions that mimic growth in the wild, rather than in the high-glucose solutions used in most laboratory studies, they exhibit a robustly periodic metabolic cycle. Over a cycle of 4 to 5 hours, yeast cells rhythmically alternate between glycolysis and respiration. The cell division cycle is tightly constrained to the reductive phase of this yeast metabolic cycle, with DNA replication taking place only during the glycolytic phase. We show that cell cycle mutants impeded in metabolic cycle–directed restriction of cell division exhibit substantial increases in spontaneous mutation rate. In addition, disruption of the gene encoding a DNA checkpoint kinase that couples the cell division cycle to the circadian cycle abolishes synchrony of the metabolic and cell cycles. Thus, circadian, metabolic, and cell division cycles may be coordinated similarly as an evolutionarily conserved means of preserving genome integrity.
Orbital and Millennial Antarctic Climate Variability over the Past 800,000 Years
Authors: Jouzel J. , Masson-Delmotte V. , Cattani O. , Dreyfus G. , Falourd S. , Hoffmann G. , Minster B. , Nouet J. , Barnola J. M. , Chappellaz J. , Fischer H. , Gallet J. C. , Johnsen S. , Leuenberger M. , Loulergue L. , Luethi D. , Oerter H. , Parrenin F. , Raisbeck G. , Raynaud D. , Schilt A. , Schwander J. , Selmo E. , Souchez R. , Spahni R. , Stauffer B. , Steffensen J. P. , Stenni B. , Stocker T. F. , Tison J. L. , Werner M. , Wolff E. W.
Published: July 2007

A high-resolution deuterium profile is now available along the entire European Project for Ice Coring in Antarctica Dome C ice core, extending this climate record back to marine isotope stage 20.2, â¼800,000 years ago. Experiments performed with an atmospheric general circulation model including water isotopes support its temperature interpretation. We assessed the general correspondence between Dansgaard-Oeschger events and their smoothed Antarctic counterparts for this Dome C record, which reveals the presence of such features with similar amplitudes during previous glacial periods. We suggest that the interplay between obliquity and precession accounts for the variable intensity of interglacial periods in ice core records.
Trench-Parallel Anisotropy Produced by Foundering of Arc Lower Crust
Authors: Behn Mark D. , Hirth Greg , Kelemen Peter B.
Published: July 2007

Many volcanic arcs display fast seismic shear-wave velocities parallel to the strike of the trench. This pattern of anisotropy is inconsistent with simple models of corner flow in the mantle wedge. Although several models, including slab rollback, oblique subduction, and deformation of water-rich olivine, have been proposed to explain trench-parallel anisotropy, none of these mechanisms are consistent with all observations. Instead, small-scale convection driven by the foundering of dense arc lower crust provides an explanation for the trench-parallel anisotropy, even in settings with orthogonal convergence and no slab rollback.
Preceramic Adoption of Peanut, Squash, and Cotton in Northern Peru
Authors: Dillehay Tom D. , Rossen Jack , Andres Thomas C. , Williams David E.
Published: July 2007

The early development of agriculture in the New World has been assumed to involve early farming in settlements in the Andes, but the record has been sparse. Peanut (
Arachis
sp.), squash (
Cucurbita moschata
), and cotton (
Gossypium barbadense
) macrofossils were excavated from archaeological sites on the western slopes of the northern Peruvian Andes. Direct radiocarbon dating indicated that these plants grew between 9240 and 5500
14
C years before the present. These and other plants were recovered from multiple locations in a tropical dry forest valley, including household clusters, permanent architectural structures, garden plots, irrigation canals, hoes, and storage structures. These data provide evidence for early use of peanut and squash in the human diet and of cotton for industrial purposes and indicate that horticultural economies in parts of the Andes took root by about 10,000 years ago.
HIV-1 Proviral DNA Excision Using an Evolved Recombinase
Authors: Sarkar Indrani , Hauber Ilona , Hauber Joachim , Buchholz Frank
Published: July 2007

HIV-1 integrates into the host chromosome and persists as a provirus flanked by long terminal repeats (LTRs). To date, treatment regimens primarily target the virus enzymes or virus-cell fusion, but not the integrated provirus. We report here the substrate-linked protein evolution of a tailored recombinase that recognizes an asymmetric sequence within an HIV-1 LTR. This evolved recombinase efficiently excised integrated HIV proviral DNA from the genome of infected cells. Although a long way from use in the clinic, we speculate that this type of technology might be adapted in future antiretroviral therapies, among other possible uses.
Buddenbrockia
Is a Cnidarian Worm
Authors: Jiménez-Guri Eva , Philippe Hervé , Okamura Beth , Holland Peter W. H.
Published: July 2007

A major evolutionary divide occurs in the animal kingdom between the so-called radially symmetric animals, which includes the cnidarians, and the bilaterally symmetric animals, which includes all worm phyla.
Buddenbrockia plumatellae
is an active, muscular, parasitic worm that belongs to the phylum Myxozoa, a group of morphologically simplified microscopic endoparasites that has proved difficult to place phylogenetically. Phylogenetic analyses of multiple protein-coding genes demonstrate that
Buddenbrockia
is a cnidarian. This active muscular worm increases the known diversity in cnidarian body plans and demonstrates that a muscular, wormlike form can evolve in the absence of overt bilateral symmetry.
Body-Centered Cubic Iron-Nickel Alloy in Earth's Core
Authors: Dubrovinsky L. , Dubrovinskaia N. , Narygina O. , Kantor I. , Kuznetzov A. , Prakapenka V. B. , Vitos L. , Johansson B. , Mikhaylushkin A. S. , Simak S. I. , Abrikosov I. A.
Published: July 2007

Cosmochemical, geochemical, and geophysical studies provide evidence that Earth's core contains iron with substantial (5 to 15%) amounts of nickel. The iron-nickel alloy Fe
0.9
Ni
0.1
has been studied in situ by means of angle-dispersive x-ray diffraction in internally heated diamond anvil cells (DACs), and its resistance has been measured as a function of pressure and temperature. At pressures above 225 gigapascals and temperatures over 3400 kelvin, Fe
0.9
Ni
0.1
adopts a body-centered cubic structure. Our experimental and theoretical results not only support the interpretation of shockwave data on pure iron as showing a solid-solid phase transition above about 200 gigapascals, but also suggest that iron alloys with geochemically reasonable compositions (that is, with substantial nickel, sulfur, or silicon content) adopt the bcc structure in Earth's inner core.
Understanding Reactivity at Very Low Temperatures: The Reactions of Oxygen Atoms with Alkenes
Authors: Sabbah Hassan , Biennier Ludovic , Sims Ian R. , Georgievskii Yuri , Klippenstein Stephen J. , Smith Ian W. M.
Published: July 2007

A remarkable number of reactions between neutral free radicals and neutral molecules have been shown to remain rapid down to temperatures as low as 20 kelvin. The rate coefficients generally increase as the temperature is lowered. We examined the reasons for this temperature dependence through a combined experimental and theoretical study of the reactions of O(
3
P) atoms with a range of alkenes. The factors that control the rate coefficients were shown to be rather subtle, but excellent agreement was obtained between the experimental results and microcanonical transition state theory calculations based on ab initio representations of the potential energy surfaces describing the interaction between the reactants.
Non-Fermi Liquid Metal Without Quantum Criticality
Authors: Pfleiderer C. , Böni P. , Keller T. , Rößler U. K. , Rosch A.
Published: July 2007

A key question in condensed matter physics concerns whether pure three-dimensional metals can always be described as Fermi liquids. Using neutron Larmor diffraction to overcome the traditional resolution limit of diffraction experiments, we studied the lattice constants of the cubic itinerant-electron magnet manganese silicide (MnSi) at low temperatures and high pressures. We were able to resolve the nature of the phase diagram of MnSi and to establish that a stable, extended non–Fermi liquid state emerges under applied pressure without quantum criticality. This suggests that new forms of quantum order may be expected even far from quantum phase transitions.
Genome Plasticity a Key Factor in the Success of Polyploid Wheat Under Domestication
Authors: Dubcovsky Jorge , Dvorak Jan
Published: July 2007

Wheat was domesticated about 10,000 years ago and has since spread worldwide to become one of the major crops. Its adaptability to diverse environments and end uses is surprising given the diversity bottlenecks expected from recent domestication and polyploid speciation events. Wheat compensates for these bottlenecks by capturing part of the genetic diversity of its progenitors and by generating new diversity at a relatively fast pace. Frequent gene deletions and disruptions generated by a fast replacement rate of repetitive sequences are buffered by the polyploid nature of wheat, resulting in subtle dosage effects on which selection can operate.
Yeast DNA Polymerase ε Participates in Leading-Strand DNA Replication
Authors: Pursell Zachary F. , Isoz Isabelle , Lundström Else-Britt , Johansson Erik , Kunkel Thomas A.
Published: July 2007

Multiple DNA polymerases participate in replicating the leading and lagging strands of the eukaryotic nuclear genome. Although 50 years have passed since the first DNA polymerase was discovered, the identity of the major polymerase used for leading-strand replication is uncertain. We constructed a derivative of yeast DNA polymerase ϵ that retains high replication activity but has strongly reduced replication fidelity, particularly for thymine-deoxythymidine 5'-monophosphate (T-dTMP) but not adenine-deoxyadenosine 5'-monophosphate (A-dAMP) mismatches. Yeast strains with this DNA polymerase ϵ allele have elevated rates of T to A substitution mutations. The position and rate of these substitutions depend on the orientation of the mutational reporter and its location relative to origins of DNA replication and reveal a pattern indicating that DNA polymerase ϵ participates in leading-strand DNA replication.
Making a New Tail
Authors: Gough Nancy R.
Published: July 2007

Adams
et al
. identified the V-ATPase H
+
pump in a pharmacological screen for ion transporters involved in
Xenopus
larval tail regeneration. When the pumping activity of the V-ATPase was inhibited with concanamycin, tail regeneration was inhibited, whereas primary tail development and wound healing were unaffected. Using a dominant-negative V-ATPase, the same inhibition of regeneration was observed, confirming V-ATPase as the target. Expression of a yeast P-type H
+
pump, which is insensitive to concanamycin, was localized to the plasma membrane and also prevented concanamycin inhibition of regeneration, confirming that it was transport of H
+
efflux at the plasma membrane that was important for regeneration. Six hours after amputation, the abundance of the mRNA for the c subunit of the V-ATPase had increased, and by 24 hours after amputation the H
+
pump was abundant in the plasma membrane of the cells of the regeneration bud. The cells of the regeneration bud were depolarized six hours after amputation; however, by 24 hours after amputation, the cells were repolarized, which is consistent with the hyperpolarizing activity of the H
+
pump. Furthermore, depolarization of the tails using a drug that converts the Na
+
,K
+
ATPase into a Na
+
/K
+
channel also inhibited regeneration, supporting the concept that membrane voltage is a critical regulator of regeneration. Inhibition of the H
+
pump decreased the number of proliferating cells in the regeneration bud and inhibited the expression of the
KCNK1
gene, which encodes a K
+
channel that is expressed at early stages of regeneration (12 hours after amputation). Axon patterning in the regeneration bud was also aberrant when the H
+
pump activity was inhibited. Thus, H
+
pump activity contributes to changes in membrane potential that are important for regulation of gene expression, cell proliferation, and proper patterning of the new tissues.

D. S. Adams. A. Masi, M. Levin, H
+
pump-dependent changes in membrane voltage are an early mechanism necessary and sufficient to induce
Xenopus
tail regeneration.
Development
134
, 1323-1335 (2007).
[Abstract]
[Full Text]
Removing Ubiquitin to Regulate NF-κB Activity
Authors: Foley John F.
Published: July 2007

As part of a negative feedback mechanism, the transcription factor nuclear factor κΒ (NF-κB) induces
IκBα
transcription, restoring the amount of its negative regulator, IκBα, in the cell. However, the rapidity with which functional IκBα recovers implies the existence of other mechanisms to stabilize IκBα, even in the face of phosphorylation by IκB kinase β (IKKβ). This event leads to ubiquitinylation of IκBα, targeting it for proteasomal degradation and resulting in the release of active NF-κB. Schweitzer
et al
. have uncovered the crucial role that the COP9 signalosome (CSN) plays in this process. CSN is an eight-subunit (CSN1-8) protein complex that controls the activities of multisubunit cullin-RING ubiquitin ligases (CRLs), one member of which, SCF
βTrCP
, ubiquitinylates IκBα. The authors performed coimmunoprecipitation studies that established that CSN2 associated with IκBα after treatment of transfected HeLa cells with tumor necrosis factor-α (TNF-α). Through coimmunoprecipitation and electrophoretic mobility shift assays, and knockdown of CSN2 by small interfering RNA (siRNA), the authors showed that the recovery in IκBα after treatment with TNF-α was much reduced in CSN2-deficient cells compared with control cells. Earlier accumulation and enhanced amounts of ubiquitinylated IκBα were also seen in cells deficient in CSN2. One component of the CSN complex is USP15, a deubiquitinylase (DUB). HeLa cells transfected with a USP15-specific siRNA showed reduced recovery of IκBα after TNF-α-stimulated degradation compared with control cells. In vitro DUB assays, using ubiquitinylated IκBα as a substrate, demonstrated that both purified CSN and USP15 deubiquitinylated IκBα. Together, these data demonstrate a previously unknown role for CSN in regulating NF-κB activity through the stabilization of IκBα.

K. Schweitzer, P. M. Bozko, W. Dubiel, M. Naumann, CSN controls NF-κB by deubiquitinylation of IκBα.
EMBO J.
26
, 1532-1541 (2007).
[PubMed]
IL-2 Antagonizes Th17 Differentiation
Authors: Adler Elizabeth M.
Published: July 2007

T helper 17 (Th17) cells are a recently identified subset of effector T cells that produce IL-17, a cytokine implicated in various autoimmune disorders as well as (more beneficially) in the defense against extracellular bacteria. Laurence
et al
. found that when naïve CD4
+
T cells were stimulated with antibodies and cultured under conditions designed to promote differentiation into Th17 cells [medium containing interleukin-6 (IL-6), transforming growth factor (TGF)-β1, and blocking antibodies directed against IL-4 and interferon-γ], addition of IL-2 led to a dose-dependent decrease in the proportion of cells producing IL-17. In contrast, antibodies to IL-2 (which is produced by activated T cells) increased the proportion of IL-17-producing cells. T cells from mice lacking the gene encoding IL-2 (
Il2
−/−
mice) generated a greater percentage of IL-17-producing cells than did T cells from wild-type mice, and
Il2
−/−
mice had increased serum concentrations of IL-17 and a greater proportion of IL-17-positive cells in peripheral lymph nodes. Decreased abundance of STAT3 (signal transducer and activator of transcription 3, which is activated by IL-6) was associated with a decrease in the proportion of Th17 cells and of the expression of
RORγT
messenger RNA, which encodes a nuclear receptor required for Th17 differentiation. Deletion of STAT5 (which is activated by IL-2), however, promoted Th17 differentiation. Moreover, STAT5 bound to the
Il-17
promoter, suggesting that it might inhibit
Il-17
transcription directly. Thus, in contrast to its well-established roles of stimulating T cell proliferation and differentiation, IL-2--once known as T cell growth factor--appears to attenuate Th17 differentiation. Stockinger provides thoughtful commentary.

A. Laurence, C. M. Tato, T. S. Davidson, Y. Kanno, Z. Chen, Z. Yao, R. B. Blank, F. Meylan, R. Siegel, L. Hennighausen, E. M. Shevach, J. J. O'Shea, Interleukin-2 signaling via STAT5 constrains T helper 17 cell generation.
Immunity
26
, 371-381 (2007).
[PubMed]

B. Stockinger, Good for goose, but not for gander: IL-2 interferes with Th17 differentiation.
Immunity
26
, 278-279 (2007).
[PubMed]