bluuebunny/crossref_metadata_2025 huggingface dataset:
The Earliest Persians in Southwestern Iran: The Textual Evidence
Authors: Waters Matthew W.
Published: August 2011

The Persians are Obscure in the Archaeological Record, and the routes and dates of their migration into Iran are uncertain. When the Persians appear in the textual record, it is in the context of their interaction with the regional powers of Elam and Assyria. Examination of the relevant sources highlights two areas of Persian settlement in the first half of the first millennium B.C.E.: the central Zagros Mountains region and modern Fars, the latter the core of the first Persian Empire (Old Persian Parsa and Greek Persis). Since there are no extant Persian inscriptions dating before the mid-sixth century, this analysis relies upon Assyrian and Elamite sources.

The Persians may have begun their arrival in southwestern Iran as early as the mid-second millennium. During the Middle Elamite period (c. 1600-1000 B.C.E.), Fars and its primary city Anshan (modern Malyan) were part of the kingdom of Elam. Sometime around 1000 B.C.E., Anshan was abandoned. Large-scale settlement cannot be traced in Fars after that until the Achaemenid period, over four hundred years later.
Electromechanical response of a curved piezoelectric nanobeam with the consideration of surface effects
Authors: Yan Zhi , Jiang Liying
Published: August 2011

This work investigates the electromechanical response of a curved piezoelectric nanobeam with the consideration of surface effects through the surface-layer-based model and the generalized Young–Laplace equations. For nanoscale piezoelectric structures, the surface effects also include surface piezoelectricity in addition to the residual surface stress and surface elasticity for elastic nanomaterials. A Euler–Bernoulli curved beam theory is used to get the explicit solutions for the electroelastic fields of a curved cantilever beam when subjected to mechanical and electrical loads. In order to apply the appropriate boundary conditions on the beam, effective axial force, shear force and moment are derived. The results indicate that the surface effects play a significant role in the electroelastic fields and the piezoelectric response of the curved piezoelectric nanobeam. It is also found that the coupling of the residual surface stress, the surface elasticity and the surface piezoelectricity may be dramatic despite that the influence of the individual one is small under some circumstances. This study is expected to be useful for design and applications of curved beam based piezoelectric nanodevices, such as the curved nanowires/nanobelts or nanorings as nanoswitches or nanoactuators for displacement control purpose.
INTEGRAL OBSERVATIONS OF THE γ-RAY BINARY 1FGL J1018.6-5856
Authors: Li Jian , Torres Diego F. , Chen Yupeng , Götz Diego , Rea Nanda , Zhang Shu , Caliandro G. Andrea , Wang Jianmin
Published: August 2011

The Fermi Large Area telescope (Fermi-LAT) collaboration has recently reported that one of their detected sources, namely, 1FGL J1018.6-5856, is a new gamma-ray binary similar to LS 5039. This has prompted efforts to study its multi-frequency behavior. In this report, we present the results from 5.78 Ms International Gamma-Ray Astrophysics Laboratory (INTEGRAL) IBIS/ISGRI observations on the source 1FGL J1018.6-5856. By combining all the available INTEGRAL data, a detection is made at a significance level of 5.4σ in the 18–40 keV band, with an average intensity of 0.074 counts s−1. However, we find that there is non-statistical noise in the image that effectively reduces the significance to about 4σ and a significant part of the signal appears to be located in a 0.2-wide phase region, at phases 0.4–0.6 (where even the corrected significance amounts to 90% of the total signal found). Given the scarcity of counts, a variability is hinted at about 3σ at the hard X-rays, with an anticorrelation with the Fermi-LAT periodicity. If this behavior were true, it would be similar to that found in LS 5039 and prompt observations with TeV telescopes at phases anticorrelated with the GeV maximum.
ARHGAP18, a GTPase-activating protein for RhoA, controls cell shape, spreading, and motility
Authors: Maeda Masao , Hasegawa Hitoki , Hyodo Toshinori , Ito Satoko , Asano Eri , Yuang Hong , Funasaka Kohei , Shimokata Kaoru , Hasegawa Yoshinori , Hamaguchi Michinari , Senga Takeshi
Published: August 2011

Rho GTPases are molecular switches that transmit biochemical signals in response to extracellular stimuli to elicit changes in the actin cytoskeleton. Rho GTPases cycle between an active, GTP-bound state and an inactive, GDP-bound state. These states are regulated by two distinct families of proteins—guanine nucleotide exchange factors and GTPase-activating proteins (GAPs). We studied the role of a previously uncharacterized GAP, ARHGAP18 (MacGAP). Overexpression of ARHGAP18 suppressed the activity of RhoA and disrupted stress fiber formation. Conversely, silencing of ARHGAP18 by small interfering RNA transfection–enhanced stress fiber formation and induced rounding of cells. We examined the role of ARHGAP18 in cell spreading and migration. Immunofluorescence analysis revealed that ARHGAP18 was localized to the leading edge during cell spreading and migration. ARHGAP18-knockdown cells showed impaired spreading, premature formation of stress fibers, and sustained activation of RhoA upon cell attachment. In addition, knockdown and overexpression of ARHGAP18 resulted in the inhibition and promotion of cell migration, respectively. Furthermore, ARHGAP18 was required for the polarization of cells for migration. Our results define ARHGAP18 as one of the crucial factors for the regulation of RhoA for the control of cell shape, spreading, and migration.
Body Banks: A History of Milk Banks, Blood Banks, and Sperm Banks in the United States
Authors: Swanson Kara W.
Published: August 2011

My dissertation traces the invention and development of a new form of banking, body banking. Today, the body bank as an institution that collects, stores, processes, and distributes a human body product is a taken-for-granted aspect of medicine in the United States. We donate to blood banks, we cherish sperm bank babies, and we contemplate many sorts of banks, including cord blood banks, gene banks, and egg banks. Such institutions have existed for the past century in the metaphorical shadow of financial banks, and like those better-studied banks have stirred considerable controversy. The driving question behind my dissertation is simply, why banks? How did we come to use “bank” to apply to bodies as well as to dollars? More intriguingly, what does this analogy show us and what is it hiding?
The relationship between mitral regurgitation and ejection fraction as predictors for the prognosis of patients with heart failure
Authors: Pecini Redi , Thune Jens Jakob , Torp‐Pedersen Christian , Hassager Christian , Køber Lars
Published: August 2011

Aims

To study whether there is interaction between mitral regurgitation (MR) and left ventricular ejection fraction (LVEF) in the mortality risk of heart failure (HF) patients.

Methods and results

We studied a large group of patients hospitalized for symptoms and clinical signs of HF in the period 2001–02. Mitral regurgitation was diagnosed on echocardiography and qualitatively graded as no/trace, mild, moderate, and severe using the colour Doppler method. Median follow‐up time was 4.5 years. Three thousand and seventy‐eight patients with HF were included, of whom 1890 patients (61%) had no/trace MR, 628 (20%) had mild MR, 452 (15%) had moderate MR, and 108 (4%) had severe MR. During follow‐up, 1660 deaths (54%) were registered. In univariate analysis, increasing severity of MR carried an increasing mortality risk, hazard ratio (HR) 1.10, 95% confidence interval (CI) 1.04–1.16, P = 0.0006 for each increasing degree of MR. In multivariable analysis, with adjustments made for age, sex, ejection fraction, serum creatinine, presence of ischaemic heart disease, chronic obstructive pulmonary disease, diabetes, and stroke, similar results were found, but only in patients with LVEF<25%, HR 1.14, 95% CI 1.03–1.26, P = 0.01 for each increasing degree of MR. This risk was driven by moderate and severe MR. For patients with LVEF≥25% the HR was 0.91, 95% CI 0.82–1.03, P = 0.2 for each increasing degree of MR.

Conclusion

Mitral regurgitation has a negative effect on prognosis of patients with HF, but only in patients with severely reduced LVEF.
SCUC With Hourly Demand Response Considering Intertemporal Load Characteristics
Authors: Khodaei Amin , Shahidehpour Mohammad , Bahramirad Shaghayegh
Published: August 2011

In this paper, the hourly demand response (DR) is incorporated into security-constrained unit commitment (SCUC) for economic and security purposes. SCUC considers fixed and responsive loads. Unlike fixed hourly loads, responsive loads are modeled with their intertemporal characteristics. The responsive loads linked to hourly market prices can be curtailed or shifted to other operating hours. The study results show that DR could shave the peak load, reduce the system operating cost, reduce fuel consumptions and carbon footprints, and reduce the transmission congestion by reshaping the hourly load profile. Numerical simulations in this paper exhibit the effectiveness of the proposed approach.
Utilization of FPAA Technology for Emulation of Multiscale Power System Dynamics in Smart Grids
Authors: Deese Anthony S. , Nwankpa Chika O.
Published: August 2011

In this paper, the authors address computational issues associated with implementation of VLSI technologies-specifically, the utilization of field programmable analog array (FPAA) technology to analyze the steady-state as well dynamic behavior of nonlinear, multiscale power systems. Emphasis is placed on the following issues: adaptation of FPAA hardware for power flow analyses, design and construction of physical prototype, optimal hardware scaling, and application of emulation to transient fault analyses.
Modal analysis of the electromechanical conversion in piezoelectric ceramic spherical shells
Authors: Aronov Boris , Brown David A. , Yan Xiang , Bachand Corey L.
Published: August 2011

The current study considers piezoelectric ceramic electromechanical transducers utilizing axisymmetric vibrations of complete and incomplete spherical shells. Analysis is focused on generating the modes of vibration that can be employed in the design of multimode unidirectional electroacoustic transducers for underwater applications and on determining the electrode configurations that achieve optimal electromechanical coupling for the different modes of vibration considered. Analytical expressions are presented for the modal and intermodal equivalent parameters characterizing the energy state of the shell vibration. Results of calculation and experimental verification of the resonance frequencies and effective coupling coefficients for different modes of vibration of the complete and incomplete spherical shells are in good agreement.
Numerical and asymptotic approach for evaluating complex wavenumbers of guided modes in viscoelastic plates
Authors: Zakharov Dmitry , Castaings Michel , Singh Dilbag
Published: August 2011

The approximate description of the dispersion curves is obtained using asymptotics of complex wavenumbers for different boundary conditions on the plate surfaces. Their comparison with the exact results shows satisfactory agreement. This approach provides an algorithm to evaluate the infinite spectrum of non-propagating modes more easily and numerically stable even for wavenumbers of big values. Results are verified by the alternative semianalytical finite element method, which also supplies the mode shapes for better identification and classification.
Acoustic analysis of a rectangular cavity with general impedance boundary conditions
Authors: Du Jing T. , Li Wen L. , Liu Zhi G. , Xu Hong A. , Ji Zhen L.
Published: August 2011

A Fourier series method is proposed for the acoustic analysis of a rectangular cavity with impedance boundary conditions arbitrarily specified on any of the walls. The sound pressure is expressed as the combination of a three-dimensional Fourier cosine series and six supplementary two-dimensional expansions introduced to ensure (accelerate) the uniform and absolute convergence (rate) of the series representation in the cavity including the boundary surfaces. The expansion coefficients are determined using the Rayleigh–Ritz method. Since the pressure field is constructed adequately smooth throughout the entire solution domain, the Rayleigh–Ritz solution is mathematically equivalent to what is obtained from a strong formulation based on directly solving the governing equations and the boundary conditions. To unify the treatments of arbitrary nonuniform impedance boundary conditions, the impedance distribution function on each specified surface is invariantly expressed as a double Fourier series expansion so that all the relevant integrals can be calculated analytically. The modal parameters for the acoustic cavity can be simultaneously obtained from solving a standard matrix eigenvalue problem instead of iteratively solving a nonlinear transcendental equation as in the existing methods. Several numerical examples are presented to demonstrate the effectiveness and reliability of the current method for various impedance boundary conditions, including nonuniform impedance distributions.
Hearing thresholds of a harbor porpoise (Phocoena phocoena) for helicopter dipping sonar signals (1.43–1.33 kHz) (L)
Authors: Kastelein Ronald A. , Hoek Lean , de Jong Christ A. F.
Published: August 2011

Helicopter long range active sonar (HELRAS), a “dipping” sonar system used by lowering transducer and receiver arrays into water from helicopters, produces signals within the functional hearing range of many marine animals, including the harbor porpoise. The distance at which the signals can be heard is unknown, and depends, among other factors, on the hearing sensitivity of the species to these particular signals. Therefore, the hearing thresholds of a harbor porpoise for HELRAS signals were quantified by means of a psychophysical technique. Detection thresholds were obtained for five 1.25 s simulated HELRAS signals, varying in their harmonic content and amplitude envelopes. The 50% hearing thresholds for the different signals were similar: 76 dB re 1 μPa (broadband sound pressure level, averaged over the signal duration). The detection thresholds were similar to those found in the same porpoise for tonal signals in the 1–2 kHz range measured in a previous study. Harmonic distortion, which occurred in three of the five signals, had little influence on their audibility. The results of this study, combined with information on the source level of the signal, the propagation conditions and ambient noise levels, allow the calculation of accurate estimates of the distances at which porpoises can detect HELRAS signals.
Effects of fundamental frequency and vocal-tract length cues on sentence segregation by listeners with hearing loss
Authors: Mackersie Carol L. , Dewey James , Guthrie Lesli A.
Published: August 2011

The purpose was to determine the effect of hearing loss on the ability to separate competing talkers using talker differences in fundamental frequency (F0) and apparent vocal-tract length (VTL). Performance of 13 adults with hearing loss and 6 adults with normal hearing was measured using the Coordinate Response Measure. For listeners with hearing loss, the speech was amplified and filtered according to the NAL-RP hearing aid prescription. Target-to-competition ratios varied from 0 to 9 dB. The target sentence was randomly assigned to the higher or lower values of F0 or VTL on each trial. Performance improved for F0 differences up to 9 and 6 semitones for people with normal hearing and hearing loss, respectively, but only when the target talker had the higher F0. Recognition for the lower F0 target improved when trial-to-trial uncertainty was removed (9-semitone condition). Scores improved with increasing differences in VTL for the normal-hearing group. On average, hearing-impaired listeners did not benefit from VTL cues, but substantial inter-subject variability was observed. The amount of benefit from VTL cues was related to the average hearing loss in the 1–3-kHz region when the target talker had the shorter VTL.
On observing acoustic backscattering from salinity turbulence
Authors: Goodman Louis , Sastre-Córdova Marcos M.
Published: August 2011

It has been hypothesized that at sufficiently high levels of oceanic salinity turbulence it should be possible to observe acoustic backscattering. However, there have been limited in situ measurements to confirm this hypothesis. Using an autonomous underwater vehicle equipped with upward and downward looking 1.2 MHz acoustic Doppler current profilers and with turbulence and fine scale sensors, measurements were performed in a region of intense turbulence and a strong salinity gradient. The approach taken was to correlate variations in the backscattered acoustic intensity, I, with a theoretical acoustic backscattering cross section per volume for salinity turbulence, σs, to obtain an estimated scattering cross section per volume, σe. Results indicated that of order 50% of the observed region was characterized by salinity turbulence induced backscattering.
An adaptive filter-based method for robust, automatic detection and frequency estimation of whistles
Authors: Johansson A.Torbjörn , White Paul R.
Published: August 2011

This paper proposes an adaptive filter-based method for detection and frequency estimation of whistle calls, such as the calls of birds and marine mammals, which are typically analyzed in the time-frequency domain using a spectrogram. The approach taken here is based on adaptive notch filtering, which is an established technique for frequency tracking. For application to automatic whistle processing, methods for detection and improved frequency tracking through frequency crossings as well as interfering transients are developed and coupled to the frequency tracker. Background noise estimation and compensation is accomplished using order statistics and pre-whitening. Using simulated signals as well as recorded calls of marine mammals and a human whistled speech utterance, it is shown that the proposed method can detect more simultaneous whistles than two competing spectrogram-based methods while not reporting any false alarms on the example datasets. In one example, it extracts complete 1.4 and 1.8 s bottlenose dolphin whistles successfully through frequency crossings. The method performs detection and estimates frequency tracks even at high sweep rates. The algorithm is also shown to be effective on human whistled utterances.
Time delay and Doppler estimation for wideband acoustic signals in multipath environments
Authors: Jiang Xue , Zeng Wen-Jun , Li Xi-Lin
Published: August 2011

Estimation of the parameters of a multipath underwater acoustic channel is of great interest for a variety of applications. This paper proposes a high-resolution method for jointly estimating the multipath time delays, Doppler scales, and attenuation amplitudes of a time-varying acoustical channel. The proposed method formulates the estimation of channel parameters into a sparse representation problem. With the ℓ1-norm as the measure of sparsity, the proposed method makes use of the basis pursuit (BP) criterion to find the sparse solution. The ill-conditioning can be effectively reduced by the ℓ1-norm regularization. Unlike many existing methods that are only applicable to narrowband signals, the proposed method can handle both narrowband and wideband signals. Simulation results are provided to verify the performance and effectiveness of the proposed algorithm, indicating that it has a super-resolution in both delay and Doppler domain, and it is robust to noise.
The influence of spectral characteristics of early reflections on speech intelligibility
Authors: Arweiler Iris , Buchholz Jörg M.
Published: August 2011

The auditory system takes advantage of early reflections (ERs) in a room by integrating them with the direct sound (DS) and thereby increasing the effective speech level. In the present paper the benefit from realistic ERs on speech intelligibility in diffuse speech-shaped noise was investigated for normal-hearing and hearing-impaired listeners. Monaural and binaural speech intelligibility tests were performed in a virtual auditory environment where the spectral characteristics of ERs from a simulated room could be preserved. The useful ER energy was derived from the speech intelligibility results and the efficiency of the ERs was determined as the ratio of the useful ER energy to the total ER energy. Even though ER energy contributed to speech intelligibility, DS energy was always more efficient, leading to better speech intelligibility for both groups of listeners. The efficiency loss for the ERs was mainly ascribed to their altered spectrum compared to the DS and to the filtering by the torso, head, and pinna. No binaural processing other than a binaural summation effect could be observed.
Bubble proliferation in the cavitation field of a shock wave lithotripter
Authors: Pishchalnikov Yuri A. , Williams James C. , McAteer James A.
Published: August 2011

Lithotripter shock waves (SWs) generated in non-degassed water at 0.5 and 2 Hz pulse repetition frequency (PRF) were characterized using a fiber-optic hydrophone. High-speed imaging captured the inertial growth-collapse-rebound cycle of cavitation bubbles, and continuous recording with a 60 fps camcorder was used to track bubble proliferation over successive SWs. Microbubbles that seeded the generation of bubble clouds formed by the breakup of cavitation jets and by bubble collapse following rebound. Microbubbles that persisted long enough served as cavitation nuclei for subsequent SWs, as such bubble clouds were enhanced at fast PRF. Visual tracking suggests that bubble clouds can originate from single bubbles.
Geoacoustic inversion in a dispersive waveguide using warping operators
Authors: Bonnel Julien , Chapman N. Ross
Published: August 2011

This paper presents a single receiver geoacoustic inversion method adapted for low-frequency impulsive sources. It is applied to light bulb data collected during the Shallow Water 2006 experiment. The inversion is carried out by extracting dispersion curves from the received signal, and comparing them to simulated replicas. To achieve dispersion curve estimation in the time-frequency domain, modal separability is improved using a signal processing method called warping. The inversion scheme allows for a reliable estimation of the New Jersey Shelf sediment properties (compressional sound speed and density). It also provides an accurate estimation of the source/receiver range.
The effects of elastic supports on the transient vibroacoustic response of a window caused by sonic booms
Authors: Ou Dayi , Mak Cheuk Ming
Published: August 2011

The transient vibration and sound radiation (TVSR) of plate-like structures with general elastic boundary conditions was investigated using the time-domain finite element method (TDFEM) and time-domain boundary element method (TDBEM). In this model, the structure can have arbitrary elastic boundary conditions and hence the effects of the boundary conditions on the TVSR can be effectively studied. The predicted results agreed well with existing experimental data using two classical boundary conditions: simply supported at all edges and clamped-free-free-free. The TVSR of a single panel with a more general boundary condition in two connected chambers was also measured. The predicted results agreed well with these experimental results. The prediction method was subsequently applied to evaluate the effects of elastic boundary supports on the TVSR of a window caused by a sonic boom. Loudness, non-audible acoustic perception, and tactile vibration thresholds were analyzed for different boundary conditions (varying between clamped and simply supported). The possibility of improving the transient vibration and noise isolation performance by selecting an appropriate boundary condition was thereby demonstrated.
Comment on “Drought-Induced Reduction in Global Terrestrial Net Primary Production from 2000 Through 2009”
Authors: Medlyn Belinda E.
Published: August 2011

Zhao and Running (Reports, 20 August 2010, p. 940) reported that global net primary production has declined over the past decade and that this reduction was caused by drought. However, their findings are not direct measurements, but rather are based on outcomes from models in which a strong temperature dependence is assumed. I examine the assumptions underlying their results and show that their findings can be explained as logical consequences of these assumptions.
Mitochondria and the Autophagy–Inflammation–Cell Death Axis in Organismal Aging
Authors: Green Douglas R. , Galluzzi Lorenzo , Kroemer Guido
Published: August 2011

Alterations of mitochondrial functions are linked to multiple degenerative or acute diseases. As mitochondria age in our cells, they become progressively inefficient and potentially toxic, and acute damage can trigger the permeabilization of mitochondrial membranes to initiate apoptosis or necrosis. Moreover, mitochondria have an important role in pro-inflammatory signaling. Autophagic turnover of cellular constituents, be it general or specific for mitochondria (mitophagy), eliminates dysfunctional or damaged mitochondria, thus counteracting degeneration, dampening inflammation, and preventing unwarranted cell loss. Decreased expression of genes that regulate autophagy or mitophagy can cause degenerative diseases in which deficient quality control results in inflammation and the death of cell populations. Thus, a combination of mitochondrial dysfunction and insufficient autophagy may contribute to multiple aging-associated pathologies.
Drawing to Learn in Science
Authors: Ainsworth Shaaron , Prain Vaughan , Tytler Russell
Published: August 2011

Emerging research suggests drawing should be explicitly recognized as a key element in science education.
A Window on the Sophistication of Plants
Authors: Jorgensen Richard A.
Published: August 2011

Chaperonin proteins are necessary for the movement of functional transcription factor KN1 between cells.
Much More Than a Telescope
Authors: Turner Michael S.
Published: August 2011

Imagine that the Hubble Space Telescope never existed—that it fell victim to budget overruns, schedule slips, and the tragedy of the Challenger disaster, and was ultimately canceled. Breakthroughs in our understanding of the universe would not have occurred, countless young people around the world would not have been inspired, and U.S. leadership in science and space would be far less. The United States is at a similar crossroads today. Last month, an appropriations committee in the House of Representatives voted to terminate Hubble's successor, the James Webb Space Telescope, as part of the 2012 budget for the National Aeronautics and Space Administration (NASA). The Senate has yet to be heard from, but the numbers in the Budget Control Act of 2011 that passed earlier this month suggest that the Senate could make the funds available to restore funding for the Webb, to the benefit of astronomy and the nation.
Hayabusa Gets to the Bottom of Deceptive Asteroid Cloaking
Authors: Kerr Richard A.
Published: August 2011

Japanese researchers dissecting the first bits of asteroid returned to Earth by a spacecraft have nailed the source of Earth's most common meteorites.
A Study of the Genetic Variability of Human Respiratory Syncytial Virus (HRSV) in Cambodia Reveals the Existence of a New HRSV Group B Genotype
Authors: Arnott Alicia , Vong Sirenda , Mardy Sek , Chu Simon , Naughtin Monica , Sovann Ly , Buecher Carole , Beauté Julien , Rith Sareth , Borand Laurence , Asgari Nima , Frutos Roger , Guillard Bertrand , Touch Sok , Deubel Vincent , Buchy Philippe
Published: August 2011

Human respiratory syncytial virus (HRSV) is the leading cause of hospitalization of children aged <5 years due to respiratory illness in industrialized countries, and pneumonia is the leading cause of mortality among children aged <5 years worldwide. Although HRSV was first identified in 1956, a preventative vaccine has yet to be developed. Here we report the results of the first study to investigate the circulation and genetic diversity of HRSV in Cambodia among an all-ages population over 5 consecutive years. The incidences of HRSV infection among all-ages outpatient and hospitalized populations were equivalent, at 9.5% and 8.2%, respectively. Infection was most prevalent among children aged <5 years, with bronchiolitis being the most frequently observed clinical syndrome in the same age group. Circulation of HRSV was seasonal, typically coinciding with the rainy season between July and November annually. Strains belonging to HRSV groups A and B were detected with equivalent frequencies; however, we observed a potentially biennial shift in the predominant circulating HRSV genotype. The majority of HRSV group B strains belonged to the recently described BA genotype, with the exception of 10 strains classified as belonging to a novel HRSV group B genotype, SAB4, first reported here.
Gypsy and the Birth of the SCAN Domain
Authors: Emerson Ryan O. , Thomas James H.
Published: August 2011

SCAN is a protein domain frequently found at the N termini of proteins encoded by mammalian tandem zinc finger (ZF) genes, whose structure is known to be similar to that of retroviral gag capsid domains and whose multimerization has been proposed as a model for retroviral assembly. We report that the SCAN domain is derived from the C-terminal portion of the gag capsid (CA) protein from the Gmr1-like family of Gypsy/Ty3-like retrotransposons. On the basis of sequence alignments and phylogenetic distributions, we show that the ancestral host SCAN domain (ESCAN for extended SCAN) was exapted from a full-length CA gene from a Gmr1-like retrotransposon at or near the root of the tetrapod animal branch. A truncated variant of ESCAN that corresponds to the annotated SCAN domain arose shortly thereafter and appears to be the only form extant in mammals. The
Anolis
lizard has a large number of tandem ZF genes with N-terminal ESCAN or SCAN domains. We predict DNA binding sites for all
Anolis
ESCAN-ZF and SCAN-ZF proteins and demonstrate several highly significant matches to
Anolis
Gmr1-like sequences, suggesting that at least some of these proteins target retroelements. SCAN is known to mediate protein dimerization, and the CA protein multimerizes to form the core retroviral and retrotransposon capsid structure. We speculate that the SCAN domain originally functioned to target host ZF proteins to retroelement capsids.
Genomic and Proteomic Characterization of the Broad-Host-Range Salmonella Phage PVP-SE1: Creation of a New Phage Genus
Authors: Santos Sílvio B. , Kropinski Andrew M. , Ceyssens Pieter-Jan , Ackermann H.-W. , Villegas Andre , Lavigne Rob , Krylov Victor N. , Carvalho Carla M. , Ferreira Eugénio C. , Azeredo Joana
Published: August 2011

(Bacterio)phage PVP-SE1, isolated from a German wastewater plant, presents a high potential value as a biocontrol agent and as a diagnostic tool, even compared to the well-studied typing phage Felix 01, due to its broad lytic spectrum against different
Salmonella
strains. Sequence analysis of its genome (145,964 bp) shows it to be terminally redundant and circularly permuted. Its G+C content, 45.6 mol%, is lower than that of its hosts (50 to 54 mol%). We found a total of 244 open reading frames (ORFs), representing 91.6% of the coding capacity of the genome. Approximately 46% of encoded proteins are unique to this phage, and 22.1% of the proteins could be functionally assigned. This myovirus encodes a large number of tRNAs (
n
=24), reflecting its lytic capacity and evolution through different hosts. Tandem mass spectrometric analysis using electron spray ionization revealed 25 structural proteins as part of the mature phage particle. The genome sequence was found to share homology with 140 proteins of the
Escherichia coli
bacteriophage rV5. Both phages are unrelated to any other known virus, which suggests that an “rV5-like virus” genus should be created within the
Myoviridae
to contain these two phages.
The HIV/AIDS Vaccine Candidate MVA-B Administered as a Single Immunogen in Humans Triggers Robust, Polyfunctional, and Selective Effector Memory T Cell Responses to HIV-1 Antigens
Authors: Gómez Carmen Elena , Nájera José Luis , Perdiguero Beatriz , García-Arriaza Juan , Sorzano Carlos Oscar S. , Jiménez Victoria , González-Sanz Rubén , Jiménez José Luis , Muñoz-Fernández María Angeles , López Bernaldo de Quirós Juan Carlos , Guardo Alberto C. , García Felipe , Gatell José M. , Plana Montserrat , Esteban Mariano
Published: August 2011

Attenuated poxvirus vectors expressing human immunodeficiency virus type 1 (HIV-1) antigens are considered promising HIV/AIDS vaccine candidates. Here, we describe the nature of T cell immune responses induced in healthy volunteers participating in a phase I clinical trial in Spain after intramuscular administration of three doses of the recombinant MVA-B-expressing monomeric gp120 and the fused Gag-Pol-Nef (GPN) polyprotein of clade B. The majority (92.3%) of the volunteers immunized had a positive specific T cell response at any time postvaccination as detected by gamma interferon (IFN-γ) intracellular cytokine staining (ICS) assay. The CD4+T cell responses were predominantly Env directed, whereas the CD8+T cell responses were similarly distributed against Env, Gag, and GPN. The proportion of responders after two doses of MVA-B was similar to that obtained after the third dose of MVA-B vaccination, and the responses were sustained (84.6% at week 48). Vaccine-induced CD8+T cells to HIV-1 antigens after 1 year were polyfunctional and distributed mainly within the effector memory (TEM) and terminally differentiated effector memory (TEMRA) T cell populations. Antivector T cell responses were mostly induced by CD8+T cells, highly polyfunctional, and of TEMRA phenotype. These findings demonstrate that the poxvirus MVA-B vaccine candidate given alone is highly immunogenic, inducing broad, polyfunctional, and long-lasting CD4 and CD8 T cell responses to HIV-1 antigens, with preference for TEM. Thus, on the basis of the immune profile of MVA-B in humans, this immunogen can be considered a promising HIV/AIDS vaccine candidate.
Bed-rest exercise, activity restriction, and high-risk pregnancies: a feasibility study
Authors: Brun Chantale R. , Shoemaker J. Kevin , Bocking Alan , Hammond Jo-Anne , Poole Monica , Mottola Michelle F.
Published: August 2011

This feasibility study investigated the response of maternal heart rate, blood pressure, and uterine contractions to a 30-min bed-rest exercise session (while listening to music) in hospitalized women with varying diagnoses of high-risk pregnancy. Eleven antenatal women who were hospitalized for activity restriction were assigned randomly to either a bed-rest exercise and music group (n = 6) or a bed-rest and music group (n = 5) that involved no exercise. The key findings were that there were no changes in maternal blood pressure or in the number of uterine contractions following the exercise intervention. A supervised bed-rest exercise intervention may, therefore, provide minimal risks and help alleviate the physiological effects of hospital activity restriction.
A PROJECTION-BASED VARIATIONAL MULTISCALE METHOD FOR LARGE-EDDY SIMULATION WITH APPLICATION TO NON-ISOTHERMAL FREE CONVECTION PROBLEMS
Authors: LÖWE JOHANNES , LUBE GERT
Published: August 2011

We consider a projection-based variational multiscale method for large-eddy simulation of the Navier–Stokes/Fourier model of incompressible, non-isothermal flows. For the semidiscrete problem, an a priori error estimate is given for rather general nonlinear, piecewise constant coefficients of the subgrid models for the unresolved scales of velocity, pressure, and temperature. Then we address aspects of the discretization in time. Finally, the design of the subgrid scale models is specified for the case of free convection problems and studied for the standard benchmark problem of free convection in a closed cavity.
Effectiveness of Heuristic Based Approach on the Performance of Indexing and Clustering of High Dimensional Data
Authors: Chen Alan , Gao Shang , Jarada Tamer N. , Zhang Ming , Pavlatos Christos , Karampelas Panagiotis , Alhajj Reda
Published: August 2011

Data in practical applications (e.g., images, molecular biology, etc) is mostly characterised by high dimensionality and huge size or number of data instances. Though, feature reduction techniques have been successful in reducing the dimensionality for certain applications, dealing with high dimensional data is still an area which has received considerable attention in the research community. Indexing and clustering of high dimensional data are two of the most challenging techniques that have a wide range of applications. However, these techniques suffer from performance issues as the dimensionality and size of the processed data increases. In our effort to tackle this problem, this paper demonstrates a general optimisation technique applicable to indexing and clustering algorithms which need to calculate distances and check them against some minimum distance condition. The optimisation technique is a simple calculation that finds the minimum possible distance between two points, and checks this distance against the minimum distance condition; thus reusing already computed values and reducing the need to compute a more complicated distance function periodically. Effectiveness and usefulness of the proposed optimisation technique has been demonstrated by applying it with successful results to clustering and indexing techniques. We utilised a number of clustering techniques, including the agglomerative hierarchical clustering, k-means clustering, and DBSCAN algorithms. Runtime for all three algorithms with this optimisation scenario was reduced, and the clusters they returned were verified to remain the same as the original algorithms. The optimisation technique also shows potential for reducing runtime by a substantial amount for indexing large databases using NAQ-tree; in addition, the optimisation technique shows potential for reducing runtime as databases grow larger both in dimensionality and size.
Comparative photophysics of sapphyrin derivatives: effects of confused and fused pyrrole rings
Authors: Lim Jong Min , Gupta Iti , Furuta Hiroyuki , Kim Dongho
Published: August 2011

We have investigated the photophysical properties of [22] π-conjugated pentapyrrolic systems, sapphyrin, N-confused and N-fused sapphyrins, with a particular focus on the effects of confused and fused pyrrole rings on their electronic structures using steady-state and time-resolved spectroscopic methods, two-photon absorption cross-section (σ(2)) measurements and quantum mechanical calculations. The absorption spectra of N-confused and N-fused sapphyrins exhibit relatively red-shifted features compared to sapphyrin. In parallel with these spectral features, the reduced HOMO–LUMO gaps were observed in going from sapphyrin to N-fused sapphyrin. In the analysis of the anisotropy of the induced current density (AICD), N-confused and N-fused sapphyrins show that extra π-electrons in confused and fused pyrrole rings contribute to the extension of their π-conjugation pathways. Slightly larger twophoton absorption cross-section values of N-confused and N-fused sapphyrins (3250 and 3900 GM) than that of sapphyrin (2900 GM) also reflect an enhanced π-conjugation effect due to bicyclic and endocyclic extensions in π-conjugation pathways, respectively. The excited singlet and triplet state lifetimes of N-confused sapphyrin were determined to be 60 ps and 1 μs, respectively, due to conformational change and acceleration of nonradiative decay processes, being in a sharp contrast with those of sapphyrin (2.4 ns and 13 μs, respectively). In the case of N-fused sapphyrin, very short singlet excited-state lifetime of 5 ps was detected probably due to the excited-state NH-tautomerization process which enhances nonradiative decay processes.
Hypoxic culture and in vivo inflammatory environments affect the assumption of pericyte characteristics by human adipose and bone marrow progenitor cells
Authors: Amos Peter J. , Mulvey Carolyn L. , Seaman Scott A. , Walpole Joseph , Degen Katherine E. , Shang Hulan , Katz Adam J. , Peirce Shayn M.
Published: August 2011

Previous studies have shown that exposure to a hypoxic in vitro environment increases the secretion of pro-angiogenic growth factors by human adipose-derived stromal cells (hASCs) [Cao Y, et al., Biochem Biophys Res Commun 332: 370–379, 2005; Kokai LE, et al., Plast Reconstr Surg 116: 1453–1460, 2005; Park BS, et al., Biomed Res (Tokyo) 31: 27–34, 2010; Rasmussen JG, et al., Cytotherapy 13: 318–328, 2010; Rehman J, et al., Circulation 109: 1292–1298, 2004]. Previously, it has been demonstrated that hASCs can differentiate into pericytes and promote microvascular stability and maintenance during angiogenesis in vivo (Amos PJ, et al., Stem Cells 26: 2682–2690, 2008; Traktuev DO, et al., Circ Res 102: 77–85, 2008). In this study, we tested the hypotheses that angiogenic induction can be increased and pericyte differentiation decreased by pretreatment of hASCs with hypoxic culture and that hASCs are similar to human bone marrow-derived stromal cells (hBMSCs) in these regards. Our data confirms previous studies showing that hASCs: 1) secrete pro-angiogenic proteins, which are upregulated following culture in hypoxia, and 2) migrate up gradients of PDGF-BB in vitro, while showing for the first time that a rat mesenteric model of angiogenesis induced by 48/80 increases the propensity of both hASCs and hBMSCs to assume perivascular phenotypes following injection. Moreover, culture of both cell types in hypoxia before injection results in a biphasic vascular length density response in this model of inflammation-induced angiogenesis. The effects of hypoxia and inflammation on the phenotype of adult progenitor cells impacts both the therapeutic and the basic science applications of the cell types, as hypoxia and inflammation are common features of natural and pathological vascular compartments in vivo.
Angiotensin receptor blockers shift the circadian rhythm of blood pressure by suppressing tubular sodium reabsorption
Authors: Fukuda Michio , Wakamatsu-Yamanaka Tamaki , Mizuno Masashi , Miura Toshiyuki , Tomonari Tatsuya , Kato Yoko , Ichikawa Tadashi , Miyagi Sota , Shirasawa Yuichi , Ito Akinori , Yoshida Atsuhiro , Kimura Genjiro
Published: August 2011

Recently, we found that an angiotensin II receptor blocker (ARB) restored the circadian rhythm of the blood pressure (BP) from a nondipper to a dipper pattern, similar to that achieved with sodium intake restriction and diuretics (Fukuda M, Yamanaka T, Mizuno M, Motokawa M, Shirasawa Y, Miyagi S, Nishio T, Yoshida A, Kimura G. J Hypertens 26: 583–588, 2008). ARB enhanced natriuresis during the day, while BP was markedly lower during the night, resulting in the dipper pattern. In the present study, we examined whether the suppression of tubular sodium reabsorption, similar to the action of diuretics, was the mechanism by which ARB normalized the circadian BP rhythm. BP and glomerulotubular balance were compared in 41 patients with chronic kidney disease before and during ARB treatment with olmesartan once a day in the morning for 8 wk. ARB increased natriuresis (sodium excretion rate; UNaV) during the day (4.5 ± 2.2 to 5.5 ± 2.1 mmol/h, P = 0.002), while it had no effect during the night (4.3 ± 2.0 to 3.8 ± 1.6 mmol/h, P = 0.1). The night/day ratios of both BP and UNaV were decreased. The decrease in the night/day ratio of BP correlated with the increase in the daytime UNaV ( r = 0.42, P = 0.006). Throughout the whole day, the glomerular filtration rate ( P = 0.0006) and tubular sodium reabsorption ( P = 0.0005) were both reduced significantly by ARB, although UNaV remained constant (107 ± 45 vs. 118 ± 36 mmol/day, P = 0.07). These findings indicate that the suppression of tubular sodium reabsorption, showing a resemblance to the action of diuretics, is the primary mechanism by which ARB can shift the circadian BP rhythm into a dipper pattern.
Increased renin excretion is associated with augmented urinary angiotensin II levels in chronic angiotensin II-infused hypertensive rats
Authors: Liu Liu , Gonzalez Alexis A. , McCormack Michael , Seth Dale M. , Kobori Hiroyuki , Navar L. Gabriel , Prieto Minolfa C.
Published: August 2011

Renin expression in principal cells of collecting ducts (CD) is upregulated in angiotensin II (ANG II)-dependent hypertensive rats; however, it remains unclear whether increased CD-derived renin undergoes tubular secretion. Accordingly, urinary levels of renin (uRen), angiotensinogen (uAGT), and ANG II (uANG II) were measured in chronic ANG II-infused Sprague-Dawley rats (80 ng/min for 14 days, n = 10) and sham-operated rats ( n = 10). Systolic blood pressure increased in the ANG II rats by day 5 and continued to increase throughout the study ( day 13; ANG II: 175 ± 10 vs. sham: 116 ± 2 mmHg; P < 0.05). ANG II infusion increased renal cortical and medullary ANG II levels (cortical ANG II: 606 ± 72 vs. 247 ± 43 fmol/g; P < 0.05; medullary ANG II: 2,066 ± 116 vs. 646 ± 36 fmol/g; P < 0.05). Although plasma renin activity (PRA) was suppressed in the ANG II-infused rats (0.3 ± 0.2 vs. 5.5 ± 1.8 ng ANG I·ml−1·h−1; P < 0.05), renin content in renal medulla was increased (12,605 ± 1,343 vs. 7,956 ± 765 ng ANG I·h−1·mg−1; P < 0.05). Excretion of uAGT and uANG II increased in the ANG II rats [uAGT: 1,107 ± 106 vs. 60 ± 26 ng/day; P < 0.0001; uANG II: 3,813 ± 431 vs. 2,080 ± 361 fmol/day; P < 0.05]. By day 13, despite suppression of PRA, urinary prorenin content increased in ANG II rats [15.7 ± 3 vs. 2.6 ± 1 × 10−3enzyme units excreted (EUE)/day, P < 0.01] as was the excretion rate of renin (8.6 ± 2 × 10−6EUE/day) compared with sham (2.8 ± 1 × 10−6EUE/day; P < 0.05). Urinary renin and prorenin protein levels examined by Western blot were augmented ∼10-fold in the ANG II-infused rats. Concomitant AT1receptor blockade with candesartan prevented the increase. Thus, in ANG II-dependent hypertensive rats with marked PRA suppression, increased urinary levels of renin and prorenin reflect their augmented secretion by CD cells into the luminal fluid. The greater availability of renin and AGT in the urine reflects the capability for intratubular ANG II formation which stimulates sodium reabsorption in distal nephron segments.
From Spheric to Aspheric Solid Polymer Lenses: A Review
Authors: Hung Kuo-Yung , Hsiao Po-Jen , Tseng Fang-Gang , Wei Miao-Chin
Published: August 2011

This paper presents a new approach in the use of MEMS technology to fabricate micro-optofluidic polymer solid lenses in order to achieve the desired profile, focal length, numerical aperture, and spot size. The resulting polymer solid lenses can be applied in optical data storage systems, imaging systems, and automated optical inspection systems. In order to meet the various needs of different applications, polymer solid lenses may have a spherical or aspherical shape. The method of fabricating polymer solid lenses is different from methods used to fabricate tunable lenses with variable focal length or needing an external control system to change the lens geometry. The current trend in polymer solid lenses is toward the fabrication of microlenses with a high numerical aperture, small clear aperture (<2 mm), and high transmittance. In this paper we focus on the use of thermal energy and electrostatic force in shaping the lens profile, including both spherical and aspherical lenses. In addition, the paper discusses how to fabricate a lens with a high numerical aperture of 0.6 using MEMS and also compares the optical characteristics of polymer lens materials, including SU-8, Norland Optical Adhesive (NOA), and cyclic olefin copolymer (COC). Finally, new concepts and applications related to micro-optofluidic lenses and polymer materials are also discussed.