bluuebunny/crossref_metadata_2025 huggingface dataset:
Model-based automated detection of echolocation calls using the link detector
Authors: Skowronski Mark D. , Fenton M. Brock
Published: July 2008

The link detector combines a model-based spectral peak tracker with an echo filter to detect echolocation calls of bats. By processing calls in the spectrogram domain, the links detector separates calls that overlap in time, including call harmonics and echoes. The links detector was validated by using an artificial recording environment, including synthetic calls, atmospheric absorption, and echoes, which provided control of signal-to-noise ratio and an absolute ground truth. Maximum hit rate (2% false positive rate) for the links detector was 87% compared to 1.5% for a spectral peak detector. The difference in performance was due to the ability of the links detector to filter out echoes. Detection range varied across species from 13 to more than 20m due to call bandwidth and frequency range. Global features of calls detected by the links detector were compared to those of synthetic calls. The error in all estimates increased as the range increased, and estimates of minimum frequency and frequency of most energy were more accurate compared to maximum frequency. The links detector combines local and global features to automatically detect calls within the machine learning paradigm and detects overlapping calls and call harmonics in a unified framework.
Mammalian laryngseal air sacs add variability to the vocal tract impedance: Physical and computational modeling
Authors: Riede Tobias , Tokuda Isao T. , Munger Jacob B. , Thomson Scott L.
Published: July 2008

Cavities branching off the main vocal tract are ubiquitous in nonhumans. Mammalian air sacs exist in human relatives, including all four great apes, but only a substantially reduced version exists in humans. The present paper focuses on acoustical functions of the air sacs. The hypotheses are investigated on whether the air sacs affect amplitude of utterances and/or position of formants. A multilayer synthetic model of the vocal folds coupled with a vocal tract model was utilized. As an air sac model, four configurations were considered: open and closed uniform tube-like side branches, a rigid cavity, and an inflatable cavity. Results suggest that some air sac configurations can enhance the sound level. Furthermore, an air sac model introduces one or more additional resonance frequencies, shifting formants of the main vocal tract to some extent but not as strongly as previously suggested. In addition, dynamic range of vocalization can be extended by the air sacs. A new finding is also an increased variability of the vocal tract impedance, leading to strong nonlinear source-filter interaction effects. The experiments demonstrated that air-sac-like structures can destabilize the sound source. The results were validated by a transmission line computational model.
On the application of the lattice Boltzmann method to the investigation of glottal flow
Authors: Kucinschi Bogdan R. , Afjeh Abdollah A. , Scherer Ronald C.
Published: July 2008

The production of voice is directly related to the vibration of the vocal folds, which is generated by the interaction between the glottal flow and the tissue of the vocal folds. In the current study, the aerodynamics of the symmetric glottis is investigated numerically for a number of static configurations. The numerical investigation is based on the lattice Boltzmann method (LBM), which is an alternative approach within computational fluid dynamics. Compared to the traditional Navier–Stokes computational fluid dynamics methods, the LBM is relatively easy to implement and can deal with complex geometries without requiring a dedicated grid generator. The multiple relaxation time model was used to improve the numerical stability. The results obtained with LBM were compared to the results provided by a traditional Navier–Stokes solver and experimental data. It was shown that LBM results are satisfactory for all the investigated cases.
Relation between perceived voice register and flow glottogram parameters in males
Authors: Salomão Gláucia Laís , Sundberg Johan
Published: July 2008

The perception of modal and falsetto registers was analyzed in a material consisting of a total of 104 vowel sounds sung by 13 choir singers, 52 sung in modal register, and 52 in falsetto register. These vowel sounds were classified by 16 expert listeners in a forced choice test and the number of votes for modal was compared to the voice source parameters: (1) closed quotient (Qclosed), (2) level difference between the two lowest source spectrum partials (H1−H2), (3) AC amplitude, (4) maximum flow declination rate (MFDR), and (5) normalized amplitude quotient (NAQ, AC amplitude/MFDR* fundamental frequency). Tones with a high value of Qclosed and low values of H1−H2 and of NAQ were typically associated with high number of votes for modal register, and vice versa, Qclosed showing the strongest correlation. Some singer subjects produced tones that could not be classified as either falsetto or modal register, suggesting that classification of registers is not always feasible.
Beamforming synthesis of binaural responses from computer simulations of acoustic spaces
Authors: Poletti Mark A. , Svensson U. Peter
Published: July 2008

Auditorium designs can be evaluated prior to construction by numerical modeling of the design. High-accuracy numerical modeling produces the sound pressure on a rectangular grid, and subjective assessment of the design requires auralization of the sampled sound field at a desired listener position. This paper investigates the production of binaural outputs from the sound pressure at a selected number of grid points by using a least squares beam forming approach. Low-frequency axisymmetric emulations are derived by assuming a solid sphere model of the head, and a spherical array of 640 microphones is used to emulate ten measured head-related transfer function (HRTF) data sets from the CIPIC database for half the audio bandwidth. The spherical array can produce high-accuracy band-limited emulation of any human subject’s measured HRTFs for a fixed listener position by using individual sets of beam forming impulse responses.
Simple vibration modeling of structural fuzzy with continuous boundary by including two-dimensional spatial memory
Authors: Friis Lars , Ohlrich Mogens
Published: July 2008

Many complicated systems of practical interest consist basically of a well-defined outer shell-like master structure and a complicated internal structure with uncertain dynamic properties. Using the “fuzzy structure theory” for predicting audible frequency vibration, the internal structure is considered as one or more fuzzy substructures that are known in some statistical sense only. Experiments have shown that such fuzzy substructures often introduce a damping in the master which is much higher than the structural losses account for. A special method for modeling fuzzy substructures with a one-dimensional continuous boundary was examined in a companion paper [L. Friis and M. Ohlrich, “Vibration modeling of structural fuzzy with continuous boundary,” J. Acoust. Soc. Am. 123, 718–728 (2008)]. In the present paper, this method is extended, such that it allows modeling of fuzzy substructures with a two-dimensional continuous boundary. Additionally, a simple method for determining the so-called equivalent coupling factor is presented. The validity of this method is demonstrated by numerical simulations of the vibration response of a master plate structure with fuzzy attachments. It is revealed that the method performs very well above a nondimensional frequency of 500 of the master, and it is shown that errors below this frequency are caused mainly by simplifying assumptions concerning the shape of the master vibration displacement.
An acoustic analysis of laughter produced by congenitally deaf and normally hearing college students
Authors: Makagon Maja M. , Funayama E. Sumie , Owren Michael J.
Published: July 2008

Relatively few empirical data are available concerning the role of auditory experience in nonverbal human vocal behavior, such as laughter production. This study compared the acoustic properties of laughter in 19 congenitally, bilaterally, and profoundly deaf college students and in 23 normally hearing control participants. Analyses focused on degree of voicing, mouth position, air-flow direction, temporal features, relative amplitude, fundamental frequency, and formant frequencies. Results showed that laughter produced by the deaf participants was fundamentally similar to that produced by the normally hearing individuals, which in turn was consistent with previously reported findings. Finding comparable acoustic properties in the sounds produced by deaf and hearing vocalizers confirms the presumption that laughter is importantly grounded in human biology, and that auditory experience with this vocalization is not necessary for it to emerge in species-typical form. Some differences were found between the laughter of deaf and hearing groups; the most important being that the deaf participants produced lower-amplitude and longer-duration laughs. These discrepancies are likely due to a combination of the physiological and social factors that routinely affect profoundly deaf individuals, including low overall rates of vocal fold use and pressure from the hearing world to suppress spontaneous vocalizations.
A straightforward method for wall impedance eduction in a flow duct
Authors: Jing Xiaodong , Peng Sen , Sun Xiaofeng
Published: July 2008

The development of the advanced liner technology for aeroengine noise control necessitates the impedance measurement method under realistic flow conditions. Currently, the methods for this need are mainly based on the inverse impedance eduction principle, confronting with the problems of initial guess, high computation cost, and low convergence. In view of this, a new strategy is developed that straightforwardly educes the impedance from the sound pressure information measured on the duct wall opposing to the test acoustic liner embedded in a flow duct. Here, the key insight is that the modal nature of the duct acoustic field renders a summed-exponential representation of the measured sound pressure; thus, the characterizing axial wave number can be readily extracted by means of Prony’s method, and further the unknown impedance is calculated from the eigenvalue and dispersion relations based on the classical mode-decomposition analysis. This straightforward method is simple in its basic principle but remarkably has the advantages of ultimately overcoming the drawbacks inherent to the inverse methods, incorporating the realistic multimode nonprogressive wave effects, high computational efficiency, possibly reducing the measurement points, and even avoiding the necessity of the duct exit impedance that bothers perhaps all the existing waveguide methods.
On the minimum audible difference in direct-to-reverberant energy ratio
Authors: Larsen Erik , Iyer Nandini , Lansing Charissa R. , Feng Albert S.
Published: July 2008

The goals of this study were to measure sensitivity to the direct-to-reverberant energy ratio (D/R) across a wide range of D/R values and to gain insight into which cues are used in the discrimination process. The main finding is that changes in D/R are discriminated primarily based on spectral cues. Temporal cues may be used but only when spectral cues are diminished or not available, while sensitivity to interaural cross-correlation is too low to be useful in any of the conditions tested. These findings are based on an acoustic analysis of these variables and the results of two psychophysical experiments. The first experiment employs wideband noise with two values for onset and offset times to determine the D/R just-noticeable difference at −10, 0, 10, and 20dB D/R. This yielded substantially higher sensitivity to D/R at 0 and 10dB D/R (2–3dB) than has been reported previously, while sensitivity is much lower at −10 and 20dB D/R. The second experiment consists of three parts where specific cues to D/R are reduced or removed, which enabled the specified rank ordering of the cues. The acoustic analysis and psychophysical experiments also provide an explanation for the “auditory horizon effect.”
Identification of SLEEPLESS, a Sleep-Promoting Factor
Authors: Koh Kyunghee , Joiner William J. , Wu Mark N. , Yue Zhifeng , Smith Corinne J. , Sehgal Amita
Published: July 2008

Sleep is an essential process conserved from flies to humans. The importance of sleep is underscored by its tight homeostatic control. Through a forward genetic screen, we identified a gene,
sleepless
, required for sleep in
Drosophila
. The
sleepless
gene encodes a brain-enriched, glycosylphosphatidylinositol-anchored protein. Loss of SLEEPLESS protein caused an extreme (>80%) reduction in sleep; a moderate reduction in SLEEPLESS had minimal effects on baseline sleep but markedly reduced the amount of recovery sleep after sleep deprivation. Genetic and molecular analyses revealed that
quiver
, a mutation that impairs
Shaker
-dependent potassium current, is an allele of
sleepless
. Consistent with this finding, Shaker protein levels were reduced in
sleepless
mutants. We propose that SLEEPLESS is a signaling molecule that connects sleep drive to lowered membrane excitability.
Addressing Complexity
Authors: Sterelny Kim
Published: July 2008

Re-Engineering Philosophy for Limited Beings
. Piecewise Approximations to Reality.
By William C. Wimsatt
. Harvard University Press, Cambridge, MA, 2007. 468 pp. $49.95, £32.95, €37.50. ISBN 9780674015456.

Although the title may offer little clue, these essays on the philosophy of science are particularly relevant to considerations of how to think about something as messy and multi-leveled as biology.
Patagonian Glacier Response During the Late Glacial–Holocene Transition
Authors: Ackert Robert P. , Becker Richard A. , Singer Brad S. , Kurz Mark D. , Caffee Marc W. , Mickelson David M.
Published: July 2008

Whether cooling occurred in the Southern Hemisphere during the Younger Dryas (YD) is key to understanding mechanisms of millennial climate change. Although Southern Hemisphere records do not reveal a distinct climate reversal during the late glacial period, many mountain glaciers readvanced. We show that the Puerto Bandera moraine (50°S), which records a readvance of the Southern Patagonian Icefield (SPI), formed at, or shortly after, the end of the YD. The exposure age (10.8 ± 0.5 thousand years ago) is contemporaneous with the highest shoreline of Lago Cardiel (49°S), which records peak precipitation east of the Andes since 13 thousand years ago. Absent similar moraines west of the Andes, these data indicate an SPI response to increased amounts of easterly-sourced precipitation—reflecting changes in the Southern Westerly circulation—rather than regional cooling.
Comment on "A 3-Hydroxypropionate/4-Hydroxybutyrate Autotrophic Carbon Dioxide Assimilation Pathway in Archaea"
Authors: Ettema Thijs J. G. , Andersson Siv G. E.
Published: July 2008

Berg
et al
. (Reports, 14 December 2007, p. 1782) reported the discovery of an autotrophic carbon dioxide–fixation pathway in Archaea and implicated a substantial role of this pathway in global carbon cycling based on sequence analysis of Global Ocean Sampling data. We question the validity of the latter claim.
When Sleep Proves Impossible
Authors: Perlis Michael L.
Published: July 2008

Insomniac
.
By Gayle Greene
. University of California Press, Berkeley, 2008. 517 pp. $29.95. ISBN 9780520246300.

Drawing on her lifelong affliction with chronic insomnia and her interviews with neurologists, sleep researchers, physicians, psychiatrists, and fellow sufferers, the author weaves a wide-ranging account of the condition, its causes, and potential remedies.
Measurement of the Humoral Immune Response following an Incident Human Papillomavirus Type 16 or 18 Infection in Young Women by a Pseudovirion-Based Neutralizing Antibody Assay
Authors: Steele Jane , Collins Stuart , Wen Kaisheng , Ryan Gordon , Constandinou-Williams Christothea , Woodman Ciaran B. J.
Published: July 2008

We have evaluated a neutralizing antibody assay which uses human papillomavirus (HPV) type 16 (HPV-16) and HPV-18 pseudovirions carrying a secretory alkaline phosphatase reporter gene and which can potentially measure functionally relevant HPV type-specific neutralizing antibodies. The reproducibility of the assay was excellent; for HPV-16, the intra- and interassay kappa values were 0.95 and 0.90, respectively; and for HPV-18, the corresponding values were 0.90 and 0.90. This assay was used to describe the kinetics of the neutralizing antibody response in a cohort of 42 young women who were recruited soon after first intercourse and who first tested positive for HPV-16 DNA or HPV-18 DNA, or both, during follow-up. Most women seroconverted following the first detection of type-specific HPV DNA and remained seropositive until the end of follow-up. Our findings are broadly consistent with those of two other cohort studies which have measured the serological response following an incident infection by using the technically simpler virus-like-particle-based enzyme-linked immunosorbent assay.
Diagnosis of Central Nervous System Tuberculosis by T-Cell-Based Assays on Peripheral Blood and Cerebrospinal Fluid Mononuclear Cells
Authors: Kim Sung-Han , Chu Kon , Choi Su-Jin , Song Kyoung-Ho , Kim Hong-Bin , Kim Nam-Joong , Park Seong-Ho , Yoon Byung-Woo , Oh Myoung-don , Choe Kang-Won
Published: July 2008

In active tuberculosis (TB),
Mycobacterium tuberculosis
-specific T cells are compartmentalized more to the site of infection than to the circulating blood. Therefore, an
M. tuberculosis
-specific enzyme-linked immunospot (ELISPOT) assay with samples from the site of infection may permit a more sensitive or specific diagnosis of active central nervous system (CNS) TB than that achieved by the assay with blood alone. Therefore, we prospectively evaluated the usefulness of circulating and compartmentalized mononuclear cell (MC; i.e., peripheral blood mononuclear cell [PBMC] and cerebrospinal fluid [CSF] MC)-based ELISPOT assays (i.e., the T-SPOT.TB test) for the diagnosis of active TB in patients with suspected CNS TB. The clinical categories of CNS TB were classified as described previously (G. E. Thwaites, T. T. Chau, K. Stepniewska, N. H. Phu, L. V. Chuong, D. X. Sinh, N. J. White, C. M. Parry, and J. J. Farrar, Lancet 360:1287-1292, 2002). Thirty-seven patients with suspected CNS TB were enrolled over a 12-month period. Of these, 31 (84%) showed clinical manifestations of suspected TB meningitis and 6 (16%) gave indications of intracranial tuberculoma with disseminated TB. The final clinical categories of the 37 patients with suspected CNS TB were as follows: 12 (32%) were classified as having CNS TB (7 with confirmed TB, 3 with probable TB, and 2 with possible TB) and 25 (68%) were classified as not having active TB. The sensitivity and specificity of the PBMC ELISPOT assay were 91% (95% confidence interval [CI], 59% to 100%) and 63% (95% CI, 41% to 81%), respectively. By comparison, the sensitivity and specificity of the CSF MC ELISPOT assay were 75% (95% CI, 19% to 99%) and 75% (95% CI, 43% to 95%), respectively. When the ratio of the CSF MC ELISPOT assay results to the PBMC ELISPOT results was 2 or more, the sensitivity and specificity were 50% (95% CI, 7% to 93%) and 100% (95% CI, 74% to 100%), respectively. The ELISPOT assay with PBMCs and CSF MCs is a useful adjunct to the current tests for the diagnosis of CNS TB.
Evaluation of CHROMagar KPC for Rapid Detection of Carbapenem-Resistant
Enterobacteriaceae
Authors: Samra Zmira , Bahar Judi , Madar-Shapiro Liora , Aziz Nazi , Israel Sara , Bishara Jihad
Published: July 2008

A new CHROMagar KPC medium was compared to MacConkey agar with carbapenem discs and PCR for the
bla
KPC
gene for rapid detection of carbapenem-resistant
Klebsiella pneumoniae
. The sensitivity and specificity relative to PCR were 100% and 98.4%, respectively, for CHROMagar KPC and 92.7% and 95.9%, respectively, for MacConkey agar.
Molecular Characterization of Human-Colonizing
Streptococcus agalactiae
Strains Isolated from Throat, Skin, Anal Margin, and Genital Body Sites
Authors: van der Mee-Marquet Nathalie , Fourny Laure , Arnault Laurence , Domelier Anne-Sophie , Salloum Mazen , Lartigue Marie-Frédérique , Quentin Roland
Published: July 2008

Streptococcus agalactiae
carriage was evaluated by sampling four body sites in a group of 249 healthy individuals including both sexes and a wide range of ages; the aims were to study the population structure of colonizing strains by multilocus sequence typing (MLST) and to evaluate their diversity by serotyping, SmaI macrorestriction analysis, and PCR screening for genetic markers of highly virulent clones for neonates. The prevalences of carriage were 27% in women and 32% in men. The major positive body site was the genital tract (23% in women and 21% in men); skin, throats, and anal margins were also positive in 2%, 4%, and 14%, respectively. These human-colonizing strains belonged mostly to serotypes III (24%), Ia (21%), V (18%), and Ib (17%). Twenty-three sequence types (STs) were identified. The MLST characteristics of the strains isolated from a single anatomic site—genital (vagina [women] or from a sample of the first urination after arising from a night's sleep [men]), throat, skin, or anal margin—suggest a body site colonization specificity for particular STs: strains of STs 2, 10, 19, and 196 were isolated only from genital sites; strains of STs 1, 8, and 23 were isolated more frequently from throat florae; and strains recovered only from anal margin samples were more closely related to strains isolated from throats than to those from genital sites. Most strains of STs 1, 8, and 23—STs that are increasingly described as being responsible for adult infections—did not carry any markers of strains virulent for neonates, suggesting that the virulence of these strains is probably associated with other genetic determinants. In addition, the genetic diversities of the strains varied between STs: STs 2, 8, 10, 23, and 196 were the most diverse; STs 1 and 19 were more homogeneous; and ST 17 strains formed three distant groups.
Evaluation of Four Selective Agars and Two Enrichment Broths in Screening for Methicillin-Resistant
Staphylococcus aureus
Authors: Böcher S. , Smyth R. , Kahlmeter G. , Kerremans J. , Vos M. C. , Skov R.
Published: July 2008

To evaluate methicillin-resistant
Staphylococcus aureus
detection, we tested in vitro four selective agars and two enrichment broths apart and in combination. Tryptone soya broth with salt, aztreonam, and cefoxitin appeared to be the most sensitive medium. This broth was superior to a phenol red mannitol broth with aztreonam and ceftizoxime.
Trends in Species Distribution and Susceptibility of Bloodstream Isolates of
Candida
Collected in Monterrey, Mexico, to Seven Antifungal Agents: Results of a 3-Year (2004 to 2007) Surveillance Study
Authors: González Gloria M. , Elizondo Mariana , Ayala Jacobo
Published: July 2008

During a 3-year surveillance program (2004 to 2007) in Monterrey, Mexico, 398 isolates of
Candida
spp. were collected from five hospitals. We established the species distribution and in vitro susceptibilities of these isolates. The species included 127
Candida albicans
strains, 151
C
.
parapsilosis
strains, 59
C
.
tropicalis
strains, 32
C
.
glabrata
strains, 11
C
.
krusei
strains, 5
C
.
guilliermondii
strains, 4
C
.
famata
strains, 2
C
.
utilis
strains, 2
C
.
zeylanoides
strains, 2
C
.
rugosa
strains, 2
C
.
lusitaniae
strains, and 1
C
.
boidinii
strain. The species distribution differed with the age of the patients. The proportion of candidemias caused by
C
.
parapsilosis
was higher among infants ≤1 year old, and the proportion of candidemias caused by
C
.
glabrata
increased with patient age (>45 years old). MICs were calculated following the criteria of the Clinical Laboratory Standards Institute reference broth macrodilution method. Overall,
C
.
albicans
,
C
.
parapsilosis
, and
C
.
tropicalis
isolates were susceptible to fluconazole and amphotericin B. However, 31.3% of
C
.
glabrata
isolates were resistant to fluconazole (MIC ≥ 64 μg/ml), 43.3% were resistant to itraconazole (MIC ≥ 1 μg/ml), and 12.5% displayed resistance to amphotericin B (MIC ≥ 2 μg/ml). Newer triazoles, namely, voriconazole, posaconazole, and ravuconazole, had a notable in vitro activity against all
Candida
species tested. Also, caspofungin was active against
Candida
sp. isolates (MIC
90
≤ 0.5 μg/ml) except
C
.
parapsilosis
(MIC
90
= 2 μg/ml). It is imperative to promote a national-level surveillance program to monitor this important microorganism.
Heart Valves Should Not Be Routinely Cultured
Authors: Muñoz Patricia , Bouza Emilio , Marín Mercedes , Alcalá Luis , Rodríguez Créixems Marta , Valerio Maricela , Pinto Angel ,   on behalf of the Group for the Management of Infective Endocarditis of the Gregorio Marañón Hospital
Published: July 2008

Heart valve (HV) culture is one of the major Duke criteria for the diagnosis of definite infectious endocarditis (IE). However, previous series suggest that heart valve culture does not have good sensitivity (7.8 to 17.6%) and may be contaminated during manipulation. Our goal was to establish the value of routine cultures of heart valves in patients with and without IE. From 2004 to 2006, resected heart valves were systematically cultured according to standard procedures. The definition and etiology of IE were based on the Duke criteria and on valve PCR of specimens from blood culture-negative patients. Bacterial and fungal broad-range PCR was performed. A total of 1,101 heart valves were studied: 1,030 (93.6%) from patients without IE and 71 (6.4%) from patients with IE (42 patients). Overall, 321 (29.2%) cultures were positive (28/71 [39.4%] IE cases and 293/1,030 [28.4%] non-IE). All IE patients with negative heart valve cultures had received antimicrobial therapy. The yield of culture of heart valves for IE diagnosis was as follows: sensitivity, 25.4%; specificity, 71.6%; positive predictive value (PPV), 5.8%; and negative predictive value, 93.3%. Because of its poor sensitivity and PPV, valve cultures should not be performed for patients without a clinical suspicion of IE. For patients with confirmed IE, heart valve cultures should be interpreted with caution.
Crystal Structure of Coxsackievirus B3 3D
pol
Highlights the Functional Importance of Residue 5 in Picornavirus Polymerases
Authors: Campagnola Grace , Weygandt Mark , Scoggin Kirsten , Peersen Olve
Published: July 2008

The crystal structure of the coxsackievirus B3 polymerase has been solved at 2.25-Å resolution and is shown to be highly homologous to polymerases from poliovirus, rhinovirus, and foot-and-mouth disease viruses. Together, these structures highlight several conserved structural elements in picornaviral polymerases, including a proteolytic activation-dependent N-terminal structure that is essential for full activity. Interestingly, a comparison of all of the picornaviral polymerase structures shows an unusual conformation for residue 5, which is always located at a distortion in the β-strand composed of residues 1 to 8. In our earlier structure of the poliovirus polymerase, we attributed this conformation to a crystal packing artifact, but the observation that this conformation is conserved among picornaviruses led us to examine the role of this residue in further detail. Here we use coxsackievirus polymerase to show that elongation activity correlates with the hydrophobicity of residue 5 and, surprisingly, more hydrophobic residues result in higher activity. Based on structural analysis, we propose that this residue becomes buried during the nucleotide repositioning step that occurs prior to phosphoryl transfer. We present a model in which the buried N terminus observed in all picornaviral polymerases is essential for stabilizing the structure during this conformational change.
Tumor Necrosis Factor Alpha Protects against Lethal West Nile Virus Infection by Promoting Trafficking of Mononuclear Leukocytes into the Central Nervous System
Authors: Shrestha Bimmi , Zhang Bo , Purtha Whitney E. , Klein Robyn S. , Diamond Michael S.
Published: July 2008

West Nile virus (WNV) is a neurotropic flavivirus that has emerged globally as a significant cause of viral encephalitis in humans, especially in immunocompromised individuals. Previous studies have shown essential protective roles for antiviral cytokines (e.g., alpha interferon [IFN-α] and IFN-γ) against WNV in mice. However, studies using cell culture offer conflicting answers regarding whether tumor necrosis factor alpha (TNF-α) has an anti-WNV function. To test the biological significance of TNF-α against WNV in vivo, experiments were performed with TNF receptor-1 (TNF-R1)-deficient and TNF-α-depleted C57BL/6 mice. TNF-R1−/−mice had enhanced mortality and decreased survival time after WNV infection compared to congenic wild-type mice. Consistent with this, administration of a neutralizing anti-TNF-α monoclonal antibody also decreased survival after WNV infection. Relatively small differences in viral burdens in peripheral tissues of TNF-R1−/−mice were observed, and this occurrence correlated with a modest antiviral effect of TNF-α on primary macrophages but not dendritic cells. In contrast, the viral titers detected in the central nervous systems of TNF-R1−/−mice were significantly increased compared to those of wild-type mice, although TNF-α did not have a direct antiviral effect in primary neuron cultures. Whereas no defect in priming of adaptive B- and T-cell responses in TNF-R1−/−mice was observed, there were significant reductions in accumulations of CD8+T cells and macrophages in the brain. Our data are most consistent with a model in which interaction of TNF-α with TNF-R1 protects against WNV infection by regulating migration of protective inflammatory cells into the brain during acute infection.
A KIND OF NONLINEAR COHERENT-ENTANGLED STATE AND SQUEEZING PROPERTY
Authors: LIU DONG-MEI , MA SHAN-JUN , KUANG MAI-HUA
Published: July 2008

Based on the technique of integration within an ordered product of nonlinear Bose operators, a new kind of nonlinear coherent entangled state, which exhibits both the property of coherent state and quantum entanglement, is constructed and its application in squeezing is discussed.
LOCAL SKEW CORRECTION IN DOCUMENTS
Authors: SARAGIOTIS P. , PAPAMARKOS N.
Published: July 2008

In this paper we propose a technique for detecting and correcting the skew of text areas in a document. The documents we work with may contain several areas of text with different skew angles. First, a text localization procedure is applied based on connected components analysis. Specifically, the connected components of the document are extracted and filtered according to their size and geometric characteristics. Next, the candidate characters are grouped using a nearest neighbor approach to form words and then based on these words text lines of any skew are constructed. Then, the top-line and baseline for each text line are estimated using linear regression. Text lines in near locations, having similar skew angles, are grown to form text areas. For each text area a local skew angle is estimated and then these text areas are skew corrected independently to horizontal or vertical orientation. The technique has been extensively tested on a variety of document images and its accuracy and robustness is compared with other existing techniques.
ROBUST FUNDAMENTAL MATRIX ESTIMATION USING COPLANAR CONSTRAINTS
Authors: TANG CHENG-YUAN , CHOU HONG-LONG , WU YI-LEH , DING YAN-HUNG
Published: July 2008

Due to degeneracy problems (e.g. corresponding point pairs are located on the same plane), it is difficult to estimate the fundamental matrix robustly and reliably using estimators even if without outliers in corresponding point pairs. In order to overcome this problem, two novel and fast methods to test the coplanarity of the corresponding point pairs are proposed. The first method is to use plane fitting. Without rectification, we formulate a plane equation to check the coplanarity of the selected corresponding point pairs. The second method employs the concept of a homography. In several experimental designs, experiments were used to test our proposed methods. According to our results, the performance of our two proposed methods is better than that of the traditional method. Furthermore, the method using homography is better than that using plane fitting. Finally, we apply our results to 3D reconstruction.
A FAST TWO-STAGE CONTENT-BASED IMAGE RETRIEVAL APPROACH IN THE DCT DOMAIN
Authors: TSAI TIENWEI , HUANG YO-PING , CHIANG TE-WEI
Published: July 2008

In this paper, a two-stage content-based image retrieval (CBIR) approach is proposed to improve the retrieval performance. To develop a general retrieval scheme which is less dependent on domain-specific knowledge, the discrete cosine transform (DCT) is employed as a feature extraction method. In establishing the database, the DC coefficients of Y, U and V components are quantized such that the feature space is partitioned into a finite number of grids, each of which is mapped to a grid code (GC). When querying an image, at coarse classification stage, the grid-based classification (GBC) and the distance threshold pruning (DTP) serve as a filter to remove those candidates with widely distinct features. At the fine classification stage, only the remaining candidates need to be computed for the detailed similarity comparison. The experimental results show that both high efficacy and high efficiency can be achieved simultaneously using the proposed two-stage approach.
LOCAL COORDINATES ALIGNMENT (LCA): A NOVEL MANIFOLD LEARNING APPROACH
Authors: ZHANG TIANHAO , LI XUELONG , TAO DACHENG , YANG JIE
Published: July 2008

Manifold learning has been demonstrated as an effective way to represent intrinsic geometrical structure of samples. In this paper, a new manifold learning approach, named Local Coordinates Alignment (LCA), is developed based on the alignment technique. LCA first obtains local coordinates as representations of local neighborhood by preserving proximity relations on a patch, which is Euclidean. Then, these extracted local coordinates are aligned to yield the global embeddings. To solve the out of sample problem, linearization of LCA (LLCA) is proposed. In addition, in order to solve the non-Euclidean problem in real world data when building the locality, kernel techniques are utilized to represent similarity of the pairwise points on a local patch. Empirical studies on both synthetic data and face image sets show effectiveness of the developed approaches.
SUPERCONVERGENCE OF FEMS AND NUMERICAL CONTINUATION FOR PARAMETER-DEPENDENT PROBLEMS WITH FOLDS
Authors: CHIEN C.-S. , HUANG H.-T. , JENG B.-W. , LI Z.-C.
Published: July 2008

We study finite element approximations for positive solutions of semilinear elliptic eigenvalue problems with folds, and exploit the superconvergence of finite element methods (FEM). In order to apply the superconvergence of FEM for Poisson's equation in [Chen & Huang, 1995; Huang et al., 2004, 2006; Lin & Yan, 1996] to parameter-dependent problems with folds, this paper provides the framework of analysis, accompanied with the proof of the strong monotonicity of the nonlinear form. It is worthy to point out that the superconvergence of the nonlinear problem in this paper is different from that in [Chen & Huang, 1995]. A continuation algorithm is described to trace solution curves of semilinear elliptic eigenvalue problems, where the Adini elements are exploited to discretize the PDEs. Numerical results on some sample test problems with folds and bifurcations are reported.
ON THE MARGIN OF COMPLETE STABILITY FOR A CLASS OF CELLULAR NEURAL NETWORKS
Authors: DI MARCO MAURO , FORTI MAURO , TESI ALBERTO
Published: July 2008

In this paper, the dynamical behavior of a class of third-order competitive cellular neural networks (CNNs) depending on two parameters, is studied. The class contains a one-parameter family of symmetric CNNs, which are known to be completely stable. The main result is that it is a generic property within the family of symmetric CNNs that complete stability is robust with respect to (small) nonsymmetric perturbations of the neuron interconnections. The paper also gives an exact evaluation of the complete stability margin of each symmetric CNN via the characterization of the whole region in the two-dimensional parameter space where the CNNs turn out to be completely stable. The results are established by means of a new technique to investigate trajectory convergence of the considered class of CNNs in the nonsymmetric case.
HOMOCLINIC SHADOWING AND ITS APPLICATION TO CHAOTIC SYSTEMS
Authors: LI XILIANG , LI XUEMEI , ZHENG ZUOHUAN
Published: July 2008

In our paper, by using shadowing techniques, we develop a general method for establishing the existence of a transversal homoclinic orbit to a periodic orbit of [Formula: see text] diffeomorphisms in Rn which implies the occurrence of chaos.
CHAOTIC VIBRATIONS OF CLOSED CYLINDRICAL SHELLS IN A TEMPERATURE FIELD
Authors: KRYSKO A. V. , AWREJCEWICZ J. , KUZNETSOVA E. S. , KRYSKO V. A.
Published: July 2008

A closed cylindrical shell with circular cross-section having constant stiffness and density and subjected to sign changeable loading and embedded into a temperature field is analyzed. Both Bubnov–Galerkin (with a higher approximation) and Fourier methods are applied to solve the derived nonlinear nondimensional partial differential equations. Among others, the novel scenario of transition from shell harmonic to chaotic vibrations via the collapse of quasi-periodic vibrations with one independent frequency and Hopf bifurcation is detected, illustrated and discussed. In addition, it is shown how for various intensities of the temperature field (including its absence) the increase of the loading yields qualitative changes in the investigated shell dynamics, and how chaotic zones are transmitted into periodic ones and vice versa.
A MINIMAL 2-D QUADRATIC MAP WITH QUASI-PERIODIC ROUTE TO CHAOS
Authors: ELHADJ ZERAOULIA , SPROTT J. C.
Published: July 2008

The aim of this paper is to present and analyze a minimal chaotic map of the plane, then we describe in detail the dynamical behavior of this map, along with some other dynamical phenomena.
RAY CHAOS IN UNDERWATER ACOUSTICS AND ITS APPLICATION
Authors: BÓDAI TAMÁS , FENWICK ALAN J. , WIERCIGROCH MARIAN
Published: July 2008

In this note we revisit the channelling effect of deep ocean acoustic wave propagation. To model propagation phenomena ray theory is used, where particular attention is payed to ray chaos. The effect of transitions between two archetypal sound speed versus depth profiles (Munk and double duct profiles) is studied. To do this the novel concept of launching basin is introduced. Its use in identifying the launching parameters of rays which remain stable is indicated, something which is highly desirable for understanding sonar system performance.
ON THE LOCATION AND CONTINUATION OF HOPF BIFURCATIONS IN LARGE-SCALE PROBLEMS
Authors: FRIEDMAN M. , QIU W.
Published: July 2008

CL_MATCONT is a MATLAB package for the study of dynamical systems and their bifurcations. It uses a minimally augmented system for continuation of the Hopf curve. The Continuation of Invariant Subspaces (CIS) algorithm produces a smooth orthonormal basis for an invariant subspace [Formula: see text] of a parameter-dependent matrix A(s). We extend a minimally augmented system technique for location and continuation of Hopf bifurcations to large-scale problems using the CIS algorithm, which has been incorporated into CL_MATCONT. We compare this approach with using a standard augmented system and show that a minimally augmented system technique is more suitable for large-scale problems. We also suggest an improvement of a minimally augmented system technique for the case of the torus continuation.
LOCALIZATION OF COMPACT INVARIANT SETS OF NONLINEAR TIME-VARYING SYSTEMS
Authors: KRISHCHENKO ALEXANDER P. , STARKOV KONSTANTIN E.
Published: July 2008

In this paper we examine the localization problem of compact invariant sets of nonlinear time-varying systems with the differentiable right-side. We extend our results respecting the localization problem obtained earlier for time-invariant systems and apply them to a damped driven pendulum and the Vallis model with regard to the seasonal cycle.
Regulation of ERK1/2 by ouabain and Na-K-ATPase-dependent energy utilization and AMPK activation in parotid acinar cells
Authors: Soltoff Stephen P. , Hedden Lee
Published: July 2008

We previously found that the phosphorylation of ERK1/2 by submaximal concentrations of the muscarinic receptor ligand carbachol was potentiated in rat parotid acinar cells exposed to ouabain, a cardiac glycoside that inhibits the Na-K-ATPase. We now report that this signaling phenomenon involves the prevention of negative regulation of extracellular signal-regulated kinase-1/2 (ERK1/2) that is normally mediated by AMP-activated protein kinase (AMPK). Carbachol increases the turnover of the ATP-consuming Na-K-ATPase, reducing intracellular ATP and promoting the phosphorylation/activation of the energy sensor AMPK. Ouabain blocks the reduction in ATP and subsequent AMPK phosphorylation, which is regulated by the AMP-to-ATP ratio. The ouabain-promoted enhancement of ERK1/2 phosphorylation was not reproduced in Par-C10 cells, an immortalized rat parotid cell line that did not respond to carbachol with an ATP reduction and that employs an upstream AMPK kinase (Ca2+/calmodulin-dependent protein kinase kinase, CaMKK) different from that (LKB1) in native cells. In native parotid cells, inhibitory effects of AMPK on ERK1/2 signaling were examined by activating AMPK with 5-aminoimidazole-4-carboxamide-1-β-d-ribofuranoside (AICAR), which is converted to an AMP mimetic but does not alter parotid ATP levels. AICAR-treated cells display increases in AMPK phosphorylation and a reduced phosphorylation of ERK1/2 subsequent to activation of muscarinic and P2X7 receptors, which promote increases in Na-K-ATPase turnover, but not upon epidermal growth factor receptor activation. These results suggest that carbachol-initiated AMPK activation can produce a negative feedback on ERK1/2 signaling in response to submaximal muscarinic receptor activation and that increases in fluid secretion can modulate receptor-initiated signaling events indirectly by producing ion transport-dependent decreases in ATP.
Expression of Fos during sham sucrose intake in rats with central gustatory lesions
Authors: Mungarndee Suriyaphun S. , Lundy Robert F. , Norgren Ralph
Published: July 2008

For humans and rodents, ingesting sucrose is rewarding. This experiment tested the prediction that the neural activity produced by sapid sucrose reaches reward systems via projections from the pons through the limbic system. Gastric cannulas drained ingested fluid before absorption. For 10 days, the rats alternated an hour of this sham ingestion between sucrose and water. On the final test day, half of them sham drank water and the other half 0.6 M sucrose. Thirty minutes later, the rats were killed and their brains immunohistochemically stained for Fos. The groups consisted of controls and rats with excitotoxic lesions in the gustatory thalamus (TTA), the medial (gustatory) parabrachial nucleus (PBN), or the lateral (visceral afferent) parabrachial nucleus. In controls, compared with water, sham ingesting sucrose produced significantly more Fos-positive neurons in the nucleus of the solitary tract, PBN, TTA, and gustatory cortex (GC). In the ventral forebrain, sucrose sham licking increased Fos in the bed nucleus of the stria terminalis, central nucleus of amygdala, and the shell of nucleus accumbens. Thalamic lesions blocked the sucrose effect in GC but not in the ventral forebrain. After lateral PBN lesions, the Fos distributions produced by distilled H2O or sucrose intake did not differ from controls. Bilateral medial PBN damage, however, eliminated the sucrose-induced Fos increase not only in the TTA and GC but also in the ventral forebrain. Thus ventral forebrain areas associated with affective responses appear to be activated directly by PBN gustatory neurons rather than via the thalamocortical taste system.
Low temperature directly activates the initial glycerol antifreeze response in isolated rainbow smelt (Osmerus mordax) liver cells
Authors: Clow Kathy A. , Ewart K. Vanya , Driedzic William R.
Published: July 2008

Rainbow smelt ( Osmerus mordax) accumulate high levels of glycerol in winter that serve as an antifreeze. Liver glycogen is a source of glycerol during the early stages of glycerol accumulation, whereas dietary glucose and amino acids are essential to maintain rates of glycerol synthesis. We presently report rates of glycerol and glucose production by isolated hepatocytes. Cells from fish held at 0.4 to –1.5°C and incubated at 0.4°C were metabolically quiescent with negligible rates of glycerol or glucose production. Hepatocytes isolated from fish maintained at 8°C and incubated at 8°C produced glucose but not glycerol. Glycerol production was activated in cells isolated from 8°C fish and incubated at 0.4°C without substrate or when glucose, aspartate, or pyruvate was available in the medium. Incubation at 0.4°C without substrate resulted in similar molar rates of glucose and glycerol production in concert with glycogen mobilization. Glycogenolysis and glycerol production were associated with increases in total in vitro activities of glycogen phosphorylase and glycerol-3-phosphate dehydrogenase. Maximal in vitro activities of hexokinase and glucokinase were not influenced by temperature, but high activities of a low- Kmhexokinase may serve to redirect glycogen-derived glucose to glycolysis as opposed to releasing it from the cells. Rates of glycerol production were not enhanced in cells from fish held at 8°C and incubated at 0.4°C with adrenergic or glucocorticoid stimulation. As such, low temperature alone is sufficient to activate the glycerol production mechanism and results in a shift from glucose to a mix of glucose and glycerol production.
Energetic responses to cold temperatures in rats lacking forebrain-caudal brain stem connections
Authors: Nautiyal Katherine M. , Dailey Megan , Brito Nilton , Brito Marcia N. d. A. , Harris Ruth B. , Bartness Timothy J. , Grill Harvey J.
Published: July 2008

Hypothalamic neurons are regarded as essential for integrating thermal afferent information from skin and core and issuing commands to autonomic and behavioral effectors that maintain core temperature (Tc) during cold exposure and for the control of energy expenditure more generally. Caudal brain stem neurons are necessary elements of the hypothalamic effector pathway and also are directly driven by skin and brain cooling. To assess whether caudal brain stem processing of thermal afferent signals is sufficient to drive endemic effectors for thermogenesis, heart rate (HR), Tc, and activity responses of chronic decerebrate (CD) and control rats adapted to 23°C were compared during cold exposure (4, 8, or 12°C) for 6 h. Other CDs and controls were exposed to 4 or 23°C for 2 h, and tissues were processed for norepinephrine turnover (NETO), a neurochemical measure of sympathetic drive. Controls maintained Tc for all temperatures. CDs maintained Tc for the 8 and 12°C exposures, but Tc declined 2°C during the 4°C exposure. Cold exposure elevated HR in CDs and controls alike. Tachycardia magnitude correlated with decreases in environmental temperature for controls, but not CDs. Cold increased NETO in brown adipose tissue, heart, and some white adipose tissue pads in CDs and controls compared with their respective room temperature controls. These data demonstrate that, in neural isolation from the hypothalamus, cold exposure drives caudal brain stem neuronal activity and engages local effectors that trigger sympathetic energetic and cardiac responses that are comparable in many, but not in all, respects to those seen in neurologically intact rats.