bluuebunny/crossref_metadata_2025 huggingface dataset:
Pitch circularity from tones comprising full harmonic series
Authors: Deutsch Diana , Dooley Kevin , Henthorn Trevor
Published: July 2008

This paper describes an algorithm for producing pitch circularity using tones that each comprise a full harmonic series, and reports an experiment that demonstrates such circularity. Banks of 12 tones (i.e., scales) were created, with F0 varying in semitone steps. For each scale, as F0 descended, the amplitudes of the odd-numbered harmonics were reduced relative to the even-numbered ones by 3.5dB for each semitone step. In consequence, the tone with the lowest F0 was heard as though displaced up an octave. In an experiment employing two such scales, all possible ordered tone pairs from each scale were presented, making 132 ordered tone pairs for each scale. Sixteen subjects judged for each tone pair whether the second tone was higher or lower than the first. The data derived from these pairwise comparisons were subjected to Kruskal’s nonmetric multidimensional scaling, and excellent circularities were obtained. Individual differences in the subjects’ judgments were also explored. The findings support the argument that musical pitch should be characterized as varying along two dimensions: the monotonic dimension of pitch height and the circular dimension of pitch class.
Monaural room acoustic parameters from music and speech
Authors: Kendrick Paul , Cox Trevor J. , Li Francis F. , Zhang Yonggang , Chambers Jonathon A.
Published: July 2008

This paper compares two methods for extracting room acoustic parameters from reverberated speech and music. An approach which uses statistical machine learning, previously developed for speech, is extended to work with music. For speech, reverberation time estimations are within a perceptual difference limen of the true value. For music, virtually all early decay time estimations are within a difference limen of the true value. The estimation accuracy is not good enough in other cases due to differences between the simulated data set used to develop the empirical model and real rooms. The second method carries out a maximum likelihood estimation on decay phases at the end of notes or speech utterances. This paper extends the method to estimate parameters relating to the balance of early and late energies in the impulse response. For reverberation time and speech, the method provides estimations which are within the perceptual difference limen of the true value. For other parameters such as clarity, the estimations are not sufficiently accurate due to the natural reverberance of the excitation signals. Speech is a better test signal than music because of the greater periods of silence in the signal, although music is needed for low frequency measurement.
Classification of Risso’s and Pacific white-sided dolphins using spectral properties of echolocation clicks
Authors: Soldevilla Melissa S. , Henderson E. Elizabeth , Campbell Gregory S. , Wiggins Sean M. , Hildebrand John A. , Roch Marie A.
Published: July 2008

The spectral and temporal properties of echolocation clicks and the use of clicks for species classification are investigated for five species of free-ranging dolphins found offshore of southern California: short-beaked common (Delphinus delphis), long-beaked common (D. capensis), Risso’s (Grampus griseus), Pacific white-sided (Lagenorhynchus obliquidens), and bottlenose (Tursiops truncatus) dolphins. Spectral properties are compared among the five species and unique spectral peak and notch patterns are described for two species. The spectral peak mean values from Pacific white-sided dolphin clicks are 22.2, 26.6, 33.7, and 37.3kHz and from Risso’s dolphins are 22.4, 25.5, 30.5, and 38.8kHz. The spectral notch mean values from Pacific white-sided dolphin clicks are 19.0, 24.5, and 29.7kHz and from Risso’s dolphins are 19.6, 27.7, and 35.9kHz. Analysis of variance analyses indicate that spectral peaks and notches within the frequency band 24–35kHz are distinct between the two species and exhibit low variation within each species. Post hoc tests divide Pacific white-sided dolphin recordings into two distinct subsets containing different click types, which are hypothesized to represent the different populations that occur within the region. Bottlenose and common dolphin clicks do not show consistent patterns of spectral peaks or notches within the frequency band examined (1–100kHz).
Gerbil middle-ear sound transmission from 100Hzto60kHz
Authors: Ravicz Michael E. , Cooper Nigel P. , Rosowski John J.
Published: July 2008

Middle-ear sound transmission was evaluated as the middle-ear transfer admittance HMY (the ratio of stapes velocity to ear-canal sound pressure near the umbo) in gerbils during closed-field sound stimulation at frequencies from 0.1to60kHz, a range that spans the gerbil’s audiometric range. Similar measurements were performed in two laboratories. The HMY magnitude (a) increased with frequency below 1kHz, (b) remained approximately constant with frequency from 5to35kHz, and (c) decreased substantially from 35to50kHz. The HMY phase increased linearly with frequency from 5to35kHz, consistent with a 20–29μs delay, and flattened at higher frequencies. Measurements from different directions showed that stapes motion is predominantly pistonlike except in a narrow frequency band around 10kHz. Cochlear input impedance was estimated from HMY and previously-measured cochlear sound pressure. Results do not support the idea that the middle ear is a lossless matched transmission line. Results support the ideas that (1) middle-ear transmission is consistent with a mechanical transmission line or multiresonant network between 5 and 35kHz and decreases at higher frequencies, (2) stapes motion is pistonlike over most of the gerbil auditory range, and (3) middle-ear transmission properties are a determinant of the audiogram.
Self-reported sleep disturbances due to railway noise: Exposure-response relationships for nighttime equivalent and maximum noise levels
Authors: Aasvang Gunn Marit , Moum Torbjørn , Engdahl Bo
Published: July 2008

The objective of the present survey was to study self-reported sleep disturbances due to railway noise with respect to nighttime equivalent noise level (Lp,A,eq,night) and maximum noise level (Lp,A,max). A sample of 1349 people in and around Oslo in Norway exposed to railway noise was studied in a cross-sectional survey to obtain data on sleep disturbances, sleep problems due to noise, and personal characteristics including noise sensitivity. Individual noise exposure levels were determined outside of the bedroom facade, the most-exposed facade, and inside the respondents’ bedrooms. The exposure-response relationships were analyzed by using logistic regression models, controlling for possible modifying factors including the number of noise events (train pass-by frequency). Lp,A,eq,night and Lp,A,max were significantly correlated, and the proportion of reported noise-induced sleep problems increased as both Lp,A,eq,night and Lp,A,max increased. Noise sensitivity, type of bedroom window, and pass-by frequency were significant factors affecting noise-induced sleep disturbances, in addition to the noise exposure level. Because about half of the study population did not use a bedroom at the most-exposed side of the house, the exposure-response curve obtained by using noise levels for the most-exposed facade underestimated noise-induced sleep disturbance for those who actually have their bedroom at the most-exposed facade.
Using impedance measurements to detect and quantify the effect of air leaks on the attenuation of earplugs
Authors: Henriksen Viggo
Published: July 2008

The impedance of a simple artificial ear occluded with an earplug and bypassed with narrow air leaks was measured along with the attenuation of sound through the air leaks. A lumped element model is suggested for the simple occluded artificial ear with an air leak. The suggested model was adapted to the impedance measurements and the attenuation was predicted from the model. The attenuation predictions were compared to the attenuation measurements and were found to be within [−3.5,+3]dB of the measured attenuation over the frequency range of 50–1000Hz and an attenuation range of −2–38dB. The average difference between the measured and predicted attenuation for four different leaks in the frequency range of 50–1000Hz was −0.7dB, indicating a very slight underestimation of the attenuation.
Model independent control of lightly damped noise/vibration systems
Authors: Yuan Jing
Published: July 2008

Feedforward control is a popular strategy of active noise/vibration control. In well-damped noise/vibration systems, path transfer functions from actuators to sensors can be modeled by finite impulse response (FIR) filters with negligible errors. It is possible to implement noninvasive model independent feedforward control by a recently proposed method called orthogonal adaptation. In lightly damped noise/vibration systems, however, path transfer functions have infinite impulse responses (IIRs) that cause difficulties in design and implementation of broadband feedforward controllers. A major source of difficulties is model error if IIR path transfer functions are approximated by FIR filters. In general, active control performance deteriorates as model error increases. In this study, a new method is proposed to design and implement model independent feedforward controllers for broadband in lightly damped noise/vibration systems. It is shown analytically that the proposed method is able to drive the convergence of a noninvasive model independent feedforward controller to improve broadband control in lightly damped noise/vibration systems. The controller is optimized in the minimum H2 norm sense. Experiment results are presented to verify the analytical results.
Prediction of energy decay in room impulse responses simulated with an image-source model
Authors: Lehmann Eric A. , Johansson Anders M.
Published: July 2008

A method is proposed that provides an approximation of the acoustic energy decay (energy–time curve) in room impulse responses generated using the image-source technique. A geometrical analysis of the image-source principle leads to a closed-form expression describing the energy decay curve, with the resulting formula being valid for a uniform as well as nonuniform definition of the enclosure’s six absorption coefficients. The accuracy of the proposed approximation is demonstrated on the basis of impulse-response simulations involving various room sizes and reverberation levels, with uniform and nonuniform sound absorption coefficients. An application example for the proposed method is illustrated by considering the task of predicting an enclosure’s reflection coefficients in order to achieve a specific reverberation level. The technique presented in this work enables designers to undertake a preliminary analysis of a simulated reverberant environment without the need for time-consuming image-method simulations.
Bottom-Up Dependent Gating of Frontal Signals in Early Visual Cortex
Authors: Ekstrom Leeland B. , Roelfsema Pieter R. , Arsenault John T. , Bonmassar Giorgio , Vanduffel Wim
Published: July 2008

The frontal eye field (FEF) is one of several cortical regions thought to modulate sensory inputs. Moreover, several hypotheses suggest that the FEF can only modulate early visual areas in the presence of a visual stimulus. To test for bottom-up gating of frontal signals, we microstimulated subregions in the FEF of two monkeys and measured the effects throughout the brain with functional magnetic resonance imaging. The activity of higher-order visual areas was strongly modulated by FEF stimulation, independent of visual stimulation. In contrast, FEF stimulation induced a topographically specific pattern of enhancement and suppression in early visual areas, but only in the presence of a visual stimulus. Modulation strength depended on stimulus contrast and on the presence of distractors. We conclude that bottom-up activation is needed to enable top-down modulation of early visual cortex and that stimulus saliency determines the strength of this modulation.
Orbitofrontal Dysfunction in Patients with Obsessive-Compulsive Disorder and Their Unaffected Relatives
Authors: Chamberlain Samuel R. , Menzies Lara , Hampshire Adam , Suckling John , Fineberg Naomi A. , del Campo Natalia , Aitken Mike , Craig Kevin , Owen Adrian M. , Bullmore Edward T. , Robbins Trevor W. , Sahakian Barbara J.
Published: July 2008

Obsessive-compulsive disorder (OCD) is characterized by repetitive thoughts and behaviors associated with underlying dysregulation of frontostriatal circuitry. Central to neurobiological models of OCD is the orbitofrontal cortex, a neural region that facilitates behavioral flexibility after negative feedback (reversal learning). We identified abnormally reduced activation of several cortical regions, including the lateral orbitofrontal cortex, during reversal learning in OCD patients and their clinically unaffected close relatives, supporting the existence of an underlying previously undiscovered endophenotype for this disorder.
Evolutionary Origins for Social Vocalization in a Vertebrate Hindbrain–Spinal Compartment
Authors: Bass Andrew H. , Gilland Edwin H. , Baker Robert
Published: July 2008

The macroevolutionary events leading to neural innovations for social communication, such as vocalization, are essentially unexplored. Many fish vocalize during female courtship and territorial defense, as do amphibians, birds, and mammals. Here, we map the neural circuitry for vocalization in larval fish and show that the vocal network develops in a segment-like region across the most caudal hindbrain and rostral spinal cord. Taxonomic analysis demonstrates a highly conserved pattern between fish and all major lineages of vocal tetrapods. We propose that the vocal basis for acoustic communication among vertebrates evolved from an ancestrally shared developmental compartment already present in the early fishes.
Ice Scour Disturbance in Antarctic Waters
Authors: Smale Dan A. , Brown Kirsty M. , Barnes David K. A. , Fraser Keiron P. P. , Clarke Andrew
Published: July 2008

The West Antarctic Peninsula is one of the fastest warming regions on Earth, and, as a consequence, most maritime glaciers and ice shelves in the region have significantly retreated over the past few decades. We collected a multiyear data set on ice scouring frequency from Antarctica by using unique experimental markers and scuba diving surveys. We show that the annual intensity of ice scouring is negatively correlated with the duration of the winter fast ice season. Because fast ice extent and duration is currently in decline in the region after recent rapid warming, it is likely that marine benthic communities are set for even more scouring in the near future.
Signal-Mediated Dynamic Retention of Glycosyltransferases in the Golgi
Authors: Tu Linna , Tai William C. S. , Chen Lu , Banfield David K.
Published: July 2008

Golgi-resident glycosyltransferases are a family of enzymes that sequentially modify glycoproteins in a subcompartment-specific manner. These type II integral membrane proteins are characterized by a short cytoplasmically exposed amino-terminal tail and a luminal enzymatic domain. The cytoplasmic tails play a role in the localization of glycosyltransferases, and coat protein complex I (COPI) vesicle–mediated retrograde transport is also involved in their Golgi localization. However, the tails of these enzymes lack known COPI-binding motifs. Here, we found that Vps74p bound to a pentameric motif present in the cytoplasmic tails of the majority of yeast Golgi-localized glycosyltransferases, as well as to COPI. We propose that Vps74p maintains the steady-state localization of Golgi glycosyltransferases dynamically, by promoting their incorporation into COPI-coated vesicles.
Anomalous Type 17 Response to Viral Infection by CD8
+
T Cells Lacking T-bet and Eomesodermin
Authors: Intlekofer Andrew M. , Banerjee Arnob , Takemoto Naofumi , Gordon Scott M. , DeJong Caitlin S. , Shin Haina , Hunter Christopher A. , Wherry E. John , Lindsten Tullia , Reiner Steven L.
Published: July 2008

When intracellular pathogens invade mammalian hosts, naïve CD8
+
T cells differentiate into cytotoxic killers, which lyse infected target cells and secrete cytokines that activate intracellular microbicides. We show that CD8
+
T cells deficient in the transcription factors T-bet and eomesodermin (Eomes) fail to differentiate into functional killers required for defense against lymphocytic choriomeningitis virus. Instead, virus-specific CD8
+
T cells lacking both T-bet and Eomes differentiate into an interleukin-17–secreting lineage, reminiscent of the helper T cell fate that has been implicated in autoimmunity and extracellular microbial defense. Upon viral infection, mice with T cells lacking both T-bet and Eomes develop a CD8
+
T cell–dependent, progressive inflammatory and wasting syndrome characterized by multi-organ infiltration of neutrophils. T-bet and Eomes, thus, ensure that CD8
+
T cells adopt an appropriate course of intracellular rather than extracellular destruction.
Rapid Immunochromatographic Strip Test for Detection of Anti-K39 Immunoglobulin G Antibodies for Diagnosis of Visceral Leishmaniasis
Authors: Welch Ryan J. , Anderson Brian L. , Litwin Christine M.
Published: July 2008

InBios International has developed an immunochromatographic rapid strip for the detection of visceral leishmaniasis that requires minimal equipment and only a small amount of blood to run a test. We compared the InBios rapid strip test with the CDC immunofluorescent antibody assay, and the agreement, sensitivity, and specificity were 98%, 90%, and 100%, respectively.
Levels of Soluble CD163 and Severity of Malaria in Children in Ghana
Authors: Kusi Kwadwo A. , Gyan Ben A. , Goka Bamenla Q. , Dodoo Daniel , Obeng-Adjei George , Troye-Blomberg Marita , Akanmori Bartholomew D. , Adjimani Jonathan P.
Published: July 2008

CD163 is an acute-phase-regulated monocyte/macrophage membrane receptor expressed late in inflammation. It is involved in the haptoglobin-mediated removal of free hemoglobin from plasma, has been identified as a naturally soluble plasma glycoprotein with potential anti-inflammatory properties, and is possibly linked to an individual's haptoglobin phenotype. High levels of soluble CD163 (sCD163) in a malaria episode may therefore downregulate inflammation and curb disease severity. In order to verify this, the relationships between sCD163 levels, malaria severity, and selected inflammatory mediators (tumor necrosis factor alpha [TNF-α], interleukin-6 [IL-6], and IL-10) were assessed by enzyme-linked immunosorbent assay using plasma samples obtained from pediatric malaria patients with uncomplicated malaria (UM [
n
= 38]), cerebral malaria (CM [
n
= 52]), and severe malarial anemia (SA [
n
= 55]) during two consecutive malaria transmission seasons (2002 and 2003). Median sCD163 levels were higher in UM (11.9 μg/ml) patients than in SA (7.7 μg/ml;
P
= 0.010) and CM (8.0 μg/ml;
P
= 0.031) patients. Levels of sCD163 were also higher in all patient groups than in a group of 81 age-matched healthy controls. The higher sCD163/TNF-α ratio in UM patients, coupled with the fact that sCD163 levels correlated with TNF-α levels in UM patients but not in CM and SA patients, suggests inflammatory dysregulation in the complicated cases. The study showed that sCD163 levels are elevated during acute malaria. High sCD163 levels in UM patients may be due to the induction of higher-level anti-inflammatory responses, enabling them to avoid disease complications. It is also possible that UM patients simply lost their CD163 receptors from macrophages in inflammatory sites while complicated-malaria patients still had their receptors attached to activated macrophages, reflecting ongoing and higher-level inflammation associated with complicated malaria.
Molecular Diagnosis of
Saksenaea vasiformis
Cutaneous Infection after Scorpion Sting in an Immunocompetent Adolescent
Authors: Lechevalier Pauline , Hermoso Dea Garcia , Carol Agnes , Bonacorsi Stephane , Ferkdadji Latifa , Fitoussi Franck , Lortholary Olivier , Bourrillon Antoine , Faye Albert , Dannaoui Eric , Angoulvant Francois
Published: July 2008

We report the first case of cutaneous mucormycosis after a scorpion sting in Tunisia. Histopathology showed broad aseptate hyphae suggestive of a Zygomycete.
Saksenaea vasiformis
was identified by PCR amplification and sequencing of the fungal DNA on a cutaneous biopsy. Successful treatment was obtained by surgery and liposomal amphotericin B.
Characterization of
Staphylococcus aureus
Isolates from Nasal Cultures Collected from Individuals in the United States in 2001 to 2004
Authors: Tenover Fred C. , McAllister Sigrid , Fosheim Gregory , McDougal Linda K. , Carey Roberta B. , Limbago Brandi , Lonsway David , Patel Jean B. , Kuehnert Matthew J. , Gorwitz Rachel
Published: July 2008

This study characterizes methicillin-susceptible
Staphylococcus aureus
(MSSA) and methicillin-resistant
S. aureus
(MRSA) isolates recovered from nasal cultures of noninstitutionalized individuals in the United States obtained in 2001 to 2004 as part of the National Health and Nutrition Examination Survey. Every tenth MSSA isolate and all MRSA isolates were typed by pulsed-field gel electrophoresis (PFGE), screened for multiple toxin genes, and tested for susceptibility to 14 antimicrobial agents. USA200, USA600, and USA900 were the predominant PFGE types among MSSA isolates in both the 2001 to 2002 and the 2003 to 2004 time periods, although they accounted for only 51.3% of 316 MSSA isolates typed in 2001 and 2002 and only 43.4% of 237 MSSA isolates typed in 2003 and 2004. In contrast, USA100, USA800, and USA700 accounted for 80.0% of the 75 MRSA isolates typed in 2001 and 2002, while USA100, USA800, and USA300 accounted for 78.4% of 134 MRSA isolates typed in 2003 and 2004. The proportion of MRSA isolates that were USA300 increased significantly from the first to the second time period (
P
= 0.03). Most USA200 isolates (both MSSA and MRSA) carried the gene for toxic shock syndrome toxin; however, carriage of the genes encoding Panton-Valentine leukocidin, while common among MRSA of PFGE type USA300, was rare among MSSA USA300 in both time periods. Most MSSA isolates remained susceptible to all antimicrobial agents except erythromycin (79.1 and 76.0% susceptibilities in the 2001 to 2002 and the 2003 to 2004 periods, respectively). In contrast, the proportions of MRSA isolates that were susceptible to chloramphenicol, clindamycin, and erythromycin were lower in 2003 and 2004 than in 2001 and 2002, although none of these differences was statistically significant.
Thymidine Kinase Sequence Analysis of Herpes Simplex Virus Type 1 Strains Present in Different Compartments in an Atypical Impetiginous Rash on the Lesional Skin of a Burn Patient
Authors: Werdin Frank , Rennekampff Hans-Oliver , Schaller Hans-Eberhard , Jahn Gerhard , Hamprecht Klaus
Published: July 2008

We report the case of a 23-year-old male burn patient with an unusual herpes simplex virus (HSV) skin manifestation. The clinical symptoms and results of HSV type 1 (HSV-1) UL23 polymorphism analysis from saliva and lesional skin underscores the need for performing molecular analysis of HSV-1 infections in burned patients presenting unusual skin lesions.
Detection of KPC-2 in a Clinical Isolate of
Proteus mirabilis
and First Reported Description of Carbapenemase Resistance Caused by a KPC β-Lactamase in
P. mirabilis
Authors: Tibbetts R. , Frye J. G. , Marschall J. , Warren D. , Dunne W.
Published: July 2008

An isolate of
Proteus mirabilis
recovered from blood cultures of a diabetic patient was shown to be resistant to imipenem, meropenem, and ertapenem by disk diffusion susceptibility testing. Amplification of whole-cell and/or plasmid DNA recovered from the isolate with primers specific for the
bla
KPC
carbapenemase gene produced an amplicon of the expected size which was confirmed to be
bla
KPC-2
by sequence analysis. Transformation of a susceptible
Escherichia coli
host with plasmid preparations from the isolate generated a transformant for which the MICs of all of the carbapenems tested were increased three- to fourfold. We believe this to be the first report of carbapenem resistance in
P
.
mirabilis
caused by the acquisition of
bla
KPC
.
Matrix Metalloproteinase 9 Facilitates West Nile Virus Entry into the Brain
Authors: Wang Penghua , Dai Jianfeng , Bai Fengwei , Kong Kok-Fai , Wong Susan J. , Montgomery Ruth R. , Madri Joseph A. , Fikrig Erol
Published: July 2008

West Nile virus (WNV) is the most-common cause of mosquito-borne encephalitis in the United States. Invasion of the brain by WNV is influenced by viral and host factors, and the molecular mechanism underlying disruption of the blood-brain barrier is likely multifactorial. Here we show that matrix metalloproteinase 9 (MMP9) is involved in WNV entry into the brain by enhancing blood-brain barrier permeability. Murine MMP9 expression was induced in the circulation shortly after WNV infection, and the protein levels remained high even when viremia subsided. In the murine brain, MMP9 expression and its enzymatic activity were upregulated and MMP9 was shown to partly localize to the blood vessels. Interestingly, we also found that cerebrospinal fluid from patients suffering from WNV contained increased MMP9 levels. The peripheral viremia and expression of host cytokines were not altered inMMP9−/−mice; however, these animals were protected from lethal WNV challenge. The resistance ofMMP9−/−mice to WNV infection correlated with an intact blood-brain barrier since immunoglobulin G, Evans blue leakage into brain, and type IV collagen degradation were markedly reduced in theMMP9−/−mice compared with their levels in controls. Consistent with this, the brain viral loads, selected inflammatory cytokines, and leukocyte infiltrates were significantly reduced in theMMP9−/−mice compared to their levels in wild-type mice. These data suggest that MMP9 plays a role in mediating WNV entry into the central nervous system and that strategies to interrupt this process may influence the course of West Nile encephalitis.
Induction of the GαqSignaling Cascade by the Human Immunodeficiency Virus Envelope Is Required for Virus Entry
Authors: Harmon Brooke , Ratner Lee
Published: July 2008

Binding of human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein (Env) with the primary receptor CD4 and one of two coreceptors, CXCR4 or CCR5, activates a signaling cascade resulting in Rac-1 GTPase activation and stimulation of actin cytoskeletal reorganizations critical for HIV-1-mediated membrane fusion. The mechanism by which HIV-1 Env induces Rac-1 activation and subsequent actin cytoskeleton rearrangement is unknown. In this study, we show that Env-mediated Rac-1 activation is dependent on the activation of Gαqand its downstream targets. Fusion and Rac-1 activation are mediated by Gαqand phospholipase C (PLC), as shown by attenuation of fusion and Rac-1 activation in cells either expressing small interfering RNA (siRNA) targeting Gαqor treated with the PLC inhibitor U73122. Rac-1 activation and fusion were also blocked by multiple protein kinase C inhibitors, by inhibitors of intracellular Ca2+release, by Pyk2-targeted siRNA, and by the Ras inhibitorS-trans,trans-farnesylthiosalicylic acid (FTS). Fusion was blocked without altering cell viability or cell surface localization of CD4 and CCR5. Similar results were obtained when cell fusion was induced by Env expressed on viral and cellular membranes and when cell lines or primary cells were the target. Treatment with inhibitors and siRNA specific for Gαior Gαssignaling mediators had no effect on Env-mediated Rac-1 activation or cell fusion, indicating that the Gαqpathway alone is responsible. These results could provide a new focus for therapeutic intervention with drugs targeting host signaling mediators rather than viral molecules, a strategy which is less likely to result in resistance.
Human Endogenous Retrovirus K (HML-2) Elements in the Plasma of People with Lymphoma and Breast Cancer
Authors: Contreras-Galindo Rafael , Kaplan Mark H. , Leissner Philippe , Verjat Thibault , Ferlenghi Ilaria , Bagnoli Fabio , Giusti Fabiola , Dosik Michael H. , Hayes Daniel F. , Gitlin Scott D. , Markovitz David M.
Published: July 2008

Actively replicating endogenous retroviruses entered the human genome millions of years ago and became a stable part of the inherited genetic material. They subsequently acquired multiple mutations, leading to the assumption that these viruses no longer replicate. However, certain human tumor cell lines have been shown to release endogenous retroviral particles. Here we show that RNA from human endogenous retrovirus K (HERV-K) (HML-2), a relatively recent entrant into the human genome, can be found in very high titers in the plasma of patients with lymphomas and breast cancer as measured by either reverse transcriptase PCR or nucleic acid sequence-based amplification. Further, these titers drop dramatically with cancer treatment. We also demonstrate the presence of reverse transcriptase and viral RNA in plasma fractions that contain both immature and correctly processed HERV-K (HML-2) Gag and envelope proteins. Finally, using immunoelectron microscopy, we show the presence of HERV-K (HML-2) virus-like particles in the plasma of lymphoma patients. Taken together, these findings demonstrate that elements of the endogenous retrovirus HERV-K (HML-2) can be found in the blood of modern-day humans with certain cancers.
Enzootic Nasal Tumor Virus Envelope Requires a Very Acidic pH for Fusion Activation and Infection
Authors: Côté Marceline , Kucharski Thomas J. , Liu Shan-Lu
Published: July 2008

Enzootic nasal tumor virus (ENTV) is a close relative of jaagsiekte sheep retrovirus (JSRV), and the two viruses use the same receptor, hyaluronidase 2 (Hyal2), for cell entry. We report here that, unlike the JSRV envelope (Env) protein, the ENTV Env protein does not induce cell fusion at pHs of 5.0 and above but requires a much lower pH (4.0 to 4.5) for fusion to occur. The entry of ENTV Env pseudovirions was substantially inhibited by bafilomycin A1 (BafA1) but was surprisingly enhanced by lysosomotropic agents and lysosomal protease inhibitors following a 4- to 6-h treatment period; of note, prolonged treatment with BafA1 or ammonium chloride completely blocked ENTV entry. Unlike typical pH-dependent viruses, ENTV Env pseudovirions were virtually resistant to inactivation at a low pH (4.5 or 5.0). Using chimeras formed from ENTV and JSRV Env proteins, we demonstrated that the transmembrane (TM) subunit of ENTV Env is primarily responsible for its unusually low pH requirement for fusion but found that the surface (SU) subunit of ENTV Env also critically influences its relatively low and pH-dependent fusion activity. Furthermore, the poor infectivity of ENTV pseudovirions in human cells was significantly improved by either replacing the SU subunit of ENTV Env with that of JSRV Env or overexpressing the functional Hyal2 receptor in target cells, suggesting that ENTV SU-Hyal2 interaction is likely to be the limiting step for viral infectivity. Collectively, our data reveal that the fusogenicity of ENTV Env is intrinsically lower than that of JSRV Env and that ENTV requires a more acidic pH for fusion, which may occur in an intracellular compartment(s) distinct from that used by JSRV.
The Transmembrane Domain of the Severe Acute Respiratory Syndrome Coronavirus ORF7b Protein Is Necessary and Sufficient for Its Retention in the Golgi Complex
Authors: Schaecher Scott R. , Diamond Michael S. , Pekosz Andrew
Published: July 2008

The severe acute respiratory syndrome coronavirus (SARS-CoV) ORF7b (also called 7b) protein is an integral membrane protein that is translated from a bicistronic open reading frame encoded within subgenomic RNA 7. When expressed independently or during virus infection, ORF7b accumulates in the Golgi compartment, colocalizing with bothcis- andtrans-Golgi markers. To identify the domains of this protein that are responsible for Golgi localization, we have generated a set of mutant proteins and analyzed their subcellular localizations by indirect immunofluorescence confocal microscopy. The N- and C-terminal sequences are dispensable, but the ORF7b transmembrane domain (TMD) is essential for Golgi compartment localization. When the TMD of human CD4 was replaced with the ORF7b TMD, the resulting chimeric protein localized to the Golgi complex. Scanning alanine mutagenesis identified two regions in the carboxy-terminal portion of the TMD that eliminated the Golgi complex localization of the chimeric CD4 proteins or ORF7b protein. Collectively, these data demonstrate that the Golgi complex retention signal of the ORF7b protein resides solely within the TMD.
Human Immunodeficiency Virus Type 1 Envelope gp120 Induces a Stop Signal and Virological Synapse Formation in Noninfected CD4+T Cells
Authors: Vasiliver-Shamis Gaia , Tuen Michael , Wu Teresa W. , Starr Toby , Cameron Thomas O. , Thomson Russell , Kaur Gurvinder , Liu Jianping , Visciano Maria Luisa , Li Hualin , Kumar Rajnish , Ansari Rais , Han Dong P. , Cho Michael W. , Dustin Michael L. , Hioe Catarina E.
Published: July 2008

Human immunodeficiency virus type 1 (HIV-1)-infected T cells form a virological synapse with noninfected CD4+T cells in order to efficiently transfer HIV-1 virions from cell to cell. The virological synapse is a specialized cellular junction that is similar in some respects to the immunological synapse involved in T-cell activation and effector functions mediated by the T-cell antigen receptor. The immunological synapse stops T-cell migration to allow a sustained interaction between T-cells and antigen-presenting cells. Here, we have asked whether HIV-1 envelope gp120 presented on a surface to mimic an HIV-1-infected cell also delivers a stop signal and if this is sufficient to induce a virological synapse. We demonstrate that HIV-1 gp120-presenting surfaces arrested the migration of primary activated CD4 T cells that occurs spontaneously in the presence of ICAM-1 and induced the formation of a virological synapse, which was characterized by segregated supramolecular structures with a central cluster of envelope surrounded by a ring of ICAM-1. The virological synapse was formed transiently, with the initiation of migration within 30 min. Thus, HIV-1 gp120-presenting surfaces induce a transient stop signal and supramolecular segregation in noninfected CD4+T cells.
DOUBLE-LAYER THIN FILMS MAGNETIC PROPERTIES DEPENDENCE ON ANISOTROPIC HEISENBERG MODEL PARAMETERS
Authors: BÎRSAN E.
Published: July 2008

The study of thin ferromagnetic films has become a field of great interest due to their importance for applications in magnetic-recording media, in order to create ultrahigh density magnetic data storage. Such an interest is also due to numerous specific phenomena related to the low dimension of these systems. In this paper we investigate the magnetic properties of bilayer thin film. The specific behavior of the mentioned system type is simulated using the Monte Carlo technique, in the extended anisotropic Heisenberg model. The magnetization, out-of-plane and in-plane magnetic susceptibilities behaviors according to temperature are investigated in order to find out the contingent magnetic ordering phase and the critical temperature, for two easy-axis anisotropy set parameter assignments. We have also presented the specific heat as a function of temperature for different direct exchange parameter values and we have found out a single-peak shape of the graphs, the critical point traveling to lower temperatures as the direct exchange parameter decreases, the similarity of the two presented cases being evident.
UNSUPERVISED LEARNING OF A HIERARCHY OF TOPOLOGICAL MAPS USING OMNIDIRECTIONAL IMAGES
Authors: ŠTIMEC ALEŠ , JOGAN MATJAŽ , LEONARDIS ALEŠ
Published: July 2008

This paper presents a novel appearance-based method for path-based map learning by a mobile robot equipped with an omnidirectional camera. In particular, we focus on an unsupervised construction of topological maps, which provide an abstraction of the environment in terms of visual aspects. An unsupervised clustering algorithm is used to represent the images in multiple subspaces, forming thus a sensory grounded representation of the environment's appearance. By introducing transitional fields between clusters we are able to obtain a partitioning of the image set into distinctive visual aspects. By abstracting the low-level sensory data we are able to efficiently reconstruct the overall topological layout of the covered path. After the high level topology is estimated, we repeat the procedure on the level of visual aspects to obtain local topological maps. We demonstrate how the resulting representation can be used for modeling indoor and outdoor environments, how it successfully detects previously visited locations and how it can be used for the estimation of the current visual aspect and the retrieval of the relative position within the current visual aspect.
ENSEMBLE VOTING SYSTEM FOR MULTICLASS PROTEIN FOLD RECOGNITION
Authors: CHEN YUEHUI , CHEN FENG , YANG JACK Y. , YANG MARY QU
Published: July 2008

Protein structure classification is an important issue in understanding the associations between sequence and structure as well as possible functional and evolutionary relationships. Recently structural genomes initiatives and other high-throughput experiments have populated the biological databases at a rapid pace. In this paper, three types of classifiers, k nearest neighbors, class center and nearest neighbor and probabilistic neural networks and their homogenous ensemble for multiclass protein fold recognition problem are evaluated firstly, and then a heterogenous ensemble Voting System is designed for the same problem. The different features and/or their combinations extracted from the protein fold dataset are used in these classification models. The heterogenous classification results are then put into a voting system to get the final result. The experimental results show that the proposed method can improve prediction accuracy by 4%–10% on a benchmark dataset containing 27 SCOP folds.
RANK ONE CHAOS: THEORY AND APPLICATIONS
Authors: WANG QIUDONG , OKSASOGLU ALI
Published: July 2008

The main purpose of this tutorial is to introduce to a more application-oriented audience a new chaos theory that is applicable to certain systems of differential equations. This new chaos theory, namely the theory of rank one maps, claims a comprehensive understanding of the complicated geometric and dynamical structures of a specific class of nonuniformly hyperbolic homoclinic tangles. For certain systems of differential equations, the existence of the indicated phenomenon of chaos can be verified through a well-defined computational process. Applications to the well-known Chua's and MLC circuits employing controlled switches are also presented to demonstrate the usefulness of the theory. We try to introduce this new chaos theory by using a balanced combination of examples, numerical simulations and theoretical discussions. We also try to create a standard reference for this theory that will hopefully be accessible to a more application-oriented audience.
STABILITY, SYMMETRY-BREAKING BIFURCATIONS AND CHAOS IN DISCRETE DELAYED MODELS
Authors: PENG MINGSHU , YUAN YUAN
Published: July 2008

In this paper, we use the standard bifurcation theory to study rich dynamics of time-delayed coupling discrete oscillators. Equivariant bifurcations including equivariant Neimark–Sacker bifurcation, equivariant pitchfork bifurcation and equivariant periodic doubling bifurcation are analyzed in detail. In the application, we consider a ring of identical discrete delayed Ikeda oscillators. Multiple oscillation patterns, such as multiple stable equilibria, stable limit cycles, stable invariant tori and multiple chaotic attractors, are shown.
NONLINEAR DYNAMICAL SYSTEM AND CHAOS SYNCHRONIZATION
Authors: KHAN AYUB , SINGH PREMPAL
Published: July 2008

Chaos synchronization of nonlinear dynamical systems has been studied through theoretical and numerical techniques. For the synchronization of two identical nonlinear chaotic dynamical systems a theorem has been constructed based on the Lyapunov function, which requires a minimal knowledge of system's structure to synchronize with an identical response system. Numerical illustrations have been provided to verify the theorem.
SYNCHRONIZATION OF IMPULSIVELY COUPLED SYSTEMS
Authors: HAN XIUPING , LU JUN-AN , WU XIAOQUN
Published: July 2008

In the past years, impulsive control for a single system and impulsive synchronization between two systems have been extensively studied. However, investigation on impulsive control and synchronization of complex networks has just started. In these studies, a network is continuously coupled, and then is synchronized by using impulsive control strategy. In this paper, a new and different coupled model is proposed, where the systems are coupled only at discrete instants through impulsive connections. Several criteria for synchronizing such kind of impulsively coupled complex dynamical systems are established. Two examples are also worked through for illustrating the main results.
EXPLOITING NONLINEAR DYNAMICS TO STORE AND PROCESS INFORMATION
Authors: MILIOTIS ABRAHAM , SINHA SUDESHNA , DITTO WILLIAM L.
Published: July 2008

By applying nonlinear dynamics to the dense storage of information, we demonstrate how a single nonlinear dynamical element can store M items, where M is variable and can be large. This provides the capability for naturally storing data in different bases or in different alphabets and can be used to implement multilevel logic. Further we show how this method of storing information can serve as a preprocessing tool for (exact or inexact) pattern matching searches. Since our scheme involves just a single procedural step, it is naturally set up for parallel implementation and can be realized with hardware currently employed for chaos-based computing architectures.
THE INTERMITTENCY ROUTE TO CHAOS OF AN ELECTRONIC DIGITAL OSCILLATOR
Authors: STAVRINIDES S. G. , MILIOU A. N. , LAOPOULOS TH. , ANAGNOSTOPOULOS A. N.
Published: July 2008

An electronic oscillator producing digital signals, formed by a second-order, nonlinear, nonautonomous, closed loop topology that is based on two integrators and nonlinear elements (a comparator and a XOR gate), was experimentally investigated. For a certain frequency and amplitude range of the periodic driving signal, the intermittency route to chaos was observed and studied.
Identification and functional characterization of a novel human and rat riboflavin transporter, RFT1
Authors: Yonezawa Atsushi , Masuda Satohiro , Katsura Toshiya , Inui Ken-ichi
Published: July 2008

Absorption of riboflavin is mediated by transporter(s). However, a mammalian riboflavin transporter has yet to be identified. In the present study, the novel human and rat riboflavin transporters hRFT1 and rRFT1 were identified on the basis of our rat kidney mRNA expression database (Horiba N, Masuda S, Takeuchi A, Saito H, Okuda M, Inui K. Kidney Int 66: 29–45, 2004). hRFT1 and rRFT1 cDNAs have an open reading frame encoding 448- and 450-amino acid proteins, respectively, that exhibit 81.1% identity and 96.4% similarity to one another. In addition, an inactive splice variant of hRFT1, hRFT1sv, was also cloned. The hRFT1sv cDNA, which encodes a 167-amino acid protein, retains an intron between exons 2 and 3 of hRFT1. Real-time PCR revealed that the sum of hRFT1 and hRFT1sv mRNAs was expressed strongly in the placenta and small intestine and was detected in all tissues examined. In addition, hRFT1 and hRFT1sv were expressed in human embryonic kidney (HEK)-293 and Caco-2 cells. HEK-293 cells transfected with green fluorescent protein-tagged hRFT1 and rRFT1 exhibited a fluorescent signal in the plasma membrane. Overexpression of hRFT1 and rRFT1, but not hRFT1sv, increased the cellular accumulation of [3H]riboflavin. The transfection of small interfering RNA targeting both hRFT1 and hRFT1sv significantly decreased the uptake of [3H]riboflavin by HEK-293 and Caco-2 cells. Riboflavin transport is Na+, potential, and pH independent. Kinetic analyses demonstrated that the Michaelis-Menten constants for the uptake by HEK-293 and Caco-2 cells were 28.1 and 63.7 nM, respectively. We propose that hRFT1 and rRFT1 are novel mammalian riboflavin transporters, which belong to a new mammalian riboflavin transporter family.
Organization of metabolic pathways in vastus lateralis of patients with chronic obstructive pulmonary disease
Authors: Green Howard J. , Bombardier Eric , Burnett Margaret , Iqbal Sobia , D'Arsigny Christine L. , O'Donnell Dennis E. , Ouyang Jing , Webb Katherine A.
Published: July 2008

The objective of this study was to determine whether patients with chronic obstructive lung disease (COPD) display differences in organization of the metabolic pathways and segments involved in energy supply compared with healthy control subjects. Metabolic pathway potential, based on the measurement of the maximal activity (Vmax) of representative enzymes, was assessed in tissue extracted from the vastus lateralis in seven patients with COPD (age 67 ± 4 yr; FEV1/FVC = 44 ± 3%, where FEV1is forced expiratory volume in 1 s and FVC is forced vital capacity; means ± SE) and nine healthy age-matched controls (age 68 ± 2 yr; FEV1/FVC = 75 ± 2%). Compared with control, the COPD patients displayed lower ( P < 0.05) Vmax(mol·kg protein−1·h−1) for cytochrome c oxidase (COX; 21.2 ± 2.0 vs. 28.7 ± 2.2) and 3-hydroxyacyl-CoA dehydrogenase (HADH; 2.54 ± 0.14 vs. 3.74 ± 0.12) but not citrate synthase (CS; 2.20 ± 0.16 vs. 3.19 ± 0.5). While no differences between groups were observed in Vmaxfor creatine phosphokinase, phosphorylase (PHOSPH), phosphofructokinase (PFK), pyruvate kinase, and lactate dehydrogenase, hexokinase (HEX) was elevated in COPD ( P < 0.05). Enzyme activity ratios were higher ( P < 0.05) for HEX/CS, HEX/COX, PHOSPH/HADH and PFK/HADH in COPD compared with control. It is concluded that COPD patients exhibit a reduced potential for both the electron transport system and fat oxidation and an increased potential for glucose phosphorylation while the potential for glycogenolysis and glycolysis remains normal. A comparison of enzyme ratios indicated greater potentials for glucose phosphorylation relative to the citric acid cycle and the electron transport chain and glycogenolysis and glycolysis relative to β-oxidation.