bluuebunny/crossref_metadata_2025 huggingface dataset:
Transmission of ultrasound through bottlenose dolphin (tursiops truncatus) jaw and skull bone
Authors: Gray Michael D. , Martin James S. , Rogers Peter H.
Published: October 2013

Measurements of ultrasound transmission through jaw (pan bone) and skull (temporal fossa) samples from an Atlantic bottlenose dolphin were performed as part of an investigation of the feasibility of performing in vivo elastography on cetacean head tissues. The pan bone and temporal fossa are both relatively thin and smooth, and are therefore of interest for acoustic imaging of the underlying tissues of the ear and brain, respectively. Field scan data will be presented, showing the influence of the bone on the quality of the focus and overall pressure levels generated by a spherically focused single-element transducer. [Work supported by ONR.]
Induced loudness reduction
Authors: Epstein Michael , Florentine Mary
Published: October 2013

Induced loudness reduction (ILR) is a phenomenon by which a preceding higher-level tone (an inducer tone) reduces the loudness of a lower-level tone (a test tone). Under certain conditions, ILR can result in loudness reductions of 10 to 15 phons for pure tones. The strength of this effect depends on a number of parameters including: (1) the levels of both the inducer and test tones; (2) the frequency separation between the inducer and test tones; (3) the durations of the inducer and test tones; (4) the time separation between the inducer and test tones; (5) individual differences; and, possibly (6) the number of exposures to inducers. Because of the sensitivity of ILR to procedural conditions, it is quite important to consider the potential effects of ILR when considering any experimental design in which level varies. The understanding of ILR has also given insight into a number of unexplained discrepancies between data sets that were collected using different procedures. In fact, some of the variability known to affect loudness judgments may be due to ILR. [Work supported by NIH/NIDCD Grant R01DC02241.]
Predicting vowel inventories: The dispersion-focalization theory revisited
Authors: Becker Roy
Published: October 2013

A revision of the dispersion-focalization theory (DFT) [Schwartz et al., J. Phonetics 25, 233–253 (1997)] is presented. Like DFT, the current computational model incorporates the center of gravity effect (COG) of 3.5-Bark spectral integration, but it deviates from DFT in that the COG contributes to the actual values and reliability weights of the perceived formants of vowels. The COG is reinterpreted as a domain of acceleration towards formant merger: the percepts of formants less than 3.5 Barks apart are perturbed towards one another in a nonlinear yet continuous fashion and their weights are increased, but perceptual merger and weight maximization occur only when the acoustic distance is about 2 Bark. Like other dispersion-based models, inventories are evaluated predominantly according to the least dispersed vowel pair, where dispersion is measured as the weighted Euclidean distance between the vowels coordinates (the first two perceived formants). Yet in the current model the weights are determined dynamically, in a well-principled manner. This model improves existing models in predicting certain universal traits, such as series of front rounded vowels in large vowel inventories, as emergent properties of certain local maxima of the inventory dispersion evaluation function, without sacrificing predictive adequacy for smaller inventories.
Matching fundamental and formant frequencies in vowels
Authors: Assmann Peter F. , Nearey Terrance M. , Chen Derrick
Published: October 2013

In natural speech, there is a moderate correlation between fundamental frequency (F0) and formant frequencies (FF) associated with differences in larynx and vocal tract size across talkers. This study asks whether listeners prefer combinations of mean F0 and mean FF that mirror the covariation of these properties. The stimuli were vowel triplets (/i/-/a/-/u/) spoken by two men and two women and subsequently processed by Kawahara’s STRAIGHT vocoder. Experiment 1 included two continua, each containing 25 vowel triplets: one with the spectrum envelope (FF) scale factor fixed at 1.0 (i.e., unmodified) and F0 varied over ±2 oct, the other with F0 scale factor fixed at 1.0 and FF scale factors between 0.63 and 1.58. Listeners used a method of adjustment procedure to find the ‘‘best voice’’ in each set. For each continuum, best matches followed a unimodal distribution centered on the mean F0 or mean FF (F1, F2, F3) observed in measurements of vowels spoken by adult males and females. Experiment 2 showed comparable results when male vowels were scaled to the female range and vice versa. Overall the results suggest that listeners have an implicit awareness of the natural covariation of F0 and FF in human voices.
Acoustic patterns of Japanese voiced velar stops
Authors: Dembowski James , Aoyama Katsura
Published: October 2013

This presentation focuses on Japanese voiced velar /g/. The phoneme /g/ in VCV contexts is said to be characterized by a distinctive wedge-shaped formant pattern in which F2 and F3 converge toward one frequency in the transition from vowel to stop closure, and then diverge as the vocal tract opens from the stop release to the following vowel. This pattern was examined using acoustic and kinematic data from an x-ray microbeam database of Japanese speakers, which is comparable to the English language x-ray microbeam speech production database [Hashi et al., J. Acoust. Soc. Am. 104, 2426–2437 (1998)]. Japanese speakers produced the expected wedge-shaped formant pattern in isolated VCV nonsense syllables, but rarely, if ever, produced this pattern in connected speech. In contrast, English speakers more frequently produced the expected formant pattern in connected speech, though the pattern was less reliably present than in isolated VCVs and varied considerably within and across speakers. These observations highlight substantial differences between controlled laboratory speech and meaningful connected speech, as well as differences in the ways that phonemes are manifested by different linguistic communities. These data also potentially illuminate the relationship among phonetic, acoustic, and kinematic levels of speech production.
Phonetic alignment to visual speech
Authors: Miller Rachel M. , Rosenblum Lawrence D. , Sanchez Kauyumari
Published: October 2013

Talkers are known to produce allophonic variation based, in part, on the speech of the person with whom they are talking. This subtle imitation, or phonetic alignment, occurs during live conversation and when a talker is asked to shadow recorded words [e.g., Shockley, et al., Percept. Psychophys. 66, 422 (2004)]. What is yet to be determined is the nature of the information to which talkers align. To examine whether this information is restricted to the acoustic modality, experiments were conducted to test if talkers align to visual speech (lipread) information. Normal-hearing subjects were asked to watch an actor silently utter words, and to identify these words by saying them out loud as quickly as possible. These shadowed responses were audio recorded and naive raters compared these responses to the actors auditory words (which had been recorded along with the actors visual tokens). Raters judged the shadowed words as sounding more like the actors words than did baseline words, which had been spoken by subjects before the shadowing task. These results show that phonetic alignment can be based on visual speech, suggesting that its informational basis is not restricted to the acoustic signal.
Effects of signal levels on vowel formant discrimination for normal-hearing listeners
Authors: Liu Chang
Published: October 2013

The goal of this study was to examine effects of signal levels on vowel formant discrimination. Thresholds of formant discrimination were measured for F1 and F2 of four vowels in isolated vowels and sentences at three intensity levels: 70, 85, and 100 dB SPL for normal-hearing listeners using a three-interval, two-alternative forced-choice procedure with a two-down, one-up tracking algorithm. Results showed that formant thresholds were significantly affected by formant frequency, linguistic context, and signal levels. Thresholds of formant discrimination were increased as formant frequency increased and linguistic context changed from isolated vowels to sentences. The signal level indicated a rollover effect in which formant thresholds at 85 dB SPL are lower than at either 70 or 100 dB SPL in both isolated vowels and sentences. This rollover level effect could be due to reduced frequency selectivity and reduction in active cochlear nonlinearity at high signal levels for normal-hearing listeners. Excitation and loudness models will be explored to account for the level effect on formant discrimination of isolated vowels.
Sequential contrast or compensation for coarticulation?
Authors: Kingston John , Mash Daniel , Chambless Della , Kawahara Shigeto
Published: October 2013

English listeners identify a stop ambiguous between /t/ and /k/ more often as ‘‘k’’ after /s/ than /sh/ (Mann and Repp, 1981). Judgments shift similarly after a fricative ambiguous between /s/ and /sh/ when its identity is predictable from a transitional probability bias but perhaps not from a lexical bias (Pitt and McQueen, 1998; cf. Samuel and Pitt, 2003). In replicating these experiments, we add a discrimination task to distinguish between the predictions of competing explanations for these findings: listeners respond ‘‘k’’ more often after /s/ because they compensate for the fronting of the stop expected from coarticulation with /s/ or because a stop with an F3 onset frequency midway between /t/’s high value and /k/’s low value sounds lower after the /s/’s high-frequency energy concentration. The second explanation predicts listeners will discriminate /s-k/ and /sh-t/ sequences better than /s-t/ and /sh-k/ sequences because sequential contrast exaggerates the spectral differences between /s-k/’s high-low intervals and /sh-t/’s low-high intervals and distinguishes them more perceptually than /s-t/’s high-high intervals and /sh-k/’s low-low intervals. Compensation for coarticulation predicts no difference in discriminability between the two pairs because it does not exaggerate differences between the two intervals. [Work supported by NIH.]
The clustering coefficient of phonological neighborhoods influences spoken word recognition
Authors: Vitevitch Michael
Published: October 2013

Neighborhood density refers to the number of words, or neighbors, that are phonologically related to a given word. For example, the words BAT, MAT, CUT, and CAN (among others) are considered phonological neighbors of the word CAT. In contrast, the clustering coefficient of the neighborhood refers to the proportion of phonological neighbors that are also neighbors of each other. Among the neighbors of CAT, the words BAT and MAT are neighbors of each other, but the words BAT and CAN are not neighbors of each other. Despite the stimulus words having the same number of neighbors overall, the results of an auditory lexical decision task showed that words with a high clustering coefficient (i.e., most neighbors were also neighbors of each other) were responded to more quickly than words with a low clustering coefficient (i.e., few neighbors were also neighbors of each other). These results suggest that some aspects of phonological similarity (i.e., clustering coefficient) might facilitate lexical activation, whereas other aspects of phonological similarity (i.e., neighborhood density) influence a later, decision stage of processing characterized by competition among activated word-forms. [Work supported by NIH.]
The use of auditory and visual information in the perception of stress in speech
Authors: Harnsberger James , Kahan Daniel , Hollien Harry
Published: October 2013

Prior work on the acoustic correlates of the perception of psychological stress in speech has suffered from the problem of quantifying and verifying the extent to which a speaker was under stress during articulation. Two experiments were conducted to address this issue. First, stressed and unstressed speech samples were elicited from 78 speakers of American English. Stressed samples were recorded by having subjects read a standard passage while under the threat of the administration of mild electric shock. Both visual and audio recordings were collected. Stress was quantified in terms of four measures: two physiological (pulse rate and galvanic skin response) and two self-report scales. Sentences from the 16 speakers showing the largest differences between the stressed and unstressed conditions were then presented in a paired comparison task to 90 naive listeners, 30 each in three conditions: (1) audio-only presentation of the stimuli, (2) visual-only presentation of the stimuli, and (3) audiovisual presentation of the stimuli. The results indicate that individual listeners are sensitive to stress cues in speech in all three conditions.
Cross-ear suppression of the verbal transformation effect: Tweaking an acoustic-phonetic level
Authors: Lenz Peter W. , Bashford James A. , Warren Richard M.
Published: October 2013

A recorded word repeating over and over undergoes a succession of illusory changes. When two images of the same repeating word are presented dichotically, with a half-cycle delay preventing fusion, the two images of the word each undergo independent illusory transformations at a rate equivalent to that of a single image [Lenz et al., J. Acoust. Soc. Am. 107, 2857 (2000)]. However, with one phoneme difference (e.g., ‘‘dark’’ versus ‘‘dart’’), transition rate is dramatically suppressed [Bashford et al., J. Acoust. Soc. Am. 110, 2658 (2001)]. Rates decrease with extent of feature mismatch at a single phoneme position (roughly 30% reduction with one feature mismatch and 45% with three). Rates also decrease with the number of mismatched phonemes (about 80% rate reduction with three out of four), suggesting a strong acoustic-phonetic basis for verbal transformation suppression. In contrast, semantic relations had no effect (e.g., transformations for ‘‘light’’ were suppressed equally by contralateral night and ‘‘might’’). Dichotic competition appears to allow us to access and selectively influence a prelexical stage of linguistic analysis. [Work supported by NIH.]
The effect of viewing angle on the visual contribution to speech intelligibility in noise
Authors: Brandewie Eugene , Brungart Douglas , Iyer Nandini , Simpson Brian
Published: October 2013

Visual cues are known to assist speech comprehension in noisy environments, but relatively little is known about the impact that viewing angle has on the visual contribution to speech intelligibility. In this experiment, four digital cameras were used to make simultaneous recordings of test phrases from the Modified Rhyme Test at four different viewing angles: 0, 45, 90, and 135 deg. These test phrases were used to measure the effect of viewing angle on the intelligibility of noise-masked speech stimuli that were presented with and without visual cues at seven different signal-to-noise ratios (SNRs). When the face was viewed from the front, the visual cues provided an intelligibility improvement that was equivalent to a 6–10-dB increase in SNR. This visual benefit remained roughly constant for viewing angles up to 90 deg, but it dropped off rapidly (to less than 2 dB) when the viewing angle increased to 135 deg. The results suggest that the visual contribution to speech perception is severely impaired when the observer does not have access to an unobstructed view of the talker’s mouth.
Multichannel active noise control system without secondary path models using the simultaneous perturbation algorithm
Authors: Kajikawa Yoshinobu , Nomura Yasuo
Published: October 2013

This paper presents a novel multichannel active noise control (ANC) system without secondary path models. This ANC system uses a simultaneous perturbation algorithm as the updating algorithm and has an advantage that secondary path models (estimation of secondary paths) are not required, unlike the MEFX (multiple error filtered-X)-based ANC. This system can consequently control noise stably because there are not modeling errors that cause system instability. The computational complexity is also very small. Experimental results demonstrate that the proposed multi-channel ANC system can operate stably under the environment where the error microphones always move.
Comparison of measurement techniques for speech intelligibility
Authors: Olson Bruce C.
Published: October 2013

A comparison of measurement techniques for speech intelligibility between two recently released measurement systems is made. EASERA (Electronic and Acoustic System Evaluation and Response Analysis) uses a standard PC and an EASERA Gateway interface attached via Firewire. The software postprocesses a variety of stimuli in order to derive the impulse response for the room under test. This impulse response is then further processed and the results are presented to the user in both graphical and textual presentations. The Ivie Technologies IE-35 is based on a Pocket PC system and uses an external modulated noise source as stimulus to produce an intelligibility score as a single number or average of a series of measurements. This paper will explore a variety of measurements made in the same locations in a room by both systems. Results will also be shown for a variety of other acoustic measures that quantify the acoustical parameters of the room.
The estimation of the room acoustic characteristic using the acoustic intensity method
Authors: Tang Yong , Shibayama Hideo , Yosida Takumi
Published: October 2013

When a sound radiates in rooms, a lot of reflection sounds are generated. From estimation of the direction where the room reflection sound comes from, we can understand the diffusion situation in the room acoustic field. By using the acoustic intensity method, we can measure the strength and the direction of the sound. In this paper, we estimate the direction of the reflection sound in the time-space by the acoustic intensity method and show the acoustic characteristic of the room.
On and Off Retinal Circuit Assembly by Divergent Molecular Mechanisms
Authors: Sun Lu O. , Jiang Zheng , Rivlin-Etzion Michal , Hand Randal , Brady Colleen M. , Matsuoka Ryota L. , Yau King-Wai , Feller Marla B. , Kolodkin Alex L.
Published: October 2013

Wiring the Retina

Starburst amacrine cells in the retina detect motion by responding to light going on or off.

L. O. Sun
et al.

(
10.1126/science.1241974
) analyzed how the cellular circuits develop in the mouse retina to form the basis of motion detection. Expression patterns of semaphorin 6A and its receptor plexin A2 defined the shape and reactivity of the starburst amacrine cells. Semaphorin 6A expression was restricted to particular cells, generating two classes of starburst amacrine cells with distinct morphologies and opposing functions.
Space Bats: Multidimensional Spatial Representation in the Bat
Authors: Yartsev Michael M.
Published: October 2013

A novel animal model, the bat, is used to elucidate place-cell and grid-cell phenomena.
A Pathway to Flowering—Why Staying Cool Matters
Authors: Nilsson Ove
Published: October 2013

Plants time flowering through temperature-sensing mechanisms involving differential RNA abundance, alternative splicing, and protein stability.

[Also see Report by

Lee
et al.

]
Brains Don't Play Dice—or Do They?
Authors: Caron Sophie J. C.
Published: October 2013

Associative brain centers are able to account for an infinite amount of possible associations through randomized sensory input.
David H. Hubel (1926–2013)
Authors: Wurtz Robert H.
Published: October 2013

A neuroscientist and Nobel laureate transformed our understanding of how input to the brain produces vision and provided new insights into brain development.
Industry Lobbying Derails Trawling Ban in Europe
Authors: Rabesandratana Tania
Published: October 2013

Two deep-sea fishing methods cause massive ecological damage, many scientists say.
French Mathematician Tapped to Head Key Funding Agency
Authors: Enserink Martin
Published: October 2013

French mathematician Jean-Pierre Bourguignon will move to Brussels to become the new president of the European Research Council, Europe's funding agency for basic research.
Structural Biology Triumph Offers Hope Against a Childhood Killer
Authors: Cohen Jon
Published: October 2013

Fine-grained structural analyses of respiratory syncytial virus have led to a promising new vaccine strategy against this devastating childhood infection.
Dark Matter's Dark Horse
Authors: Cho Adrian
Published: October 2013

A rare yes/no effort promises to prove either that hypothetical particles called axions are the universe's elusive dark matter—or that they can't be.
Hepatitis C Virus RNA Replication and Virus Particle Assembly Require Specific Dimerization of the NS4A Protein Transmembrane Domain
Authors: Kohlway Andrew , Pirakitikulr Nathan , Barrera Francisco N. , Potapova Olga , Engelman Donald M. , Pyle Anna M. , Lindenbach Brett D.
Published: October 2013

Hepatitis C virus (HCV) NS4A is a single-pass transmembrane (TM) protein essential for viral replication and particle assembly. The sequence of the NS4A TM domain is highly conserved, suggesting that it may be important for protein-protein interactions. To test this hypothesis, we measured the potential dimerization of the NS4A TM domain in a well-characterized two-hybrid TM protein interaction system. The NS4A TM domain exhibited a strong homotypic interaction that was comparable in affinity to glycophorin A, a well-studied human blood group antigen that forms TM homodimers. Several mutations predicted to cluster on a common surface of the NS4A TM helix caused significant reductions in dimerization, suggesting that these residues form an interface for NS4A dimerization. Mutations in the NS4A TM domain were further examined in the JFH-1 genotype 2a replicon system; importantly, all mutations that destabilized NS4A dimers also caused defects in RNA replication and/or virus assembly. Computational modeling of NS4A TM interactions suggests a right-handed dimeric interaction of helices with an interface that is consistent with the mutational effects. Furthermore, defects in NS4A oligomerization and virus particle assembly of two mutants were rescued by NS4A A15S, a TM mutation recently identified through forward genetics as a cell culture-adaptive mutation. Together, these data provide the first example of a functionally important TM dimer interface within an HCV nonstructural protein and reveal a fundamental role of the NS4A TM domain in coordinating HCV RNA replication and virus particle assembly.
Sodium Hydrogen Exchangers Contribute to Arenavirus Cell Entry
Authors: Iwasaki Masaharu , Ngo Nhi , de la Torre Juan C.
Published: October 2013

Several arenaviruses, chiefly Lassa virus (LASV), cause hemorrhagic fever (HF) disease in humans and pose a great public health concern in the regions in which they are endemic. Moreover, evidence indicates that the worldwide-distributed prototypic arenavirus lymphocytic choriomeningitis virus (LCMV) is a neglected human pathogen of clinical significance. The limited existing armamentarium to combat human-pathogenic arenaviruses underscores the importance of developing novel antiarenaviral drugs, a task that would be facilitated by the identification and characterization of virus-host cell factor interactions that contribute to the arenavirus life cycle. A genome-wide small interfering RNA (siRNA) screen identified sodium hydrogen exchanger 3 (NHE3) as required for efficient multiplication of LCMV in HeLa cells, but the mechanisms by which NHE activity contributed to the life cycle of LCMV remain unknown. Here we show that treatment with the NHE inhibitor 5-(
N
-ethyl-
N
-isopropyl) amiloride (EIPA) resulted in a robust inhibition of LCMV multiplication in both rodent (BHK-21) and human (A549) cells. EIPA-mediated inhibition was due not to interference with virus RNA replication, gene expression, or budding but rather to a blockade of virus cell entry. EIPA also inhibited cell entry mediated by the glycoproteins of the HF arenaviruses LASV and Junin virus (JUNV). Pharmacological and genetic studies revealed that cell entry of LCMV in A549 cells depended on actin remodeling and Pak1, suggesting a macropinocytosis-like cell entry pathway. Finally, zoniporide, an NHE inhibitor being explored as a therapeutic agent to treat myocardial infarction, inhibited LCMV propagation in culture cells. Our findings indicate that targeting NHEs could be a novel strategy to combat human-pathogenic arenaviruses.
The Innate Immune Factor Apolipoprotein L1 Restricts HIV-1 Infection
Authors: Taylor Harry E. , Khatua Atanu K. , Popik Waldemar
Published: October 2013

Apolipoprotein L1 (APOL1) is a major component of the human innate immune response against African trypanosomes. Although the mechanism of the trypanolytic activity of circulating APOL1 has been recently clarified, the intracellular function(s) of APOL1 in human cells remains poorly defined. Like that of many genes linked to host immunity, APOL1 expression is induced by proinflammatory cytokines gamma interferon (IFN-γ) and tumor necrosis factor alpha (TNF-α). Additionally, IFN-γ-polarized macrophages that potently restrict HIV-1 replication express APOL1, which suggests that APOL1 may contribute to HIV-1 suppression. Here, we report that APOL1 inhibits HIV-1 replication by multiple mechanisms. We found that APOL1 protein targeted HIV-1 Gag for degradation by the endolysosomal pathway. Interestingly, we found that APOL1 stimulated both endocytosis and lysosomal biogenesis by promoting nuclear localization of transcription factor EB (TFEB) and expression of TFEB target genes. Moreover, we demonstrated that APOL1 depletes cellular viral accessory protein Vif, which counteracts the host restriction factor APOBEC3G, via a pathway involving degradation of Vif in lysosomes and by secretion of Vif in microvesicles. As a result of Vif depletion by APOL1, APOBEC3G was not degraded and reduced infectivity of progeny virions. In support of this model, we also showed that endogenous expression of APOL1 in differentiated U937 monocytic cells stimulated with IFN-γ resulted in a reduced production of virus particles. This finding supports the hypothesis that induction of APOL1 contributes to HIV-1 suppression in differentiated monocytes. Deciphering the precise mechanism of APOL1-mediated HIV-1 restriction may facilitate the design of unique therapeutics to target HIV-1 replication.
Reselection of a Genomic Upstream Open Reading Frame in Mouse Hepatitis Coronavirus 5′-Untranslated-Region Mutants
Authors: Wu Hung-Yi , Guan Bo-Jhih , Su Yu-Pin , Fan Yi-Hsin , Brian David A.
Published: October 2013

An AUG-initiated upstream open reading frame (uORF) encoding a potential polypeptide of 3 to 13 amino acids (aa) is found within the 5′ untranslated region (UTR) of >75% of coronavirus genomes based on 38 reference strains. Potential CUG-initiated uORFs are also found in many strains. The AUG-initiated uORF is presumably translated following genomic 5′-end cap-dependent ribosomal scanning, but its function is unknown. Here, in a reverse-genetics study with mouse hepatitis coronavirus, the following were observed. (i) When the uORF AUG-initiating codon was replaced with a UAG stop codon along with a U112A mutation to maintain a uORF-harboring stem-loop 4 structure, an unimpaired virus with wild-type (WT) growth kinetics was recovered. However, reversion was found at all mutated sites within five virus passages. (ii) When the uORF was fused with genomic (main) ORF1 by converting three in-frame stop codons to nonstop codons, a uORF-ORF1 fusion protein was made, and virus replicated at WT levels. However, a frameshifting G insertion at virus passage 7 established a slightly 5′-extended original uORF. (iii) When uAUG-eliminating deletions of 20, 30, or 51 nucleotides (nt) were made within stem-loop 4, viable but debilitated virus was recovered. However, a C80U mutation in the first mutant and an A77G mutation in the second appeared by passage 10, which generated alternate uORFs that correlated with restored WT growth kinetics.
In vitro
, the uORF-disrupting nondeletion mutants showed enhanced translation of the downstream ORF1 compared with the WT. These results together suggest that the uORF represses ORF1 translation yet plays a beneficial but nonessential role in coronavirus replication in cell culture.
Ultradeep Pyrosequencing and Molecular Modeling Identify Key Structural Features of Hepatitis B Virus RNase H, a Putative Target for Antiviral Intervention
Authors: Hayer Juliette , Rodriguez Christophe , Germanidis Georgios , Deléage Gilbert , Zoulim Fabien , Pawlotsky Jean-Michel , Combet Christophe
Published: October 2013

Last-generation nucleoside/nucleotide analogues are potent against hepatitis B virus (HBV) and have a high barrier to resistance. However, delayed responses have been observed in patients previously exposed to other drugs of the same class, long-term resistance is possible, and cure of infection cannot be achieved with these therapies, emphasizing the need for alternative therapeutic approaches. The HBV RNase H represents an interesting target because its enzyme activity is essential to the HBV life cycle. The goal of our study was to characterize the structure of the HBV RNase H by computing a 3-dimensional molecular model derived from
E. coli
RNase H and analyzing 2,326 sequences of all HBV genotypes available in public databases and 958,000 sequences generated by means of ultradeep pyrosequencing of sequences from a homogenous population of 73 treatment-naive patients infected with HBV genotype D. Our data revealed that (i) the putative 4th catalytic residue displays unexpected variability that could be explained by the overlap of the HBx gene and has no apparent impact on HBV replicative capacity and that (ii) the C-helix-containing basic protrusion, which is required to guide the RNA/DNA heteroduplex into the catalytic site, is highly conserved and bears unique structural properties that can be used to target HBV-specific RNase H inhibitors without cross-species activity. The model shows substantial differences from other known RNases H and paves the way for functional and structural studies as a prerequisite to the development of new inhibitors of the HBV cell cycle specifically targeting RNase H activity.
Acupuncture with Non-Steroidal Anti-Inflammatory Drugs (Nsaids) versus Acupuncture Or Nsaids Alone for the Treatment of Chronic Neck Pain: An Assessor-Blinded Randomised Controlled Pilot Study
Authors: Cho Jae-Heung , Nam Dong-Hyun , Kim Ki-Tack , Lee Jun-Hwan
Published: October 2013

Objective

To investigate the feasibility and sample size required for a full-scale randomised controlled trial of the effectiveness of acupuncture with non-steroidal anti-inflammatory drugs (NSAIDs) for chronic neck pain compared with acupuncture or NSAID treatment alone.

Methods

A total of 45 patients with chronic neck pain participated in the study. For 3 weeks the acupuncture with NSAIDs treatment group took NSAIDs (zaltoprofen, 80 mg) daily while receiving acupuncture treatment three times a week. The acupuncture treatment group received treatment three times a week and the NSAID treatment group took NSAIDs daily. The primary outcomes were to determine the feasibility and to calculate the sample size. As secondary outcomes, pain intensity and pain-related symptoms for chronic neck pain were measured.

Results

With regard to enrolment and dropout rates, 88.2% of patients consented to be recruited to the trial and 15.6% of participants were lost to follow-up. The sample size for a full-scale trial was estimated to be 120 patients. Although preliminary, there was a significant change in the visual analogue scale (VAS) for neck pain intensity between the baseline measurement and each point of assessment in all groups. However, there was no difference in VAS scores between the three groups.

Conclusions

This pilot study has provided the feasibility and sample size for a full-scale trial of acupuncture with NSAIDs for chronic neck pain compared with acupuncture or NSAID treatment alone. Further research is needed to validate the effects of acupuncture with NSAIDs.

Clinical Trial Registration

NIH ClinicalTrials.gov NCT01205958.
Acquired male urethral diverticulum: a complication following artificial urethral sphincter implantation
Authors: Peralta João Pedro , Reis Mário , Rabaça Carlos , Sismeiro Amilcar
Published: October 2013

The authors report a case of a 72-year-old patient who underwent radical prostatectomy in 2003 due to prostate cancer. During follow-up, he presented with permanent and severe urinary stress incontinence for which he underwent an artificial urinary sphincter implantation in 2009. After infection of the device, followed by the development of a urinary fistula, the artificial urinary sphincter was removed. He presented no new signs or symptoms for 2 years, during which he remained completely incontinent. In April 2012, he developed a painless scrotal swelling close to the median raphe. On manual compression, it showed urinary leakage and disappeared completely, only to reappear several hours later. Auxiliary examinations revealed a bulbar urethral diverticulum which was subsequently excised. A urethroplasty was performed during the same procedure. The patient presented with no further complications. Although still suffering from complete urinary incontinence, he refused any kind of surgery for the time being.
Genetic effects of marine stock enhancement: a case study based on the highly piscivorous Japanese Spanish mackerel
Authors: Nakajima Kaori , Kitada Shuichi , Habara Yoko , Sano Shoko , Yokoyama Emi , Sugaya Takuma , Iwamoto Akio , Kishino Hirohisa , Hamasaki Katsuyuki
Published: October 2013

We used a before–after control–impact design to quantify the genetic effects of the large piscivorous Japanese Spanish mackerel (Scomberomorus niphonius) stock enhancement program on wild populations in the Seto Inland Sea. Samples of 1424 wild and 230 hatchery fish collected from 13 sites around Japan were genotyped using five microsatellite markers. A total of 758 wild and 103 hatchery fish were sequenced for the mitochondrial DNA D-loop region. The population structure of Japanese Spanish mackerel was panmictic around Japan. Hatchery fish had significantly lower genetic diversity indices than did wild fish. However, there was no significant change in any of the diversity indices in the Seto Inland Sea, despite the substantial genetic mixing proportion of hatchery-origin genes (7.8%–14.5% from releases in 2001 and 2002), a conclusion supported by simulations. The estimated effective population size was surprisingly small (∼430–970) but stable in the Seto Inland Sea compared with the large census size. A Ryman–Laikre effect was not likely in the Japanese Spanish mackerel.
EXPLICIT SOLUTION FOR QUEUE LENGTH DISTRIBUTION OF M/T-SPH/1 QUEUE
Authors: ZHANG HONGBO , SHI DINGHUA , HOU ZHENTING
Published: October 2013

In this paper we study an M/T-SPH/1 queue system, where T-SPH denotes the continuous time phase type distribution defined on a birth and death process with countably many states. The queue model can be described by a quasi-birth-and-death (QBD) process with countable phases. For the QBD process, we give the computation scheme of the joint stationary distribution. Furthermore, the obtained results enable us to give the stationary queue length distribution for the M/T-SPH/1 queue.
INDIRECT SEARCHES FOR DECAYING DARK MATTER
Authors: IBARRA ALEJANDRO , TRAN DAVID , WENIGER CHRISTOPH
Published: October 2013

Numerous observations point towards the existence of an unknown elementary particle with no electromagnetic interactions, a large population of which was presumably produced in the early stages of the history of the Universe. This so-called dark matter has survived until the present day, accounting for the 26% of the present energy budget of the Universe. It remains an open question whether the particles comprising the dark matter are absolutely stable or whether they have a finite but very long lifetime, which is a possibility since there is no known general principle guaranteeing perfect stability. In this paper, we review the observational limits on the lifetime of dark matter particles with mass in the GeV–TeV range using observations of the cosmic fluxes of antimatter, gamma-rays and neutrinos. We also examine some theoretically motivated scenarios that provide decaying dark matter candidates.
ANALYTIC STUDY OF FIRST-ORDER PHASE TRANSITION IN HOLOGRAPHIC SUPERCONDUCTOR AND SUPERFLUID
Authors: HUANG WUNG-HONG
Published: October 2013

We use the matching method to investigate the first-order phase transition in holographic superconductor and superfluid. We first use the simple holographic superconductor model to describe the matching method and mention how to see the first-order phase transition. Next, we study the holographic superconductor with Stückelberg term and see that the analytic results indicate the existence of first-order phase transition. Finally, we study the holographic superfluid and show that the first-order phase transition can be found for some values of parameters. We determine the critical value analytically and compare it with the previous numerical result.
OPTIMAL FOLDING OF DATA FLOW GRAPHS BASED ON FINITE PROJECTIVE GEOMETRY USING VECTOR SPACE PARTITIONING
Authors: CHOUDHARY SWADESH , SHARMA HRISHIKESH , PATKAR SACHIN
Published: October 2013

A number of computations exist, especially in area of error-control coding and matrix computations, whose underlying data flow graphs are based on finite projective-geometry (PG) based balanced bipartite graphs. Many of these applications of finite projective geometry are actively being researched upon, especially in coding theory. Almost all these applications need large bipartite graphs, whose nodes represent parallel computations. To reduce its implementation cost, reducing amount of system/hardware resources during design is an important engineering objective. In this context, we present a scheme to reduce resource utilization while designing systems modeled using PG-based graphs. In such systems, the number of processing units is equal to the number of vertices, each performing an atomic computation. We present a novel way of partitioning the vertex set assigned to various atomic computations, into blocks. Each block of partition is then assigned to a processing unit. A processing unit performs the computations corresponding to the vertices in the block assigned to it in a sequential fashion, thus creating the effect of folding the overall computation. The symmetric properties of projective space lattices enable us to develop a conflict-free communication schedule. We employed the technique of coset decomposition of a finite field for partitioning. The folding scheme achieves the best possible throughput, in lack of any overhead of shuffling data across memories while scheduling another computation on the same processing unit. We first provide a scheme for a finite projective space of dimension five, and the corresponding schedules. This specific scheme is then generalized for arbitrary finite projective spaces. Both the folding schemes have been verified by both simulation as well as hardware prototyping. For example, a semi-parallel decoder architecture for a new class of expander codes was designed and implemented using this scheme, with potential deployment in DVD-R/CD-ROM drives.
Abnormal functional connectivity between motor cortex and pedunculopontine nucleus following chronic dopamine depletion
Authors: Valencia Miguel , Chavez Mario , Artieda Julio , Bolam J. Paul , Mena-Segovia Juan
Published: October 2013

The activity of the basal ganglia is altered in Parkinson's disease (PD) as a consequence of the degeneration of dopamine neurons in the substantia nigra pars compacta. This results in aberrant discharge patterns and expression of exaggerated oscillatory activity across the basal ganglia circuit. Altered activity has also been reported in some of the targets of the basal ganglia, including the pedunculopontine nucleus (PPN), possibly due to its close interconnectivity with most regions of the basal ganglia. However, the nature of the involvement of the PPN in the pathophysiology of PD has not been fully elucidated. Here, we recorded local field potentials in the motor cortex and the PPN in the 6-hydroxydopamine (6-OHDA)-lesioned rat model of PD under urethane anesthesia. By means of linear and nonlinear statistics, we analyzed the synchrony between the motor cortex and the PPN and the delay in the interaction between these two structures. We observed the presence of coherent activity between the cortex and the PPN in low (5–15 Hz)- and high (25–35 Hz)-frequency bands during episodes of cortical activation. In each case, the cortex led the PPN. Dopamine depletion strengthened the interaction of the low-frequency activities by increasing the coherence specifically in the theta and alpha ranges and reduced the delay of the interaction in the gamma band. Our data show that cortical inputs play a determinant role in leading the coherent activity with the PPN and support the involvement of the PPN in the pathophysiology of PD.
Differential contributions of basal ganglia and thalamus to song initiation, tempo, and structure
Authors: Chen J. R. , Stepanek L. , Doupe A. J.
Published: October 2013

Basal ganglia-thalamocortical circuits are multistage loops critical to motor behavior, but the contributions of individual components to overall circuit function remain unclear. We addressed these issues in a songbird basal ganglia-thalamocortical circuit (the anterior forebrain pathway, AFP) specialized for singing and critical for vocal plasticity. The major known afferent to the AFP is the premotor cortical nucleus, HVC. Surprisingly, previous studies found that lesions of HVC alter song but do not eliminate the ability of the AFP to drive song production. We therefore used this AFP-driven song to investigate the role of basal ganglia and thalamus in vocal structure, tempo, and initiation. We found that lesions of the striatopallidal component (Area X) slowed song and simplified its acoustic structure. Elimination of the thalamic component (DLM) further simplified the acoustic structure of song and regularized its rhythm but also dramatically reduced song production. The acoustic structure changes imply that sequential stages of the AFP each add complexity to song, but the effects of DLM lesions on song initiation suggest that thalamus is a locus of additional inputs important to initiation. Together, our results highlight the cumulative contribution of stages of a basal ganglia-thalamocortical circuit to motor output along with distinct involvement of thalamus in song initiation or “gating.”
Lymphoepithelioma-Like Carcinoma of the Lung: An Unusual Case and Literature Review
Authors: Huang Yuan-Chun , Hsueh Ching , Ho Shang-Yun , Liao Chiung-Ying
Published: October 2013

We described a case of lymphoepithelioma-like carcinoma (LELC) of the lung of a 65-year-old man with initial symptoms of intermittent chest pain and mild shortness of breath for 2 weeks. A right-lung mass was noted on chest computed tomography (CT) scan and was proved histopathologically as LELC of lung after video-assisted thorascopic lobectomy. He was successfully treated with lobectomy with postoperative adjuvant chemotherapy and is alive without signs of recurrence for 36 months after the diagnosis. It is important for clinicians, pathologists, and radiologists to understand the clinical, pathological, and radiological presentations of this neoplasm to avoid improper clinical decision making and misdiagnosis.
Measurement of Additional Strains in Shaft Lining Using Differential Resistance Sensing Technology
Authors: Zhao Guangsi , Pei HuaFu , Liang Hengchang
Published: October 2013

As is well known, shaft lining fracture is the main disaster resulting in a large amount of fatalities and property loss. Thus, the additional strain is a key parameter to evaluate the safety condition of existing shaft linings. In this study, a new type of safety monitoring system based on differential resistance sensing technology is developed to measure the additional strain in shaft linings. In this paper, the theatrical study, the working principle, and the function of the newly developed monitoring system are fully presented. To investigate the reliability and effectiveness of the monitoring system, the differential resistance sensors are used to measure the horizontal and vertical strains at different elevations in a shaft lining during reinforcing the fracture inside the shaft lining. It can be found that from the test results the monitoring system based on differential resistance sensing technology can measure the deformation of the existing wall lining during stratum grouting. Therefore, it can be concluded that the newly developed monitoring system is significant for fracture warning and reinforcement engineering.
Sufficient Conditions for Non-Bazilevič Functions
Authors: Cui Qun-Fa , Wang Zhi-Gang , Chen Xiao-Hong , Wen Feng-Hua
Published: October 2013

The main purpose of this paper is to derive some sufficient conditions for analytic functions to be of non-Bazilevič type.
Maximally Flat Waveforms with Finite Number of Harmonics in Class-FPower Amplifiers
Authors: Juhas Anamarija , Novak Ladislav A.
Published: October 2013

In this paper general solution to the problem of finding maximally flat waveforms with finite number of harmonics (maximally flat trigonometric polynomials) is provided. Waveform coefficients are expressed in closed form as functions of harmonic orders. Two special cases of maximally flat waveforms (so-called maximally flat even harmonic and maximally flat odd harmonic waveforms), which proved to play an important role in class-Fand inverse class-Fpower amplifier (PA) operations, are also considered. For these two special types of waveforms, coefficients are expressed as functions of two parameters only. Closed form expressions for efficiency and power output capability of class-Fand inverse class-FPA operations with maximally flat waveforms are also provided as explicit functions of number of a harmonics.
A Nonlinear Finite Element Method for Magnetoelectric Composite and the Study on the Influence of Interfacial Bonding
Authors: Wang He-Ling , Liu Bin , Fang Dai-Ning
Published: October 2013

Magnetoelectric composite material is effective in transferring magnetic field into electric signal. In this paper, a nonlinear finite element method is present to model the magnetoelectric composite of ferroelectric and magnetostrictive material. In the method, the nonlinear and coupling behavior of magnetostrictive material such as Terfenol-D is considered. The nonuniform magnetic, electric, and mechanical field distributions are present. An interfacial transferring coefficient is defined to investigate the performance of interfacial mechanical coupling quantitatively, and the influence of the properties of interfacial bonding material and interfacial cracks on magnetoelectric coefficient is discussed. A new laminate ME composite of curved interface is proposed to overcome weak interfacial bonding.