bluuebunny/crossref_metadata_2025 huggingface dataset:
Ventilation and Speech Characteristics During Submaximal Aerobic Exercise
Authors: Baker Susan E. , Hipp Jenny , Alessio Helaine
Published: July 2008

Purpose

This study examined alterations in ventilation and speech characteristics as well as perceived dyspnea during submaximal aerobic exercise tasks.

Method

Twelve healthy participants completed aerobic exercise-only and simultaneous speaking and aerobic exercise tasks at 50% and 75% of their maximum oxygen consumption (VO
2
max). Measures of ventilation, oxygen consumption, heart rate, perceived dyspnea, syllables per phrase, articulation rate, and inappropriate linguistic pause placements were obtained at baseline and throughout the experimental tasks.

Results

Ventilation was significantly lower during the speaking tasks compared with the nonspeaking tasks. Oxygen consumption, however, did not significantly differ between speaking and nonspeaking tasks. The perception of dyspnea was significantly higher during the speaking tasks compared with the nonspeaking tasks. All speech parameters were significantly altered over time at both task intensities.

Conclusions

It is speculated that decreased ventilation without a reduction in oxygen consumption implies that utilization of oxygen by the working muscles was increased during the speaking tasks to meet the metabolic needs. A greater ability to utilize oxygen from inspired air is found in individuals who are at higher fitness levels, and therefore these findings may have implications for individuals who must complete simultaneous speech and exercise for occupational purposes (e.g., fitness/military drill instructors, singers performing choreography).
Measurement of Phonated Intervals During Four Fluency-Inducing Conditions
Authors: Davidow Jason H. , Bothe Anne K. , Andreatta Richard D. , Ye Jun
Published: July 2008

Purpose

Previous investigations of persons who stutter have demonstrated changes in vocalization variables during fluency-inducing conditions (FICs). A series of studies has also shown that a reduction in short intervals of phonation, those from 30 to 200 ms, is associated with decreased stuttering. The purpose of this study, therefore, was to test the hypothesis that the distribution of phonated intervals (PIs) should change during 4 of the most well-known FICs.

Method

A repeated-measures design was used to explore the relationship between PIs and stuttering during 4 FICs: chorus reading, prolonged speech, singing, and rhythmic stimulation. Most conditions were conducted at 2 different speech rates. The distribution of PIs was measured during these conditions and was compared with PI distributions obtained during control conditions.

Results

Overall PI distributions were significantly different during all 4 FICs, as compared with control conditions. PIs in the range of 30–150 ms were reduced across all FICs, at all speech rates.

Conclusion

These results provide further evidence of the importance of phonation variables to (a) our understanding of how FICs may operate and (b) the treatment of stuttering. These findings, along with previous studies that showed how purposefully reducing the number of short PIs resulted in the elimination of stuttering, suggest that treatment programs based on prolonged speech—or PIs, in particular—may benefit from emphasizing a reduction in the number of short PIs and a simultaneous increase in the number of longer PIs.
Stimulus, Task, and Learning Effects on Measures of Temporal Resolution: Implications for Predictors of Language Outcome
Authors: Smith Nicholas A. , Trainor Laurel J. , Gray Kellie , Plantinga Judy A. , Shore David I.
Published: July 2008

Purpose

Some studies find that temporal processing ability predicts language outcome whereas other studies do not. Resolution of this debate is hindered by the variety of temporal measures used, nonsensory loading of the tasks, and differential amounts of practice across studies. The goal of this study was to examine the effects of stimulus properties, experimental task, and perceptual learning on listeners' gap detection performance.

Method

Gap detection thresholds were obtained from adults with normal hearing and language ability. The effects of marker frequency similarity and marker duration on thresholds were examined in yes-no, two-interval forced-choice (2IFC), and dual-pair comparison tasks (which vary in nonsensory loading) over 4 days of testing.

Results

Thresholds were highest for gaps defined by markers with disparate frequencies (1000 and 4000 Hz; i.e., between-channel gap detection), and with longer (300 ms) trailing markers, obtained using yes-no and 2IFC tasks. However, these effects were attenuated with training or the initial use of the dual-pair comparison task.

Conclusions

These results suggest that gap detection thresholds reflect a variety of sensory and nonsensory factors. Understanding these underlying factors is critical to any evaluation of the relation between temporal processing and language outcome.
An Experimental Clinical Trial of a Cognitive-Behavior Therapy Package for Chronic Stuttering
Authors: Menzies Ross G. , O’Brian Sue , Onslow Mark , Packman Ann , St Clare Tamsen , Block Susan
Published: July 2008

Purpose

The aims of the present study were to (a) examine the rate of social phobia among adults who stutter, (b) study the effects of speech restructuring treatment on social anxiety, and (c) study the effects on anxiety and stuttering of a cognitive-behavior therapy (CBT) package for social anxiety.

Method

Thirty-two adults with chronic stuttering were randomly allocated to receive either speech restructuring following a CBT package for social anxiety or speech restructuring alone. Data were obtained on a variety of speech and psychological measures at pre-treatment, post-CBT, post–speech restructuring, and 12 months follow-up.

Results

Sixty percent of our cohort were diagnosed with social phobia. Speech restructuring treatment alone had no impact on the social phobia of our cohort at 12 months follow-up. At follow-up, participants who had received CBT showed no social phobia and greater improvements than control participants on a range of psychological measures of anxiety and avoidance. However, the CBT package made no difference to the speech outcomes of those with social phobia.

Conclusion

The CBT treatment was associated with significant and sustained improvements in psychological functioning but did not improve fluency.
Effects of Stimulus Bandwidth on the Imitation of English Fricatives by Normal-Hearing Children
Authors: Stelmachowicz Patricia G. , Nishi Kanae , Choi Sangsook , Lewis Dawna E. , Hoover Brenda M. , Dierking Darcia , Lotto Andrew
Published: July 2008

Purpose

Recent studies from the authors' laboratory have suggested that reduced audibility in the high frequencies (because of the bandwidth of hearing instruments) may play a role in the delays in phonological development often exhibited by children with hearing impairment. The goal of the current study was to extend previous findings on the effect of bandwidth on fricatives/affricates to more complex stimuli.

Method

Nine fricatives/affricates embedded in 2-syllable nonsense words were filtered at 5 and 10 kHz and presented to normal-hearing 6- to 7-year-olds who repeated words exactly as heard. Responses were recorded for subsequent phonetic and acoustic analyses.

Results

Significant effects of talker gender and bandwidth were found, with better performance for the male talker and the wider bandwidth condition. In contrast to previous studies, relatively small (5%) mean bandwidth effects were observed for /s/ and /z/ spoken by the female talker. Acoustic analyses of stimuli used in the previous and the current studies failed to explain this discrepancy.

Conclusions

It appears likely that a combination of factors (i.e., dynamic cues, prior phonotactic knowledge, and perhaps other unidentified cues to fricative identity) may have facilitated the perception of these complex nonsense words in the current study.
Candidacy for Bilateral Hearing Aids: A Retrospective Multicenter Study
Authors: Boymans Monique , Goverts S. Theo , Kramer Sophia E. , Festen Joost M. , Dreschler Wouter A.
Published: July 2008

Purpose

The goal of this study was to find factors for refining candidacy criteria for bilateral hearing aid fittings. Clinical files of 1,000 consecutive hearing aid fittings were analyzed.

Method

Case history, audiometric, and rehabilitation data were collected from clinical files, and an extensive questionnaire on long-term outcome measures was conducted. After at least 2 years of hearing aid use, 505 questionnaires were returned. In order to compare differences in benefits between unilateral and bilateral fittings, two subgroups were composed in which most relevant variables (age, degree of hearing loss, and audiometric asymmetry) were matched for unilateral fittings (n= 212) and bilateral fittings (n= 477).

Results

The bilateral group had significantly higher benefit scores than the unilateral group for detection, speech intelligibility in reverberation, and localization, but poorer scores for comfort of loud sounds. The benefit of bilateral hearing aids was not significantly related to the level of technology of the hearing aids.

Conclusion

The analysis of the relation between objective parameters and the subjective outcome measures showed that candidacy for a successful bilateral fitting could not be predicted from age, maximum speech intelligibility, employment, exposure to background noise, or social activities.
Subjective and Objective Effects of Fast and Slow Compression on the Perception of Reverberant Speech in Listeners With Hearing Loss
Authors: Shi Lu-Feng , Doherty Karen A.
Published: July 2008

Purpose

The purpose of the current study was to assess the effect of fast and slow attack/release times (ATs/RTs) on aided perception of reverberant speech in quiet.

Method

Thirty listeners with mild-to-moderate sensorineural hearing loss were tested monaurally with a commercial hearing aid programmed in 3 AT/RT settings: linear, fast (AT = 9 ms, RT = 90 ms), and slow (AT = 900 ms, RT = 1,500 ms). Stimuli consisted of 200 low-predictability Speech-Perception-in-Noise sentences, presented at 60 dB SPL at 4 reverberation levels (RT60= 0, 0.6, 1.2, and 3.6 s). Listeners were randomly presented with 12 listening conditions (3 AT/RT settings × 4 reverberation levels). Intelligibility scores and clarity ratings of the sentences were obtained.

Results

Aided speech intelligibility and clarity significantly decreased as reverberation increased. Both fast and slow ATs/RTs resulted in significantly higher speech intelligibility than linear, but no significant difference was observed between fast and slow ATs/RTs. Clarity rating was similar across 3 settings; however, rating decreased the fastest with fast AT/RT as reverberation increased. Slow AT/RT resulted in significantly higher real-ear aided response than fast AT/RT and linear, despite the same programmed gain for all settings.

Conclusion

Reverberation had a more significant effect on aided speech perception than AT/RT, but fast and slow AT/RT resulted in improved speech intelligibility over linear amplification.
Phase transition induced by a shock wave in hard-sphere and hard-disk systems
Authors: Zhao Nanrong , Sugiyama Masaru , Ruggeri Tommaso
Published: August 2008

Dynamic phase transition induced by a shock wave in hard-sphere and hard-disk systems is studied on the basis of the system of Euler equations with caloric and thermal equations of state. First, Rankine–Hugoniot conditions are analyzed. The quantitative classification of Hugoniot types in terms of the thermodynamic quantities of the unperturbed state (the state before a shock wave) and the shock strength is made. Especially Hugoniot in typical two possible cases (P-1 and P-2) of the phase transition is analyzed in detail. In the case P-1 the phase transition occurs between a metastable liquid state and a stable solid state, and in the case P-2 the phase transition occurs through coexistence states, when the shock strength changes. Second, the admissibility of the two cases is discussed from a viewpoint of the recent mathematical theory of shock waves, and a rule with the use of the maximum entropy production rate is proposed as the rule for selecting the most probable one among the possible cases, that is, the most suitable constitutive equation that predicts the most probable shock wave. According to the rule, the constitutive equation in the case P-2 is the most promising one in the dynamic phase transition. It is emphasized that hard-sphere and hard-disk systems are suitable reference systems for studying shock wave phenomena including the shock-induced phase transition in more realistic condensed matters.
Classical Wigner theory of gas surface scattering
Authors: Pollak Eli , Sengupta Santanu , Miret-Artés Salvador
Published: August 2008

The scattering of atoms from surfaces is studied within the classical Wigner formalism. A new analytical expression is derived for the angular distribution and its surface temperature dependence. The expression is valid in the limit of weak coupling between the vertical motion with respect to the surface and the horizontal motion of the atom along the periodic surface. The surface temperature dependence is obtained in the limit of weak coupling between the horizontal atomic motion and the surface phonons. The resulting expression, which takes into account the surface corrugation, leads to an almost symmetric double peaked angular distribution, with peaks at the rainbow angles. The analytic expression agrees with model numerical computations. It provides a good qualitative description for the experimentally measured angular distribution of Ne and Ar scattered from a Cu surface.
Resonance energy transfer from a dye molecule to graphene
Authors: Swathi R. S. , Sebastian K. L.
Published: August 2008

We study the distance dependence of the rate of resonance energy transfer from the excited state of a dye to the π system of graphene. Using the tight-binding model for the π system and the Dirac cone approximation, we obtain the analytic expression for the rate of energy transfer from an electronically excited dye to graphene. While in traditional fluorescence resonance energy transfer, the rate has a (distance)−6 dependence, we find that the distance dependence in this case is quite different. Our calculation of rate in the case of the two dyes, pyrene and nile blue, shows that the distance dependence is Yukawa type. We have also studied the effect of doping on energy transfer to graphene. Doping does not modify the rate for electronic excitation energy transfer significantly. However, in the case of vibrational transfer, the rate is found to be increased by an order of magnitude due to doping. This can be attributed to the nonzero density of states at the Fermi level that results from doping.
Improved virtual orbital multireference Møller–Plesset study of the ground and excited electronic states of protonated acetylene, C2H3+
Authors: Chaudhuri Rajat K. , Freed Karl F.
Published: August 2008

The ground state geometries and associated normal mode frequencies of the classical and nonclassical protonated acetylene ion, i.e., the vinyl cation C2H3+, are computed using the complete active space self-consistent field and improved virtual orbital (IVO) complete active space configuration interaction methods. In addition, the minimum-energy reaction path for the classical to nonclassical interconversion is determined (as are excitation energies) using the IVO modification of multireference Møller–Plesset (MRMP) perturbation theory. The IVO-MRMP treatment predicts the nonclassical structure to be 4.8kcal∕mol more stable than the classical one, which is consistent with other high level theoretical estimates. The proton affinity of acetylene from the IVO-MRMP treatment (154.8kcal∕mol) also agrees well with experiment (153.3kcal∕mol) and with earlier CASPT2 calculations (154.8kcal∕mol). We further report geometries and vibrational frequencies of low lying excited states of C2H3+, which have not been observed and/or studied before. Comparisons with previous highly correlated calculations further demonstrate the computational efficiency of the IVO-MRPT methods.
Real-time, local basis-set implementation of time-dependent density functional theory for excited state dynamics simulations
Authors: Meng Sheng , Kaxiras Efthimios
Published: August 2008

We present a method suitable for large-scale accurate simulations of excited state dynamics within the framework of time-dependent density functional theory (DFT). This is achieved by employing a local atomic basis-set representation and real-time propagation of excited state wave functions. We implement the method within SIESTA, a standard ground-state DFT package with local atomic basis, and demonstrate its potential for realistic and accurate excited state dynamics simulations using small and medium-sized molecules as examples (H2, CO, O3, and indolequinone). The method can be readily applied to problems involving nanostructures and large biomolecules.
Adsorption of oxygen atoms on the Mg3Nd(001) surface
Authors: Wang Na , Zhang Wei-Bing , Li Wen , Zeng Xiao-Qin , Ding Wen-Jiang , Tang Bi-Yu
Published: August 2008

Based on the density functional theory, the stability of three possible Mg3Nd(001) surfaces is investigated, and the structural and electronic properties of O adsorption on the most stable Mg3Nd(001) surface are studied. The calculated results show that the most favorable adsorption site is the (2Nd+Mg) hollow site, and the adsorption energy decreases as the coverage increases. At low coverage O atoms prefer Nd atoms to Mg atoms as nearest neighbors. When the coverage increases to a full monolayer, some O atoms sink into the alloy surface and stay between Nd and Mg atoms. The electronic structures of the adsorption system show that for all coverage the interaction between O and the alloy surface mainly arises from the hybridization of O 2p states and Nd 5d states, while the interaction between Mg 3s states and O 2p states becomes noticeable at the high coverage. The present study reveals that during the initial oxidation stage of the alloy, Nd atoms can get a priority of oxidation, followed by Nd rich oxide film.
Effects of interaction range and compressibility on the microphase separation of diblock copolymers: Mean-field analysis
Authors: Wang Qiang
Published: August 2008

Using the random-phase approximation and self-consistent field calculations, we have investigated the effects of finite interaction range and compressibility on the order-disorder transition (ODT) and the lamellar structure of symmetric diblock copolymers. While the compressibility does not affect the ODT, both the values of χN and bulk lamellar period at the ODT increase with increasing interaction range. On the other hand, both the free-energy density and bulk period of the lamellae increase with either increasing interaction range or decreasing compressibility. Even with a finite compressibility, the mean-field ODT is still a second-order phase transition. The scaling exponent of bulk lamellar period with χN, however, decreases with increasing compressibility. Our mean-field analysis provides a well understood reference for the study of fluctuation effects in diblock copolymers with finite interaction range and compressibility.
Reflection and diffraction of internal waves analyzed with the Hilbert transform
Authors: Mercier Matthieu J. , Garnier Nicolas B. , Dauxois Thierry
Published: August 2008

We apply the Hilbert transform to the physics of internal waves in two-dimensional fluids. Using this demodulation technique, we can discriminate internal waves propagating in different directions: This is very helpful in answering several fundamental questions in the context of internal waves. We focus more precisely in this paper on phenomena associated with dissipation, diffraction, and reflection of internal waves.
Dislocation nucleation from a sharp corner in silicon
Authors: Izumi Satoshi , Yip Sidney
Published: August 2008

By combining molecular dynamics simulation with reaction pathway sampling, we have observed the nucleation of a three-dimensional dislocation loop from a sharp corner in silicon and investigated the shear stress dependence of the activation energy and saddle-point configuration. The nucleated shuffle-set half-loop consisted of two 60° segments and one screw segment, each lying along a Peierls valley. The half-hexagonal shape is in good agreement with experiments at low temperature. Under high stress (90%–95% of athermal shear stress), the dislocation embryo is far from perfect, with half-size Burgers vector (about 0.2 nm) and a 0.4–0.7 nm radius forming a diffuse core region. A consequence is that the Rice–Thompson theory gives incorrect predictions regarding the activation energy and saddle-point configuration. With decreasing applied stress (less than 70%), the embryo approaches that of a perfect dislocation.
Full-spectrum phonon relaxation times in crystalline Si from molecular dynamics simulations
Authors: Zhao Hong , Freund Jonathan B.
Published: August 2008

The lattice vibrations of a periodic silicon crystal are simulated by a molecular dynamics simulation. The history of atomic displacements and velocities obtained is used to compute the amplitudes of all phonon modes supported by the lattice. The phonon amplitude autocorrelation coefficients are found to decay exponentially in time, in agreement with single-mode relaxation time models for phonon scattering. However, the relaxation times extracted from the correlation curves are found to differ significantly from the empirical formulas currently used in models for microscale thermal transport, suggesting that improved relaxation time models are needed for accurate predictions in complex small-scale heat transfer systems.
Laser action in nanowires: Observation of the transition from amplified spontaneous emission to laser oscillation
Authors: Zimmler Mariano A. , Bao Jiming , Capasso Federico , Müller Sven , Ronning Carsten
Published: August 2008

Direct evidence of the transition from amplified spontaneous emission to laser action in optically pumped zinc oxide (ZnO) nanowires, at room temperature, is presented. The optical power evolves from a superlinear to a linear regime as the pump power exceeds threshold, concomitant with a transition to directional emission along the nanowire and the emergence of well defined cavity Fabry–Pérot modes around a wavelength of ≈385 nm, the intensity of which exceeds the spontaneous emission background by orders of magnitude. The laser oscillation threshold is found to be strongly dependent on nanowire diameter, with no laser oscillation observed for diameters smaller than ∼150 nm. Finally, we use an alternative “head on” detection geometry to measure the output power of a single nanowire laser.
Ferroelectric, electrical and magnetic properties of Cr, Mn, Co, Ni, Cu added polycrystalline BiFeO3 films
Authors: Naganuma Hiroshi , Miura Jun , Okamura Soichiro
Published: August 2008

Cr, Mn, Co, Ni, and Cu were added to polycrystalline BiFeO3 films, and their influence on the ferroelectric, electrical, and magnetic properties was investigated. All the additives except Ni reduced the leakage current density in the high electric field region. The addition of Cu and Co decreased the coercive field without reducing remanent polarization. The addition of Co caused spontaneous magnetization at room temperature, which exhibited a large coercive field of 16kOe at 10K. It was revealed that Co addition suppressed the leakage current density, decreased the electric coercive field, and induced spontaneous magnetization and large magnetic coercivity.
Terahertz conductivity of thin metal films
Authors: Laman N. , Grischkowsky D.
Published: August 2008

The conductivities of thin Al, Au, and Ag films were measured via their transmission at terahertz frequencies. The conductivities of all the films, particularly the thinner films and Al films, were much smaller than their bulk dc values. This reduced conductivity can be quantitatively understood in terms of an increased scattering rate from defects. The transmission is consistent with a frequency independent conductivity, implying a very fast electron scattering time.
Decisions and Transitions: Meeting the Needs of the ‘Knowledge Economy’
Authors: Warrington Molly
Published: August 2008

Governments worldwide have focused attention on improving educational attainment in order to meet the labour demands of the knowledge economy. I explore decisions taken concerning further and higher education among seventy-one students from a highly successful comprehensive school in North East England, and argue that the postulated links between attainment, higher education, and secure well-paid employment are more complicated than policy documents suggest. Instead, I argue for a greater understanding among policy makers of the specificity of place and of the impact of relative differences in economic, social, and cultural capital.
Evaluating the ability of the differenced Normalized Burn Ratio (dNBR) to predict ecologically significant burn severity in Alaskan boreal forests
Authors: Murphy Karen A. , Reynolds Joel H. , Koltun John M.
Published: August 2008

During the 2004 fire season ~6.6 million acres (~2.7 million ha) burned across Alaska. Nearly 2 million of these were on National Wildlife Refuge System lands inaccessible from the state’s limited road system. Many fires burned through September, driven by unusually warm and dry temperatures throughout the summer. Using several fires from this season, we assessed the national burn severity methodology’s performance on refuge lands. Six fires, spanning 814 489 acres (329 613 ha), were sampled on five boreal forest refuges. In total, 347 sites were sampled for vegetation composition and ground-based burn severity estimates following the national protocols. The relationship between the differenced Normalized Burn Ratio (dNBR) and composite burn index (CBI) was unexpectedly weak (R2adjusted, 0.11–0.64). The weak relationship was not a result of data or image processing errors, nor of any biotic or abiotic confounding variable. The inconsistent results, and dNBR’s limited ability to discern the ecologically significant differences within moderate and high severity burn sites, indicate that the current methodology does not satisfy key Alaskan boreal forest management objectives.
Cumulative cultural evolution in the laboratory: An experimental approach to the origins of structure in human language
Authors: Kirby Simon , Cornish Hannah , Smith Kenny
Published: July 2008

We introduce an experimental paradigm for studying the cumulative cultural evolution of language. In doing so we provide the first experimental validation for the idea that cultural transmission can lead to the appearance of design without a designer. Our experiments involve the iterated learning of artificial languages by human participants. We show that languages transmitted culturally evolve in such a way as to maximize their own transmissibility: over time, the languages in our experiments become easier to learn and increasingly structured. Furthermore, this structure emerges purely as a consequence of the transmission of language over generations, without any intentional design on the part of individual language learners. Previous computational and mathematical models suggest that iterated learning provides an explanation for the structure of human language and link particular aspects of linguistic structure with particular constraints acting on language during its transmission. The experimental work presented here shows that the predictions of these models, and models of cultural evolution more generally, can be tested in the laboratory.
Novelties of the flowering plant pollen tube underlie diversification of a key life history stage
Authors: Williams Joseph H.
Published: August 2008

The origin and rapid diversification of flowering plants has puzzled evolutionary biologists, dating back to Charles Darwin. Since that time a number of key life history and morphological traits have been proposed as developmental correlates of the extraordinary diversity and ecological success of angiosperms. Here, I identify several innovations that were fundamental to the evolutionary lability of angiosperm reproduction, and hence to their diversification. In gymnosperms pollen reception must be near the egg largely because sperm swim or are transported by pollen tubes that grow at very slow rates (< ≈20 μm/h). In contrast, pollen tube growth rates of taxa in ancient angiosperm lineages (
Amborella
,
Nuphar
, and
Austrobaileya
) range from ≈80 to 600 μm/h. Comparative analyses point to accelerated pollen tube growth rate as a critical innovation that
preceded
the origin of the true closed carpel, long styles, multiseeded ovaries, and, in monocots and eudicots, much faster pollen tube growth rates. Ancient angiosperm pollen tubes all have callosic walls and callose plugs (in contrast, no gymnosperms have these features). The early association of the callose-walled growth pattern with accelerated pollen tube growth rate underlies a striking repeated pattern of faster and longer-distance pollen tube growth often within solid pathways in phylogenetically derived angiosperms. Pollen tube innovations are a key component of the spectacular diversification of carpel (flower and fruit) form and reproductive cycles in flowering plants.
A triallelic system of
S5
is a major regulator of the reproductive barrier and compatibility of indica–japonica hybrids in rice
Authors: Chen Jiongjiong , Ding Jihua , Ouyang Yidan , Du Hongyi , Yang Jiangyi , Cheng Ke , Zhao Jie , Qiu Shuqing , Zhang Xuelian , Yao Jialing , Liu Kede , Wang Lei , Xu Caiguo , Li Xianghua , Xue Yongbiao , Xia Mian , Ji Qing , Lu Jufei , Xu Mingliang , Zhang Qifa
Published: August 2008

Hybrid sterility is a major form of postzygotic reproductive isolation. Although reproductive isolation has been a key issue in evolutionary biology for many decades in a wide range of organisms, only very recently a few genes for reproductive isolation were identified. The Asian cultivated rice (
Oryza sativa
L.) is divided into two subspecies,
indica
and
japonica
. Hybrids between
indica
and
japonica
varieties are usually highly sterile. A special group of rice germplasm, referred to as wide-compatibility varieties, is able to produce highly fertile hybrids when crossed to both
indica
and
japonica
. In this study, we cloned
S5
, a major locus for
indica–japonica
hybrid sterility and wide compatibility, using a map-based cloning approach. We show that
S5
encodes an aspartic protease conditioning embryo-sac fertility. The
indica
(
S5
-i) and
japonica
(
S5
-j) alleles differ by two nucleotides. The wide compatibility gene (
S5
-n) has a large deletion in the N terminus of the predicted S5 protein, causing subcellular mislocalization of the protein, and thus is presumably nonfunctional. This triallelic system has a profound implication in the evolution and artificial breeding of cultivated rice. Genetic differentiation between
indica
and
japonica
would have been enforced because of the reproductive barrier caused by
S5
-i and
S5
-j, and species coherence would have been maintained by gene flow enabled by the wide compatibility gene.
Phylocom: software for the analysis of phylogenetic community structure and trait evolution
Authors: Webb Campbell O. , Ackerly David D. , Kembel Steven W.
Published: August 2008

Motivation: The increasing availability of phylogenetic and trait data for communities of co-occurring species has created a need for software that integrates ecological and evolutionary analyses.

Capabilities: Phylocom calculates numerous metrics of phylogenetic community structure and trait similarity within communities. Hypothesis testing is implemented using several null models. Within the same framework, it measures phylogenetic signal and correlated evolution for species traits. A range of utility functions allow community and phylogenetic data manipulation, tree and trait generation, and integration into scientific workflows.

Availability: Open source at: http://phylodiversity.net/phylocom/

Contact:  cwebb@oeb.harvard.edu
VistaClara: an expression browser plug-in for Cytoscape
Authors: Kincaid Robert , Kuchinsky Allan , Creech Michael
Published: August 2008

Summary: VistaClara is a plug-in for Cytoscape which provides a more flexible means to visualize gene and protein expression within a network context. An extended attribute browser is provided in the form of a graphical and interactive permutation matrix that resembles the heat map displays popular in gene-expression analysis. This extended browser permits a variety of display options and interactions not currently available in Cytoscape.

Availability:  http://chianti.ucsd.edu/cyto_web/plugins/index.php

Contact:  robert_kincaid@agilent.com
1-[(4,5-Dimethylcyclohexa-1,4-dien-1-yl)sulfonyl]-4-methylbenzene
Authors: Gray Ryan H. , Fronczek Frank R. , Vicente M. Graça H.
Published: August 2008

In the title molecule, C15H18O2S, the dimethylcyclohexadiene unit is slightly non-planar, having a folded conformation with the two double-bond planes forming a dihedral angle of 3.9 (6)°. Methyl groups of the dimethylcyclohexadiene ring tilt away from each other, forming internal C—C—C(Me) angles approximately 11° greater than the exterior angles.
Poly[zinc(II)-[μ-1,4-bis(imidazol-1-ylmethyl)benzene]-μ-4,4′-oxydibenzoato]
Authors: Yu Chun-Hui
Published: August 2008

In the title compound, [Zn(C14H8O5)(C14H14N4)]
n
, the coordination polyhedron around each ZnII atom is a distorted tetrahedron. The ligands bridge the Zn atoms to form a two-dimensional (4,4)-network.
catena-Poly[[triaquazinc(II)]-μ-1H-1,2,4-triazole-3,5-dicarboxylato]
Authors: Sun Yan-Yan , Zhang Ya-Wen , Zhang Gong , Cheng Lin
Published: August 2008

In the title compound, [Zn(C4HN3O4)(H2O)3]
n
, each ZnII atom adopts a distorted octahedral coordination geometry, being surrounded by one chelating and one monodentate 1H-1,2,4-triazole-3,5-dicarboxylate ligand and three water molecules. Adjacent ZnII cations are linked by a 1H-1,2,4-triazole-3,5-dicarboxylate ligand in a μ2,κ3 fashion to form a chain running along the c axis. The crystal packing is stabilized by N—H...O, O—H...N and O—H...O hydrogen bonds.
Low-temperature redetermination of aquachloridotriphenyltin(IV)–1,10-phenanthroline (1/1)
Authors: Ng Seik Weng
Published: August 2008

The crystal structure of the title compound, [Sn(C6H5)3Cl(H2O)]·C12H8N2, which was refined in the triclinic space group P\overline{1} [Fu, Gao, Ma & Zhang (2005). Chin. J. Synth. Chem. 13, 55–57], has been redetermined in the monoclinic space group C2/c from low-temperature diffraction measurements. The Sn atom is five-coordinate in a trans-C3SnClO trigonal-bipyramidal geometry; the coordinated water molecule forms a pair of hydrogen bonds to the nitrogen heterocycle.
7,9-Dimethyl-5-phenylsulfonyl-5H-benzo[b]carbazole
Authors: Chakkaravarthi G. , Dhayalan V. , Mohanakrishnan A. K. , Manivannan V.
Published: August 2008

In the title compound, C24H19NO2S, the mean plane of the benzo[b]carbazole ring system makes a dihedral angle of 79.26 (5)° with the phenyl ring. The S atom is in a distorted tetrahedral configuration. The crystal structure exhibits weak C—H...O and C—H...π interactions.
5H-1-Benzothiopyrano[2,3-b]pyridin-5-one
Authors: Khan Muhammad Naeem , Tahir M. Nawaz , Khan Misbahul Ain , Khan Islam Ullah , Arshad Muhammad Nadeem
Published: August 2008

Molecules of the title compound, C12H7NOS, with one half-molecule in the asymmetric unit, are disordered about a crystallographic centre of inversion. Refinement showed that the C=O group is disordered with the S atom and the N atom is disordered over four positions. Adjacent molecules are connected through C—H...O hydrogen bonds and π...π interactions (centroid–centroid distances of 3.635 and 3.858 Å).
9-Methoxy-5-phenylsulfonyl-5H-benzo[b]carbazole
Authors: Chakkaravarthi G. , Dhayalan V. , Mohanakrishnan A. K. , Manivannan V.
Published: August 2008

In the title compound, C23H17NO3S, the mean plane of the benzo[b]carbazole ring system makes a dihedral angle of 77.17 (4)° with the phenyl ring. The S atom is in a distorted tetrahedral configuration. There are three intramolecular C—H...O interactions forming five- and six-membered rings with graph-set motifs S(5) and S(6), respectively.
N-Methylisosalsoline from Hammada scoparia
Authors: Jarraya Raoudha Mezghani , Bouaziz Amira , Hamdi Besma , Ben Salah Abdelhamid , Damak Mohamed
Published: August 2008

The title compound (systematic name: 1,2-dimethyl-6-methoxy-1,2,3,4-tetrahydroisoquinolin-7-ol), C12H17NO2, is a major alkaloid isolated from Hammada scoparia leaves. It belongs to the isoquinoline family and it was characterized by NMR spectroscopy and X-ray crystallographic techniques. The absolute configuration could not be reliably determined. An intermolecular O—H...N hydrogen bond is present in the crystal structure.
2-Methyl-3-(4-nitrophenyl)acrylic acid
Authors: Muhammad Niaz , Tahir M. Nawaz , Zia-ur-Rehman  , Ali Saqib
Published: August 2008

The title compound, C10H9NO4, forms R
2
2(8) dimers due to intermolecular O—H...O hydrogen bonding in the crystal structure. Two dimers are further linked to each other through two intermolecular C—H...O hydrogen bonds, forming an R
3
3(7) ring motif. The nitro groups form an intramolecular C—H...O hydrogen bond mimicking a five-membered ring. As a result of these hydrogen bonds, polymeric sheets are formed. The aromatic ring makes a dihedral angle of 42.84 (8)° with the carboxylate group and an angle of 8.01 (14)° with the nitro group. There is a π-interaction (N—O...π) between the nitro group and the aromatic ring, with a distance of 3.7572 (14) Å between the N atom and the centroid of the aromatic ring.
Genetic variation among females affects paternity in a dioecious plant
Authors: Teixeira Sara , Burkhardt Anne , Bernasconi Giorgina
Published: July 2008

Flowering plants rely on vectors for pollen transfer, and cannot choose their mates. Although recipient plants are unable to choose which pollen they receive, post‐pollination selection (acting pre‐ or post‐zygotically) may modify the outcome of pollination. Here we show that genetic variation among pollen recipients can predict the outcome of pollen competition (seed paternity) in the dioecious white campion. To investigate whether genetic variation among pollen recipients affects paternity, we applied the same pollen mixture from two males to three females, two of which full sisters and the third one chosen at random (unrelated). To control for maternal environmental effects, the plants used for these crosses were greenhouse‐reared F1. We replicated this in two populations, for a total of 51 crosses, and genotyped a total of 772 offspring to assign paternity. If genetic variation affects paternity, we expected greater similarity of paternity success of the focal male with the sisters, compared to the unrelated female. Paternity of the focal male was significantly more repeatable over sisters, compared to repeatability over the mean of sisters and the unrelated females. When populations were analyzed separately, this was significant in one of the two populations. Paternity was not significantly correlated with stigma size. This provides evidence that in at least one population, genetic variation among individual plants influences the donors’ paternity success, as assessed through genetic analysis of the seedling. Since due to gravity‐dispersed seeds natural patches may often consist of related plants, the observed effect may contribute to variation in male reproductive success.
Linking dendritic network structures to population demogenetics: The downside of connectivity
Authors: Labonne Jacques , Ravigné Virginie , Parisi Bruno , Gaucherel Cédric
Published: July 2008

Spatial structures strongly influence ecological processes. Connectivity is known to positively influence metapopulation demography and genetics by increasing the rescue effect and thus favoring individual and gene flow between populations. This result has not been tested in the special case of dendritic networks, which encompass stream and cave ecosystem for instance. We propose a first approach using an individual based model to explore the population demography and genetics in various dendritic networks. To do so, we first generate a large number of different networks, and we analyze the relationship between their hydrographical characteristics and connectivity. We show that connectivity mean and variance of connectivity are strongly correlated in dendritic networks. Connectivity segregates two types of networks: Hortonian and non‐Hortonian networks. We then simulate the population dynamics for a simple life cycle in each of the generated networks, and we analyze persistence time as well as populations structure at quasi‐stationary state. Our main results show that connectivity in dendritic networks can promote local extinction and genetic isolation by distance at low dispersal and diminish the size of the metapopulation at high dispersal. We discuss these unexpected findings in the light of connectivity spatial distribution in dendritic networks in the case of our model.
Discovery of a SNP in exon 7 of thelipoprotein lipasegene and its association with fatness traits in native and Cherry Valley Peking ducks
Authors: Wu Y. , Zhang H. L. , Wang J. , Liu X. L.
Published: July 2008

Lipoprotein lipase (LPL) is a multifunctional protein, playing a major role in the hydrolysis of triglycerides in chylomicrons and very low‐density lipoproteins. This study was designed to investigate the effects of variants in exon 7 of theLPLgene on duck growth and fatness traits. Two populations (native and Cherry Valley Peking duck populations) were used in this study. Growth and fatness traits were measured in them. Primers for exon 7 of theLPLgene were designed from chicken genomic and cDNA sequences. Polymorphisms were detected by DNA sequencing, and a PCR–SSCP method was developed to genotype the two populations. The results showed one novel polymorphism: a synonymous alteration in exon 7 of theLPLgene (c.91C>T;EU834120andEU834121). It was associated with abdominal fat weight and percentage of abdominal fat weight of native Peking duck and with percentage of subcutaneous fat plus skin weight and abdominal fat weight of Cherry Valley Peking duck. The alteration in exon 7 ofLPLmay be linked with potential major loci or genes affecting some fatness traits.
Sodium nitrite promotes regional blood flow in patients with sickle cell disease: a phase I/II study
Authors: Mack A. Kyle , McGowan II Vicki R. , Tremonti Carole K. , Ackah Diana , Barnett Christopher , Machado Roberto F. , Gladwin Mark T. , Kato Gregory J.
Published: July 2008

In addition to vaso‐occlusion by sickled erythrocytes, the pathophysiology of sickle cell disease (SCD) is compounded by the diminished bioavailability of nitric oxide (NO), associated with vasoconstriction, endothelial activation and cell adhesion. We tested the ability of sodium nitrite, which can be converted to NO by deoxyhaemoglobin at acid pH and low oxygen tension, to improve blood flow in patients with SCD. In a phase I/II clinical trial, sodium nitroprusside, NG‐monomethyl‐L‐arginine, and sodium nitrite were infused sequentially into the brachial artery in 14 patients at steady state. In a dose‐dependent manner, sodium nitrite infusion rates of 0·4, 4 and 40 μmol/min into the brachial artery augmented mean venous plasma nitrite concentrations (P < 0·0001) and stimulated forearm blood flow up to 77 ± 11% above baseline (P < 0·0001), measured by venous occlusion strain gauge plethysmography. This nitrite response was blunted significantly compared to controls without SCD, as previously seen with other NO donors. Sodium nitrite infusions were well tolerated without hypotension, clinically significant methaemoglobinaemia or other untoward events. The unique pharmacological properties of nitrite as a hypoxia‐potentiated vasodilator and cytoprotective agent in the setting of ischaemia‐reperfusion injury make this anion a plausible NO donor for future clinical trials in SCD.
Rivaroxaban – an oral, direct Factor Xa inhibitor – has potential for the management of patients with heparin‐induced thrombocytopenia
Authors: Walenga Jeanine M. , Prechel Margaret , Jeske Walter P. , Hoppensteadt Debra , Maddineni Jyothi , Iqbal Omer , Messmore Harry L. , Bakhos Mamdouh
Published: July 2008

Rivaroxaban is an oral, direct activated Factor Xa (FXa) inhibitor in advanced clinical development for the prevention and treatment of thromboembolic disorders. Currently available anticoagulants include unfractionated heparin (UFH) and low molecular weight heparins (LMWHs); however, their use can be restricted by heparin‐induced thrombocytopenia (HIT). HIT is usually caused by the production of antibodies to a complex of heparin and platelet factor‐4 (PF4). This study was performed to evaluate, in vitro, the potential of rivaroxaban as an anticoagulant for the management of patients with HIT. UFH, the LMWH enoxaparin, fondaparinux and the direct thrombin inhibitor argatroban were tested to enable comparative analyses. Rivaroxaban did not cause platelet activation or aggregation in the presence of HIT antibodies, unlike UFH and enoxaparin, suggesting that rivaroxaban does not cross‐react with HIT antibodies. Furthermore, rivaroxaban did not cause the release of PF4 from platelets and did not interact with PF4, unlike UFH and enoxaparin. These findings suggest that rivaroxaban may be a suitable anticoagulant for the management of patients with HIT.
Road age and its importance in earthworm invasion of northern boreal forests
Authors: Cameron Erin K. , Bayne Erin M.
Published: August 2008

Roads are an important conduit for the spread of invasive species. Road age is a key factor that could influence the susceptibility of roads to invasion as older roads are typically subject to higher cumulative levels of human disturbance and propagule pressure than younger roads. We investigated the effects of road age on the spread of non‐native earthworms, which act as ecosystem engineers.

We sampled earthworms and habitat variables at 98 roads in the boreal forest of Alberta, Canada, to determine the influence of road age on non‐native earthworm occurrence at the landscape level. The extent and rate of local spread were also assessed at seven sites adjacent to old and young roads. Generalized estimating equations and zero‐inflated negative binomial regression were used to analyze landscape‐ and local‐level results, respectively. We used our models to create maps that predict the current and potential future extent of earthworms in north‐eastern Alberta.

Probability of earthworm occurrence and extent of spread increased as road age increased. Areas closer to agriculture and towards the south and west of our study area were also significantly more likely to be invaded by earthworms.

Our spread model indicated that approximately 9% of the boreal forest of north‐eastern Alberta is likely invaded by earthworms currently. This is projected to increase to 49% of suitable forest habitat over the next 50 years as human development intensifies in this region.

Synthesis and applications. Although the effects of roads and linear features are commonly investigated in relation to native species, our results emphasize the importance of considering the impacts of linear feature creation on the spread of invasive species. We demonstrate that road age in particular can be an important factor affecting the spread of invasive species. In the boreal forest, reducing the number of roads being constructed, restricting traffic, and reclaiming temporary roads will be critical to reduce the future extent of earthworm invasions.