bluuebunny/crossref_metadata_2025 huggingface dataset:
Stuttering in English–Mandarin Bilingual Speakers: The Influence of Language Dominance on Stuttering Severity
Authors: Lim Valerie P. C. , Lincoln Michelle , Chan Yiong Huak , Onslow Mark
Published: August 2008

Purpose

English and Mandarin are the 2 most spoken languages in the world, yet it is not known how stuttering manifests in English–Mandarin bilinguals. In this research, the authors investigated whether the severity and type of stuttering is different in English and Mandarin in English–Mandarin bilinguals, and whether this difference was influenced by language dominance.

Method

Thirty English–Mandarin bilinguals who stutter (BWS), ages 12–44 years, were categorized into 3 groups (15 English-dominant, 4 Mandarin-dominant, and 11 balanced bilinguals) using a self-report classification tool. Three 10-min conversations in English and Mandarin were assessed by 2 English–Mandarin bilingual clinicians for percent syllables stuttered (%SS), perceived stuttering severity (SEV), and types of stuttering behaviors using the Lidcombe Behavioral Data Language (LBDL; Packman & Onslow, 1998; Teesson, Packman, & Onslow, 2003).

Results

English-dominant and Mandarin-dominant BWS exhibited higher %SS and SEV scores in their less dominant language, whereas the scores for the balanced bilinguals were similar for both languages. The difference in the percentage of stutters per LBDL category between English and Mandarin was not markedly different for any bilingual group.

Conclusions

Language dominance appeared to influence the severity but not the types of stuttering behaviors in BWS. Clinicians working with BWS need to assess language dominance when diagnosing stuttering severity in bilingual clients.
Modulation Detection Interference for Asynchronous Presentation of Masker and Target in Listeners With Normal and Impaired Hearing
Authors: Koopman Jan , Houtgast Tammo , Dreschler Wouter A.
Published: August 2008

Purpose

The sensitivity to sinusoidal amplitude modulations (SAMs) is reduced when other modulated maskers are presented simultaneously at a distant frequency (also referred to as
modulation detection interference
[MDI]). This article describes the results of onset differences between masker and target as a parameter.

Method

Carrier frequencies were 1 kHz (target: 625 ms, 8 Hz SAM) and 2 kHz (masker: 625 ms, 8 Hz SAM; modulation depth = 1) presented at 25 dB SL for listeners with impaired hearing (
n
= 8) and at 25 dB SL and 50 dB SL for listeners with normal hearing (
n
= 6). Masker was delayed by 0, 125, 250, 500, 625, or 750 ms relative to the target.

Results

Sensitivity to SAMs was reduced in both groups by a modulated masker simultaneous presentation. Reducing the temporal overlap (i.e., increasing the onset delay between masker and target) increased the sensitivity to SAMs in the presence of modulated maskers.

Conclusion

The gradual reduction in MDI with increasing asynchrony between masker and target suggests that MDI is not solely related to perceptual grouping. Reduced sensitivity to SAMs due to prior stimulation with SAM stimuli (forward masking), and deficits in across-channel integration, are other factors that may play a role.
Long-Term Trajectories of the Development of Speech Sound Production in Pediatric Cochlear Implant Recipients
Authors: Tomblin J. Bruce , Peng Shu-Chen , Spencer Linda J. , Lu Nelson
Published: August 2008

Purpose

This study characterized the development of speech sound production in prelingually deaf children with a minimum of 8 years of cochlear implant (CI) experience.

Method

Twenty-seven pediatric CI recipients' spontaneous speech samples from annual evaluation sessions were phonemically transcribed. Accuracy for these speech samples was evaluated in piecewise regression models.

Results

As a group, pediatric CI recipients showed steady improvement in speech sound production following implantation, but the improvement rate declined after 6 years of device experience. Piecewise regression models indicated that the slope estimating the participants' improvement rate was statistically greater than 0 during the first 6 years postimplantation, but not after 6 years. The group of pediatric CI recipients' accuracy of speech sound production after 4 years of device experience reasonably predicts their speech sound production after 5–10 years of device experience.

Conclusions

The development of speech sound production in prelingually deaf children stabilizes after 6 years of device experience, and typically approaches a plateau by 8 years of device use. Early growth in speech before 4 years of device experience did not predict later rates of growth or levels of achievement. However, good predictions could be made after 4 years of device use.
Past Tense Marking by African American English–Speaking Children Reared in Poverty
Authors: Pruitt Sonja , Oetting Janna
Published: August 2008

Purpose

This study examined past tense marking by African American English (AAE)-speaking children from low- and middle-income backgrounds to determine if poverty affects children’s marking of past tense in ways that mirror the clinical condition of specific language impairment (SLI).

Method

Participants were 15 AAE-speaking 6-year-olds from low-income backgrounds, 15 AAE-speaking 6-year-olds from middle-income backgrounds who served as age-matched controls, and 15 AAE-speaking 5-year-olds from middle-income backgrounds who served as language-matched controls. Data were drawn from language samples and probes.

Results

Results revealed high rates of regular marking, variable rates of irregular marking, high rates of over-regularizations, and absence of dialect-inappropriate errors of commission. For some analyses, marking was affected by the phonological characteristics of the items and the children’s ages, but none of the analyses revealed effects for the children’s socioeconomic level.

Conclusions

Within AAE, poverty status as a variable affects past tense marking in ways that are different from the clinical condition of SLI.
Are Working Memory Measures Free of Socioeconomic Influence?
Authors: Engel Pascale Marguerite Josiane , Santos Flávia Heloísa , Gathercole Susan Elizabeth
Published: August 2008

Purpose

This study evaluated the impact of socioeconomic factors on children’s performance on tests of working memory and vocabulary.

Method

Twenty Brazilian children, aged 6 and 7 years, from low-income families, completed tests of working memory (verbal short-term memory and verbal complex span) and vocabulary (expressive and receptive). A further group of Brazilian children from families of higher socioeconomic status matched for age, gender, and nonverbal ability also participated in the study.

Results

Children from the low socioeconomic group obtained significantly lower scores on measures of expressive and receptive vocabulary than their higher income peers but no significant group differences were found on the working memory measures.

Conclusion

Measures of working memory provide assessments of cognitive abilities that appear to be impervious to substantial differences in socioeconomic background. As these measures are highly sensitive to language ability and learning in general, they appear to provide useful methods for diagnosing specific learning difficulties that are independent of environmental opportunity.
On a partial differential equation method for determining the free energies and coexisting phase compositions of ternary mixtures from light scattering data
Authors: Ross David S. , Thurston George M. , Lutzer Carl V.
Published: August 2008

In this paper we present a method for determining the free energies of ternary mixtures from light scattering data. We use an approximation that is appropriate for liquid mixtures, which we formulate as a second-order nonlinear partial differential equation. This partial differential equation (PDE) relates the Hessian of the intensive free energy to the efficiency of light scattering in the forward direction. This basic equation applies in regions of the phase diagram in which the mixtures are thermodynamically stable. In regions in which the mixtures are unstable or metastable, the appropriate PDE is the nonlinear equation for the convex hull. We formulate this equation along with continuity conditions for the transition between the two equations at cloud point loci. We show how to discretize this problem to obtain a finite-difference approximation to it, and we present an iterative method for solving the discretized problem. We present the results of calculations that were done with a computer program that implements our method. These calculations show that our method is capable of reconstructing test free energy functions from simulated light scattering data. If the cloud point loci are known, the method also finds the tie lines and tie triangles that describe thermodynamic equilibrium between two or among three liquid phases. A robust method for solving this PDE problem, such as the one presented here, can be a basis for optical, noninvasive means of characterizing the thermodynamics of multicomponent mixtures.
Quantum molecular dynamics study of water on TiO2(110) surface
Authors: Zhang Wenhua , Yang Jinlong , Luo Yi , Monti Susanna , Carravetta Vincenzo
Published: August 2008

The adsorption of water on perfect TiO2(110) surface is studied by quantum molecular dynamics simulation adopting a periodic model formed by five water molecules on a (5×1) surface unit cell of a five layer slab of TiO2. The total simulation time is 3.2ps. At about 1.3ps, one water molecule dissociates with the help of other adsorbed waters and surface bridging oxygens. During the remaining 1.9ps, the waters and OH groups vibrate, but no more dissociation or recombination is observed. By comparing recent experimental O1s photoemission (x-ray photoelectron spectroscopy) spectra of H2O∕TiO2(110) to the computed spectrum of the adsorbate in the configurations supplied by the molecular dynamics simulation, the observed peaks can be attributed to different oxygen species. The proposed assignment of the main spectral features supports the occurrence of partial water dissociation (∼20%) also on a perfect TiO2 surface.
High-rate deposition of microcrystalline silicon p-i-n solar cells in the high pressure depletion regime
Authors: Smets A. H. M. , Matsui T. , Kondo M.
Published: August 2008

Hydrogenated microcrystalline silicon films (μc-Si:H) deposited at high deposition rates (∼2 nm/s) by means of the very-high-frequency (VHF) deposition technique in the high pressure depletion regime have been integrated into single junction p-i-n solar cells. It is demonstrated that μc-Si:H solar cells can be optimized using a twofold approach. First the bulk properties, deposited under steady-state plasma conditions, are optimized by monitoring the presence of crystalline grain boundaries in μc-Si:H. These hydrogenated crystalline grain boundaries can easily be detected via the crystalline surface hydrides contribution to the narrow high stretching modes by infrared transmission spectroscopy. The crystalline grain boundaries suffer from postdeposition oxidation which results in a reduced red response of the solar cell. The absence of these crystalline surfaces in an as-deposited μc-Si:H matrix reflects the device grade microcrystalline bulk material. Second, the prevention of silane backdiffusion from the background during the initial growth is a necessity to deposit a uniform μc-Si:H phase over the entire film thickness. The initial growth is optimized while preserving the optimized bulk properties deposited under steady-state conditions, using initial profiling of plasma parameters such as the silane flow and the VHF power density. Solar cell devices with efficiency of 8.0% at a μc-Si:H deposition rate of 2.0 nm/s are obtained using the presented approach.
Influence of thermodynamics and local geometry on glass formation in Zr based alloys
Authors: Ray P. K. , Chattopadhyay K. , Murty B. S.
Published: August 2008

A theoretical approach for predicting glass forming ability of transition metal alloys is proposed. This is an attempt for synergistic understanding of the effects of thermodynamics and local geometry on glass forming ability. The enthalpy of formation has been estimated by a modified Miedema’s model and used as a criterion for stability. The lattice strain energy has been estimated by a modified Miracle’s model. The coordination numbers of the solute centered clusters have been used for establishing a set of inequalities that demarcate geometrically favored composition regimes. Glass formation within the geometrically favored areas is dictated by thermodynamics.
Modeling of ion-acoustic soliton excitation through decay process of a localized perturbation
Authors: Pajouh H. Hakimi , Abbasi H.
Published: August 2008

The possibility of the nonlinear decay of a localized perturbation into the ion-acoustic solitons is studied. The present paper is a theoretical attempt to model the experimental soliton excitation [S. Yi et al., Phys. Plasmas 4, 2436 (1997)] in which solitons are excited by a grid modulating near the ion plasma frequency. It has been reported that a localized wave was created near the grid that would decay nonlinearly into the ion-acoustic soliton and a wave packet [T. E. Sheridan et al., Phys. Plasmas 5, 3165 (1998)]. For this purpose, an unbounded plasma composed of the cold positively charged ions and hot electrons is considered. Electron trapping is included in the model as the result of their nonlinear resonant interaction with the localized potential well. A Gaussian initial perturbation is used to model the localized perturbation. The numerical calculation through a modified Korteweg–de Vries equation simulates the decay of the initial Gaussian perturbation into several ion-acoustic solitons and a wave packet. It is shown that the electron trapping has an essential influence on the decay process.
Quantitative characterization of micromixing simulation
Authors: Zhang Zhiyi , Yim ChaeHo , Lin Min , Cao Xudong
Published: August 2008

Micromixers with floor-grooved microfluidic channels have been successfully demonstrated in experiment. In this work, we numerically simulated the mixing within the devices and used the obtained concentration versus channel length profiles to quantitatively characterize the process. It was found that the concentration at any given cross-section location of the microfluidic channel periodically oscillates along the channel length, in coordination with the groove-caused helical flow during the mixing, and eventually converges to the neutral concentration value of two the mixing fluids. With these data, the specific channel length required for each helical flow to complete, the mixing efficiency of the devices, and the total channel length required to complete a mixing were easily defined and quantified, and were used to directly and comprehensively characterize the micromixing. This concentration versus channel length profile-based characterization method was also demonstrated in quantitatively analyzing the micromixing within a classic T mixer. It has clear advantages over the traditional concentration image-based characterization method that is only able to provide qualitative or semiquantitative information about a micromixing, and is expected to find an increasing use in studying mixing and optimizing device structure through numerical simulations.
Electron low energy-loss functions of Pb(Mg1/3Nb2/3)O3: Theory and experiment
Authors: Lu Ning , Zhu Jing
Published: August 2008

Local low energy-loss functions (ELFs) of chemical ordered nanodomains in relaxor Pb(Mg1/3Nb2/3)O3 (PMN) were obtained by using Kramers–Krönig analysis of experimental electron low energy-loss spectra. Electronic structures and dielectric functions were calculated via ab initio calculation using the full-potential linearized augmented plane-wave method on a 30 atom PMN supercell with B-site cation ordering along the [111] direction. The theoretical ELFs are fundamentally in agreement with the experimental ELFs. Furthermore, we systematically elucidate all the peaks in the low ELF based on the ab initio calculated densities of states. It is found that the Nb 4d–O 2p hybridization is enhanced through ferroelectric transition, which makes the O 2p collective excitation energy upper shift in ELF, while Mg, also as the B-site ion, presents no covalent bonding effect with O.
Enhanced nonresonant optical pumping based on turnstile transport in a chaotic microcavity laser
Authors: Yang Juhee , Lee Sang-Bum , Shim Jeong-Bo , Moon Songky , Lee Soo-Young , Kim Sang Wook , Lee Jai-Hyung , An Kyungwon
Published: August 2008

We report efficient nonresonant optical pumping based on turnstile transport in a chaotic microcavity laser. We observed more than tenfold enhancement in the pumping efficiency at a particular pumping angle and at a particular boundary position of the microcavity while these angle and position are consistent with the turnstile transport mechanism in chaotic ray dynamics. The pumping efficiency distribution resembles that of the output emission for the same cavity, supporting the concept of time-reversed ray transport.
Investigation of local electrical properties of coincidence-site-lattice boundaries in location-controlled silicon islands using scanning capacitance microscopy
Authors: Matsuki Nobuyuki , Ishihara Ryoichi , Baiano Alessando , Beenakker Kees
Published: August 2008

We used scanning capacitance microscopy (SCM) to investigate the electrical activity of grain boundaries consisting of random and coincidence-site-lattice (CSL) boundaries in location-controlled silicon islands, which were fabricated using the μ-Czochralski process with an excimer laser. The SCM results suggest that the electrical activity of the {122}∑9 CSL boundary is much smaller than that of a random boundary, and the {111}∑3 CSL boundary is negligible. This is consistent with previous theoretical predictions and experimental results for thin-film transistors.
Magnetization dependence on dynamic strain in ferromagnetic shape memory Ni–Mn–Ga
Authors: Sarawate N. N. , Dapino M. J.
Published: August 2008

The characterization of commercial Ni–Mn–Ga for use as a dynamic deformation sensor is addressed. The flux density is experimentally determined as a function of cyclic strain loading at frequencies from 0.2to160Hz. With increasing frequency, the stress versus strain response remains almost unchanged whereas the flux density versus strain response shows increasing hysteresis. This behavior indicates that twin-variant reorientation occurs in concert with the mechanical loading, whereas the rotation of magnetization vectors occurs with a delay as the loading frequency increases. The increasing magnetization hysteresis must be considered when utilizing the material in dynamic sensing applications.
Modified permittivity observed in bulk gallium arsenide and gallium phosphide samples at 50K using the whispering gallery mode method
Authors: Hartnett John G. , Mouneyrac David , Le Floch Jean-Michel , Krupka Jerzy , Tobar Michael E. , Cros D.
Published: August 2008

Whispering gallery modes in bulk cylindrical gallium arsenide and gallium phosphide samples have been examined both in darkness and under white light at 50K. In both samples we observed change in permittivity under light and dark conditions. This results from a change in the polarization state of the semiconductor, which is consistent with a free electron-hole creation/recombination process. The permittivity of the semiconductor is modified by free photocarriers in the surface layers of the sample which is the region sampled by whispering gallery modes.
AIMP2/p38, the scaffold for the multi-tRNA synthetase complex, responds to genotoxic stresses via p53
Authors: Han Jung Min , Park Bum-Joon , Park Sang Gyu , Oh Young Sun , Choi So Jung , Lee Sang Won , Hwang Soon-Kyung , Chang Seung-Hee , Cho Myung-Haing , Kim Sunghoon
Published: August 2008

AIMP2/p38 is a scaffolding protein required for the assembly of the macromolecular tRNA synthetase complex. Here, we describe a previously unknown function for AIMP2 as a positive regulator of p53 in response to genotoxic stresses. Depletion of AIMP2 increased resistance to DNA damage-induced apoptosis, and introduction of AIMP2 into AIMP2-deficient cells restored the susceptibility to apoptosis. Upon DNA damage, AIMP2 was phosphorylated, dissociated from the multi-tRNA synthetase complex, and translocated into the nuclei of cells. AIMP2 directly interacts with p53, thereby preventing MDM2-mediated ubiquitination and degradation of p53. Mutations in AIMP2, affecting its interaction with p53, hampered its ability to activate p53. Nutlin-3 recovered the level of p53 and the susceptibility to UV-induced cell death in AIMP2-deficient cells. This work demonstrates that AIMP2, a component of the translational machinery, functions as proapoptotic factor via p53 in response to DNA damage.
A role for a lithium-inhibited Golgi nucleotidase in skeletal development and sulfation
Authors: Frederick Joshua P. , Tafari A. Tsahai , Wu Sheue-Mei , Megosh Louis C. , Chiou Shean-Tai , Irving Ryan P. , York John D.
Published: August 2008

Sulfation is an important biological process that modulates the function of numerous molecules. It is directly mediated by cytosolic and Golgi sulfotransferases, which use 3′-phosphoadenosine 5′-phosphosulfate to produce sulfated acceptors and 3′-phosphoadenosine 5′-phosphate (PAP). Here, we identify a Golgi-resident PAP 3′-phosphatase (gPAPP) and demonstrate that its activity is potently inhibited by lithium
in vitro
. The inactivation of
gPAPP
in mice led to neonatal lethality, lung abnormalities resembling atelectasis, and dwarfism characterized by aberrant cartilage morphology. The phenotypic similarities of gPAPP mutant mice to chondrodysplastic models harboring mutations within components of the sulfation pathway lead to the discovery of undersulfated chondroitin in the absence of functional enzyme. Additionally, we observed loss of gPAPP leads to perturbations in the levels of heparan sulfate species in lung tissue and whole embryos. Our data are consistent with a model that clearance of the nucleotide product of sulfotransferases within the Golgi plays an important role in glycosaminoglycan sulfation, provide a unique genetic basis for chondrodysplasia, and define a function for gPAPP in the formation of skeletal elements derived through endochondral ossification.
Differentiation of regulatory Foxp3+T cells in the thymic cortex
Authors: Liston Adrian , Nutsch Katherine M. , Farr Andrew G. , Lund Jennifer M. , Rasmussen Jeffery P. , Koni Pandelakis A. , Rudensky Alexander Y.
Published: August 2008

Regulatory Foxp3+T cells (TR) are indispensable for preventing autoimmune pathology in multiple organs and tissues. During thymic differentiation T cell receptor (TCR)–ligand interactions within a certain increased affinity range, in conjunction with γc-containing cytokine receptor signals, induce Foxp3 expression and thereby commit developing thymocytes to the TRlineage. The contribution of distinct MHC class II–expressing accessory cell types to the differentiation process of Foxp3+thymocytes remains controversial, because a unique role in this process has been ascribed to either thymic dendritic cells (tDC) or to medullary thymic epithelial cells (mTEC). Furthermore, it was suggested that the thymic medulla, where the bulk of the negative selection of self-reactive thymocytes takes place, provides a specialized microenvironment supporting TRdifferentiation. Here, we report that the cortex, as defined by cortical thymic epithelial cells (cTEC), is sufficient for supporting TRdifferentiation. MHC class II expression restricted to both cTEC and mTEC or to cTEC alone did not significantly affect the numbers of Foxp3+thymocytes. Furthermore, genetic or pharmacologic blockade of thymocyte migration resulted in a prominent accumulation of Foxp3+thymocytes in the cortex, demonstrating that secondary signals required for Foxp3 up-regulation exist in the cortex. Our results suggest that mTEC or tDC do not serve as a cell type singularly responsible for TRdifferentiation and that neither the cortex nor the medulla exclusively provides an environment suitable for Foxp3 induction. Instead, multiple accessory cell types probably contribute to the thymic generation of regulatory Foxp3+T cells.
Where does biodiversity go from here? A grim business-as-usual forecast and a hopeful portfolio of partial solutions
Authors: Ehrlich Paul R. , Pringle Robert M.
Published: August 2008

The threats to the future of biodiversity are many and well known. They include habitat conversion, environmental toxification, climate change, and direct exploitation of wildlife, among others. Moreover, the projected addition of 2.6 billion people by mid-century will almost certainly have a greater environmental impact than that of the last 2.6 billion. Collectively, these trends portend a grim future for biodiversity under a business-as-usual scenario. These threats and their interactions are formidable, but we review seven strategies that, if implemented soundly and scaled up dramatically, would preserve a substantial portion of global biodiversity. These are actions to stabilize the human population and reduce its material consumption, the deployment of endowment funds and other strategies to ensure the efficacy and permanence of conservation areas, steps to make human-dominated landscapes hospitable to biodiversity, measures to account for the economic costs of habitat degradation, the ecological reclamation of degraded lands and repatriation of extirpated species, the education and empowerment of people in the rural tropics, and the fundamental transformation of human attitudes about nature. Like the carbon “stabilization wedges” outlined by Pacala and Socolow [Pacala S, Socolow R (2004) Stabilization wedges: Solving the climate problem for the next 50 years with current technologies.Science305:968–972] (1), the science and technologies needed to effect this vision already exist. The remaining challenges are largely social, political, and economic. Although academic conservation biology still has an important role to play in developing technical tools and knowledge, success at this juncture hinges more on a massive mobilization of effort to do things that have traditionally been outside the scope of the discipline.
Extinction as the loss of evolutionary history
Authors: Erwin Douglas H.
Published: August 2008

Current plant and animal diversity preserves at most 1–2% of the species that have existed over the past 600 million years. But understanding the evolutionary impact of these extinctions requires a variety of metrics. The traditional measurement is loss of taxa (species or a higher category) but in the absence of phylogenetic information it is difficult to distinguish the evolutionary depth of different patterns of extinction: the same species loss can encompass very different losses of evolutionary history. Furthermore, both taxic and phylogenetic measures are poor metrics of morphologic disparity. Other measures of lost diversity include: functional diversity, architectural components, behavioral and social repertoires, and developmental strategies. The canonical five mass extinctions of the Phanerozoic reveals the loss of different, albeit sometimes overlapping, aspects of loss of evolutionary history. The end-Permian mass extinction (252 Ma) reduced all measures of diversity. The same was not true of other episodes, differences that may reflect their duration and structure. The construction of biodiversity reflects similarly uneven contributions to each of these metrics. Unraveling these contributions requires greater attention to feedbacks on biodiversity and the temporal variability in their contribution to evolutionary history. Taxic diversity increases after mass extinctions, but the response by other aspects of evolutionary history is less well studied. Earlier views of postextinction biotic recovery as the refilling of empty ecospace fail to capture the dynamics of this diversity increase.
Resistance, resilience, and redundancy in microbial communities
Authors: Allison Steven D. , Martiny Jennifer B. H.
Published: August 2008

Although it is generally accepted that plant community composition is key for predicting rates of ecosystem processes in the face of global change, microbial community composition is often ignored in ecosystem modeling. To address this issue, we review recent experiments and assess whether microbial community composition is resistant, resilient, or functionally redundant in response to four different disturbances. We find that the composition of most microbial groups is sensitive and not immediately resilient to disturbance, regardless of taxonomic breadth of the group or the type of disturbance. Other studies demonstrate that changes in composition are often associated with changes in ecosystem process rates. Thus, changes in microbial communities due to disturbance may directly affect ecosystem processes. Based on these relationships, we propose a simple framework to incorporate microbial community composition into ecosystem process models. We conclude that this effort would benefit from more empirical data on the links among microbial phylogeny, physiological traits, and disturbance responses. These relationships will determine how readily microbial community composition can be used to predict the responses of ecosystem processes to global change.
Species invasions and extinction: The future of native biodiversity on islands
Authors: Sax Dov F. , Gaines Steven D.
Published: August 2008

Predation by exotic species has caused the extinction of many native animal species on islands, whereas competition from exotic plants has caused few native plant extinctions. Exotic plant addition to islands is highly nonrandom, with an almost perfect 1 to 1 match between the number of naturalized and native plant species on oceanic islands. Here, we evaluate several alternative implications of these findings. Does the consistency of increase in plant richness across islands imply that a saturation point in species richness has been reached? If not, should we expect total plant richness to continue to increase as new species are added? Finally, is the rarity of native plant extinctions to date a misleading measure of the impact of past invasions, one that hides an extinction debt that will be paid in the future? By analyzing historical records, we show that the number of naturalized plant species has increased linearly over time on many individual islands. Further, the mean ratio of naturalized to native plant species across islands has changed steadily for nearly two centuries. These patterns suggest that many more species will become naturalized on islands in the future. We also discuss how dynamics of invasion bear upon alternative saturation scenarios and the implications these scenarios have for the future retention or extinction of native plant species. Finally, we identify invasion-motivated research gaps (propagule pressure, time-lags to extinction, abundance shifts, and loss of area) that can aid in forecasting extinction and in developing a more comprehensive theory of species extinctions.
Bacterial species exhibit diversity in their mechanisms and capacity for protein disulfide bond formation
Authors: Dutton Rachel J. , Boyd Dana , Berkmen Mehmet , Beckwith Jon
Published: August 2008

Protein disulfide bond formation contributes to the folding and activity of many exported proteins in bacteria. However, information about disulfide bond formation is limited to only a few bacterial species. We used a multifaceted bioinformatic approach to assess the capacity for disulfide bond formation across this biologically diverse group of organisms. We combined data from a cysteine counting method, in which a significant bias for even numbers of cysteine in proteins is taken as an indicator of disulfide bond formation, with data on the presence of homologs of known disulfide bond formation enzymes. These combined data enabled us to make predictions about disulfide bond formation in the cell envelope across bacterial species. Our bioinformatic and experimental results suggest that many bacteria may not generally oxidatively fold proteins, and implicate the bacterial homolog of the enzyme vitamin K epoxide reductase, a protein required for blood clotting in humans, as part of a disulfide bond formation pathway present in several major bacterial phyla.
Therapeutic RNAi targeting PCSK9 acutely lowers plasma cholesterol in rodents and LDL cholesterol in nonhuman primates
Authors: Frank-Kamenetsky Maria , Grefhorst Aldo , Anderson Norma N. , Racie Timothy S. , Bramlage Birgit , Akinc Akin , Butler David , Charisse Klaus , Dorkin Robert , Fan Yupeng , Gamba-Vitalo Christina , Hadwiger Philipp , Jayaraman Muthusamy , John Matthias , Jayaprakash K. Narayanannair , Maier Martin , Nechev Lubomir , Rajeev Kallanthottathil G. , Read Timothy , Röhl Ingo , Soutschek Jürgen , Tan Pamela , Wong Jamie , Wang Gang , Zimmermann Tracy , de Fougerolles Antonin , Vornlocher Hans-Peter , Langer Robert , Anderson Daniel G. , Manoharan Muthiah , Koteliansky Victor , Horton Jay D. , Fitzgerald Kevin
Published: August 2008

Proprotein convertase subtilisin/kexin type 9 (PCSK9) regulates low density lipoprotein receptor (LDLR) protein levels and function. Loss of PCSK9 increases LDLR levels in liver and reduces plasma LDL cholesterol (LDLc), whereas excess PCSK9 activity decreases liver LDLR levels and increases plasma LDLc. Here, we have developed active, cross-species, small interfering RNAs (siRNAs) capable of targeting murine, rat, nonhuman primate (NHP), and human PCSK9. For
in vivo
studies, PCSK9 and control siRNAs were formulated in a lipidoid nanoparticle (LNP). Liver-specific siRNA silencing of PCSK9 in mice and rats reduced PCSK9 mRNA levels by 50–70%. The reduction in PCSK9 transcript was associated with up to a 60% reduction in plasma cholesterol concentrations. These effects were shown to be mediated by an RNAi mechanism, using 5′-RACE. In transgenic mice expressing human PCSK9, siRNAs silenced the human PCSK9 transcript by >70% and significantly reduced PCSK9 plasma protein levels. In NHP, a single dose of siRNA targeting PCSK9 resulted in a rapid, durable, and reversible lowering of plasma PCSK9, apolipoprotein B, and LDLc, without measurable effects on either HDL cholesterol (HDLc) or triglycerides (TGs). The effects of PCSK9 silencing lasted for 3 weeks after a single bolus i.v. administration. These results validate PCSK9 targeting with RNAi therapeutics as an approach to specifically lower LDLc, paving the way for the development of PCSK9-lowering agents as a future strategy for treatment of hypercholesterolemia.
Forced extraction of targeted components from complex macromolecular assemblies
Authors: Moore Sean D. , Baker Tania A. , Sauer Robert T.
Published: August 2008

When individual protein components of supramolecular complexes are required for assembly, determining whether they play additional structural or functional roles can be difficult. Removing a protein from the complex after assembly can circumvent this problem. Here, we show that an AAA+ unfoldase/protease can extract an essential assembly protein from the ribosome. Specifically, Mg
2+
depletion allowed ClpXP to remove an ssrA-tagged variant of ribosomal protein L22 from the 50S subunit of
E. coli
ribosomes without disrupting either the structural integrity or hydrodynamic properties of the modified particle. Forced extraction using AAA+ enzymes and targeted component proteins should be broadly applicable to the study of macromolecular complexes.
The replicative DNA polymerase of herpes simplex virus 1 exhibits apurinic/apyrimidinic and 5′-deoxyribose phosphate lyase activities
Authors: Bogani Federica , Boehmer Paul E.
Published: August 2008

Base excision repair (BER) is essential for maintaining genome stability both to counter the accumulation of unusual bases and to protect from base loss in the DNA. Herpes simplex virus 1 (HSV-1) is a large dsDNA virus that encodes its own DNA replication machinery, including enzymes involved in nucleotide metabolism. We report on a replicative family B and a herpesvirus-encoded DNA Pol that possesses DNA lyase activity. We have discovered that the catalytic subunit of the HSV-1 DNA polymerase (Pol) (UL30) exhibits apurinic/apyrimidinic (AP) and 5′-deoxyribose phosphate (dRP) lyase activities. These activities are integral to BER and lead to DNA cleavage on the 3′ side of abasic sites and 5′-dRP residues that remain after cleavage by 5′-AP endonuclease. The UL30-catalyzed reaction occurs independently of divalent cation and proceeds via a Schiff base intermediate, indicating that it occurs via a lyase mechanism. Partial proteolysis of the Schiff base shows that the DNA lyase activity resides in the Pol domain of UL30. These observations together with the presence of a virus-encoded uracil DNA glycosylase indicates that HSV-1 has the capacity to perform critical steps in BER. These findings have implications on the role of BER in viral genome maintenance during lytic replication and reactivation from latency.
Communication strategies in translation
Authors: Rabab'ah Ghaleb Ahmed
Published: August 2008

According to Nord’s approach (1991) strategic competence is believed to be crucial in dealing with translation problems. It plays an important role as a regulating mechanism, compensating for deficiencies in the other sub-competencies and contributes towards solving the problems that arise. Nord also argues that there is a need for further research that can provide empirical data derived from the problems encountered by translators. The data can also be relevant to the mechanisms the translators use in solving problems.

Based on Nord’s claim, this study has investigated the communication strategies used by a sample of thirty six Saudi majors at the College of Languages and Translation at King Saud University in Riyadh. First, the strategies employed by Saudi students to compensate for any difficulties they encountered during translation process were examined. The subjects involved were asked to translate a one- page text from their native language, Arabic, into English. It was found that approximation was the most frequently used communication strategy. The other strategies used in order of frequency were circumlocution, message abandonment/reduction, and literal translation. These strategies are elaborated along with recommendations to provide more insights into how to develop students’ strategic competence in translation.
Are animated demonstrations the clearest and most comfortable way to communicate on-screen instructions?
Authors: Souza José Marconi Bezerra de , Dyson Mary C.
Published: August 2008

This study uses preference measurements to compare participants’ perceptions of nine versions of on-screen instructions and aims to discover the ones users consider to be the clearest and most comfortable to use. Instructions are divided into 3 categories: composite instructions, synoptic instructions and animated demonstrations. A group of twenty-four adult participants ranked instructions, first within the same category and then between categories. Even though no data was gathered to suggest which type of instruction will lead to better learning, the results show that animations are perceived as being the clearest and most comfortable to use. Users are likely to welcome animations, particularly for learning highly dynamic and non-intuitive software drawing tasks (i.e., using Bezier tools).
T cell–independent development and induction of somatic hypermutation in human IgM+IgD+CD27+ B cells
Authors: Scheeren Ferenc A. , Nagasawa Maho , Weijer Kees , Cupedo Tom , Kirberg Jörg , Legrand Nicolas , Spits Hergen
Published: August 2008

IgM+IgD+CD27+ B cells from peripheral blood have been described as circulating marginal zone B cells. It is still unknown when and where these cells develop. These IgM+IgD+CD27+ B cells exhibit somatic hypermutations (SHMs) in their B cell receptors, but the exact nature of the signals leading to induction of these SHMs remains elusive. Here, we show that IgM+IgD+CD27+ B cells carrying SHMs are observed during human fetal development. To examine the role of T cells in human IgM+IgD+CD27+ B cell development we used an in vivo model in which Rag2−/−γC−/− mice were repopulated with human hematopoietic stem cells. Using Rag2−/−γC−/− mice on a Nude background, we demonstrated that development and induction of SHMs of human IgM+IgD+CD27+ B cells can occur in a T cell–independent manner.
Functional skewing of the global CD8 T cell population in chronic hepatitis B virus infection
Authors: Das Abhishek , Hoare Matthew , Davies Nathan , Lopes A. Ross , Dunn Claire , Kennedy Patrick T.F. , Alexander Graeme , Finney Helene , Lawson Alistair , Plunkett Fiona J. , Bertoletti Antonio , Akbar Arne N. , Maini Mala K.
Published: August 2008

The inflamed liver in chronic hepatitis B virus (HBV) infection (CHB) is characterized by a large influx of non–virus-specific CD8 T cells. Little is known about the functional capacity of these lymphocytes, which could provide insights into mechanisms of failure of viral control and liver damage in this setting. We compared the effector function of total circulating and intrahepatic CD8 T cells in CHB patients and healthy donors. We demonstrated that CD8 T cells from CHB patients, regardless of their antigen specificity, were impaired in their ability to produce interleukin-2 and proliferate upon TCR-dependent stimulation. In contrast, these CD8 T cells had preserved production of the proinflammatory cytokines interferon-γ and tumor necrosis factor-α. This aberrant functional profile was partially attributable to down-regulation of the proximal T cell receptor signaling molecule CD3ζ, and could be corrected in vitro by transfection of CD3ζ or replenishment of the amino acid arginine required for its expression. We provide evidence for depletion of arginine in the inflamed hepatic microenvironment as a potential mechanism for these defects in global CD8 T cell signaling and function. These data imply that polarized CD8 T cells within the HBV-infected liver may impede proliferative antiviral effector function, while contributing to the proinflammatory cytokine environment.
ADAMTS13: a new link between thrombosis and inflammation
Authors: Chauhan Anil K. , Kisucka Janka , Brill Alexander , Walsh Meghan T. , Scheiflinger Friedrich , Wagner Denisa D.
Published: August 2008

von Willebrand factor (VWF) levels are elevated and a disintegrin-like and metalloprotease with thrombospondin type I repeats–13 (ADAMTS13) activity is decreased in both acute and chronic inflammation. We hypothesized that by cleaving hyperactive ultralarge VWF (ULVWF) multimers, ADAMTS13 down-regulates both thrombosis and inflammation. Using intravital microscopy, we show that ADAMTS13 deficiency results in increased leukocyte rolling on unstimulated veins and increased leukocyte adhesion in inflamed veins. Both processes were dependent on the presence of VWF. Depletion of platelets in Adamts13−/− mice reduced leukocyte rolling, suggesting that platelet interaction with ULVWF contributes to this process. Increased levels of endothelial P-selectin and plasma VWF in Adamts13−/− compared with wild-type (WT) mice indicated an elevated release of Weibel-Palade bodies. ULVWF multimers released upon stimulation with histamine, a secretagogue of Weibel-Palade bodies, slowed down leukocyte rolling in Adamts13−/− but not in WT mice. Furthermore, in inflammatory models, ADAMTS13 deficiency resulted in enhanced extravasation of neutrophils, and this process was also dependent on VWF. Our findings reveal an important role for ADAMTS13 in preventing excessive spontaneous Weibel-Palade body secretion, and in the regulation of leukocyte adhesion and extravasation during inflammation.
Comparison of algorithms for pre-processing of SELDI-TOF mass spectrometry data
Authors: Cruz-Marcelo Alejandro , Guerra Rudy , Vannucci Marina , Li Yiting , Lau Ching C. , Man Tsz-Kwong
Published: August 2008

Motivation: Surface-enhanced laser desorption and ionization (SELDI) time of flight (TOF) is a mass spectrometry technology. The key features in a mass spectrum are its peaks. In order to locate the peaks and quantify their intensities, several pre-processing steps are required. Though different approaches to perform pre-processing have been proposed, there is no systematic study that compares their performance.

Results: In this article, we present the results of a systematic comparison of various popular packages for pre-processing of SELDI-TOF data. We evaluate their performance in terms of two of their primary functions: peak detection and peak quantification. Regarding peak quantification, the performance of the algorithms is measured in terms of reproducibility. For peak detection, the comparison is based on sensitivity and false discovery rate. Our results show that for spectra generated with low laser intensity, the software developed by Ciphergen Biosystems (ProteinChip© Software 3.1 with the additional tool Biomarker Wizard) produces relatively good results for both peak quantification and detection. On the other hand, for the data produced with either medium or high laser intensity, none of the methods show uniformly better performances under both criteria. Our analysis suggests that an advantageous combination is the use of the packages MassSpecWavelet and PROcess, the former for peak detection and the latter for peak quantification.

Contact:  rguerra@rice.edu; marina@rice.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
4,4′-Diazenediyldipyridinium (4-pyridyldiazenyl)pyridinium octacyanidomolybdate(V) tetrahydrate
Authors: Liu Wen-Yan , Zhou Hu , Yuan Ai-Hua
Published: August 2008

The structure of the title complex, (C10H10N4)(C10H9N4)[Mo(CN)8]·4H2O, consists of 4,4′-diazenediyldipyridinium and (4-pyridyldiazenyl)pyridinium cations disordered over the same site, an [Mo(CN)8]3− anion and four uncoordinated water molecules. The cations (crystallographic symmetry, 2) and the [Mo(CN)8]3− anion (crystallographic symmetry, 222) are arranged in an alternating fashion, forming a two-dimensional layered structure through hydrogen bonds. Hydrogen bonds, π–π stacking interactions (shortest distance = 4.7872 Å) and van der Waals forces between adjacent layers generate a three-dimensional supramolecular structure.
1′,5-Dinitro-2′-phenyl-2′,3′,5′,6′,7′,7a'-hexahydrospiro[indoline-3,3′-1′H-pyrrolizin]-2-one
Authors: Sarrafi Yaghoub , Alimohammadi Kamal
Published: August 2008

In the title cycloadduct, C20H18N4O5, the rings of the pyrrolizine system adopt envelope conformations. A centrosymmetric dimer is formed via intermolecular N—H...O hydrogen bonds between the indolinone rings.
4-Nitrophenyl methacrylate
Authors: Xu Yun-Hua , Qu Fanqi
Published: August 2008

The title compound, C10H9NO4, was obtained serendipitously during the preparation of benzyl cyclohexylcarbamate. The molecule consists of two approximately planar parts, the nitrophenyl ring and the rest of the non-H atoms, with a dihedral angle of 55.05 (6)° between the two segments. The crystal structure is stabilized by weak C—H...O interactions and π stacking [3.753 (1) Å] along the b axis.
2-(7,8-Diphenyl-1H-imidazo[4,5-f]quinoxalin-2-yl)phenol methanol disolvate
Authors: Fun Hoong-Kun , Kia Reza , Raithby Paul R.
Published: August 2008

The title compound, C27H18N4O·2CH4O, is a unsymmetrically substituted quinoxaline. An intramolecular O—H...N hydrogen bond involving the hydroxy and imino groups generates an S(6) ring motif. Intermolecular C—H...O and N—H...O hydrogen bonds form an R
2
1(7) ring motif involving a methanol O atom and two H atoms of the imidazole and benzene rings, respectively. The latter links neighbouring molecules into one-dimensional extended chains along the a axis. The two benzene rings are inclined towards each other, as indicated by the dihedral angle of 52.13 (10)°. The phenol ring is almost coplanar with the basic quinoxaline unit, making a dihedral angle of 2.43 (6)°. The short distances between the centroids of the five- and six-membered rings prove the existence of π–π interactions [centroid–centroid distances = 3.5234 (9)–3.7885 (10) Å]. The crystal structure is stabilized by intramolecular O—H...N, intermolecular O—H...O, N—H...O and C—H...O (× 2) hydrogen bonds and weak intermolecular C—H...π and π–π interactions.