bluuebunny/crossref_metadata_2025 huggingface dataset:
The Effect of Feedback and Practice on the Acquisition of Novel Speech Behaviors
Authors: Kim In-sop , LaPointe Leonard L. , Stierwalt Julie A. G.
Published: May 2012

Purpose

This study examined the effect of manipulating several parameters of motor learning theory on participants' phonetic acquisition and retention of utterances in a foreign language (Korean).

Method

Thirty-two native English-speaking participants naïve to the Korean language were each given 10 Korean sentences to practice and learn. The independent variables in the study were the number of practice trials and the feedback schedule. The participants listened to sentences delivered by a native speaker and received feedback according to the schedule. Participant responses were then judged by a panel of native Korean speakers in terms of their intelligibility, naturalness, and precision.

Results

The combination of 20% feedback and 100 practice trials was more effective than other combinations of feedback and practice trial schedule for the retention of novel phonetic productions of Korean phrases both 1 day after training and 1 week later.

Conclusions

These findings are in agreement with previously reported applications of motor learning–guided principles on the acquisition of motoric skills. These findings may have direct implications for both second-language learning and the treatment of neuromotor speech disorders such as apraxia of speech.
Acquired Apraxia of Speech: The Effects of Repeated Practice and Rate/Rhythm Control Treatments on Sound Production Accuracy
Authors: Wambaugh Julie L. , Nessler Christina , Cameron Rosalea , Mauszycki Shannon C.
Published: May 2012

Purpose

This investigation was designed to elucidate the effects of repeated practice treatment on sound production accuracy in individuals with apraxia of speech (AOS) and aphasia. A secondary purpose was to determine if the addition of rate/rhythm control to treatment provided further benefits beyond those achieved with repeated practice.

Method

A single-subject design was employed with 10 speakers with chronic AOS and aphasia. Articulation accuracy served as the dependent measure. Participants received repeated practice treatment until a plateau in performance was observed or high levels of accuracy were achieved. If performance criterion was not reached, rate/rhythm control was added to the treatment to determine if additional gains would be made.

Results

For 8 of the participants, improvements were evident for all applications of repeated practice treatment, and positive response generalization was observed in most cases. When rate/rhythm control treatment was applied, modest additional gains were apparent for the majority of the applications. The 2 participants who did not benefit from repeated practice treatment also did not show improvements with rate/rhythm control treatment.

Conclusions

Repeated practice treatment resulted in improved articulation for the majority of participants. The amount of improvement varied within and across participants. Rate/rhythm control appeared to have limited additional benefits for some participants.

Supplemental Material

https://doi.org/10.23641/asha.6170201
The Feasibility of a Structured Cognitive Training Protocol to Address Progressive Cognitive Decline in Individuals With Vascular Dementia
Authors: Mayer Jamie F. , Bishop Lilli A. , Murray Laura L.
Published: May 2012

Purpose

Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy, better known as CADASIL, is a rare, genetic form of early-onset vascular dementia. The purpose of this study was to use a modified version of Attention Process Training—II (APT–II; Sohlberg, Johnson, Paule, Raskin, & Mateer, 2001) with an individual with early-stage CADASIL.

Method

APT–II, modified to include strategy training, was applied in an A-B, multiple-probe design for an individual who had been diagnosed with early-stage CADASIL. Outcome measures included pre–post neuropsychological testing of attention, memory, and executive function; within-treatment probes of visual and auditory attention; and a measure of subjective experience of cognitive functioning in daily living.

Results

The participant demonstrated nominal gains on visual and auditory attention probes but improved performance on several posttreatment measures of processing speed and executive function. The participant also reported substantially improved functional outcomes following the intervention protocol.

Conclusion

This case illustrates the potential utility of behavioral intervention for individuals with CADASIL and highlights issues for speech-language pathologists to consider when using structured cognitive training protocols in the setting of progressive cognitive decline. These data suggest that further controlled studies for treating this population are warranted.
Attention and Other Cognitive Deficits in Aphasia: Presence and Relation to Language and Communication Measures
Authors: Murray Laura L.
Published: May 2012

Purpose

This study was designed to further elucidate the relationship between cognition and aphasia, with a focus on attention. It was hypothesized that individuals with aphasia would display variable deficit patterns on tests of attention and other cognitive functions and that their attention deficits, particularly those of complex attention functions, would be related to their language and communication status.

Method

A group of individuals with varying types and severity of aphasia and a group of age- and education-matched adults with no brain damage completed tests of attention, short-term and working memory, and executive functioning.

Results

Overall, the group with aphasia performed significantly more poorly than the control group on the cognitive measures but displayed variability in the presence, types, and severity of their attention and other cognitive deficits. Correlational and regression analyses yielded significant relations between participants' attention deficits and their language and communication status.

Conclusion

The findings accorded well with prior research identifying (a) attention and other cognitive deficits in most but not all individuals with aphasia; (b) heterogeneity in the types and severity of attention and other cognitive symptoms among individuals with cognitive impairments; and (c) potent associations among attention, language, and other cognitive domains. Implications for clinical practice and future research are discussed.
Effects of Word Frequency and Modality on Sentence Comprehension Impairments in People With Aphasia
Authors: DeDe Gayle
Published: May 2012

Purpose

It is well known that people with aphasia have sentence comprehension impairments. The present study investigated whether lexical factors contribute to sentence comprehension impairments in both the auditory and written modalities using online measures of sentence processing.

Method

People with aphasia and non brain–damaged controls participated in the experiment (
n
= 8 per group). Twenty-one sentence pairs containing high- and low-frequency words were presented in self-paced listening and reading tasks. The sentences were syntactically simple and differed only in the critical words. The dependent variables were response times for critical segments of the sentence and accuracy on the comprehension questions.

Results

The results showed that word frequency influences performance on measures of sentence comprehension in people with aphasia. The accuracy data on the comprehension questions suggested that people with aphasia have more difficulty understanding sentences containing low-frequency words in the written compared to auditory modality. Both group and single-case analyses of the response time data also indicated that people with aphasia experience more difficulty with reading than listening.

Conclusion

Sentence comprehension in people with aphasia is influenced by word frequency and presentation modality.
Short-Form Philadelphia Naming Test: Rationale and Empirical Evaluation
Authors: Walker Grant M. , Schwartz Myrna F.
Published: May 2012

Purpose

To create two matched short forms of the Philadelphia Naming Test (PNT; Roach, Schwartz, Martin, Grewal, & Brecher, 1996) that yield similar results to the PNT for measuring anomia.

Method

In Study 1, archived naming data from 94 individuals with aphasia were used to identify which PNT items should be included in the short forms. The 2 constructed sets of 30 items, PNT30-A and PNT30-B, were validated using archived data from a separate group of 56 individuals with aphasia. In Study 2, the reliability of the PNT, PNT30-A, and PNT30-B across independent test administrations was evaluated with a new group of 25 individuals with aphasia who were selected to represent the full range of naming impairment.

Results

In Study 1, PNT30-A and PNT30-B were found to be internally consistent, and accuracy scores on these subsets of items were highly correlated with the full PNT. In Study 2, PNT accuracy was extremely reliable over the span of 1 week, and independent administrations of PNT30-A and PNT30-B produced similar results to the PNT and to each other.

Conclusion

The short forms of the PNT can be used to reliably estimate PNT performance, and the results can be compared to the provided norms. The 2 matched tests allow for the measurement of change in an individual’s naming ability.
Development of a Theoretically Based Treatment for Sentence Comprehension Deficits in Individuals With Aphasia
Authors: Kiran Swathi , Caplan David , Sandberg Chaleece , Levy Joshua , Berardino Alex , Ascenso Elsa , Villard Sarah , Tripodis Yorghos
Published: May 2012

Purpose

Two new treatments, 1 based on sentence to picture matching (SPM) and the other on object manipulation (OM), that train participants on the thematic roles of sentences using pictures or by manipulating objects were piloted.

Method

Using a single-subject multiple-baseline design, sentence comprehension was trained on the affected sentence type in 1 task-related protocol in 15 participants with aphasia. The 2 tasks were SPM and OM; the treatment stimuli were object relatives, object clefts, passives, and unaccusatives, as well as two control structures—object relatives with a complex noun phrase (NP) and active sentences with three NPs.

Results

The criteria for efficacious treatment was an increase in the level of performance from the pretreatment probes to the posttreatment probes for the treated structure such that accuracy rose from at or below chance to above chance and either (a) accuracy rose by 33% or (b) the effect size was 2.6. Based on these criteria, the success rate for training the target structure was 2/6 participants in the SPM condition and 4/7 participants in the OM condition.

Conclusion

The outcome of this study illustrates the utility of this theoretically motivated and efficacious treatment for sentence comprehension deficits in individuals with aphasia.
The Time-Course of Lexical Activation During Sentence Comprehension in People With Aphasia
Authors: Ferrill Michelle , Love Tracy , Walenski Matthew , Shapiro Lewis P.
Published: May 2012

Purpose

To investigate the time-course of processing of lexical items in auditorily presented canonical (subject–verb–object) constructions in young, neurologically unimpaired control participants and participants with left-hemisphere damage and agrammatic aphasia.

Method

A cross modal picture priming (CMPP) paradigm was used to test 114 control participants and 8 participants with agrammatic aphasia for priming of a lexical item (direct object noun) immediately after it is initially encountered in the ongoing auditory stream and at 3 additional time points at 400-ms intervals.

Results

The control participants demonstrated immediate activation of the lexical item, followed by a rapid loss (decay). The participants with aphasia demonstrated delayed activation of the lexical item.

Conclusion

This evidence supports the hypothesis of a delay in lexical activation in people with agrammatic aphasia. The delay in lexical activation feeds syntactic processing too slowly, contributing to comprehension deficits in people with agrammatic aphasia.
Developmental Trajectories of Verbal and Nonverbal Skills in Individuals With a History of Specific Language Impairment: From Childhood to Adolescence
Authors: Conti-Ramsden Gina , St Clair Michelle C. , Pickles Andrew , Durkin Kevin
Published: May 2012

Purpose

To investigate the longitudinal trajectories of verbal and nonverbal skills in individuals with a history of specific language impairment (SLI) from childhood to adolescence. This study focuses on SLI only and investigates within-participant measures across abilities.

Method

Verbal and nonverbal skills were assessed in 242 children with a history of SLI at ages 7, 8, 11, 14, 16, and 17. Discrete factor growth modeling was used to examine developmental trajectories for the whole group and to identify subgroups on the basis of a novel, developmental, multidimensional approach.

Results

When expressive language, receptive language, and nonverbal skills were scaled to a common metric, the group of individuals with a history of SLI as a whole had stable skills growth throughout the 10-year time frame. Seven language subgroups were identified, but these differed only in severity and did not display mutually distinctive patterns of growth development. In contrast, 6 nonverbal skills subgroups were identified, and their trajectories did differ significantly, with evidence of deceleration in around one third of the sample.

Conclusion

Individuals with a history of SLI show steady language growth from age 7. However, different patterns of growth of nonverbal skills are observed from childhood to adolescence.
The Effects of Concurrent Cognitive Load on Phonological Processing in Adults Who Stutter
Authors: Jones Robin M. , Fox Robert A. , Jacewicz Ewa
Published: May 2012

Purpose

To determine whether phonological processing in adults who stutter (AWS) is disrupted by increased amounts of cognitive load in a concurrent attention-demanding task.

Method

Nine AWS and 9 adults who do not stutter (AWNS) participated. Using a dual-task paradigm, the authors presented word pairs for rhyme judgments and, concurrently, letter strings for memory recall. The rhyme judgment task manipulated rhyming type (rhyming/nonrhyming) and orthographic representation (similar/dissimilar). The memory recall task varied stimulus complexity (no letters, 3 letters, 5 letters). Rhyme judgment accuracy and reaction time (RT) were used to assess phonological processing, and letter recall accuracy was used to measure memory recall.

Results

For rhyme judgments, AWS were as accurate as AWNS, and the increase in the cognitive load did not affect rhyme judgment accuracy of either group. Significant group differences were found in RTs (delays by AWS were 241 ms greater). RTs of AWS were also slower in the most demanding rhyme condition and varied with the complexity of the memory task. Accuracy of letter recall of AWS was comparatively worse in the most demanding 5-letter condition.

Conclusion

Phonological and cognitive processing of AWS is more vulnerable to disruptions caused by increased amounts of cognitive load in concurrent attention-demanding tasks.
The analysis of NMR J-couplings of saturated and unsaturated compounds by the localized second order polarization propagator approach method
Authors: Zarycz Natalia , Aucar Gustavo A.
Published: May 2012

Calculations of NMR J-coupling with polarization propagators are not invariant under unitary transformations at second order level of approach, second order polarization propagator approach (SOPPA). They are only invariant at first order or random phase level of approach (RPA). We performed “localized” SOPPA (Loc-SOPPA), calculations of J-couplings applying two different schemes for the localization of molecular orbitals(LMO): Foster-Boys and Pipek-Mezey. We show here that results of such Loc-SOPPA calculations are different though not much: they are less than 6% different in the worst case. Therefore it is possible to apply them with confidence in the analysis of the transmission of different coupling mechanisms within the molecule. We are able now to get reliable information on what LMOs are the most important (and so which are not important) for a given J-coupling in a molecule. This information can then be used for selecting which are the paths that should be described with the highest possible accuracy for that J-coupling calculation. A few unsaturated compounds are analyzed: ethene, trans-difluoroethene or DiF-ethene, and imine. It is shown that different lone pairs (of pz or px/y type) are responsible for the vicinal F-F J-coupling in DiF-ethene; and also the fact that the main LP contributor is not the same for the fermi contact and the spin-dipolar mechanisms. We also studied phosphorous containing compounds such as phosphine and cis-propylene phosphine. In both cases the analysis of the main LMO contributing to one-bond P-H coupling and through-space P-C coupling were performed. The above mentioned unsaturated molecular systems have quasiinstability problems that arise at RPA level of approach. We show here that they are mostly originated in the antibonding π* LMO, corresponding to the C=C or C=N double bonds. We performed the analysis of the origin of quasiinstabilities for the SD mechanism. The contribution of each kind of excitation terms to SOPPA calculations were considered, meaning the main contributions by single and double excitations. It is shown that one can get more than 97% of the total electron correlation contribution when including terms that mainly contain single excitations (though double-excitation matrix elements should still be calculated).
Non-stationary forward flux sampling
Authors: Becker Nils B. , Allen Rosalind J. , ten Wolde Pieter Rein
Published: May 2012

We present a method, Non-Stationary Forward Flux Sampling, that allows efficient simulation of rare events in both stationary and non-stationary stochastic systems. The method uses stochastic branching and pruning to achieve uniform sampling of trajectories in phase space and time, leading to accurate estimates for time-dependent switching propensities and time-dependent phase space probability densities. It is suitable for equilibrium or non-equilibrium systems, in or out of stationary state, including non-Markovian or externally driven systems. We demonstrate the validity of the technique by applying it to a one-dimensional barrier crossing problem that can be solved exactly, and show its usefulness by applying it to the time-dependent switching of a genetic toggle switch.
Rare switching events in non-stationary systems
Authors: Becker Nils B. , Rein ten Wolde Pieter
Published: May 2012

Physical systems with many degrees of freedom can often be understood in terms of transitions between a small number of metastable states. For time-homogeneous systems with short-term memory these transitions are fully characterized by a set of rate constants. We consider the question how to extend such a coarse-grained description to non-stationary systems and to systems with finite memory. We identify the physical regimes in which time-dependent rates are meaningful, and state microscopic expressions that can be used to measure both externally time-dependent and history-dependent rates in microscopic simulations. Our description can be used to generalize Markov state models to time-dependent Markovian or non-Markovian systems.
Two-dimensional stimulated resonance Raman spectroscopy of molecules with broadband x-ray pulses
Authors: Biggs Jason D. , Zhang Yu , Healion Daniel , Mukamel Shaul
Published: May 2012

Expressions for the two-dimensional stimulated x-ray Raman spectroscopy (2D-SXRS) signal obtained using attosecond x-ray pulses are derived. The 1D- and 2D-SXRS signals are calculated for trans-N-methyl acetamide (NMA) with broad bandwidth (181 as, 14.2 eV FWHM) pulses tuned to the oxygen and nitrogen K-edges. Crosspeaks in 2D signals reveal electronic Franck-Condon overlaps between valence orbitals and relaxed orbitals in the presence of the core-hole.
The free energy of expansion and contraction: Treatment of arbitrary systems using the Jarzynski equality
Authors: Davie Stuart J. , Reid James C. , Searles Debra J.
Published: May 2012

Thermodynamic integration, free energy perturbation, and slow change techniques have long been utilised in the calculation of free energy differences between two states of a system that has undergone some transformation. With the introduction of the Jarzynski equality and the Crooks relation, new approaches are possible. This paper investigates an important phenomenon – systems undergoing a change in volume/density – and derives both the Jarzynski equality and Crooks relation of such systems using a statistical mechanical approach. These results apply to systems with arbitrary particle interactions and densities. The application of this approach to the expansion/compression of particles confined within a vessel with a piston and within a periodic system is considered.
First passage times for a tracer particle in single file diffusion and fractional Brownian motion
Authors: Sanders Lloyd P. , Ambjörnsson Tobias
Published: May 2012

We investigate the full functional form of the first passage time density (FPTD) of a tracer particle in a single-file diffusion (SFD) system whose population is: (i) homogeneous, i.e., all particles having the same diffusion constant and (ii) heterogeneous, with diffusion constants drawn from a heavy-tailed power-law distribution. In parallel, the full FPTD for fractional Brownian motion [fBm—defined by the Hurst parameter, H ∈ (0, 1)] is studied, of interest here as fBm and SFD systems belong to the same universality class. Extensive stochastic (non-Markovian) SFD and fBm simulations are performed and compared to two analytical Markovian techniques: the method of images approximation (MIA) and the Willemski-Fixman approximation (WFA). We find that the MIA cannot approximate well any temporal scale of the SFD FPTD. Our exact inversion of the Willemski-Fixman integral equation captures the long-time power-law exponent, when H ⩾ 1/3, as predicted by Molchan [Commun. Math. Phys. 205, 97 (1999)10.1007/s002200050669] for fBm. When H < 1/3, which includes homogeneous SFD (H = 1/4), and heterogeneous SFD (H < 1/4), the WFA fails to agree with any temporal scale of the simulations and Molchan's long-time result. SFD systems are compared to their fBm counter parts; and in the homogeneous system both scaled FPTDs agree on all temporal scales including also, the result by Molchan, thus affirming that SFD and fBm dynamics belong to the same universality class. In the heterogeneous case SFD and fBm results for heterogeneity-averaged FPTDs agree in the asymptotic time limit. The non-averaged heterogeneous SFD systems display a lack of self-averaging. An exponential with a power-law argument, multiplied by a power-law pre-factor is shown to describe well the FPTD for all times for homogeneous SFD and sub-diffusive fBm systems.
Crystal structure of ammonia dihydrate II
Authors: Griffiths Gareth I. G. , Fortes A. Dominic , Pickard Chris J. , Needs R. J.
Published: May 2012

We have used density-functional-theory (DFT) methods together with a structure searching algorithm to make an experimentally constrained prediction of the structure of ammonia dihydrate II (ADH-II). The DFT structure is in good agreement with neutron diffraction data and verifies the prediction. The structure consists of the same basic structural elements as ADH-I, with a modest alteration to the packing, but a considerable reduction in volume. The phase diagram of the known ADH and ammonia monohydrate + water-ice structures is calculated with the Perdew-Burke-Ernzerhof density functional, and the effects of a semi-empirical dispersion corrected functional are investigated. The results of our DFT calculations of the finite-pressure elastic constants of ADH-II are compared with the available experimental data for the elastic strain coefficients.
Theoretical analysis of photoinduced H-atom elimination in thiophenol
Authors: Venkatesan T. S. , Ramesh S. G. , Lan Z. , Domcke W.
Published: May 2012

The photoinduced hydrogen elimination reaction in thiophenol via the conical intersections of the dissociative 1πσ* excited state with the bound 1ππ* excited state and the electronic ground state has been investigated with ab initio electronic-structure calculations and time-dependent quantum wave-packet calculations. A screening of the coupling constants of the symmetry-allowed coupling modes at the 1ππ*-1πσ* and 1πσ*-S0 conical intersection shows that the SH torsional mode is by far the most important coupling mode at both conical intersections. A model including three intersecting potential-energy surfaces (S0, 1ππ*, 1πσ*) and two nuclear degrees of freedom (SH stretch and SH torsion) has been constructed on the basis of ab initio complete-active-space self-consistent field and multireference second-order perturbation theory calculations. The nonadiabatic quantum wave-packet dynamics initiated by optical excitation of the 1ππ* and 1πσ* states has been explored for this three-state two-coordinate model. The photodissociation dynamics is characterized in terms of snapshots of time-dependent wave packets, time-dependent electronic population probabilities, and the branching ratio of the 2σ/2π electronic states of the thiophenoxyl radical. The dependence of the timescale of the photodissociation process and the branching ratio on the initial excitation of the SH stretching and SH torsional vibrations has been analyzed. It is shown that the node structure, which is imposed on the nuclear wave packets by the initial vibrational preparation as well as by the transitions through the conical intersections, has a profound effect on the photodissociation dynamics. The effect of additional weak coupling modes of CC twist (ν16a) and ring-distortion (ν16b) character has been investigated with three-dimensional and four-dimensional time-dependent wave-packet calculations, and has been found to be minor.
Multicomponent density functional theory study of the interplay between electron-electron and electron-proton correlation
Authors: Sirjoosingh Andrew , Pak Michael V. , Hammes-Schiffer Sharon
Published: May 2012

The interplay between electron-electron and electron-proton correlation is investigated within the framework of the nuclear-electronic orbital density functional theory (NEO-DFT) approach, which treats electrons and select protons quantum mechanically on the same level. Recently two electron-proton correlation functionals were developed from the electron-proton pair densities obtained from explicitly correlated wavefunctions. In these previous derivations, the kinetic energy contribution arising from electron-proton correlation was neglected. In this paper, an electron-proton correlation functional that includes this kinetic energy contribution is derived using the adiabatic connection formula in multicomponent DFT. The performance of the NEO-DFT approach using all three electron-proton correlation functionals in conjunction with three well-established electronic exchange-correlation functionals is assessed. NEO-DFT calculations with these electron-proton correlation functionals capture the increase in the hydrogen vibrational stretching frequencies arising from the inclusion of electron-electron correlation in model systems. Electron-proton and electron-electron correlation are found to be uncoupled and predominantly additive effects to the total energy for the model systems studied. Thus, electron-proton correlation functionals and electronic exchange-correlation functionals can be developed independently and subsequently combined together without re-parameterization.
Bifurcation transitions in a photochemical system under low magnetic fields
Authors: Kipriyanov A. A. , Purtov P. A.
Published: May 2012

In the last decades, the effect of low magnetic fields on biochemical and chemical systems has been an urgent problem. By now numerous experimental and theoretical studies have been conducted to demonstrate that commonly this effect is of no essence as it does not exceed 10%. However, there are experimental works which testify that in some systems, magnetic field effects are more significant. Thus, of great interest is an active search for rather simple but realistic models that are based on physically explicit assumptions and able to account for a strong effect of low magnetic fields. The present work not only offers a theoretical study on the simplest photochemical system, describing a reversible reaction of photodissociation, but also shows how a low magnetic field can strongly modify its properties under highly nonequilibrium conditions. It is assumed that external magnetic field can have effect on the rates of radical reactions occurring in a system. This, in turn, leads to bifurcation of the nonequilibrium stationary state and, thus, to a drastic change in the properties of chemical systems (temperature and reagent concentration).
Influence of the nonlinear dynamic plasma screening on the electron-dust collision in dusty plasmas
Authors: Ki Dae-Han , Jung Young-Dae
Published: May 2012

The nonlinear dynamic plasma screening effects on the elastic electron-dust grain collision are investigated in dusty plasmas. The results show that the nonlinear dynamic screening effect significantly increases the magnitude of the eikonal phase shift. It is also found that the magnitude of the phase shift decreases with an increase of the thermal energy. In addition, it is found that the differential eikonal cross section shows the oscillatory behavior, and the oscillating peaks approach to the collision center with increasing thermal energy. It is also found that the total eikonal cross section decreases with an increase of the thermal energy.
Vortex mode dynamics and bandwidth tunability in a two-dimensional array of interacting magnetic disks
Authors: Montoncello Federico , Giovannini Loris
Published: May 2012

We calculate the spin wave spectrum and band diagram of a planar array of interacting disks in the vortex state at zero and finite applied field. We found that the circular polarization of modes depends on the Bloch wavevector k, and that the apparent spin wave profile can change as k increases from Γ to zone boundary as a consequence of the array periodicity, although the cell function remains the same. Focusing on the gyrotropic mode, we found that application of an external field can reduce or enhance the mode bandwidth, and hence slow down or boost the information carrier propagation along orthogonal directions.
Fractal structures in two-metal electrodeposition systems II: Cu and Zn
Authors: Nakouzi Elias , Sultan Rabih
Published: May 2012

In this second part of our study on fractal co-electrochemical deposition, we investigate the Cu-Zn system. Macroscopic and microscopic inspection shows a sensitive dependence of the morphology of the final pattern on initial concentrations. The pattern is seen to undergo a transition from classical dendrites to randomly ramified deposits, with each slight increase in [Cu2+]0, while [Zn2+]0 is maintained constant. The variational trends in chemical composition, growth velocity, and fractal dimension with increasing [Cu2+]0 are analyzed. The latter is seen to generally increase with copper (II) ion concentration. In contrast, the growth rate of the deposits is seen to decrease with increasing concentration of Cu2+ ions. A new probe of dense ramified morphology, the pattern density, is introduced and seen to increase with [Cu2+]0. XRD measurements reveal that the observed properties correlate with the birth of copper-rich nuclei, which disrupt the crystalline anisotropy of the two-metal alloy.
Optically recorded tunable microlenses based on dye-doped liquid crystal cells
Authors: Lucchetti Liana , Tasseva Jordanka
Published: May 2012

We report on optically recorded microlenses in conventional liquid crystal cells doped with the azo-dye methyl-red. The focal length can be tuned electrically and changed in a wide range with just a small variation of the applied dc voltage. No patterned electrodes, built-in polymeric lens, or patterned molecular reorientation are required.
Electron heating mode transition induced by ultra-high frequency in atmospheric microplasmas for biomedical applications
Authors: Kwon H. C. , Won I. H. , Lee J. K.
Published: May 2012

The electron heating mode transition induced by ultra-high frequency in atmospheric-pressure microplasmas was investigated using particle-in-cell simulation with a Monte Carlo collision. Interestingly, this discharge mode transition is accompanied by non-monotonic evolution of electron kinetics such as effective electron temperature, plasma density, and electron energy on the electrode. In this study, the highest flux of energetic electrons (ɛ > 4 eV) usable for tailoring the surface chemistry in atmospheric microplasmas is obtained at the specific frequency (400 MHz), where an optimal trade-off is established between the amplitude of sheath oscillations and the power coupled to electrons for sub-millimeter dimensions (200 µm).
Electron energy-loss spectroscopy study of MgH2 in the plasmon energy range
Authors: Paik B. , Walton A. , Mann V. , Book D. , Jones I. P. , Harris I. R.
Published: May 2012

Electron energy loss spectroscopy of MgH2 in the plasmon energy range is reported here as a part of a study to determine the dielectric function of this hydride. From the dielectric function, we have estimated the unperturbed plasmon energy of MgH2 as 11.34 eV. Interband transitions are also inferred from the dielectric function. Contribution of these interband transitions to the perturbed plasmon energy has been discussed within the scope of dielectric theory. Our analysis suggests that the MgH2 band gap lies within the range ∼4.3–4.5 eV.
Nanoscale integration of SiC/SiO2 core-shell nanocables in diamond through a simultaneous hybrid structure fabrication
Authors: Zhuang Hao , Zhang Lei , Staedler Thorsten , Jiang Xin
Published: May 2012

The nanoscale integration of SiC nanocables in a diamond thin film is achieved through a novel synthetic pathway, which combines Fe catalyst and detonation nanodiamond seeding technique in a microwave plasma chemical vapor deposition process. The obtained hybrid structures show controllable SiC nanocable fraction depending on the relative fraction of iron catalyst and diamond seeds. The SiC nanocable has a conical structure with 10 nm diameter SiC core, surrounded by SiO2 shell. The diamond crystals show high quality/crystallinity even for hybrid structures featuring an increasing SiC nanocable fraction. In the end, the growth behavior of the hybrid structure is discussed.
In situ microwave characterization of microwire composites with external magnetic field
Authors: Qin F. X. , Brosseau C. , Peng H. X. , Wang H. , Sun J.
Published: May 2012

Rubber composites containing Co68.15Fe4.35Si12.25B15.25 glass-covered amorphous microwires were fabricated. For samples containing 5 mm long wires and randomly dispersed in the polymer matrix, our results demonstrate that the current induces resonance of circumferential permeability (magnetoimpedance resonance) resulting in a significant change of the effective permittivity of the wire-filled composites with application of a high magnetic field. For samples containing longer wires (70 mm) periodically arranged in the polymer matrix, the permittivity spectrum shows two resonance peaks due to, respectively, dipole and magnetoimpedance resonance. The induced magnetoimpedance resonance has a narrower linewidth than the dipole one as magnetic field is increased.
Optical-electrical simulation of organic solar cells: Influence of light trapping by photonic crystal and ZnO spacer on electrical characteristics
Authors: Vervisch Wilfried , Rivière Guillaume , Vedraine Sylvain , Biondo Stéphane , Torchio Philippe , Duché David , Simon Jean-Jacques , Escoubas Ludovic
Published: May 2012

This paper deals with organic solar cells (OSC) simulation using finite element method. Optical modeling is performed via finite difference time domain method whilst the continuity and Poisson’s equations are solved to obtain electrical characteristics of the OSC. In this work, simulation results point out the OSC structure influence on its performances, either by the interface grating or by the ZnO optical spacer introduced between the active layer (P3HT:PCBM layer) and the metallic electrode. The comparison of modeling results and experimental measurement allows us to confirm and forecast the enhancement of the photovoltaic properties such as the power conversion efficiency.
Quasi-exact treatment of the relativistic generalized isotonic oscillator
Authors: Agboola D.
Published: May 2012

We investigate the pseudospin symmetry case of a spin-\documentclass[12pt]{minimal}\begin{document}$\frac{1}{2}$\end{document}12 particle governed by the generalized isotonic oscillator, by presenting quasi-exact polynomial solutions of the Dirac equation with pseudospin symmetry vector and scalar potentials. The resulting equation is found to be quasi-exactly solvable owing to the existence of a hidden sl(2) algebraic structure. A systematic and closed form solution to the basic equation is obtained using the Bethe ansatz method. Analytic expression for the energy is obtained and the wavefunctions are derived in terms of the roots to a set of Bethe ansatz equations.
Uniform yeast cell assembly via microfluidics
Authors: Chang Ya-Wen , He Peng , Marquez Samantha M. , Cheng Zhengdong
Published: May 2012

This paper reports the use of microfluidic approaches for the fabrication of yeastosomes (yeast-celloidosomes) based on self-assembly of yeast cells onto liquid-solid or liquid-gas interfaces. Precise control over fluidic flows in droplet- and bubble-forming microfluidic devices allows production of monodispersed, size-selected templates. The general strategy to organize and assemble living cells is to tune electrostatic attractions between the template (gel or gas core) and the cells via surface charging. Layer-by-Layer (LbL) polyelectrolyte deposition was employed to invert or enhance charges of solid surfaces. We demonstrated the ability to produce high-quality, monolayer-shelled yeastosome structures under proper conditions when sufficient electrostatic driving forces are present. The combination of microfluidic fabrication with cell self-assembly enables a versatile platform for designing synthetic hierarchy bio-structures.
MHC class II distribution in dendritic cells and B cells is determined by ubiquitin chain length
Authors: Ma Jessica K. , Platt Mia Y. , Eastham-Anderson Jeffrey , Shin Jeoung-Sook , Mellman Ira
Published: May 2012

Dendritic cells (DCs) and B cells present antigen-derived peptides bound to MHC class II (MHC II) molecules for recognition by CD4-positive T lymphocytes. DCs control the intracellular traffic of peptide–MHC II complexes by regulating the ubiquitination of MHC II. In resting or “immature” DCs, ubiquitinated MHC II molecules are targeted to lysosomes, but upon pathogen-induced “maturation,” ubiquitination is down-regulated and MHC II can accumulate on the plasma membrane of mature DCs. Although B cells constitutively ubiquitinate their MHC II, it unexpectedly remains at the surface. We find that DCs and B cells differ in MHC II-conjugated ubiquitin (Ub) chain length: four to six Ub in immature DCs vs. two to three in B cells. In both cell types, experimentally increasing Ub chain length led to efficient lysosomal transport of MHC II, whereas MHC II with fewer than two Ubs did not reach lysosomes. Thus, Ub chain length plays a crucial role in regulating the intracellular fate and function of MHC II in DCs and B cells.
Role of phosphorylation of Cdc20 in p31
comet
-stimulated disassembly of the mitotic checkpoint complex
Authors: Miniowitz-Shemtov Shirly , Eytan Esther , Ganoth Dvora , Sitry-Shevah Danielle , Dumin Elena , Hershko Avram
Published: May 2012

The mitotic checkpoint system delays anaphase until all chromosomes are correctly attached to the mitotic spindle. When the checkpoint is turned on, it promotes the formation of the mitotic checkpoint complex (MCC), which inhibits the ubiquitin ligase anaphase-promoting complex/cyclosome (APC/C). MCC is composed of the checkpoint proteins BubR1, Bub3, and Mad2 bound to the APC/C activator Cdc20. When the checkpoint is satisfied, MCC is disassembled and APC/C becomes active. Previous studies have shown that the Mad2-binding protein p31
comet
promotes the dissociation of Cdc20 from BubR1 in MCC in a process that requires ATP. We now show that a part of MCC dissociation is blocked by inhibitors of cyclin-dependent kinases (Cdks) and that purified Cdk1–cyclin B stimulates this process. The mutation of all eight potential Cdk phosphorylation sites of Cdc20 partially prevented its release from BubR1. Furthermore, p31
comet
stimulated Cdk-catalyzed phosphorylation of Cdc20 in MCC. It is suggested that the binding of p31
comet
to Mad2 in MCC may trigger a conformational change in Cdc20 that facilitates its phosphorylation by Cdk, and that the latter process may promote its dissociation from BubR1.
Joint Bayesian inference of condition-specific miRNA and transcription factor activities from combined gene and microRNA expression data
Authors: Zacher Benedikt , Abnaof Khalid , Gade Stephan , Younesi Erfan , Tresch Achim , Fröhlich Holger
Published: May 2012

Motivation: There have been many successful experimental and bioinformatics efforts to elucidate transcription factor (TF)-target networks in several organisms. For many organisms, these annotations are complemented by miRNA-target networks of good quality. Attempts that use these networks in combination with gene expression data to draw conclusions on TF or miRNA activity are, however, still relatively sparse.

Results: In this study, we propose Bayesian inference of regulation of transcriptional activity (BIRTA) as a novel approach to infer both, TF and miRNA activities, from combined miRNA and mRNA expression data in a condition specific way. That means our model explains mRNA and miRNA expression for a specific experimental condition by the activities of certain miRNAs and TFs, hence allowing for differentiating between switches from active to inactive (negative switch) and inactive to active (positive switch) forms. Extensive simulations of our model reveal its good prediction performance in comparison to other approaches. Furthermore, the utility of BIRTA is demonstrated at the example of Escherichia coli data comparing aerobic and anaerobic growth conditions, and by human expression data from pancreas and ovarian cancer.

Availability and implementation: The method is implemented in the R package birta, which is freely available for Bio-conductor (>=2.10) on http://www.bioconductor.org/packages/release/bioc/html/birta.html.

Contact:  frohlich@bit.uni-bonn.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
BRAT-BW: efficient and accurate mapping of bisulfite-treated reads
Authors: Harris Elena Y. , Ponts Nadia , Le Roch Karine G. , Lonardi Stefano
Published: May 2012

Summary: We introduce BRAT-BW, a fast, accurate and memory-efficient tool that maps bisulfite-treated short reads (BS-seq) to a reference genome using the FM-index (Burrows–Wheeler transform). BRAT-BW is significantly more memory efficient and faster on longer reads than current state-of-the-art tools for BS-seq data, without compromising on accuracy. BRAT-BW is a part of a software suite for genome-wide single base-resolution methylation data analysis that supports single and paired-end reads and includes a tool for estimation of methylation level at each cytosine.

Availability: The software is available in the public domain at http://compbio.cs.ucr.edu/brat/.

Contact:  elenah@cs.ucr.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
The Oregon Health Insurance Experiment: Evidence from the First Year*
Authors: Finkelstein Amy , Taubman Sarah , Wright Bill , Bernstein Mira , Gruber Jonathan , Newhouse Joseph P. , Allen Heidi , Baicker Katherine ,   Oregon Health Study Group
Published: May 2012

In 2008, a group of uninsured low-income adults in Oregon was selected by lottery to be given the chance to apply for Medicaid. This lottery provides an opportunity to gauge the effects of expanding access to public health insurance on the health care use, financial strain, and health of low-income adults using a randomized controlled design. In the year after random assignment, the treatment group selected by the lottery was about 25 percentage points more likely to have insurance than the control group that was not selected. We find that in this first year, the treatment group had substantively and statistically significantly higher health care utilization (including primary and preventive care as well as hospitalizations), lower out-of-pocket medical expenditures and medical debt (including fewer bills sent to collection), and better self-reported physical and mental health than the control group.
Semipersistent Whitefly Transmission of Squash vein yellowing virus, Causal Agent of Viral Watermelon Vine Decline
Authors: Webb Susan E. , Adkins Scott , Reitz Stuart R.
Published: May 2012

Squash vein yellowing virus (SqVYV), a recently described Ipomovirus sp. in the family Potyviridae, is the cause of viral watermelon vine decline, a devastating disease in Florida. SqVYV is known to be transmitted by the whitefly, Bemisia tabaci (Gennadius) B strain, but details of the transmission process have not previously been investigated. We completed a series of experiments to determine efficiency of transmission, effects of different acquisition and inoculation access periods, the length of time that whiteflies retained transmissible virus, and the minimum time needed to complete a cycle of acquisition and inoculation. Efficiency was low, with at least 30 whiteflies per plant needed for consistent transmission. Acquisition leading to later transmission peaked at 4 h, and inoculation access periods longer than 4 to 8 h led to no increase in infection rates. Whiteflies retained virus only a short time, with no transmission by 24 h after removal from infected plants. A minimum of 3 h was needed to complete a cycle of transmission under laboratory conditions. These results demonstrate semipersistent transmission of SqVYV and will help refine models of the epidemiology of this virus and the disease it causes.