bluuebunny/crossref_metadata_2025 huggingface dataset:
Depth Properties of scaled attachment random recursive trees
Authors: Devroye Luc , Fawzi Omar , Fraiman Nicolas
Published: December 2011

We study depth properties of a general class of random recursive trees where each node i attaches to the random node \documentclass{article} \usepackage{mathrsfs, amsmath, amssymb}\pagestyle{empty} \begin{document} \begin{align*}\left\lfloor iX_i\right\rfloor\end{align*} \end{document}
and X0,…,Xn is a sequence of i.i.d. random variables taking values in [0,1). We call such trees scaled attachment random recursive trees (sarrt). We prove that the typical depth Dn, the maximum depth (or height) Hn and the minimum depth Mn of a sarrt are asymptotically given by Dn ∼μ‐1 log n, Hn ∼ αmax log n and Mn ∼ αmin log n where μ,αmax and αmin are constants depending only on the distribution of X0 whenever X0 has a density. In particular, this gives a new elementary proof for the height of uniform random recursive trees Hn ∼ elog n that does not use branching random walks.© 2011 Wiley Periodicals, Inc. Random Struct. Alg., 2011
Fifty Years of Mössbauer Spectroscopy in Solid State Research – Remarkable Achievements, Future Perspectives
Authors: Gütlich Philipp
Published: December 2011

Mössbauer spectroscopy was founded more than fifty years ago based on an outstanding discovery by the young German physicist Rudolf Ludwig Mössbauer while working on his Ph.D. thesis. He discovered the recoilless nuclear resonance fluorescence of gamma radiation and was awarded the Nobel Prize in Physics in 1961 as one of the youngest recipients of this most prestigious award. His discovery led to the development of a new technique for measurements of hyperfine interactions between nuclear moments and electromagnetic fields. This method, with highest sharpness of tuning of 10–13, yields information on valence state, symmetry, magnetic behavior, phase transition, lattice dynamics and other solid state properties.
A Further Extension of Pnictide Oxide Chemistry – Synthesis and Structure of La2AuP2O
Authors: Eul Matthias , Möller Manfred H. , Hoffmann Rolf‐Dieter , Jeitschko Wolfgang , Pöttgen Rainer
Published: December 2011

The phosphide oxide La2AuP2O was synthesized from lanthanum filings, dried La2O3, gold pieces, and ground red phosphorus in the ideal 1.33:0.33:1:2 ratio in an evacuated silica tube at 1473 K. Small single crystals were obtained by recrystallization in a NaCl/KCl flux. The structure was determined on the basis of single‐crystal X‐ray diffractometer data: new type, C2/m, a = 1537.3(3), b = 427.39(8), c = 1009.2(2) pm, β = 131.02(1) °, wR2 = 0.046, 1102 F2 values, 38 variables. La2AuP2O contains two striking structural motifs: The oxygen atoms are located in La4 tetrahedra. The latter are cis‐edge‐shared forming polymeric cationic [La2O]4+ chains. These cationic units are separated and charge‐balanced by [AuP2]4– polyanions which have monovalent gold in distorted trigonal planar phosphorus coordination. Two crystallographically independent phosphorus sites occur in the polyanion, i.e. isolated P3– besides dumb‐bells P24– (P2–P2 223 pm). La2AuP2O, which crystallizes in the form of ruby red transparent crystals, is an electron precise phosphide oxide (4La3+)(2Au+)(2P3–)(P24–)(2O2–).
Stability and bifurcation in a gene regulatory network model with delay
Authors: Wang Z. , Liu Z. , Yuan R.
Published: December 2011

A delayed gene regulatory network model with positive and negative feedbacks is considered. We investigate the stability of the positive equilibrium and the existence of Hopf bifurcation of the model by analyzing the associated characteristic transcendental equation. Applying the normal form theory and center manifold theorem, we consider the direction of the Hopf bifurcation and stability of the bifurcating periodic solutions. An example is given and numerical simulations are performed to illustrate the obtained results.
Full Engagement! Inspire, Motivate, and Bring out the Best in Your People
Authors: Castelluccio Donna
Published: December 2011

Full Engagement! Inspire, Motivate, and Bring out the Best in Your People Brian Tracy 2011, AMACOM 262 pages, hardcover
Comma N' cents in pricing: The effects of auditory representation encoding on price magnitude perceptions
Authors: Coulter Keith S. , Choi Pilsik , Monroe Kent B.
Published: December 2011

Numbers and prices can be processed and encoded in three different forms: 1) visual [based on their written form in Arabic numerals (e.g., 72)], 2) verbal [based on spoken word‐sounds (e.g., “seventy” and “two”), and 3) analog (based on judgments of relative “size” or amount (e.g., more than 70 but less than 80)]. In this paper, we demonstrate that including commas (e.g., $1599 vs. $1599) and cents (e.g., $1599.85 vs. $1599) in a price's Arabic written form (i.e., how it is perceived visually) can change how the price is encoded and represented verbally in a consumer's memory. In turn, the verbal encoding of a written price can influence assessments of the numerical magnitude of the price. These effects occur because consumers non‐consciously perceive that there is a positive relationship between syllabic length and numerical magnitude. Three experiments are presented demonstrating this important effect.
In silico comparative analysis of conserved genes expressed in solanaceous plants under abiotic stresses
Authors: gupta sanchita , dhawan sunita singh , sharma ashok
Published: December 2011

The gene expression data was studied in order to analyze genes involved in different abiotic stresses in solanaceous plants. Salt, temperature (heat & cold) and drought are the main abiotic stresses to the plants. Abiotic stress responses are important for sessile organisms like plants because they have to cope with environmental changes to survive. The idea was to analyze those differentially expressed genes, which show common expression in response to different abiotic stress conditions in each plant. Mitogen activated protein kinases (MAPK) are important mediators in signal transmission, connecting the perception of external stimuli to cellular responses. In plants, MAPKs plays a major role in the signaling of abiotic stresses. The expression data were retrieved from gene expression omnibus (GEO) database at NCBI. The set of genes were selected showing up or down regulation in at least two abiotic stresses. These genes were used for searching their involvement in different steps of MAP kinase pathway. Our findings suggest that a common set of genes are the key players in signaling pathway responsible for initiation of cascade of reaction in response to stress. The study will help to understand how the conserved genes are expressing differentially in response to various abiotic stresses. The common genes affecting the MAP kinase pathway might be highly conserved. These genes may be used to study the response of different abiotic stresses in other plant species.
Lack of Generalization of Auditory Learning in Typically Developing Children
Authors: Halliday Lorna F. , Taylor Jenny L. , Millward Kerri E. , Moore David R.
Published: December 2011

Purpose

To understand the components of auditory learning in typically developing children by assessing generalization across stimuli, across modalities (i.e., hearing, vision), and to higher level language tasks.

Method

Eighty-six 8- to 10-year-old typically developing children were quasi-randomly assigned to 4 groups. Three of the groups received twelve 30-min training sessions on multiple standards using either an auditory frequency discrimination task (AFD group), auditory phonetic discrimination task (PD group), or visual frequency discrimination task (VFD group) over 4 weeks. The 4th group, which was the no-intervention control (NI) group, did not receive any training. Thresholds on all tasks (AFD, PD, and VFD) were assessed immediately before and after training, along with performance on a battery of language assessments.

Results

Relative to the other groups, both the AFD group and the PD group, but not the VFD group, showed significant learning on the stimuli upon which they were trained. However, in those instances where learning was observed, it did not generalize to the nontrained stimuli or to the language assessments.

Conclusions

Nonspeech (AFD) or speech (PD) discrimination training can lead to auditory learning in typically developing children of this age range. However, this learning does not always generalize across stimuli or tasks, across modalities, or to higher level measures of language ability.
Dialect Variation and Reading: Is Change in Nonmainstream American English Use Related to Reading Achievement in First and Second Grades?
Authors: Terry Nicole Patton , Connor Carol McDonald , Petscher Yaacov , Conlin Catherine Ross
Published: December 2011

Purpose

In this study, we examined (a) whether children who spoke Nonmainstream American English (NMAE) frequently in school at the beginning of 1st grade increased their use of Mainstream American English (MAE) through the end of 2nd grade, and whether increasing MAE use was associated with (b) language and reading skills and school context and (c) greater gains in reading skills.

Method

A longitudinal design was implemented with 49 children who spoke NMAE moderately to strongly. Spoken production of NMAE forms, word reading, and reading comprehension were measured at the beginning, middle, and end of 1st and 2nd grades. Various oral language skills were also measured at the beginning of 1st grade.

Results

Results indicate that most children increased their MAE production during 1st grade and maintained these levels in 2nd grade. Increasing MAE use was predicted by children’s expressive vocabulary and nonword repetition skills at the beginning of 1st grade. Finally, the more children increased their MAE production, the greater were their reading gains from 1st grade through 2nd grade.

Conclusions

The findings extend previous reports of a significant association between NMAE use and specific reading skills among young children and have implications for theory, educational practice, and future research.
General and Specific Effects of Lexicon in Grammar: Determiner and Object Pronoun Omissions in Child Spanish
Authors: Pérez-Leroux Ana Teresa , Castilla-Earls Anny Patricia , Brunner Jerry
Published: December 2011

Purpose

This study explores the hypothesis that vocabulary growth can have 2 types of effects in morphosyntactic development. One is a general effect, where vocabulary growth globally determines utterance complexity, defined in terms of sentence length and rates of subordination. There are also specific effects, where vocabulary size has a selective impact on the acquisition of grammatical markers and where lexicon is a prerequisite for typological convergence. The study compares the differential effects of vocabulary in 2 measures of morphosyntactic development: omissions of object clitic pronouns and definite articles.

Method

Correlation analysis and structural equation models were used to analyze the statistical effects of measures of vocabulary and grammatical development in 110 Spanish-speaking monolingual children ages 3–5 years.

Results

The data revealed general effects of vocabulary growth on utterance length and subordination rates and on the use of definite determiners and object pronouns. Specific effects of vocabulary growth were identified for object pronouns but not for determiners.

Conclusions

The study found support for a 2-dimensional model separating lexicon and syntax and for 2 types of relationships. Vocabulary development generally determines sentence complexity and further evidence for specific effects in object pronoun use.
Selective Auditory Attention in Adults: Effects of Rhythmic Structure of the Competing Language
Authors: Reel Leigh Ann , Hicks Candace Bourland
Published: December 2011

Purpose

The authors assessed adult selective auditory attention to determine effects of (a) differences between the vocal/speaking characteristics of different mixed-gender pairs of masking talkers and (b) the rhythmic structure of the language of the competing speech.

Method

Reception thresholds for English sentences were measured for 50 monolingual English-speaking adults in conditions with 2-talker (male–female) competing speech spoken in a stress-based (English, German), syllable-based (Spanish, French), or mora-based (Japanese) language. Two different masking signals were created for each language (i.e., 2 different 2-talker pairs). All subjects were tested in 10 competing conditions (2 conditions for each of the 5 languages).

Results

A significant difference was noted between the 2 masking signals within each language. Across languages, significantly greater listening difficulty was observed in conditions where competing speech was spoken in English, German, or Japanese, as compared with Spanish or French.

Conclusions

Results suggest that (a) for a particular language, masking effectiveness can vary between different male–female 2-talker maskers and (b) for stress-based vs. syllable-based languages, competing speech is more difficult to ignore when spoken in a language from the native rhythmic class as compared with a nonnative rhythmic class, regardless of whether the language is familiar or unfamiliar to the listener.
Effect of Onset and Rhyme Primes in Preschoolers With Typical Development and Specific Language Impairment
Authors: Gray Shelley , Reiser Mark , Brinkley Shara
Published: December 2011

Purpose

In this study, the authors used cued shadowing to examine children’s phonological word-form representations by studying the effects of onset and rhyme primes on lexical access.

Method

Twenty-five preschoolers with specific language impairment (SLI; hereafter known as the SLI group), 24 age- and gender-matched children (AM group), and 20 vocabulary- and gender-matched children (VM group) participated. Children listened to pairs of words and repeated the second word as quickly as they could. Primes included words with overlapping onsets, words with overlapping rimes, and identical or unrelated words.

Results

As expected, unrelated words inhibited production in the AM and VM groups. Overlapping rimes primed production in the AM group. No inhibitory or priming effects were found for the SLI group.

Conclusion

Phonological priming may be used to study the phonological representations of preschool-age children. Results suggest that none of the groups accessed words incrementally. Priming for overlapping rimes by the AM but not the VM or SLI groups may indicate that the AM group benefited from lexical organization favoring nucleus + rime organization that has not yet developed for the VM or SLI groups. The lack of inhibition in the SLI group suggests that their phonological representations were not detailed enough to prime words in their lexicon or that they did not process the prime or target words.
Examining Success of Communication Strategies Used by Formal Caregivers Assisting Individuals With Alzheimer’s Disease During an Activity of Daily Living
Authors: Wilson Rozanne , Rochon Elizabeth , Mihailidis Alex , Leonard Carol
Published: December 2011

Purpose

To examine how formal (i.e., employed) caregivers' use verbal and nonverbal communication strategies while assisting individuals with moderate to severe Alzheimer’s disease (AD) during the successful completion of an activity of daily living (ADL). Based on the literature, the authors hypothesized that caregivers' use of 1 proposition, closed-ended questions, and repetition would be of most benefit.

Method

Twelve caregiver–AD dyads participated in this observational study. Each dyad was videorecorded on 6 separate occasions while completing handwashing. Handwashing sessions were transcribed and systematically coded for the use of communication strategies during completion of the ADL.

Results

Caregiver–AD dyads successfully completed 90% of all handwashing sessions, and caregivers employed a variety of communication strategies. Consistent with our hypotheses, during successful task completion, caregivers most frequently provided individuals with AD with 1 direction or idea (i.e., proposition) at a time, closed-ended questions, and paraphrased repetition. Caregivers also frequently used encouraging comments and the resident’s name during the task; however, use of these strategies was not correlated to task success rate.

Conclusion

This study adds to the limited body of evidence supporting the use of specific communication strategies by caregivers assisting individuals with moderate to severe AD during successful completion of ADLs.
Contribution of Linguistic Variables to Bilingual Listeners' Perception of Degraded English Sentences
Authors: Shi Lu-Feng
Published: December 2011

Purpose

The present study was designed to investigate what linguistic variables best predict bilingual recognition of acoustically degraded sentences and how to identify bilingual individuals who might have more difficulty than their monolingual counterparts on such tasks.

Method

Four hundred English speech-perception-in-noise (SPIN) sentences with high and low context were presented in combinations of noise (signal-to-noise ratio: +6 and 0 dB) and reverberation (reverberation time: 1.2 and 3.6 s) to 10 monolingual and 50 bilingual listeners. A detailed linguistic profile was obtained for bilingual listeners using the Language Experience and Proficiency Questionnaire.

Results

Variables per reading in English (age of fluency, proficiency, and preference) emerged as strong predictors of performance across noise, reverberation, and context effects. Via discriminant analyses, bilingual listeners who rated their accent to be perceptible and reported shorter length of immersion in an English-spoken country or school tended to score significantly lower on the SPIN test than monolingual listeners.

Conclusions

Bilingual listeners' linguistic background plays a major role in their use of context in degraded English sentences. Rather than conventional variables such as age of acquisition, variables pertaining to reading, proficiency, immersion, and accent severity may be obtained for improved prediction of bilingual performance on the task.
Sentence Comprehension in Postinstitutionalized School-Age Children
Authors: Desmarais Chantal , Roeber Barbara J. , Smith Mary E. , Pollak Seth D.
Published: December 2011

Purpose

In this study, the authors investigated sentence comprehension and spatial working memory abilities in a sample of internationally adopted, postinstitutionalized (PI) children. The authors compared the performance of these PI children with that of an age-matched group of children living with their birth families. They hypothesized that PI children would perform below clinical threshold on tasks of sentence comprehension and that poor sentence comprehension would be associated with poor performance in working memory.

Method

Twenty-three PI children and 36 comparison children were administered sentence comprehension and spatial memory tasks from standardized assessments.

Results

Some oral sentence comprehension skills and the spatial working memory skills were weaker in the school-age PI children than in the age-matched comparison children. A mediational analysis demonstrated that poor spatial working memory performance partially explains the sentence comprehension differences between the 2 groups.

Conclusion

These findings provide valuable information to better plan early intervention and special education for PI children.
Semantic Deficits in Spanish–English Bilingual Children With Language Impairment
Authors: Sheng Li , Peña Elizabeth D. , Bedore Lisa M. , Fiestas Christine E.
Published: December 2011

Purpose

To examine the nature and extent of semantic deficits in bilingual children with language impairment (LI).

Method

Thirty-seven Spanish–English bilingual children with LI (ranging from age 7;0 [years;months] to 9;10) and 37 typically developing (TD) age-matched peers generated 3 associations to 12 pairs of translation equivalents in English and Spanish. Responses were coded as paradigmatic (e.g.,
dinner
–
lunch,
cena–desayuno
[
dinner
–
breakfast
]), syntagmatic (e.g.,
delicious
–
pizza,
delicioso
–
frijoles
[
delicious
–
beans
]), and errors (e.g.,
wearing
–
where,
vestirse
–
mal
[
to get dressed–bad
]). A semantic depth score was derived in each language and conceptually by combining children’s performance in both languages.

Results

The LI group achieved significantly lower semantic depth scores than the TD group after controlling for group differences in vocabulary size. Children showed higher conceptual scores than single-language scores. Both groups showed decreases in semantic depth scores across multiple elicitations. Analyses of individual performances indicated that semantic deficits (1
SD
below the TD mean semantic depth score) were manifested in 65% of the children with LI and in 14% of the TD children.

Conclusion

School-age bilingual children with and without LI demonstrated spreading activation of semantic networks. Consistent with the literature on monolingual children with LI, sparsely linked semantic networks characterize a considerable proportion of bilingual children with LI.
The Influence of Stimulus Taste and Chemesthesis on Tongue Movement Timing in Swallowing
Authors: Steele Catriona M. , van Lieshout Pascal H. H. M. , Pelletier Cathy A.
Published: December 2011

Purpose

To explore the influence of taste and trigeminal irritation (chemesthesis) on durational aspects of tongue movement in liquid swallowing, controlling for the influence of perceived taste intensity.

Method

Electromagnetic midsagittal articulography was used to trace tongue movements during discrete liquid swallowing with 5 liquids: water, 3 moderate concentration tastants without odor (sweet, sour, sweet-sour), and a high concentration of citric acid (sour taste plus chemesthesis). Participants were 33 healthy adults in 2 gender-balanced, age-stratified groups (under/over 50). Perceived taste intensity was measured using the Generalized Labeled Magnitude Scale (Bartoshuk, 2000; Bartoshuk et al., 2004). Tongue movement sequencing and durations of the composite tongue movement envelope and component events (rise phase, location of first movement peak, release phase) were calculated.

Results

No obligate sequence of tongue segment movement was observed. Overall durations and the timing of the first movement peak were significantly longer with water than with the moderate concentration of sweet-sour liquid. Perceived taste intensity did not modulate stimulus effects in a significant way. The expected pattern of shorter movement durations with the high concentration of citric acid was not seen.

Conclusions

A chemesthetic-taste stimulus of high citric acid did not influence the durations of tongue movements compared with those seen during the swallowing of moderate concentration tastants and water.
Vocabulary and Working Memory in Children Fit With Hearing Aids
Authors: Stiles Derek J. , McGregor Karla K. , Bentler Ruth A.
Published: December 2011

Purpose

To determine whether children with mild-to-moderately severe sensorineural hearing loss (CHL) present with disturbances in working memory and whether these disturbances relate to the size of their receptive vocabularies.

Method

Children 6 to 9 years of age participated. Aspects of working memory were tapped by articulation rate, forward and backward digit span in the auditory and visual modalities, Corsi span, parent surveys, and a sequential encoding task. Articulation rate, digit spans, and Corsi spans were also administered in low-level broadband noise.

Results

CHL and children with normal hearing (CNH) demonstrated auditory advantage in forward serial recall. CHL demonstrated slower articulation rates than CNH, but similar memory spans. CHL with poor executive function presented with poorer performance on the Corsi span task. The presence of background noise had no effect on performance in either group. CHL presented with significantly smaller receptive vocabularies than their CNH peers. Across groups, receptive vocabulary size was positively correlated with digit span in quiet, Corsi span in noise, and articulation rate.

Conclusions

In the presence of mild-to-moderately severe hearing loss, children demonstrated resilient working memory systems. For all children, working memory and vocabulary were related; that is, children with poorer working memory had smaller vocabulary sizes.
Optoelectronic behaviors and carrier dynamics of individual localized luminescent centers in InGaN quantum-well light emitting diodes
Authors: De Suman , Kumar Das Dibyendu , Layek Arunasish , Raja Archana , Kumar Singh Manoj , Bhattacharya Arnab , Dhar Subhabrata , Chowdhury Arindam
Published: December 2011

Spatially, spectrally, and temporally resolved photoluminescence (PL) microscopy was performed on InGaN quantum-well light emitting diodes to probe individual localized luminescent centers arising from disorder induced potential fluctuations. Two energetically distinct localization centers were identified where the photoemission quantum-efficiency (QE) are correlated to the transition energies. PL lifetime measurements on emission centers suggest that activation barrier for non-radiative recombination (NR) processes determines their QE. The disparity in carrier dynamics not only substantiate two diverse mechanisms for localization processes, but also indicate the presence of multiple NR channels even within the trap centers implying their lateral dimensions to span several nanometers.
Flexible, ultrathin, and transparent sound-emitting devices using silver nanowires film
Authors: Tian He , Xie Dan , Yang Yi , Ren Tian-Ling , Lin Yu-Xuan , Chen Yu , Wang Yu-Feng , Zhou Chang-Jian , Peng Ping-Gang , Wang Li-Gang , Liu Li-Tian
Published: December 2011

We demonstrated flexible, ultrathin, and transparent sound-emitting devices (SEDs) using silver nanowires (AgNWs). Large area of AgNWs film on substrate was made by dry transfer technique. The sound emission from the AgNWs was measured as a function of power, distance, and frequency. Significant flat and wide frequency responses occurred between 15 and 45 kHz. The sound pressure was in good agreement with theoretical results. This indicates that a thermoacoustic effect exists in AgNWs. The AgNWs-SEDs can be integrated with the liquid crystal display, which shows the potential to be an important component in flexible electronic systems.
Quantum efficiency control of InGaN/GaN multi-quantum-well structures using Ag/SiO2 core-shell nanoparticles
Authors: Jang Lee-Woon , Sahoo Trilochan , Jeon Dae-Woo , Kim Myoung , Jeon Ju-Won , Jo Dong-Seob , Kim Min-Kyu , Yu Yeon-Tae , Polyakov Alexander Y. , Lee In-Hwan
Published: December 2011

Photoluminescence (PL) efficiency increase up to 2.8 times was observed for GaN/InGaN multi-quantum-well (MQW) structures as a result of deposition of a thin layer of about 40-nm-diameter Ag nanoparticles (NPs) surrounded by SiO2 shell. These Ag/SiO2 NPs were prepared by sol-gel method. The amount of PL intensity enhancement decreased with increasing the SiO2 shell thickness. PL intensity increase was accompanied by corresponding decrease of PL decay time and is ascribed to a strong coupling of MQW region to localized surface plasmons (LSPs) associated with Ag/SiO2 NPs.
Asymmetry of carrier transport leading to efficiency droop in GaInN based light-emitting diodes
Authors: Meyaard David S. , Lin Guan-Bo , Shan Qifeng , Cho Jaehee , Fred Schubert E. , Shim Hyunwook , Kim Min-Ho , Sone Cheolsoo
Published: December 2011

The effect of the asymmetry in carrier concentration and mobility is studied in GaInN pn-junction light-emitting diodes (LEDs). We propose and present experimental evidence that the asymmetry in carrier concentration and mobility, and associated high-level injection phenomena, cause efficiency droop in GaInN LEDs. Low temperatures exacerbate the degree of asymmetry of the junction by reducing acceptor ionization, and shift high-injection-phenomena to lower currents. Accordingly, at temperatures near 80 K, we measure a greater droop compared to room temperature. The analysis of temperature-dependent I–V curves shows an excellent correlation between the onset of high-level injection and the onset of droop.
Detecting surface acoustic wave gyroscopic signal by acousto-optic coupling
Authors: Lu Shuxiang , Chen Shufen , Li Honglang , Fu Lei , Zou Zhengfeng , Meng Yanbin
Published: December 2011

A technique for surface acoustic wave (SAW) gyroscopic signal detection by acousto-optic coupling is presented in this article. The principles of the technique and the detection structure were analyzed, and experiments were conducted using the gyroscope. The static results show that the maximum coupling efficiency obtained using this technique is 80.02% when the acousto-optic interaction length is maintained at 15 mm, the SAW electrical power is 99 mW, and the SAW frequency is 168.201 MHz. When the gyroscope was rotating, a linear voltage-rotation response curve was obtained and the sensitivity was approximately 1.2 mV/deg/s.
Origin of the collapse of tunnel magnetoresistance at high annealing temperature in CoFeB/MgO perpendicular magnetic tunnel junctions
Authors: Gan H. D. , Sato H. , Yamanouchi M. , Ikeda S. , Miura K. , Koizumi R. , Matsukura F. , Ohno H.
Published: December 2011

We have investigated a tunnel magnetoresistance (TMR) ratio of CoFeB/MgO perpendicular magnetic tunnel junctions (p-MTJs) with a 40 nm diameter as a function of an annealing temperature Ta. The TMR ratio at room temperature (RT) increases with increasing Ta and reaches 149% at Ta = 350 °C, and further increase of Ta results in a strong reduction of the TMR ratio, i.e., 2% at Ta = 400 °C. The temperature dependence of the junction resistance versus magnetic field loops reveals that the reduced TMR ratio at RT is due to the disappearance of a stable antiparallel magnetization configuration. We find that reduction of dipole coupling restores the TMR ratio.
Stabilized G protein binding site in the structure of constitutively active metarhodopsin-II
Authors: Deupi Xavier , Edwards Patricia , Singhal Ankita , Nickle Benjamin , Oprian Daniel , Schertler Gebhard , Standfuss Jörg
Published: December 2011

G protein-coupled receptors (GPCR) are seven transmembrane helix proteins that couple binding of extracellular ligands to conformational changes and activation of intracellular G proteins, GPCR kinases, and arrestins. Constitutively active mutants are ubiquitously found among GPCRs and increase the inherent basal activity of the receptor, which often correlates with a pathological outcome. Here, we have used the M257Y
6.40
constitutively active mutant of the photoreceptor rhodopsin in combination with the specific binding of a C-terminal fragment from the G protein alpha subunit (GαCT) to trap a light activated state for crystallization. The structure of the M257Y/GαCT complex contains the agonist all-
trans
-retinal covalently bound to the native binding pocket and resembles the G protein binding metarhodopsin-II conformation obtained by the natural activation mechanism; i.e., illumination of the prebound chromophore 11-
cis
-retinal. The structure further suggests a molecular basis for the constitutive activity of 6.40 substitutions and the strong effect of the introduced tyrosine based on specific interactions with Y223
5.58
in helix 5, Y306
7.53
of the NPxxY motif and R135
3.50
of the E(D)RY motif, highly conserved residues of the G protein binding site.
Assembly of vorticity-aligned hard-sphere colloidal strings in a simple shear flow
Authors: Cheng Xiang , Xu Xinliang , Rice Stuart A. , Dinner Aaron R. , Cohen Itai
Published: December 2011

Colloidal suspensions self-assemble into equilibrium structures ranging from face- and body-centered cubic crystals to binary ionic crystals, and even kagome lattices. When driven out of equilibrium by hydrodynamic interactions, even more diverse structures can be accessed. However, mechanisms underlying out-of-equilibrium assembly are much less understood, though such processes are clearly relevant in many natural and industrial systems. Even in the simple case of hard-sphere colloidal particles under shear, there are conflicting predictions about whether particles link up into string-like structures along the shear flow direction. Here, using confocal microscopy, we measure the shear-induced suspension structure. Surprisingly, rather than flow-aligned strings, we observe log-rolling strings of particles normal to the plane of shear. By employing Stokesian dynamics simulations, we address the mechanism leading to this out-of-equilibrium structure and show that it emerges from a delicate balance between hydrodynamic and interparticle interactions. These results demonstrate a method for assembling large-scale particle structures using shear flows.
Two surfaces on the histone chaperone Rtt106 mediate histone binding, replication, and silencing
Authors: Zunder Rachel M. , Antczak Andrew J. , Berger James M. , Rine Jasper
Published: December 2011

The histone chaperone Rtt106 binds histone H3 acetylated at lysine 56 (H3K56ac) and facilitates nucleosome assembly during several molecular processes. Both the structural basis of this modification-specific recognition and how this recognition informs Rtt106 function are presently unclear. Guided by our crystal structure of Rtt106, we identified two regions on its double-pleckstrin homology domain architecture that mediated histone binding. When histone binding was compromised, Rtt106 localized properly to chromatin but failed to deliver H3K56ac, leading to replication and silencing defects. By mutating analogous regions in the structurally homologous chromatin-reorganizer Pob3, we revealed a conserved histone-binding function for a basic patch found on both proteins. In contrast, a loop connecting two β-strands was required for histone binding by Rtt106 but was dispensable for Pob3 function. Unlike Rtt106, Pob3 histone binding was modification-independent, implicating the loop of Rtt106 in H3K56ac-specific recognition in vivo. Our studies described the structural origins of Rtt106 function, identified a conserved histone-binding surface, and defined a critical role for Rtt106:H3K56ac-binding specificity in silencing and replication-coupled nucleosome turnover.
PathVisio-Validator: a rule-based validation plugin for graphical pathway notations
Authors: Chandan Kumar , van Iersel Martijn P. , Aladjem Mirit I. , Kohn Kurt W. , Luna Augustin
Published: December 2011

Purpose: The PathVisio-Validator plugin aims to simplify the task of producing biological pathway diagrams that follow graphical standardized notations, such as Molecular Interaction Maps or the Systems Biology Graphical Notation. This plugin assists in the creation of pathway diagrams by ensuring correct usage of a notation, and thereby reducing ambiguity when diagrams are shared among biologists. Rulesets, needed in the validation process, can be generated for any graphical notation that a developer desires, using either Schematron or Groovy. The plugin also provides support for filtering validation results, validating on a subset of rules, and distinguishing errors and warnings.

Availability: The PathVisio-Validator plugin works with versions of PathVisio 2.0.11 and later on Windows, Mac OS X and Linux. The plugin along with the instructions, example rulesets for Groovy and Schematron, and Java source code can be downloaded at http://pathvisio.org/wiki/PathVisioValidatorHelp. The software is developed under the open-source Apache 2.0 License and is freely available for both commercial and academic use.

Contact:  chandankmit@gmail.com; augustin@mail.nih.gov

Supplementary information:  Supplementary data are available at Bioinformatics online.
htSeqTools: high-throughput sequencing quality control, processing and visualization in R
Authors: Planet Evarist , Attolini Camille Stephan-Otto , Reina Oscar , Flores Oscar , Rossell David
Published: December 2011

Summary: We provide a Bioconductor package with quality assessment, processing and visualization tools for high-throughput sequencing data, with emphasis in ChIP-seq and RNA-seq studies. It includes detection of outliers and biases, inefficient immuno-precipitation and overamplification artifacts, de novo identification of read-rich genomic regions and visualization of the location and coverage of genomic region lists.

Availability:  www.bioconductor.org

Contact:  david.rossell@irbbarcelona.org

Supplementary information:  Supplementary data available at Bioinformatics online.
PIE the search: searching PubMed literature for protein interaction information
Authors: Kim Sun , Kwon Dongseop , Shin Soo-Yong , Wilbur W. John
Published: December 2011

Motivation: Finding protein-protein interaction (PPI) information from literature is challenging but an important issue. However, keyword search in PubMed® is often time consuming because it requires a series of actions that refine keywords and browse search results until it reaches a goal. Due to the rapid growth of biomedical literature, it has become more difficult for biologists and curators to locate PPI information quickly. Therefore, a tool for prioritizing PPI informative articles can be a useful assistant for finding this PPI-relevant information.

Results: PIE (Protein Interaction information Extraction) the search is a web service implementing a competition-winning approach utilizing word and syntactic analyses by machine learning techniques. For easy user access, PIE the search provides a PubMed-like search environment, but the output is the list of articles prioritized by PPI confidence scores. By obtaining PPI-related articles at high rank, researchers can more easily find the up-to-date PPI information, which cannot be found in manually curated PPI databases.

Availability:  http://www.ncbi.nlm.nih.gov/IRET/PIE/

Contact:  sun.kim@nih.gov

Supplementary information:  Supplementary data are available at Bioinformatics online.
Propofol Neurotoxicity Is Mediated by p75 Neurotrophin Receptor Activation
Authors: Pearn Matthew L. , Hu Yue , Niesman Ingrid R. , Patel Hemal H. , Drummond John C. , Roth David M. , Akassoglou Katerina , Patel Piyush M. , Head Brian P.
Published: December 2011

Background

Propofol exposure to neurons during synaptogenesis results in apoptosis, leading to cognitive dysfunction in adulthood. Previous work from our laboratory showed that isoflurane neurotoxicity occurs through p75 neurotrophin receptor (p75(NTR)) and subsequent cytoskeleton depolymerization. Given that isoflurane and propofol both suppress neuronal activity, we hypothesized that propofol also induces apoptosis in developing neurons through p75(NTR).

Methods

Days in vitro 5-7 neurons were exposed to propofol (3 μM) for 6 h and apoptosis was assessed by cleaved caspase-3 (Cl-Csp3) immunoblot and immunofluorescence microscopy. Primary neurons from p75(NTR-/-) mice or wild-type neurons were treated with propofol, with or without pretreatment with TAT-Pep5 (10 μM, 15 min), a specific p75(NTR) inhibitor. P75(NTR-/-) neurons were transfected for 72 h with a lentiviral vector containing the synapsin-driven p75(NTR) gene (Syn-p75(NTR)) or control vector (Syn-green fluorescent protein) before propofol. To confirm our in vitro findings, wild-type mice and p75(NTR-/-) mice (PND5) were pretreated with either TAT-Pep5 or TAT-ctrl followed by propofol for 6 h.

Results

Neurons exposed to propofol showed a significant increase in Cl-Csp3, an effect attenuated by TAT-Pep5 and hydroxyfasudil. Apoptosis was significantly attenuated in p75(NTR-/-) neurons. In p75(NTR-/-) neurons transfected with Syn-p75(NTR), propofol significantly increased Cl-Csp3 in comparison with Syn-green fluorescent protein-transfected p75(NTR-/-) neurons. Wild-type mice exposed to propofol exhibited increased Cl-Csp3 in the hippocampus, an effect attenuated by TAT-Pep5. By contrast, propofol did not induce apoptosis in p75(NTR-/-) mice.

Conclusion

These results demonstrate that propofol induces apoptosis in developing neurons in vivo and in vitro and implicate a role for p75(NTR) and the downstream effector RhoA kinase.
Additional Value of Upper GI Tract Endoscopy in the Diagnostic Assessment of Childhood IBD
Authors: Hummel Thalia Z. , ten Kate Fiebo J.W. , Reitsma Johannes B. , Benninga Marc A. , Kindermann Angelika
Published: December 2011

Objectives:

For the choice of treatment in children with inflammatory bowel disease (IBD), it is important to make a distinction between Crohn disease (CD) and ulcerative colitis (UC). To look for pathognomonic features of CD, upper gastrointestinal tract (UGT) endoscopy has become part of the routine evaluation of children with suspected IBD; however, pathological changes can also be found in the UGT in patients with UC. The aims of the present study were to establish the role of UGT involvement in the diagnostic assessment of suspected IBD in children and to detect histopathological changes in the UGT mucosa, which can distinguish CD from non‐CD (UC and non‐IBD).

Methods:

Biopsies (colon, ileum, duodenum, stomach, esophagus) from children suspected of having IBD who underwent endoscopy between 2003 and 2008 were reassessed by a blinded, expert pathologist. The histological findings of the UGT were compared with the diagnosis based on ileocolonic biopsies and the final diagnosis.

Results:

In 11% of the children with CD, the diagnosis was based solely on the finding of granulomatous inflammation in the UGT. Focal cryptitis of the duodenum and focally enhanced gastritis were found significantly more frequently in children with CD compared with children with UC and non‐IBD, with a specificity and positive predictive value of 99% and 93% and 87.1% and 78.6%, respectively.

Conclusions:

Histology on ileocolonic biopsies alone is insufficient for a correct diagnosis of CD or UC in children. UGT endoscopy should, therefore, be performed in the diagnostic assessment of all children suspected of having IBD.
Congenital Hepatic Fibrosis and Autosomal Recessive Polycystic Kidney Disease
Authors: Srinath Arvind , Shneider Benjamin L.
Published: December 2011

Objectives:

The published natural history of congenital hepatic fibrosis (CHF) was examined to inform clinical decision making in autosomal recessive polycystic kidney disease (ARPKD).

Methods:

A systematic literature search of the data on CHF, ARPKD, Caroli disease, Caroli syndrome, and type V choledochal cyst was performed to extract data related to portal hypertension, infection, malignancy, mortality, and transplantation.

Results:

Information related to 1230 patients with CHF was extracted from 155 articles. Median and mean age at diagnosis were 2 and 11.2 years, respectively. Median and mean time followed after diagnosis were 5.0 and 7.5 years, respectively (range 0–38 years). Sequelae of portal hypertension (n = 409), cholangitis (n = 152), and malignancy (n = 21) were noted. The nature of the portal hypertension was similar to that in other pediatric conditions (164 with varices, 74 bleeding varices, 81 underwent portosystemic shunting). Documented cholangitis was fatal in 3 of 23 children who were infected after renal transplantation. Twenty‐one patients developed hepatobiliary cancer, with the majority having cholangiocarcinoma (n = 19). Cholangiocarcinoma (CCA) was predominant in individuals older than 40 years with either Caroli syndrome or isolated CHF, not ARPKD (median and mean age at CCA diagnosis were 70.3 and 60.1 years, respectively; range 33–75 years). There was a relative paucity of data on combined liver‐kidney transplantation.

Conclusions:

Clinical decision making in ARPKD should reflect an understanding of the potential issues emanating from CHF. Accepted pediatric specific approaches to portal hypertension are warranted but must take into consideration the stage of renal insufficiency and potential plans for renal transplantation. Cholangitis is a major issue and necessitates anticipatory guidance and awareness. CCA, although a dreaded complication, does not appear to be a major issue during childhood. The indications for liver and combined liver‐kidney transplantation are controversial and warrant further analysis.
Socioenvironmental Factors Associated With Constipation in Hong Kong Children and Rome III Criteria
Authors: Tam Yuk H. , Li Albert M. , So Hung K. , Shit Kam Y. , Pang Kristine K. , Wong Yuen S. , Tsui Siu Y. , Mou Jennifer W. , Chan Kin W. , Lee Kim H.
Published: December 2011

Objective:

Data regarding the prevalence of constipation in the general population of Asian children using internationally standardized definitions are scarce. Environmental factors surrounding a child's day to day living may trigger or perpetuate constipation and encourage postponement of defecation.

Methods:

A territory‐wide cross‐sectional questionnaire survey was conducted in 2318 Hong Kong Chinese elementary school students. Constipation was defined by pediatric Rome III criteria.

Results:

The mean age of the children was 9 ± 1.9 years; 51% were boys. Two hundred eighty‐two children (12.2%, 95% confidence interval [CI] 10.9%–13.5%) were found to have constipation. Children ages 6 to 7 years had the highest prevalence (16.8%, 95% CI 13.8%–19.8%). There was no difference in prevalence between boys and girls (11.6% vs 12.3%; P > 0.05) and between obese and nonobese children (11.5% vs 11.1%; P > 0.05). In univariate analysis, constipation was found to be significantly more prevalent among those children who lived with neither parent, had inadequate company of parents at home, refused to pass bowel movements in school, spent long hours doing homework, had inadequate sleep, and had decreased fiber intake and frequent consumption of fast food (P < 0.05). Multivariate analysis identified refusal to pass bowel movements in school toilets (odds ratio [OR] 1.97, 95% CI 1.42%–2.74%), having dinner with one/both parents <50% of time (OR 1.52, 95% CI 1.01%–2.31%), nighttime sleep <7 hours (OR 1.87, 95% CI 1.04%–3.33%), and frequent consumption of fast food (OR 1.14, 95% CI 1.03%–1.26%) to be independent factors associated with constipation.

Conclusions:

Socioenvironmental factors are associated with childhood constipation, and bringing them to the awareness of the public may help prevent or stop the progression of childhood constipation at its early stages.
Thermosulfurimonas dismutans gen. nov., sp. nov., an extremely thermophilic sulfur-disproportionating bacterium from a deep-sea hydrothermal vent
Authors: Slobodkin A. I. , Reysenbach A.-L. , Slobodkina G. B. , Baslerov R. V. , Kostrikina N. A. , Wagner I. D. , Bonch-Osmolovskaya E. A.
Published: December 2011

An extremely thermophilic, anaerobic, chemolithoautotrophic bacterium (strain S95T) was isolated from a deep-sea hydrothermal vent chimney located on the Eastern Lau Spreading Center, Pacific Ocean, at a depth of 1910 m. Cells of strain S95Twere oval to short Gram-negative rods, 0.5–0.6 µm in diameter and 1.0–1.5 µm in length, growing singly or in pairs. Cells were motile with a single polar flagellum. The temperature range for growth was 50–92 °C, with an optimum at 74 °C. The pH range for growth was 5.5–8.0, with an optimum at pH 7.0. Growth of strain S95Twas observed at NaCl concentrations ranging from 1.5 to 3.5 % (w/v). Strain S95Tgrew anaerobically with elemental sulfur as an energy source and bicarbonate/CO2as a carbon source. Elemental sulfur was disproportionated to sulfide and sulfate. Growth was enhanced in the presence of poorly crystalline iron(III) oxide (ferrihydrite) as a sulfide-scavenging agent. Strain S95Twas also able to grow by disproportionation of thiosulfate and sulfite. Sulfate was not used as an electron acceptor. Analysis of the 16S rRNA gene sequence revealed that the isolate belongs to the phylumThermodesulfobacteria. On the basis of its physiological properties and results of phylogenetic analyses, it is proposed that the isolate represents the sole species of a new genus,Thermosulfurimonas dismutansgen. nov., sp. nov.; S95T( = DSM 24515T = VKM B-2683T) is the type strain of the type species. This is the first description of a thermophilic micro-organism that disproportionates elemental sulfur.