bluuebunny/crossref_metadata_2025 huggingface dataset:
Insertion of parylene-N films in electron transport layer: An effective approach for efficiency improvement of organic light emitting diodes
Authors: Hu Y. M. , He Y. , Chen X. Q. , Zhan Y. Q. , You Y. T. , Xuxie H. N. , Peng H.
Published: November 2012

Efficiency of tris (8-hydroxyquinolato) aluminum (Alq3) based organic light emitting diodes has been obviously improved by inserting a parylene-N (PPXN) buffer layer with proper thickness and location in the Alq3 layer. For an optimized PPXN inserted structure, current efficiency of 6.89 cd/A and luminous power efficiency of 1.85 lm/W were achieved; both are 42% higher than the 4.84 cd/A and 1.30 lm/W of the buffer free structure, respectively. The light emitting spectra of 4-dicyanomethylene-2-methyl-6-p-dimethylaminostyryl-4H-pyran (DCM) doped Alq3 (Alq3:DCM) strips showed the electron current enhancement resulted in the observed efficiency improvement of PPXN inserted devices. The device current evolutions were explained by nonuniform potential distribution in the organic layer and the tunneling barrier reduction.
Enhancing the spin properties of shallow implanted nitrogen vacancy centers in diamond by epitaxial overgrowth
Authors: Staudacher T. , Ziem F. , Häussler L. , Stöhr R. , Steinert S. , Reinhard F. , Scharpf J. , Denisenko A. , Wrachtrup J.
Published: November 2012

Scaling of diamond defect center based quantum registers relies on the ability to position nitrogen vacancy (NV) centers with high spatial resolution. Using ion implantation, shallow (<10 nm) NVs can be placed with accuracy below 20 nm, but generally show reduced spin properties compared to bulk NVs. We demonstrate the enhancement of spin properties for shallow implanted NVs using a diamond overgrowth technique. An increase of coherence times up to an order of magnitude (T2 = 250 μs) was achieved, ms decoherence times were realized using dynamical decoupling. This marks a further step towards achieving strong coupling among defects positioned with nm precision.
Strain dependence of transition temperatures and structural symmetry of BiFeO3 within the tetragonal-like structure
Authors: Siemons W. , MacDougall G. J. , Aczel A. A. , Zarestky J. L. , Biegalski M. D. , Liang S. , Dagotto E. , Nagler S. E. , Christen H. M.
Published: November 2012

The influence of strain-imposed in-plane lattice symmetry on the structural and magnetic properties of tetragonal-like BiFeO3 is investigated by x-ray and elastic neutron scattering. We find that an increase in the in-plane distortion results in an increase of the Néel temperature from 313 ± 5 K to 324 ± 3 K for films grown on YAlO3 and LaAlO3, respectively. The change in magnetic ordering temperature is reproduced in three-dimensional Heisenberg Monte-Carlo simulations. These results show that strain cannot be treated as a single scalar number or simply as a direct consequence of the lattice mismatch between the film material and the substrate.
Dynamic nuclear spin polarization in an all-semiconductor spin injection device with (Ga,Mn)As/n-GaAs spin Esaki diode
Authors: Shiogai J. , Ciorga M. , Utz M. , Schuh D. , Arakawa T. , Kohda M. , Kobayashi K. , Ono T. , Wegscheider W. , Weiss D. , Nitta J.
Published: November 2012

We investigate the dynamic nuclear spin polarization in an n-GaAs lateral channel induced by electrical spin injection from a (Ga,Mn)As/n-GaAs spin Esaki diode. Signatures of nuclear spin polarization are studied in both three-terminal and non-local voltage signals, where a strong electron spin depolarization feature is observed close to zero magnetic field. This is due to the large nuclear field induced in the channel through hyperfine interaction between injected electron spins and localized nuclear spins. We study the time evolution of the dynamic nuclear spin polarization and evaluate polarization and relaxation times of nuclear spins in the channel.
Complex charge ordering phenomena in La1−xSrxFeO3−δ investigated by mechanical spectroscopy
Authors: Ying X. N.
Published: November 2012

The presence of complex charge ordering phenomena in La1−xSrxFeO3−δ (x = 0.55, 0.60, 0.67, and 0.72) has been studied by kilohertz mechanical spectroscopy. With the decrease in temperature, a step increase of the modulus and decrease of internal friction were observed around the charge ordering transition temperature in La0.33Sr0.67FeO3−δ. This characteristic behavior preserves in La1−xSrxFeO3−δ (x = 0.55, 0.60, and 0.72), which suggests the existence of charge ordering. An internal friction peak around 160 K in La1−xSrxFeO3−δ (x = 0.55 and 0.60) is identified as an elastic manifestation of magnetic freezing. The description of the electronic phase diagram is obtained and it supports an ionic picture.
Enhanced output of nanostructured piezoelectric arrays via controlled matrix/transducer interfacial interactions
Authors: Kim Kanguk , Sirbuly Donald J.
Published: November 2012

Here we investigate the effects of interfacial interactions and the mechanical properties of the matrix on the piezoelectric output of vertically aligned ZnO nanowires (NWs) embedded in a polymer matrix. This matrix-assisted energy conversion platform allows non-mechanical energy sources to apply stress to the NWs, producing direct-current outputs. The slip conditions at the matrix/transducer interface were experimentally modified using adhesion promoters and different molecular weight matrices which were compared to finite element method simulations. The no-slip conditions showed a 2-fold enhancement in the output whereas a 72% increase in the matrix modulus resulted in a 2.5-fold enhancement.
An all C60 vertical transistor for high frequency and high current density applications
Authors: Fischer Axel , Scholz Reinhard , Leo Karl , Lüssem Björn
Published: November 2012

We present a vertical organic transistor with high operating frequencies and high current densities based on the organic semiconductor C60. In this vertical organic triode (VOT), doped layers can easily be inserted to efficiently reduce the contact resistance without the need for additional structuring. Combined with annealing at elevated temperatures (150°C for 2 h), we achieve a current density of 1 A/cm2 at a driving voltage of 3 V together with an extremely high transconductance of 30 mS. The transistor retains a voltage gain above 1 up to 1.5 MHz in a simple inverter circuit.
Vibrational absorption and vibrational circular dichroism spectra of leucine in water under different pH conditions: Hydrogen-bonding interactions with water
Authors: Poopari Mohammad Reza , Zhu Peiyan , Dezhahang Zahra , Xu Yunjie
Published: November 2012

Vibrational absorption (VA) and vibrational circular dichroism (VCD) spectroscopy have been used to study leucine, a flexible branched-chain amino acid, in aqueous solution. The VA spectra in the range of 1800–1250 cm−1 of leucine in D2O under three representative pHs from strongly acidic (pH = 1), near neutral (pH = 6), to strongly basic (pH = 13), have been measured. The related VCD spectrum has been obtained under near neutral condition. Searches have been carried out to identify the most stable conformers of the Zwitterionic, protonated, and deprotonated forms of leucine in water. The geometry optimization, harmonic frequency calculations, and VA and VCD intensities have been computed at the B3LYP/6-311++G(d,p) level with the implicit polarizable continuum solvation model. While the observed VA spectra under three pHs can be well interpreted with the inclusion of the implicit solvation model, both implicit and explicit solvation models have been found to be crucial for the adequate interpretation of the complex VCD features observed. Molecular dynamics simulations and radial distribution functions have been used to aid the modeling of the leucine-(water)N clusters. It has been recognized that the insertion of a water molecule between the COO− and NH3+ functional groups in the explicit solvated clusters is critical to reproduce the VCD signatures observed. Furthermore, the inclusion of the implicit bulk water environment has been found to be essential to lock water molecules, which are directly hydrogen bonded to leucine, into the positions expected in solution. The application of the explicit and implicit solvation models simultaneously allows new insights into the hydrogen bonding network surrounding leucine in aqueous solution and the role of the surrounding bulk water in stabilizing such hydrogen-bonding network.
Quantum coherence effects in hybrid nanoparticle molecules in the presence of ultra-short dephasing times
Authors: Sadeghi S. M.
Published: November 2012

We study quantum coherence effects in single nanoparticle systems consisting of a semiconductor quantum dot and a metallic nanoparticle in the presence of the ultra-short dephasing times of the quantum dots. The results suggest that coherent exciton-plasmon coupling can sustain the collective molecular resonances (plasmonic meta-resonances) of these systems at about room temperature. We investigate quantum optical properties of the quantum dots under this condition, demonstrating formation of ultranarrow gain and absorption spectral lines. These results are discussed in terms of plasmonic normalization of coherent population oscillation and the collective states of the nanoparticle systems.
Tip expansion in a laser assisted scanning tunneling microscope
Authors: Xie Nan , Gong Huiqi , Yan Shichao , Zhao Jimin , Shan Xinyan , Guo Yang , Sun Qian , Lu Xinghua
Published: November 2012

The thermal expansion of a scanning tunneling microscope tip induced by femtosecond laser is investigated with various parameters including laser power, modulation frequency, illumination spot, and laser wavelength. The magnitude of tip expansion is measured to be proportional to the laser power. The response bandwidth is closely related to the length of the tip cone section, which is consistent with a two-rod model simulation. While visible lasers produce significant tip expansion, deep ultraviolet and near infrared lasers result in significantly reduced expansion magnitude, which can be explained with the tip induced surface plasmon in the tunneling junction.
Surface leakage investigation via gated type-II InAs/GaSb long-wavelength infrared photodetectors
Authors: Chen G. , Huang E. K. , Hoang A. M. , Bogdanov S. , Darvish S. R. , Razeghi M.
Published: November 2012

By using gating technique, surface leakage generated by SiO2 passivation in long-wavelength infrared type-II superlattice photodetector is suppressed, and different surface leakage mechanisms are disclosed. By reducing the SiO2 passivation layer thickness, the saturated gated bias is reduced to −4.5 V. At 77 K, dark current densities of gated devices are reduced by more than 2 orders of magnitude, with 3071 Ω cm2 differential-resistance-area product at −100 mV. With quantum efficiency of 50%, the 11μm 50% cut-off gated photodiode has a specific detectivity of 7 × 1011 Jones, and the detectivity stays above 2 × 1011 Jones from 0 to −500 mV operation bias.
Role of ethylene on surface oxidation of TiO2(110)
Authors: Murata Y. , Petrova V. , Petrov I. , Ciobanu C. V. , Kodambaka S.
Published: November 2012

Using in situ high-temperature (700-1000 K) scanning tunneling microscopy (STM), we studied the influence of ethylene on the surface dynamics of oxygen-deficient, rutile-structured TiO2(110). STM images were acquired during annealing the sample as a function of time, oxygen and ethylene pressures, and temperature. With increasing oxygen pressure and/or decreasing temperature, TiO2(110) surface mass increased, consistent with previous results. Interestingly, annealing the sample in ethylene with traces of oxygen also results in the growth of TiO2 at higher rates than those observed during annealing in pure oxygen. Our results indicate that ethylene promotes oxidation of TiO2(110).
Densification of functional plasma polymers by momentum transfer during film growth
Authors: Hegemann Dirk , Körner Enrico , Blanchard Noémi , Drabik Martin , Guimond Sébastien
Published: November 2012

Functional plasma polymers were deposited from pure ethylene discharges and with the addition of carbon dioxide or ammonia. The incorporation of oxygen and nitrogen-containing functional groups depends on the fragmentation in the gas phase as well as on the densification during film growth. While a minimum energy per deposited carbon atom is required for cross-linking, the densification and accompanying reduction of functional group incorporation was found to scale linearly with momentum transfer through ion bombardment during film growth.
Enhanced thermoelectric figure-of-merit in spark plasma sintered nanostructured n-type SiGe alloys
Authors: Bathula Sivaiah , Jayasimhadri M. , Singh Nidhi , Srivastava A. K. , Pulikkotil Jiji , Dhar Ajay , Budhani R. C.
Published: November 2012

We report a significant enhancement in the thermoelectric figure-of-merit of phosphorous doped nanostructured n-type Si80Ge20 alloys, which were synthesized employing high energy ball milling followed by rapid-heating using spark plasma sintering. The rapid-heating rates, used in spark plasma sintering, allow the achievement of near-theoretical density in the sintered alloys, while retaining the nanostructural features introduced by ball-milling. The nanostructured alloys display a low thermal conductivity (2.3 W/mK) and a high value of Seebeck coefficient (−290 μV/K) resulting in a significant enhancement in ZT to about 1.5 at 900 °C, which is so far the highest reported value for n-type Si80Ge20 alloys.
Ultraviolet whispering-gallery-mode lasing in ZnO micro/nano sphere crystal
Authors: Okazaki Kota , Shimogaki Tetsuya , Fusazaki Koshi , Higashihata Mitsuhiro , Nakamura Daisuke , Koshizaki Naoto , Okada Tatsuo
Published: November 2012

We report ultraviolet (UV) whispering-gallery-mode (WGM) lasing in a zinc oxide (ZnO) micro/nanosphere crystal fabricated by simply ablating a ZnO sintered target, which was much more productive method without any time-consuming crystal-growth process. The lasing spectral mode spacing was controlled by changing the diameters, and single-mode lasing was realized from a ZnO nanosphere. Experimental results were in good agreement with predictions from WGM theories. Since the ZnO sphere can operate as an active WGM refractometric sensor for small molecules in UV region, high sensitivity enhanced by high quality factor, refractive index, and wavelength dispersion can be expected.
Highly crystallized poly (lactic acid) under high pressure
Authors: Zhang Jin , Yan Ding-Xiang , Xu Jia-Zhuang , Huang Hua-Dong , Lei Jun , Li Zhong-Ming
Published: November 2012

Biodegradable poly (lactic acid) (PLA) usually has a crystallinity less than 10% due to its poor crystallization ability. In this work, we found high pressure could significantly facilitate formation of crystallites of PLA, resulting in a crystallinity high up to 66.3% at pressure and temperature of 300 MPa and 185 ºC. High-pressure induced crystalline reorganization and lamellar thickening led to two melting temperatures in the highly crystallized PLA but without cold crystallization compared to the normal-pressure crystallized PLA. Temperature dependence of high-pressure crystallization of PLA suggested desirable crystallization temperatures for highly crystallized PLA products.
Heptahelical protein PQLC2 is a lysosomal cationic amino acid exporter underlying the action of cysteamine in cystinosis therapy
Authors: Jézégou Adrien , Llinares Elisa , Anne Christine , Kieffer-Jaquinod Sylvie , O’Regan Seana , Aupetit Joëlle , Chabli Allel , Sagné Corinne , Debacker Cécile , Chadefaux-Vekemans Bernadette , Journet Agnès , André Bruno , Gasnier Bruno
Published: November 2012

Cystinosin, the lysosomal cystine exporter defective in cystinosis, is the founding member of a family of heptahelical membrane proteins related to bacteriorhodopsin and characterized by a duplicated motif termed the PQ loop. PQ-loop proteins are more frequent in eukaryotes than in prokaryotes; except for cystinosin, their molecular function remains elusive. In this study, we report that three yeast PQ-loop proteins of unknown function, Ypq1, Ypq2, and Ypq3, localize to the vacuolar membrane and are involved in homeostasis of cationic amino acids (CAAs). We also show that PQLC2, a mammalian PQ-loop protein closely related to yeast Ypq proteins, localizes to lysosomes and catalyzes a robust, electrogenic transport that is selective for CAAs and strongly activated at low extracytosolic pH. Heterologous expression of PQLC2 at the yeast vacuole rescues the resistance phenotype of an
ypq2
mutant to canavanine, a toxic analog of arginine efficiently transported by PQLC2. Finally, PQLC2 transports a lysine-like mixed disulfide that serves as a chemical intermediate in cysteamine therapy of cystinosis, and PQLC2 gene silencing trapped this intermediate in cystinotic cells. We conclude that PQLC2 and Ypq1–3 proteins are lysosomal/vacuolar exporters of CAAs and suggest that small-molecule transport is a conserved feature of the PQ-loop protein family, in agreement with its distant similarity to SWEET sugar transporters and to the mitochondrial pyruvate carrier. The elucidation of PQLC2 function may help improve cysteamine therapy. It may also clarify the origin of CAA abnormalities in Batten disease.
Identification of nonferritin mitochondrial iron deposits in a mouse model of Friedreich ataxia
Authors: Whitnall Megan , Rahmanto Yohan Suryo , Huang Michael L.-H. , Saletta Federica , Lok Hiu Chuen , Gutiérrez Lucía , Lázaro Francisco J. , Fleming Adam J. , St. Pierre Tim G. , Mikhael Marc R. , Ponka Prem , Richardson Des R.
Published: November 2012

There is no effective treatment for the cardiomyopathy of the most common autosomal recessive ataxia, Friedreich ataxia (FA). This disease is due to decreased expression of the mitochondrial protein, frataxin, which leads to alterations in mitochondrial iron (Fe) metabolism. The identification of potentially toxic mitochondrial Fe deposits in FA suggests Fe plays a role in its pathogenesis. Studies using the muscle creatine kinase (MCK) conditional frataxin knockout mouse that mirrors the disease have demonstrated frataxin deletion alters cardiac Fe metabolism. Indeed, there are pronounced changes in Fe trafficking away from the cytosol to the mitochondrion, leading to a cytosolic Fe deficiency. Considering Fe deficiency can induce apoptosis and cell death, we examined the effect of dietary Fe supplementation, which led to body Fe loading and limited the cardiac hypertrophy in MCK mutants. Furthermore, this study indicates a unique effect of heart and skeletal muscle-specific frataxin deletion on systemic Fe metabolism. Namely, frataxin deletion induces a signaling mechanism to increase systemic Fe levels and Fe loading in tissues where frataxin expression is intact (i.e., liver, kidney, and spleen). Examining the mutant heart, native size-exclusion chromatography, transmission electron microscopy, Mössbauer spectroscopy, and magnetic susceptibility measurements demonstrated that in the absence of frataxin, mitochondria contained biomineral Fe aggregates, which were distinctly different from isolated mammalian ferritin molecules. These mitochondrial aggregates of Fe, phosphorus, and sulfur, probably contribute to the oxidative stress and pathology observed in the absence of frataxin.
Calaxin drives sperm chemotaxis by Ca
2+
-mediated direct modulation of a dynein motor
Authors: Mizuno Katsutoshi , Shiba Kogiku , Okai Masahiko , Takahashi Yusuke , Shitaka Yuji , Oiwa Kazuhiro , Tanokura Masaru , Inaba Kazuo
Published: November 2012

Sperm chemotaxis occurs widely in animals and plants and plays an important role in the success of fertilization. Several studies have recently demonstrated that Ca
2+
influx through specific Ca
2+
channels is a prerequisite for sperm chemotactic movement. However, the regulator that modulates flagellar movement in response to Ca
2+
is unknown. Here we show that a neuronal calcium sensor, calaxin, directly acts on outer-arm dynein and regulates specific flagellar movement during sperm chemotaxis. Calaxin inhibition resulted in significant loss of sperm chemotactic movement, despite normal increases in intracellular calcium concentration. Using a demembranated sperm model, we demonstrate that calaxin is essential for generation and propagation of Ca
2+
-induced asymmetric flagellar bending. An in vitro motility assay revealed that calaxin directly suppressed the velocity of microtubule sliding by outer-arm dynein at high Ca
2+
concentrations. This study describes the missing link between chemoattractant-mediated Ca
2+
signaling and motor-driven microtubule sliding during sperm chemotaxis.
Is the Dutch Delay of Principle B Effect dependent on verb type?
Authors: Akker Saskia van den , Hoeks John , Spenader Jennifer K. , Hendriks Petra
Published: November 2012

Dutch children interpret reflexives correctly from age 4 on, but frequently misinterpret object pronouns as coreferring with the local subject until age 6. We investigated whether this so-called Delay of Principle B Effect (DPBE) differs by verb type. We tested 47 children between 4 and 6 years old with regular transitive verbs (e.g., to hit) and grooming verbs (e.g., to wash), verbs that often refer to self-directed actions. In general, children displaying the DPBE performed equally well on both verb types. In contrast, children who performed poorly on pronouns and reflexives made significantly more errors interpreting pronouns with grooming verbs than with transitive verbs. This suggests that young children are aware of the tendency for certain events to be self-directed. However, our results show they only apply this information when interpreting pronouns but not reflectives, indicating that they also use their grammatical knowledge.
Deaccentuation in Dutch as a second language
Authors: Caspers Johanneke , Bosma Evelyn , Kramm Frida , Reya Polona
Published: November 2012

A non-native accent in a second language is usually not restricted to the segmental domain — consonants and vowels — but is also noticeable in the suprasegmental domain, which includes phenomena such as word stress and sentence accent. The central question in this paper is whether advanced non-native speakers of Dutch produce pitch accent errors as a result of deaccentuation of given information in ‘verum focus’ sentences (‘… but I don’t READ books’). We expected the correct position of the pitch accent to be problematic for speakers with a non-Germanic mother tongue (L1) as compared to speakers with a Germanic L1. Non-native speakers of Dutch with Hungarian or German as L1 and a control group of native Dutch speakers read aloud a text containing a number of verum focus sentences. The results reveal that the Hungarian speakers tend to focus the negation, while the German speakers of Dutch as a second language highlight the finite verb, just as the native speakers do.
Neuter gender in a sexless language
Authors: de Dreu Merijn , Buell Leston
Published: November 2012

In some Germanic languages, neuter gender is used both as a lexical gender and for certain grammatical functions, while in Romance languages, neuter gender is only employed for grammatical functions. Zulu, a Bantu language, has a much more elaborate noun class system than those languages, but one not rooted in sex or animacy as in Germanic or Romance. However, it is shown that Zulu noun class 17 is used for the same range of grammatical functions as neuter gender in Indo-European. Specifically, Indo-European neuter gender and Zulu class 17 are used when the referent has no specific noun class properties, for expletive subjects, and as the subject of nominal predication, even when the referent is human. Aside from its use in some languages as a gender for nouns, then, neuter gender can be understood as a cluster of grammatical functions, independently of the way the lexicon is organized.
Can speech pitch perception be measured language-independently?
Authors: Heeren Willemijn , Avram Andrei A. , Cardinaletti Anna , Coene Martine , Volpato Francesca
Published: November 2012

Recently, a test battery was developed with the goal of assessing perception of F0 in linguistic, but language-independent, contexts by listeners from different language backgrounds. Test validation using Dutch, Italian and Romanian listeners generally showed comparable performance. In this study we present cross-language results on how F0 contributes to prominence perception in Dutch (a Germanic language) and Italian and Romanian (Romance languages), as well as on how F0 trades off with duration, a second important cue to prominence. We discuss implications of these results for the language-independent set-up of the test battery.
Obviation properties of the d-pronoun in Dutch
Authors: van Kampen Jacqueline
Published: November 2012

The present paper discusses a decisive difference in Dutch between the d(emonstrative)-pronoun and the p(ersonal)-pronoun. The d-pronoun is a grammatical device for focus-to-topic-shift. Van Kampen (2010) derived this from two properties of the d-pronoun
, neither of them present in the p-pronoun. (i) The d-pronoun obviates as antecedent all arguments except the first preceding focus. (ii) The d-pronoun introduces the new topic of its sentence. The present paper derives three other properties of the d-pronoun. The d-pronoun allows a bound variable reading in certain complex CPs (Section 2). A d-pronoun in a temporal adjunct CP can bind a quantifier in the matrix CP
, but it does not do so in non-temporal adjunct CPs (Section 3), nor in complement CPs (Section 4). Since the d-pronoun is not only an anaphor locally bound by the first preceding focus
, but also a discourse anaphor
, it invites a reconsideration of the notion ‘bound anaphor’ in the Binding Theory.
Subject interpretation of object questions by Dutch 5-year-olds
Authors: Metz Marijke , van Hout Angeliek , Lely Heather van der
Published: November 2012

We investigated the interpretation of Dutch wie ‘who’- and welke ‘which’-questions in Dutch 5-year-olds. In contrast to wh-questions in many languages, Dutch wh-questions are structurally ambiguous between a subject and an object reading. We used test items in which the ambiguity was resolved by number agreement. The participants (N = 20) heard a wh-question and had to choose the corresponding picture out of a set of four; this method revealed their interpretation as either subject or object question. The results show that 5-year-olds interpret all question types as subject questions, independent of the agreement cues. Thus, they effectively do not attend to the agreement mismatch that this interpretation causes for the object questions. These errors suggest an overly strong subject-first bias in 5-year-olds. We argue that number agreement is too weak a cue for children to overcome this tendency.
The 12321 model of Dutch spelling acquisition
Authors: Neijt Anneke , Peters M. , Zuidema Johan
Published: November 2012

We propose that Dutch children acquire and use knowledge of Dutch spelling through a series of stages we call the 12321 model. At first, a single phase for the mapping of speech onto writing suffices, but in later stages of instruction, two or three mapping phases are needed. This is one aspect of our hypothesis about spelling development. The other aspect relates to experience, which allows for storage of the mapping relation between larger parts of speech and concomitant larger strings of letters. As a consequence, the necessary number of mapping phases for words or parts of words that are frequently used decreases from three to two, and ultimately to one once more — hence the name 12321 model.
Easy to (re)analyse
Authors: Zwart C. Jan-Wouter
Published: November 2012

Within minimalism, we may assume derivations to involve subderivations, connected by the interface components dealing with sound and meaning (layered derivations). If so, complex adjectival constructions involving predicates like tough/easy (as in John is easy to please) receive a natural account in terms of reanalysis taking place at these interface components, turning a complex adjectival construction into a simplex adjective which can be merged in predicative or attributive position in the next derivation layer. Arguments against reanalysis address earlier, more complicated conceptions of reanalysis, and fail to distinguish plain and expanded tough-constructions, the latter not showing any reanalysis characteristics. In a layered-derivation cum reanalysis approach, the arguments for empty operator movement in the embedded infinitival clause disappear, and the reanalysed construction shows the properties of an adjectival passive instead.
Functional analysis in the study of second language acquisition
Authors: Dressler Wolfgang U. , Dziubalska-Kolaczyk Katarzyna
Published: November 2012

Studies of second language acquisition (SLA) are often devoid of sufficient theoretical background. With this contribution we want to demonstrate the suitability of a theoretical functional approach to this area and especially to the analysis of the learner's perspective. The theoretical background is, on the one hand, functional explanation, and on the other, semiotically based "natural linguistics", with an emphasis on phonology and text linguistics. We will differentiate two types of functional explanation, both applicable to SLA (3.2) and deal with several problems of functional analysis which correspond to recurrent problems of SLA analysis (3.3), such as goal conflicts, competition of strategies (multiple strategies), multi-functionality, alternative explanations, and the vexing question as to what extent form follows function. Having established and illustrated (with SLA material) four types of functional deficiencies (3.4), we will deal with the learner's progress from a functional point of view as against the background of selected current views on SLA (4).
The role of psychological resilience and positive affect in risky decision‐making
Authors: Xing Cai , Sun Jian‐min
Published: November 2012

Past studies suggest that positive affect produces a wide range of desirable outcomes because it helps people build lasting resources. It may be assumed that these resources build on positive affect over time, which in turn may explain the beneficial effect of positive affect in stressful encounters. However, this assumption has not been directly tested by empirical studies. This question is important in that it helps clarify the underlying mechanism through which individuals with more positive affect might respond adaptively to adverse situations. Using a stressful task that included 20 rounds of risky investment choices, the current study examined whether psychological resilience, an important personal resource fuelled by positive affect, could account for the beneficial effects of positive affect. Specifically, we examined the relationship between individuals’ baseline levels of positive affect, their levels of psychological resilience, their choices in a risky investment decision task, and their levels of positive affect on the final investment task. The results demonstrate that psychological resilience could indeed help explain happier people's enhanced outcomes: They chose higher return although more risky investment options and experienced more positive affect at the end of the task. The current study supports the notion that individuals who experience frequent positive affect thrive through various challenges not simply because they feel good, but because they have resources that they can utilize to deal with these challenges. Findings from the present study support further investigation of the important relationship between specific positive affect, psychological resilience, and performance in risky investment tasks.
A Pilot Study of Interpersonal Psychotherapy for Alcohol-Dependent Women with Co-Occurring Major Depression
Authors: Gamble Stephanie A. , Talbot Nancy L. , Cashman-Brown Sarah M. , He Hua , Poleshuck Ellen L. , Connors Gerard J. , Conner Kenneth R.
Published: November 2012

Background

Co-occurring major depression is prevalent among alcohol-dependent women and is a risk factor for poor treatment outcomes. This uncontrolled pilot study tested the feasibility, acceptability, and initial effects of interpersonal psychotherapy (IPT) for women with co-occurring alcohol dependence and major depression (AD-MD) in an outpatient community addiction treatment program.

Methods

Fourteen female patients with concurrent diagnoses of alcohol dependence and major depression participated. Assessments were conducted at baseline, midtreatment (8 and 16 weeks), posttreatment (24 weeks), and follow-up (32 weeks).

Results

Participants attended a mode of 8 out of 8 possible sessions of IPT in addition to their routine addiction care, and reported high treatment satisfaction on the Client Satisfaction Questionnaire-8. Women's drinking behavior, depressive symptoms, and interpersonal functioning improved significantly over the treatment period and were sustained at follow-up.

Conclusions

These preliminary findings suggest that IPT is a feasible, highly acceptable adjunctive behavioral intervention for AD-MD women.
Infections Acquired by Adults Who Receive Extracorporeal Membrane Oxygenation Risk Factors and Outcome
Authors: Aubron Cecile , Cheng Allen C. , Pilcher David , Leong Tim , Magrin Geoff , Cooper D. Jamie , Scheinkestel Carlos , Pellegrino Vince
Published: November 2012

Objectives.

To analyze infectious complications that occur in patients who receive extracorporeal membrane oxygenation (ECMO), associated risk factors, and consequences on patient outcome.

Design.

Retrospective observational survey from 2005 through 2011.

Participants and Setting.

Patients who required ECMO in an Australian referral center.

Methods.

Cases of bloodstream infection (BSI), catheter-associated urinary tract infection (CAUTI), and ventilator-associated pneumonia (YAP) that occurred in patients who received ECMO were analyzed.

Results.

A total of 146 ECMO procedures were performed for more than 48 hours in 139 patients, and 36 patients had a total of 46 infections (30.1 infectious episodes per 1,000 days of ECMO). They included 24 cases of BSI, 6 of them secondary to VAP; 23 cases of VAP; and 5 cases of CAUTI. The most frequent pathogens were Enterobacteriaceae (found in 16 of 46 cases), and Candida was the most common cause of BSI (in 9 of 24 cases). The Sequential Organ Failure Assessment score before ECMO initiation and the number of days of support were independenuy associated with a risk of BSI, with odds ratios of 1.23 (95% confidence interval [CI], 1.03-1.47; P = .019) and 1.08(95% CI, 1.03-1.19]; P = .006), respectively. Infected patients did not have a significantly higher mortality compared with uninfected patients (41.7% vs 32%; P = .315), but intensive care unit length of stay (16 days [interquartile range, 8-26 days] vs 11 days [IQR, 4-19 days]; P = .012) and hospital length of stay (33.5 days [interquartile range, 15.5-55.5] vs 24 days [interquartile range, 9-42 days]; P = .029) were longer.

Conclusion.

The probability of infection increased with the duration of support and the severity of illness before initiation of ECMO. Infections affected length of stay but did not have an impact on mortality.
Defining Relatedness in Studies of Transmission of Antimicrobial-Resistant Organisms Variability in Definitions across Studies and Impact of Different Approaches on Study Conclusions
Authors: Greenblatt Rachel M. , Han Jennifer H. , Nachamkin Irving , Tolomeo Pam , Lautenbach Ebbing
Published: November 2012

Objective.

Comparison of studies evaluating patient-to-patient transmission of organisms is difficult, given the lack of standardized criteria. We used fluoroquinolone-resistantEscherichia coli(FQREC) as a model to characterize variability in definitions of relatedness across studies and to evaluate the resultant impact on study conclusions.

Design.

Narrative review and cohort study.

Methods.

The narrative review compared relatedness criteria across studies of FQREC. Additionally, an existing database was used to compare relatedness of isolates on the basis of molecular criteria alone versus molecular plus clinical criteria with different temporal cutoffs (hospitalization overlap of ≥1 day or allowance for nonoverlap of hospitalization dates of ≤7 days or ≤30 days).

Results.

Forty-six articles met narrative review inclusion criteria. Sixteen studies exclusively utilized molecular criteria to define relatedness. Thirty studies included molecular and clinical criteria. Of these, 6 included temporal data (ie, time period of isolate identification), 10 included patient location, and 14 included proximity and temporal criteria. For the database analysis, 353 patients were colonized with FQREC. There were 2 main clusters containing 48 and 17 related isolates within 49 pulsed-field gel electrophoresis types. Among the clusters, 18.4% of isolates were related by molecular criteria. Incorporating clinical criteria, fewer isolates were considered related: 5.7% of isolates using 30-day criteria, 3.1% using 7-day criteria, and 1.4% using 1-day overlap.

Conclusions.

There is considerable variability in definitions of relatedness of FQREC. Utilizing molecular criteria alone to define relatedness overestimates transmission compared with definitions including clinical criteria. Standard definitions of relatedness in studies of antimicrobial-resistant organisms are needed.
An empirical Bayes approach for analysis of diverse periodic trends in time-course gene expression data
Authors: Kocak Mehmet , Olusegun George E. , Pyne Saumyadipta , Pounds Stanley
Published: November 2012

Motivation: There is a substantial body of works in the biology literature that seeks to characterize the cyclic behavior of genes during cell division. Gene expression microarrays made it possible to measure the expression profiles of thousands of genes simultaneously in time-course experiments to assess changes in the expression levels of genes over time. In this context, the commonly used procedures for testing include the permutation test by de Lichtenberg et al. and the Fisher’s G-test, both of which are designed to evaluate periodicity against noise. However, it is possible that a gene of interest may have expression that is neither cyclic nor just noise. Thus, there is a need for a new test for periodicity that can identify cyclic patterns against not only noise but also other non-cyclic patterns such as linear, quadratic or higher order polynomial patterns.

Results: To address this weakness, we have introduced an empirical Bayes approach to test for periodicity and compare its performance in terms of sensitivity and specificity with that of the permutation test and Fisher’s G-test through extensive simulations and by application to a set of time-course experiments on the Schizosaccharomyces pombe cell-cycle gene expression. We use ‘conserved’ and ‘cycling’ genes by Lu et al. to assess the sensitivity and CESR genes by Chenet al. to assess the specificity of our new empirical Bayes method.

Availability and implementation: The SAS Macro for our empirical Bayes test for periodicity is included in the supplementary materials along with a sample run of the MACRO program.

Contact:  mkocak1@uthsc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
High-throughput microbial population genomics using the Cortex variation assembler
Authors: Iqbal Zamin , Turner Isaac , McVean Gil
Published: November 2012

Summary: We have developed a software package, Cortex, designed for the analysis of genetic variation by de novo assembly of multiple samples. This allows direct comparison of samples without using a reference genome as intermediate and incorporates discovery and genotyping of single-nucleotide polymorphisms, indels and larger events in a single framework. We introduce pipelines which simplify the analysis of microbial samples and increase discovery power; these also enable the construction of a graph of known sequence and variation in a species, against which new samples can be compared rapidly. We demonstrate the ease-of-use and power by reproducing the results of studies using both long and short reads.

Availability:  http://cortexassembler.sourceforge.net (GPLv3 license).

Contact:  zam@well.ox.ac.uk, mcvean@well.ox.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.
Non-redundant compendium of human ncRNA genes in GeneCards
Authors: Belinky Frida , Bahir Iris , Stelzer Gil , Zimmerman Shahar , Rosen Naomi , Nativ Noam , Dalah Irina , Iny Stein Tsippi , Rappaport Noa , Mituyama Toutai , Safran Marilyn , Lancet Doron
Published: November 2012

Motivation: Non-coding RNA (ncRNA) genes are increasingly acknowledged for their importance in the human genome. However, there is no comprehensive non-redundant database for all such human genes.

Results: We leveraged the effective platform of GeneCards, the human gene compendium, together with the power of fRNAdb and additional primary sources, to judiciously unify all ncRNA gene entries obtainable from 15 different primary sources. Overlapping entries were clustered to unified locations based on an algorithm employing genomic coordinates. This allowed GeneCards’ gamut of relevant entries to rise ∼5-fold, resulting in ∼80 000 human non-redundant ncRNAs, belonging to 14 classes. Such ‘grand unification’ within a regularly updated data structure will assist future ncRNA research.

Availability and implementation: All of these non-coding RNAs are included among the ∼122 500 entries in GeneCards V3.09, along with pertinent annotation, automatically mined by its built-in pipeline from 100 data sources. This information is available at www.genecards.org.

Contact: Frida.Belinky@weizmann.ac.il

Supplementary information:  Supplementary data are available at Bioinformatics online.
Scribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web
Authors: Miller Chase A. , Anthony Jon , Meyer Michelle M. , Marth Gabor
Published: November 2012

Motivation: High-throughput biological research requires simultaneous visualization as well as analysis of genomic data, e.g. read alignments, variant calls and genomic annotations. Traditionally, such integrative analysis required desktop applications operating on locally stored data. Many current terabyte-size datasets generated by large public consortia projects, however, are already only feasibly stored at specialist genome analysis centers. As even small laboratories can afford very large datasets, local storage and analysis are becoming increasingly limiting, and it is likely that most such datasets will soon be stored remotely, e.g. in the cloud. These developments will require web-based tools that enable users to access, analyze and view vast remotely stored data with a level of sophistication and interactivity that approximates desktop applications. As rapidly dropping cost enables researchers to collect data intended to answer questions in very specialized contexts, developers must also provide software libraries that empower users to implement customized data analyses and data views for their particular application. Such specialized, yet lightweight, applications would empower scientists to better answer specific biological questions than possible with general-purpose genome browsers currently available.

Results: Using recent advances in core web technologies (HTML5), we developed Scribl, a flexible genomic visualization library specifically targeting coordinate-based data such as genomic features, DNA sequence and genetic variants. Scribl simplifies the development of sophisticated web-based graphical tools that approach the dynamism and interactivity of desktop applications.

Availability and implementation: Software is freely available online at http://chmille4.github.com/Scribl/ and is implemented in JavaScript with all modern browsers supported.

Contact:  gabor.marth@bc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Inhaled Nitric Oxide Attenuates the Adverse Effects of Transfusing Stored Syngeneic Erythrocytes in Mice with Endothelial Dysfunction after Hemorrhagic Shock
Authors: Lei Chong , Yu Binglan , Shahid Mohd , Beloiartsev Arkadi , Bloch Kenneth D. , Zapol Warren M.
Published: November 2012

Background

The authors investigated whether transfusion with stored erythrocytes would increase tissue injury, inflammation, oxidative stress, and mortality (adverse effects of transfusing stored erythrocytes) in a murine model of hemorrhagic shock. They tested whether the adverse effects associated with transfusing stored erythrocytes were exacerbated by endothelial dysfunction and ameliorated by inhaling nitric oxide.

Methods

The authors studied mice fed a high-fat diet (HFD-fed; to induce endothelial dysfunction) or a standard diet for 4-6 weeks. Mice were subjected to 90 min of hemorrhagic shock, followed by resuscitation with leukoreduced syngeneic erythrocytes stored less than 24 h (fresh erythrocytes) or stored for 2 weeks (stored erythrocytes).

Results

In standard-diet-fed mice at 2 h after resuscitation, transfusion with stored erythrocytes increased tissue injury more than transfusion with fresh erythrocytes. The adverse effects of transfusing stored erythrocytes were more marked in HFD-fed mice and associated with increased lactate levels and short-term mortality. Compared with fresh erythrocytes, resuscitation with stored erythrocytes was associated with a reduction in P50, increased plasma hemoglobin levels, and increased indices of inflammation and oxidative stress, effects that were exacerbated in HFD-fed mice. Inhaled nitric oxide reduced tissue injury, lactate levels, and indices of inflammation and oxidative stress and improved short-term survival in HFD-fed mice resuscitated with stored erythrocytes.

Conclusions

Resuscitation with stored erythrocytes adversely impacts outcome in mice with hemorrhagic shock, an effect that is exacerbated in mice with endothelial dysfunction. Inhaled nitric oxide reduces tissue injury and improves short-term survival in HFD-fed mice resuscitated with stored erythrocytes.
Guillain–Barré Syndrome After Influenza Vaccination in the United States, A Report From the CDC/FDA Vaccine Adverse Event Reporting System (1990–2009)
Authors: Souayah Nizar , Yacoub Hussam A. , Khan Hafiz M.R. , Farhad Khosro , Mehyar Lubna Shafiq , Maybodi Leila , Menkes Daniel L. , Qureshi Adnan I.
Published: November 2012

Objectives:

To determine the rate of Guillain–Barré syndrome (GBS) after administration of influenza vaccine in the United States and to provide further information about the characteristics and temporal profile of these incidents.

Methods:

Data were acquired from the Vaccine Adverse Event Reporting System, supplemented by data from the Center for Biologics and Research under the Freedom of Information Act between 1990 and 2009.

Results:

There were 802 cases (mean age, 54.72 ± 18.4 years) of GBS reported after influenza vaccination in the United States between 1990 and 2009. Among the 802 vaccinated patients with available data, 624 (77.8%) developed GBS within 6 weeks and 78 (9.7%) after 6 weeks, whereas these data were unavailable for the remaining 100 patients (13%). The reporting rate of post–influenza vaccine GBS was within the range expected in the general population or approximately 0.46 cases per million vaccinations. A non-Gaussian distribution of GBS within the first 6 weeks post-vaccination was noted, given that the peak incidence occurred in the second week.

Conclusions:

The incidence of post–influenza vaccine GBS is similar to the incidence of idiopathic GBS in the general population. Although the nonnormal distribution of post-vaccination GBS suggests that some cases may be triggered by vaccination, the greater risk of complications from influenza virus infections makes vaccination the first-line strategy for infection prevention and support the current guidelines on vaccination.