bluuebunny/crossref_metadata_2025 huggingface dataset:
Pressure-induced changes in the dielectric response of polymer relaxors
Authors: Hilczer B. , Szafrański M. , Hilczer A.
Published: February 2012

The effect of hydrostatic pressure on the dielectric response of P(VDF/TrFE)(50/50) irradiated with fast electrons has been studied. A non-linear upward shift of the glass transition temperature Tg and the Curie temperature TC of the polymer relaxors was observed under pressure with the initial slope dTg/dp being considerably smaller than dTC/dp. Moreover, pressure was found to reduce the contribution to the low-frequency dielectric absorption originating from segmental motions in the amorphous phase whereas the contribution related to ferroelectric-paraelectric transition and that of polar nanoclusters in the crystalline phase were found to be enhanced.
High-efficiency thin-film InGaP/InGaAs/Ge tandem solar cells enabled by controlled spalling technology
Authors: Shahrjerdi D. , Bedell S. W. , Ebert C. , Bayram C. , Hekmatshoar B. , Fogel K. , Lauro P. , Gaynes M. , Gokmen T. , Ott J. A. , Sadana D. K.
Published: February 2012

In this letter, we demonstrate the effectiveness of the controlled spalling technology for producing high-efficiency (28.7%) thin-film InGaP/(In)GaAs/Ge tandem solar cells. The controlled spalling technique was employed to separate the as-grown solar cell structure from the host Ge wafer followed by its transfer to an arbitrary Si support substrate. The structural and electrical properties of the thin-film tandem cells were examined and compared against those on the original bulk Ge substrate. The comparison of the electrical data suggests the equivalency in cell parameters for both the thin-film (spalled) and bulk (non-spalled) cells, confirming that the controlled spalling technology does maintain the integrity of all layers in such an elaborate solar cell structure.
Temperature dependence of the intraexcitonic AC Stark effect in semiconductor quantum wells
Authors: Wagner M. , Teich M. , Helm M. , Stehr D.
Published: February 2012

We have investigated the temperature-dependent, intraexcitonic AC Stark effect that manifests itself in a line splitting of the heavy-hole 1s exciton transition in a GaAs/AlGaAs multi quantum well when the 1s-2p intraexciton transition is driven by intense THz light. The observed wavelength-dependent splitting at Helium temperature can still be distinguished at elevated temperatures up to 200 K. Although the thermal energy exceeds the exciton binding energy by a factor of 1.7, thermal exciton ionization influences the coherent nonlinear effect only indirectly via thermal line broadening. With a threefold transmission change on ultrafast timescales in a region accessible to Peltier-cooling the scheme could be promising for optical modulators.
Fabrication of flower-like silver nanostructure on the Al substrate for surface enhanced fluorescence
Authors: Dong Jun , Zheng Hairong , Yan Xiaoqing , Sun Yu , Zhang Zhenglong
Published: February 2012

Surface-enhanced fluorescence (SEF) substrates consisting of flower-like nanostructure of electromagnetically coupled silver dendrites on Al surface were manufactured by modified galvanic displacement process between Ag ion and Al at room temperature. Substrate enhancement efficiency, which was evaluated from SEF intensities of the adsorbed Rhodamine 6 G(Rh6G), was found to increase rapidly with reaction time. The observation highlights the importance of strong coupling effects between nanobranches in SEF. The variation of SEF efficiency can be qualitatively explained with local surface plasmon resonance model of coupled silver nanostructures.
Note: Self-sensing based on charge control improves the performance of active damping using piezoelements
Authors: Liu Yong Bin , Zhang Lian Sheng , Feng Zhi Hua
Published: February 2012

A piezoelectric element can be used separately as a sensor or an actuator. A self-sensing strategy based on a charge driver can utilize a piezoelectric element as a sensor while actuating. The strategy was proven via experiments on a cantilever vibrator using a piezoelectric plate with both sensing and actuating functions. The amplitude of the vibration was actively damped by a factor exceeding 90%. The method can be used in numerous fields, including scanning probe microscopy, vibration suppression, and monitoring the health of structures.
Optimal parameters for morphology of bulk heterojunction solar cells from simulations
Authors: Xue Junwei , Hou Tingjun , Li Youyong
Published: February 2012

We combine atomistic simulation with mesoscale simulation to predict the morphology of bulk heterojunction (BHJ) solar cells. We show that good morphology is formed for weight fraction of PCBM in the region of 0.41–0.62 for poly(3-hexylthiophene)/[6,6]-phenyl-C61 butyric acid methyl ester BHJ solar cells, which agrees with experimental results. Our simulation results indicate that the enhanced phase separation is achieved by increasing the temperature, which is consistent with transmission electron microscopy results. We find that Flory-Huggins parameter (χ) > 1 is required for phase separation and good morphology. Our simulation method is useful for predicting the morphology of BHJ polymer solar cells.
Power management strategy based on adaptive neuro-fuzzy inference system for fuel cell-battery hybrid vehicle
Authors: Li Qi , Chen Weirong , Liu Shukui , You Zhiyu , Tao Shiyong , Li Yankun
Published: February 2012

A power management strategy based on an adaptive neuro-fuzzy inference system is proposed to enhance the fuel economy of fuel cell-battery hybrid vehicle and increase the mileage of continuation of journey. The model of hybrid vehicle for fuel cell-battery structure is developed by electric vehicle simulation software advisor. The simulation results demonstrate that the proposed strategy can satisfy the power requirement of four standard drive cycles and achieve the power distribution between fuel cell system and battery. The comprehensive comparisons with a power tracking control strategy which is widely adopted in advisor verify that the proposed strategy has better validity in terms of fuel economy in four standard drive cycles. Hence, the proposed strategy will take important effect for designing advanced power management system of hybrid vehicle.
Finite-difference time-domain simulation of light induced charge dynamics in silver nanoparticles
Authors: Hu Zixuan , Ratner Mark A. , Seideman Tamar
Published: February 2012

We use a finite-difference time-domain (FDTD) approach to describe and control light-induced charge dynamics via two constructs consisting of nanoscale silver cylinders. The charge dynamics is found to be significantly different from the energy dynamics intensively studied in the past in similar systems. It is shown that two-color sources with a tunable relative phase introduce the opportunity to control the charge dynamics via a simple and interesting control mechanism, namely, the time evolution of the charge is directly tied to the instantaneous value of the source fields. Hence, our ability to shape laser pulses and tailor their relative phases and amplitudes translates directly into the possibility of manipulating charge oscillations within metal nanoparticle arrays.
Field-effect devices utilizing LaAlO3-SrTiO3 interfaces
Authors: Förg B. , Richter C. , Mannhart J.
Published: February 2012

Using LaAlO3-SrTiO3 bilayers, we have fabricated field-effect devices that utilize the two-dimensional electron liquid generated at the bilayers’ n-type interfaces as drain-source channels and the LaAlO3 layers as gate dielectrics. With gate voltages well below 1 V, the devices are characterized by voltage gain and current gain. The devices were operated at temperatures up to 100 °C.
Effect of overgrowth temperature on the mid-infrared response of Ge/Si(001) quantum dots
Authors: Yakimov A. I. , Bloshkin A. A. , Timofeev V. A. , Nikiforov A. I. , Dvurechenskii A. V.
Published: February 2012

Ge/Si quantum dots fabricated by molecular-beam epitaxy at 500 °C are overgrown with Si at different temperatures Tcap, and their mid-infrared photoresponse is investigated. The photocurrent maximum shifts from 2.3 to 3.9 μm with increasing Tcap from 300 to 750 °C. The best performance is achieved for the detector with Tcap = 600 °C in a photovoltaic mode. At a sample temperature of 90 K and no applied bias, a responsivity of 0.43 mA/W and detectivity of 6.2 × 1010 cmHz1/2/W at λ = 3 μm were measured under normal incidence infrared radiation. The device exhibits very low dark current (Idark = 2 nA/cm2 at T = 90 K and U = −0.2 V) and operates until 200 K.
Self consistently calibrated photopyroelectric calorimeter for the high resolution simultaneous absolute measurement of the specific heat and of the thermal conductivity
Authors: Zammit U. , Paoloni S. , Mercuri F. , Marinelli M. , Scudieri F.
Published: February 2012

High temperature resolution study of the specific heat and of the thermal conductivity over the smecticA-nematic and nematic-isotropic phase transitions in octylcynobephenyl liquid crystal using a new photopyroelectric calorimetry configuration are reported, where, unlike previously adopted ones, no calibration is required other than the procedure used during the actual measurement. This makes photopyroelectric calorimetry suitable for “absolute” measurements of the thermal parameters like most other existing conventional calorimetric techniques where, however, the thermal conductivity cannot be measured.
Membrane-localized β-subunits alter the PIP
2
regulation of high-voltage activated Ca
2+
channels
Authors: Suh Byung-Chang , Kim Dong-Il , Falkenburger Björn H. , Hille Bertil
Published: February 2012

The β-subunits of voltage-gated Ca
2+
(Ca
V
) channels regulate the functional expression and several biophysical properties of high-voltage–activated Ca
V
channels. We find that Ca
V
β-subunits also determine channel regulation by the membrane phospholipid phosphatidylinositol 4,5-bisphosphate (PIP
2
). When Ca
V
1.3, -2.1, or -2.2 channels are cotransfected with the β3-subunit, a cytosolic protein, they can be inhibited by activating a voltage-sensitive lipid phosphatase to deplete PIP
2
. When these channels are coexpressed with a β2a-subunit, a palmitoylated peripheral membrane protein, the inhibition is much smaller. PIP
2
sensitivity could be increased by disabling the two palmitoylation sites in the β2a-subunit. To further test effects of membrane targeting of Ca
V
β-subunits on PIP
2
regulation, the N terminus of Lyn was ligated onto the cytosolic β3-subunit to confer lipidation. This chimera, like the Ca
V
β2a-subunit, displayed plasma membrane localization, slowed the inactivation of Ca
V
2.2 channels, and increased the current density. In addition, the Lyn-β3 subunit significantly decreased Ca
V
channel inhibition by PIP
2
depletion. Evidently lipidation and membrane anchoring of Ca
V
β-subunits compete with the PIP
2
regulation of high-voltage–activated Ca
V
channels. Compared with expression with Ca
V
β3-subunits alone, inhibition of Ca
V
2.2 channels by PIP
2
depletion could be significantly attenuated when β2a was coexpressed with β3. Our data suggest that the Ca
V
currents in neurons would be regulated by membrane PIP
2
to a degree that depends on their endogenous β-subunit combinations.
Psycholinguistic perspectives on second language learning and bilingualism
Authors: F. Kroll Judith , A. Bogulski Cari , McClain Rhonda
Published: February 2012

Recent psycholinguistic research demonstrates that using a second language has consequences for the first language (e.g. Dussias, 2003; Van Hell & Dijkstra, 2002) and for domain-general cognitive processes (Bialystok, 2005). This work suggests that the language system is permeable, with cross-language exchange at every level of processing (Malt & Sloman, 2003). Critically, even proficient bilinguals appear unable to switch off the language not in use when they hear, read, or speak one language alone (e.g. Dijkstra, 2005; Kroll, Bobb, & Wodniecka, 2006; Marian & Spivey, 2003), creating cross-language competition. In this article, we describe research that considers how cross-language activation is modulated during spoken production and during the earliest stages of second language learning. We hypothesize that the open nature of the bilingual�s language system may create optimal conditions for new language learning and also for enhanced cognitive control that enables effective selection of the language to be spoken.
Modeling morphological variation and development
Authors: McCarthy Corrine
Published: February 2012

This paper proposes a model of morphological variation and development grounded in feature-geometric theory. It tests two hypotheses that follow from this model on a corpus of data from speakers of Spanish as a second language (L2). First, variation is systematic; default, underspecified feature values are adopted when errors occur. This hypothesis is supported for person, number, and finiteness, as 3rd, singular, and nonfinite defaults surface in place of 1st, plural, and finite verbs. Second, developmental trends are observed as nodes are added to the geometry; the unmarked/less specified feature value is successfully produced prior to the marked/more specified one. This hypothesis is partially supported, as accuracy in 3rd person emerges prior to 1st. However, no developmental pattern is found for number. Errors in finiteness are limited to lower-proficiency speakers, whereas intermediate speakers favor 3rd person, finite defaults. Together, these results suggest systematic variation and gradual development in the morphology.
Identifying graphematic units
Authors: Berg Kristian
Published: February 2012

It is a matter of debate how far the description of a writing system should be based on the units and categories of the respective spoken language. The present paper pursues the idea of relative autonomy: accordingly, writing systems should be based on as little phonological information as possible. Otherwise, existing structures may be superimposed by structures from the spoken language and not be discovered. As a necessary step in this direction, the present paper proposes a procedure to identify vowel and consonant letters across languages without reverting to phonology. This is achieved by making use of the different distribution of vowel and consonant letters. The proposed identification procedure is shown to work for English, Dutch, and German. Keywords: letter distribution; written minimal pairs; multi-dimensional scaling
Grain-size units of phonological awareness among Russian first graders
Authors: Kerek Eugenia , Niemi Pekka
Published: February 2012

This article presents the results of a study of phonological awareness development with 43 grade 1 children in Russian primary school. It is suggested that languagespecific factors, such as the complexity of syllabic structure, as well as the salience of consonant-vowel (CV) units in Russian phonology and orthography influence the course of phonological awareness development of Russian schoolchildren. The findings suggest that the special cohesion of CV units in Russian orthography promotes rapid development of explicit awareness of CV units in Russian-speaking beginning readers, while the instability of syllabic boundaries slows down the process of developing explicit syllabic awareness. The results are discussed in terms of phonological units prominent at different levels of explicitness in connection with the qualitative shift in phonological awareness brought about by the onset of literacy acquisition. Keywords: reading development; phonological awareness; language-specific phonological patterns; orthographic depth; grain-size units; Russian-speaking beginning readers
Linguistic landscape and heritage language literacy education
Authors: Leung Genevieve Y. , Wu Ming-Hsuan
Published: February 2012

This paper investigates the ways languages are used in Philadelphia Chinatown through qualitative content analysis of 330 photos. Examining the linguistic landscape of public spaces exposes issues of linguistic tensions, language vitality, and language shift in multilingual settings. While Chinese in the form of Mandarin is highly publicized, thereby placing disproportionate emphasis upon one language over others, Philadelphia Chinatown shows diversity, coexistence, and creative uses of multiple Chinese languages alongside English. The signage suggests linguistic rescaling connecting real and imagined audiences, conforming to broader ‘Chinese’ linguistic norms while localized to connect to a range of Chineses. We show how linguistic and cultural pluralism of ‘Chinese’ have always existed – and continue to exist – and the importance of developing socially sensitive literacy pedagogy, especially when there is a mismatch between the informal, community-level signage and what is formally taught in ‘Chinese’ language classrooms in the U.S. Keywords: linguistic landscape; Chinatown; Chinese languages; literacy education; heritage language; education
Growth regulators.
Authors: Hancock J. , Retamales J.
Published: February 2012

This chapter examines plant growth regulators used for blueberries (Vaccinium spp.) in regard to their application and the factors that affect their performance. Current and potential uses of these substances (control vegetative growth, enhancement of leaf development, delay flowering, inhibition of flower bud formation or elimination of flowers in nursery plants, flower and fruit thinning, fruit set improvement, and harvest regulation) are presented.
Pre- and postharvest management of fruit quality.
Authors: Hancock J. , Retamales J.
Published: February 2012

This chapter discusses the pre- and postharvest management of blueberry (Vaccinium sp.) fruit quality. The attributes (fruit size, weight loss, aroma, scar, colour, firmness, seediness, soluble solids, titratable acidity, ratio of soluble solids to titratable acids, pH, antioxidant capacity, and fruit decay) and factors (cultivar, climate, nutrition, plant water status, canopy management, and harvesting method) affecting fruit quality are defined, as well as the factors that influence the postharvest life of the fruit and the approaches used (cooling, controlled and modified atmosphere storage, and control of postharvest spoilage by chemical and physical means) to extend fruit quality.
Effects of Stocking Catchable‐Sized Hatchery Rainbow Trout on Wild Rainbow Trout Abundance, Survival, Growth, and Recruitment
Authors: Meyer Kevin A. , High Brett , Elle F. Steven
Published: February 2012

The Idaho Department of Fish and Game has proactively dealt with the potential adverse genetic effects of stocking catchable‐sized hatchery trout in waters that support native salmonids by adopting a policy in 2001 whereby only sterile rainbow trout Oncorhynchus mykiss are stocked in flowing waters; however, concerns regarding the competitive effects of introducing hatchery trout into streams and rivers supporting wild trout have not been addressed. We stocked fish in the middle 3 years of a 5‐year study to assess whether stocking hatchery rainbow trout of catchable size (hereafter, catchables) reduced the abundance, survival, growth, or recruitment of wild rainbow trout in streams. Catchables averaging 249 mm total length (TL) were stocked from 2006 to 2008 at an annual density of 4.2 fish/100 m2 into 12 treatment reaches of stream that were paired with control reaches at least 3 km apart in the same stream in which no stocking occurred. Wild rainbow trout abundance (including all fish ≥75 mm TL), recruitment, survival, and growth were determined from population estimates and recaptures of fish tagged with passive integrated transponder (PIT) tags during mark–recapture electrofishing sampling. The abundance of wild rainbow trout averaged 13.2 fish/100 m2 but varied substantially across sites and years, ranging from a low of 0.5 to a high of 131.3 fish/100 m2; similar variability was observed in recruitment to age 1. Estimates of total annual survival averaged 0.53 based on the population abundance estimates (which allowed for emigration and immigration) and 0.26 based on the PIT‐tag recaptures (which allowed for emigration but not immigration). Our paired study design demonstrated that the abundance, survival, growth, and recruitment to age 1 of wild rainbow trout were all unaffected by stocking catchables. The lack of population‐level effects from stocking catchables was not surprising considering the high short‐term mortality and the socially and physiologically naive behavior typically exhibited by hatchery catchables stocked in lotic systems.
Modeling the Effect of Environmental Parameters on Feeding Ecology of the Shortnose Sturgeon in the Saint John River, New Brunswick
Authors: Usvyatsov Sima , Watmough James , Litvak Matthew K.
Published: February 2012

We examined the effects of spatial, temporal, and environmental parameters on the feeding habits of the shortnose sturgeon Acipenser brevirostrum. We sampled sturgeon gut contents using colonic flushing, a new, low‐impact technique. We found that heavy feeding continued until at least November, when water temperature reached 8°C. In all seasons, foraging shortnose sturgeon used shallow water (2–8 m); however, in late fall this trend was even stronger, when 50% of the sturgeon were captured in less than 3 m depth. Over 60 families of prey items were identified from 166 colonic samples collected at four points between spring and late fall from seven locations throughout the lower Saint John River, New Brunswick. Samples from freshwater sites contained mainly Gastropoda, Sphaeriidae, Chironomidae, and Gammaridae. Samples from saline and brackish environments contained mostly Gammaridae, Corophiidae, softshell clam Mya arenaria, Cyathura polita, and Chironomidae. We used sensitivity analysis to determine the number of shortnose sturgeon required to obtain a representative sample of the diet. We found that 20–40 gut samples from sturgeons in both brackish and freshwater environments would suffice for a general description of the diet but that complete knowledge of the sturgeon diet and a comparison among several sites would require the sampling of hundreds of fish. The digestibility of prey varied from 77% of the ingested volume in a saline environment to only 6% in freshwater samples. Shortnose sturgeon from freshwater sites had higher ingested volumes and more prey per ingested volume than did those from brackish sites, which indicated further differences in feeding efficiency between the environments. Salinity was a significant parameter in the redundancy analysis of ingested prey items. In freshwater sites the significant factors were season, sturgeon length, ingested volume, number of ingested prey, and number of ingested taxa. In saline sites the significant factors were season, location, ingested volume, and the number of ingested prey. Our findings identified the spatial and temporal gradients in shortnose sturgeon foraging and provided insight into foraging efficiency in this species.
Does Anaerobic Activity Differ Seasonally or between Sexes in Yellow Perch Populations?
Authors: Schoenebeck Casey W. , Brown Michael L.
Published: February 2012

Anaerobic activities, such as those associated with spawning, foraging for prey, and predator avoidance, may vary seasonally and by sex as energetic demands change. We quantified the glycolytic muscle enzyme lactate dehydrogenase (LDH) to determine whether enzyme concentrations differed seasonally or between sexes in yellow perch Perca flavescens populations that exhibited female‐biased sexual size dimorphism (SSD). Patterns in LDH for a yellow perch population with fast‐growing fish and one with slow‐growing fish varied significantly among seasons and between sexes. The LDH concentration was lower during spring than during summer and fall, indicating that activity costs associated with nonspawning burst‐swimming activities (e.g., foraging for prey or predator avoidance) are greater than costs associated with spawning activity. In addition, LDH concentrations were greater in males than in females for both populations. Therefore, we hypothesize that greater cumulative, year‐round anaerobic activity (rather than just spawning activity) by males is responsible for female‐biased SSD in yellow perch.
Sport imagery ability predicts trait confidence, and challenge and threat appraisal tendencies
Authors: Williams Sarah E. , Cumming Jennifer
Published: February 2012

The present study investigated the interplay among athletes' sport imagery ability, trait confidence, and tendency to appraise situations as a challenge and threat. The potential mediating role of trait confidence was also tested. A total of 207 athletes (M age =19.44; s=1.26; 90 female, 117 male) completed the Sport Imagery Ability Questionnaire to assess ease of imaging skill, strategy, goal, affect and mastery imagery, the confidence subscale of the Competitive Trait Anxiety Inventory to measure trait confidence, and the Cognitive Appraisal Scale to assess tendencies to appraise sport situations as a challenge and as a threat. Structural equation modelling supported a model wherein mastery and goal imagery ability both positively predicted confidence, which in sequence positively predicted challenge appraisal and negatively predicted threat appraisal tendency. Partial support was found for confidence mediating the relationship between mastery imagery ability and appraisal tendencies. In addition, ease of imaging mastery and affect imagery directly predicted challenge appraisal tendency (positive direction), and ease of imaging mastery imagery directly predicted threat appraisal tendency (negative direction). Results highlight the importance of motivational imagery ability and the need to assess athletes' ability to image different content.
Hole-mediated ferromagnetic enhancement and stability in Cu-doped ZnOS alloy thin films
Authors: Li Y F , Pan H L , Yao B , Deng R , Xu Y , Li J C , Zhang L G , Zhao H F , Shen D Z , Wu T
Published: February 2012

We report room temperature ferromagnetism enhancement of Cu-doped ZnOS (Zn1−x
Cu
x
O1−y
S
y
) alloy thin films with high hole concentration. The Zn0.91Cu0.09O0.92S0.08 alloy thin films with a hole concentration of 4.3 × 1019 cm−3 show the strongest magnetization of 1.5μB/Cu. First-principles calculation shows that high hole concentration stabilizes the ferromagnetic ordering in the Zn1−x
Cu
x
O1−y
S
y
system, indicating a strong correlation between ferromagnetic stability and hole concentration. These results suggest that the Zn1−x
Cu
x
O1−y
S
y
alloy with high hole concentration is promising to find applications in spintronic devices.
The effects of polymer side-chain structure on roughness formation of ArF photoresist in plasma etching processes
Authors: Uesugi Takuji , Okada Takeru , Wada Akira , Kato Keisuke , Yasuda Atsushi , Maeda Shinichi , Samukawa Seiji
Published: February 2012

Low etching resistance and roughness formation of ArF photoresist during plasma etching are serious problems. We have previously found that decisive factors affecting the plasma resistance and roughness formation in an ArF photoresist are determined by ultraviolet/vacuum ultraviolet radiation and roughness formation is dominated by chemical reactions. In this paper, on the basis of our previous findings on the interaction between radiation species from plasma and ArF photoresist polymers, we investigated the polymer structural dependence for the degradation mechanism of ArF photoresist in the plasma etching processes. The etching resistance of ArF photoresist was improved by controlling the elemental ratio of oxygen atoms and ring structures in photoresist polymer. Furthermore, lactone C=O bond is found to be a key factor for roughness formation during the etching process. We have revealed the importance of the molecular structure of ArF photoresist for improving the surface roughness and etching resistance during the plasma etching process.
Initiation mechanism of a positive streamer in pressurized carbon dioxide up to liquid and supercritical phases with nanosecond pulsed voltages
Authors: Ihara T , Furusato T , Kameda S , Kiyan T , Katsuki S , Hara M , Akiyama H
Published: February 2012

In this work, the initiation process of an electrical discharge in pressurized carbon dioxide up to the liquid and supercritical phases was investigated using Schlieren and photomultiplier techniques. A pulsed positive voltage with a rise time of about 40 ns and half-width of 150 ns was applied to a point-to-plane gap. The experimental results showed that the discharge started with a primary streamer consisting of a burst primary streamer and a successive primary streamer, and a back discharge followed them. It was predicted from an analysis of the experimental results that the initiation criterion of a burst primary streamer was electron multiplication on the order of 108 independent of the medium conditions. That is, a direct ionization process without bubble formation is supported as an initiation mechanism of nanosecond positive discharges in pressurized carbon dioxide. The medium state in the burst primary streamer channel was a gas or pseudo-gas of 50–200 kg m−3 density.
ArchTEx: accurate extraction and visualization of next-generation sequence data
Authors: Lai William K. M. , Bard Jonathan E. , Buck Michael J.
Published: February 2012

Motivation: The extension of mapped sequence tags is a common step in the analysis of single-end next-generation sequencing (NGS) data from protein localization and chromatin studies. The optimal extension can vary depending on experimental and technical conditions. Improper extension of sequence tags can obscure or mislead the interpretation of NGS results. We present an algorithm, ArchTEx (Architectural Tag Extender), which identifies the optimal extension of sequence tags based on the maximum correlation between forward and reverse tags and extracts and visualizes sites of interest using the predicted extension.

Availability and implementation: ArchTEx requires Java 1.6 or newer. Source code and the compiled program are freely available at http://sourceforge.net/projects/archtex/

Contact:  mjbuck@buffalo.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads
Authors: Sun Ruping , Love Michael I. , Zemojtel Tomasz , Emde Anne-Katrin , Chung Ho-Ryun , Vingron Martin , Haas Stefan A.
Published: February 2012

Summary: We developed Breakpointer, a fast algorithm to locate breakpoints of structural variants (SVs) from single-end reads produced by next-generation sequencing. By taking advantage of local non-uniform read distribution and misalignments created by SVs, Breakpointer scans the alignment of single-end reads to identify regions containing potential breakpoints. The detection of such breakpoints can indicate insertions longer than the read length and SVs located in repetitve regions which might be missd by other methods. Thus, Breakpointer complements existing methods to locate SVs from single-end reads.

Availability:  https://github.com/ruping/Breakpointer

Contact:  ruping@molgen.mpg.de

Supplementary information:  Supplementary material is available at Bioinformatics online.
A functional generalized method of moments approach for longitudinal studies with missing responses and covariate measurement error
Authors: Yi Grace Y. , Ma Yanyuan , Carroll Raymond J.
Published: February 2012

Covariate measurement error and missing responses are typical features in longitudinal data analysis. There has been extensive research on either covariate measurement error or missing responses, but relatively little work has been done to address both simultaneously. In this paper, we propose a simple method for the marginal analysis of longitudinal data with time-varying covariates, some of which are measured with error, while the response is subject to missingness. Our method has a number of appealing properties: assumptions on the model are minimal, with none needed about the distribution of the mismeasured covariate; implementation is straightforward and its applicability is broad. We provide both theoretical justification and numerical results.
Labor Makes the News: Newspapers, Journalism, and Organized Labor, 1933–1955
Authors: Glende Philip M.
Published: February 2012

Labor Makes the Newsexamines newspaper coverage of organized labor during the burst of union activity that began in the early 1930s. For activists and sympathizers, it was an article of faith that newspapers were deliberately unfair. However, publishers and their employees responded to the labor movement with great diversity, in part because publishers recognized that many readers were union members. For reporters, covering labor tested the boundary between personal and political interests and the professional ideal of neutrality on news pages. While publicly condemning the press, labor officials used newspapers to establish their legitimacy and wage war against enemies. Examining the treatment of organized labor provides a window for viewing the interplay among the sociopolitical, economic, and occupational goals of the publisher, the editorial worker, and the labor leader.
Corporate Social Responsibility of Dutch Entrepreneurs in the Twentieth Century
Authors: Sluyterman Keetie
Published: February 2012

On the basis of articles in contemporary periodicals, literature, and company archives, this article explores the views of entrepreneurs and society about what constitutes the responsibility of entrepreneurs. From the mid-nineteenth century, we can trace discussions about how entrepreneurs should behave in their own company and toward society, but these ideas were far from constant over time. The changing views on the social responsibilities of entrepreneurs give us therefore important information about changes in the national business system. Though focused on the Dutch entrepreneurs in their relationship to Dutch society, the article includes the influence of ideas from abroad. International management literature abounded in the Netherlands, and multinational companies often picked up ideas from other countries. How companies and entrepreneurs defined their responsibilities depended to a large extent on the criticisms launched by the outside world. Entrepreneurs and company managers responded to concerns in the society of which they formed part, and the progressive ones among them, the true leaders, searched for ways of reconciling the requirements of their business with the demands of the society.
Suppression of progenitor differentiation requires the long noncoding RNA ANCR
Authors: Kretz Markus , Webster Dan E. , Flockhart Ross J. , Lee Carolyn S. , Zehnder Ashley , Lopez-Pajares Vanessa , Qu Kun , Zheng Grace X.Y. , Chow Jennifer , Kim Grace E. , Rinn John L. , Chang Howard Y. , Siprashvili Zurab , Khavari Paul A.
Published: February 2012

Long noncoding RNAs (lncRNAs) regulate diverse processes, yet a potential role for lncRNAs in maintaining the undifferentiated state in somatic tissue progenitor cells remains uncharacterized. We used transcriptome sequencing and tiling arrays to compare lncRNA expression in epidermal progenitor populations versus differentiating cells. We identified ANCR (anti-differentiation ncRNA) as an 855-base-pair lncRNA down-regulated during differentiation. Depleting ANCR in progenitor-containing populations, without any other stimuli, led to rapid differentiation gene induction. In epidermis, ANCR loss abolished the normal exclusion of differentiation from the progenitor-containing compartment. The ANCR lncRNA is thus required to enforce the undifferentiated cell state within epidermis.
Endocrine fibroblast growth factors 15/19 and 21: from feast to famine
Authors: Potthoff Matthew J. , Kliewer Steven A. , Mangelsdorf David J.
Published: February 2012

We review the physiology and pharmacology of two atypical fibroblast growth factors (FGFs)—FGF15/19 and FGF21—that can function as hormones. Both FGF15/19 and FGF21 act on multiple tissues to coordinate carbohydrate and lipid metabolism in response to nutritional status. Whereas FGF15/19 is secreted from the small intestine in response to feeding and has insulin-like actions, FGF21 is secreted from the liver in response to extended fasting and has glucagon-like effects. FGF21 also acts in an autocrine fashion in several tissues, including adipose. The pharmacological actions of FGF15/19 and FGF21 make them attractive drug candidates for treating metabolic disease.
Copy number variation of individual cattle genomes using next-generation sequencing
Authors: Bickhart Derek M. , Hou Yali , Schroeder Steven G. , Alkan Can , Cardone Maria Francesca , Matukumalli Lakshmi K. , Song Jiuzhou , Schnabel Robert D. , Ventura Mario , Taylor Jeremy F. , Garcia Jose Fernando , Van Tassell Curtis P. , Sonstegard Tad S. , Eichler Evan E. , Liu George E.
Published: February 2012

Copy number variations (CNVs) affect a wide range of phenotypic traits; however, CNVs in or near segmental duplication regions are often intractable. Using a read depth approach based on next-generation sequencing, we examined genome-wide copy number differences among five taurine (three Angus, one Holstein, and one Hereford) and one indicine (Nelore) cattle. Within mapped chromosomal sequence, we identified 1265 CNV regions comprising ∼55.6-Mbp sequence—476 of which (∼38%) have not previously been reported. We validated this sequence-based CNV call set with array comparative genomic hybridization (aCGH), quantitative PCR (qPCR), and fluorescent in situ hybridization (FISH), achieving a validation rate of 82% and a false positive rate of 8%. We further estimated absolute copy numbers for genomic segments and annotated genes in each individual. Surveys of the top 25 most variable genes revealed that the Nelore individual had the lowest copy numbers in 13 cases (∼52%, χ2 test; P-value <0.05). In contrast, genes related to pathogen- and parasite-resistance, such as CATHL4 and ULBP17, were highly duplicated in the Nelore individual relative to the taurine cattle, while genes involved in lipid transport and metabolism, including APOL3 and FABP2, were highly duplicated in the beef breeds. These CNV regions also harbor genes like BPIFA2A (BSP30A) and WC1, suggesting that some CNVs may be associated with breed-specific differences in adaptation, health, and production traits. By providing the first individualized cattle CNV and segmental duplication maps and genome-wide gene copy number estimates, we enable future CNV studies into highly duplicated regions in the cattle genome.
Cell death, non‐invasively assessed by intrinsic fluorescence intensity of NADH, is a predictive indicator of functional differentiation of embryonic stem cells
Authors: Buschke David G. , Squirrell Jayne M. , Fong Jimmy J. , Eliceiri Kevin W. , Ogle Brenda M.
Published: February 2012

Background information

Continued advances in stem cell biology and stem cell transplantation rely on non‐invasive biomarkers to characterise cells and stem cell aggregates. The non‐invasive quality of such biomarkers is essential because exogenous labels, probes or reporters can unintentionally and dramatically alter stem cell state as can disruption of cell–cell and cell–matrix interactions. Here, we investigate the utility of the autofluorescent metabolite, nicotinamide adenine dinucleotide (NADH), as a non‐invasive, intrinsic biomarker of cell death when detected with multi‐photon optical‐based approaches. To test this possibility, cell death was induced in murine embryoid bodies (EBs) at an early stage (day 3) of differentiation using staurosporine, an ATP‐competitive kinase inhibitor of electron transport. Several hours after staurosporine treatment, EBs were stained with a single‐colour, live/dead probe. A single‐cross‐sectional plane of each EB was imaged to detect the fluorescence intensity of the live/dead probe (extrinsic fluorescence) as well as the fluorescence intensity of NADH (intrinsic fluorescence). EBs were assessed at subsequent time points (days 6–12) for the formation of beating areas as an indicator of functional differentiation.

Results

Statistical comparison indicated a strong positive correlation between extrinsic fluorescence intensity of the live/dead stain and intrinsic fluorescence of NADH, suggesting that the intensity of NADH fluorescence could be used to reliably and non‐invasively assess death of cells of EBs. Furthermore, EBs that had high levels of cell death soon after aggregate formation had limited ability to give rise to functional cardiomyocytes at later time points.

Conclusions

We demonstrate the utility of NADH fluorescence intensity as a non‐invasive indicator of cell death in stem cell aggregates when measured using multi‐photon excitation. In addition, we show that the degree of stem cell death at early stages of differentiation is predictive for the formation of functional cardiomyocytes.
Pro-tumour activity of interleukin-22 in HPAFII human pancreatic cancer cells
Authors: Curd L M , Favors S E , Gregg R K
Published: February 2012

Interleukin (IL)-22 is a cytokine involved in inflammatory and wound healing processes that is secreted primarily by T helper type 17 (Th17) cells. IL-22 receptor (IL-22R) expression is limited to epithelial cells of the digestive organs, respiratory tract and skin. Most tumours originating in these sites over-express IL-22R. Interestingly, there is an increase in Th17 frequency within the peripheral blood and tumour microenvironment of advanced cancer patients. Subsequently, IL-17 has been shown to display both pro-tumour and anti-tumour functions. Because many tumours lack expression of the IL-17 receptor, the effects of IL-17 on tumour growth are generated by cells that surround the tumour cells. Like IL-17, high levels of IL-22 have been detected in tumour tissues and the peripheral blood of cancer patients; however, the direct effect of IL-22 on tumour cells has remained largely unknown. In this report, we show that IL-22 stimulated production of vascular endothelial growth factor (VEGF) and the anti-apoptotic factor Bcl-XL in IL-22R-positive HPAFII human pancreatic cancer cells. Additionally, IL-22 augmented HPAFII cell production of immunosuppressive cytokines. We show further that IL-22 activation of HPAFII cells diminished T cell production of interferon (IFN)-γ through the action of IL-10. Strikingly, we show for the first time that IL-22 can fully protect cancer cells from natural killer (NK) cell-mediated cytotoxicity by stimulating tumour production of IL-10 and transforming growth factor (TGF)-β1. Our data support the idea that IL-22 may act to promote the pathogenesis of cancers rather than function in anti-tumour immunity.
A novel approach to quantify and locate potential microrefugia using topoclimate, climate stability, and isolation from the matrix
Authors: Ashcroft Michael B. , Gollan John R. , Warton David I. , Ramp Daniel
Published: February 2012

Ecologists are increasingly recognizing the conservation significance of microrefugia, but it is inherently difficult to locate these small patches with unusual climates, and hence they are also referred to as cryptic refugia. Here we introduce a new methodology to quantify and locate potential microrefugia using fine‐scale topoclimatic grids that capture extreme conditions, stable climates, and distinct differences from the surrounding matrix. We collected hourly temperature data from 150 sites in a large (200 km by 300 km) and diverse region of New South Wales, Australia, for a total of 671 days over 2 years. Sites spanned a range of habitats including coastal dune shrublands, eucalypt forests, exposed woodland ridges, sheltered rainforest gullies, upland swamps, and lowland pastures. Climate grids were interpolated using a regional regression approach based on elevation, distance to coast, canopy cover, latitude, cold‐air drainage, and topographical exposure to winds and radiation. We identified extreme temperatures on two separate climatic gradients: the 5th percentile of minimum temperatures and the 95th percentile of maximum temperatures. For each gradient, climatic stability was assessed on three different time scales (intra‐seasonal, intra‐annual and inter‐annual). Differences from the matrix were assessed using a moving window with a 5 km radius. We averaged the Z‐scores for these extreme, stable and isolated climates to identify potential locations of microrefugia. We found that our method successfully predicted the location of communities that were considered to occupy refugia, such as rainforests that have progressively contracted in distribution over the last 2.5 million years, and alpine grasslands that have contracted over the last 15 thousand years. However, the method was inherently sensitive to the gradient selected and other aspects of the modelling process. These uncertainties could be dealt with in a conservation planning context by repeating the methodology with various parameterizations and identifying areas that were consistently identified as microrefugia.
Malondialdehyde content as a potential biochemical indicator of tolerant Cenchrus ciliaris L. genotypes under heat stress treatment
Authors: Tommasino E. , Griffa S. , Grunberg K. , Ribotta A. , López Colomba E. , Carloni E. , Quiroga M. , Luna C. M.
Published: February 2012

Buffel grass (Cenchrus ciliaris L.) is an important forage grass in arid and semiarid regions. As part of a genetic improvement programme, four genotypes [Biloela (Bl), Americana (Am), Texas (Tx) and Sexual (Sx)] were categorized by tolerance to heat stress in a greenhouse experiment. At 30 d after sowing, half of the plants (control plants) were transferred to growth chambers (28°C day per night), and the other half (pre‐treated plants, Prt) were exposed to heat stress treatment (0, 24, 48 and 72 h; 45°C day per night). Malondialdehyde (MDA) content, an indicator of oxidative damage, was determined from foliar samples. During heat stress, Sx showed the earliest increase in MDA (at 24 h) followed by Tx (48 h) and Am and Bl (72 h). Results were compared with heat‐stress tolerance evaluated as morphological traits at the end of recuperation (60 d after sowing). Fresh weight and aerial plant height were lowest in the Prt‐Sx genotype and highest in Am and Bl genotypes; Tx showed intermediate tolerance. Results suggest that tolerance to heat stress in C. ciliaris genotypes could be related to the capacity for regulating the oxidative damage increase. Foliar MDA content might therefore be used in a genetic improvement programme of C. ciliaris as a potential biochemical indicator for a rapid, simple and low‐cost identification of heat‐stress tolerant genotypes.