bluuebunny/crossref_metadata_2025 huggingface dataset:
Preparation of radiation-grafted powders for use as anion exchange ionomers in alkaline polymer electrolyte fuel cells
Authors: Poynton Simon D. , Slade Robert C. T. , Omasta Travis J. , Mustain William E. , Escudero-Cid Ricardo , Ocón Pilar , Varcoe John R.
Published: February 2014

The use of radiation-grafted anion exchange ionomer powders leads to surprisingly high alkaline membrane fuel cell performances.
A highly permeable polyimide with enhanced selectivity for membrane gas separations
Authors: Rogan Yulia , Malpass-Evans Richard , Carta Mariolino , Lee Michael , Jansen Johannes C. , Bernardo Paola , Clarizia Gabriele , Tocci Elena , Friess Karel , Lanč Marek , McKeown Neil B.
Published: February 2014

Introducing the highly rigid ethanoanthracene unit into polyimides of intrinsic microporosity provides an impressive enhancement of gas selectivity by molecular sieving.
Efficient implementation of iterative multi‐input–multi‐output orthogonal frequency‐division multiplexing receiver using minimum‐mean‐square error interference cancellation
Authors: Han Bing , Yang Zengli , Zheng Yahong Rosa
Published: February 2014

An efficient hardware implementation scheme is proposed for iterative multi‐input–multi‐output orthogonal frequency‐division multiplexing receiver which includes an MMSE‐IC (minimum‐mean‐square error interference cancellation) detector, a channel estimator, a low‐density parity‐check (LDPC) decoder and other supporting modules. The proposed implementation uses the QR decomposition (QRD) of the complex‐valued matrices with four coordinate rotation digital computer (CORDIC) cores and a back substitution to solve the MMSE‐IC equations while the existing systolic array architectures require 15–38 CORDIC cores to achieve a similar throughput. The proposed 4‐CORDIC QRD architecture can be configured as a 16‐matrix or a 64‐matrix pipelining by using a different number of multipliers combined with one‐dimensional (1D) or 2D arrays of the back substitution, respectively. The channel estimator implements a commonly‐used frequency domain least squares channel estimation with the canonic‐signed‐digits method, thanks to the character of the Zadroff‐Chu sequence used as the pilot. In the LDPC decoder, the min‐sum algorithm is implemented for the quasicyclic LDPC decoding. The two schemes for the MMSE‐IC detector with different throughput and resource usages have been implemented in a Field Programmable Gate Array for a complete baseband turbo receiver. Their resource usages, throughputs and latencies are compared with the classic systolic array architectures, which demonstrate that the proposed receiver architecture achieves the best tradeoff between the throughput and the resource usage.
Effect of morphology on electrical treeing in low density polyethylene nanocomposites
Authors: Alapati Sridhar , Meledath Joy Thomas , Karmarkar Ajay
Published: February 2014

Influence of polymer morphology on the inception and the growth of electrical trees in unfilled low density polyethylene (LDPE) as well as LDPE filled with 1, 3 and 5% by weight nanoalumina samples stressed with 50 Hz ac voltage has been studied. It is seen that there is a significant improvement in tree inception voltage with filler loading in LDPE filled with nanoparticles. Tree inception voltage increased with the filler loading up to 3% by weight nanoalumina loading and showed a reduction at 5% by weight loading. Change in tree growth patterns from branch to bush as well as a slower tree growth with increase in filler loading in LDPE alumina nanocomposites were observed. The degree of crystallinity and change in crystalline morphology induced by the presence of alumina nanoparticles in LDPE was studied using differential scanning calorimetry (DSC) and scanning electron microscopy (SEM). DSC results show a similar melting behaviour for both unfilled LDPE and LDPE nanocomposites. However, there is a reduction in the degree of crystallinity for LDPE filled with 5% by weight nanoalumina. An increase in lamellae packing with increase in filler loadings and a highly disordered spherulitic structure for LDPE filled with 5% by weight nanoalumina was observed from the SEM images. The slow propagation of tree growth as well as reduction in tree inception voltage with increase in filler loadings were attributed to the morphological changes observed in the LDPE nanocomposites.
Efficient numerical–analytical tool for time domain obstacles detection
Authors: Di Mattia Valentina , Russo Paola , De Leo Alfredo , Scalise Lorenzo , Mariani Primiani Valter , Cerri Graziano
Published: February 2014

The aim of this work is to implement a mixed approach able to provide an efficient time domain solution of the electromagnetic (EM) coupling between an antenna and an obstacle distant few meters away. The idea is to divide the problem into a small number of less complex sub‐problems exploiting the advantage of solving some of them by analytical models and the others by numerical codes. To this end, the electric field radiated by the antenna just close to the object has been sampled in time and spatial domains by means of a small number of plane waves; for each plane wave impinging on the object, the scattering problem has been solved by a commercial code; finally, the total echo has been obtained as analytical summation of all the scattering contributions at the antenna position. The resulting echo has been compared with that coming from a full‐wave numerical solution, whereas the voltage signal received at the antenna port has been compared with that measured by experimental investigations. The positive results obtained demonstrate the possibility of using the tool to effectively study obstacle detection problems, for example as support to the design of an EM obstacles detector to improve visually impaired mobility.
One-Stage Open Reduction of an Old Cervical Subluxation: Case Report
Authors: Barrenechea Ignacio J.
Published: February 2014

Study Design

Case report.

Objective

The recommended treatment of cervical subluxation is currently closed or open reduction. These treatments are better accomplished in the acute setting, when muscular and ligamentous laxity allows the required maneuvers to realign the dislocated segments. However, subsets of patients are still being treated subacutely. The majority of the literature addressing subacute subluxations reports treatment through “front and back” approaches, many of them performed in two, three, or even four stages. Other authors recommend days or weeks of traction to reduce the subluxation, followed by anterior or posterior approaches. Herein, we present a one-stage open posterior surgical treatment of a 2-month standing C5–C6 subluxation with “jumped facets,” describing a useful technique to reduce these challenging cases without the need of traction or multistage procedures.

Methods

After opening and exposing the posterior elements, we performed a wide C5–6 bilateral foraminotomy; we then put lateral mass screws and rods from C4 to C6. Resembling the technique used in the reduction of high-grade lumbar spondylolisthesis, we used a rod reducer to bring back the C5 screw head toward the rod, thus realigning the lateral mass screw heads and reducing the subluxation.

Results

No changes were observed in the motor evoked or somatosensory potentials during this maneuver. Following an uneventful procedure, the patient was transferred to the postanesthetic care unit and discharged 3 days later.

Conclusions

This open single-stage posterior approach dramatically reduces operating time. This technique could be added into the decision-making armamentarium for cases without disk herniation.
Sensitivities to parameterization in the size-modified Poisson-Boltzmann equation
Authors: Harris Robert C. , Boschitsch Alexander H. , Fenley Marcia O.
Published: February 2014

Experimental results have demonstrated that the numbers of counterions surrounding nucleic acids differ from those predicted by the nonlinear Poisson-Boltzmann equation, NLPBE. Some studies have fit these data against the ion size in the size-modified Poisson-Boltzmann equation, SMPBE, but the present study demonstrates that other parameters, such as the Stern layer thickness and the molecular surface definition, can change the number of bound ions by amounts comparable to varying the ion size. These parameters will therefore have to be fit simultaneously against experimental data. In addition, the data presented here demonstrate that the derivative, SK, of the electrostatic binding free energy, ΔGel, with respect to the logarithm of the salt concentration is sensitive to these parameters, and experimental measurements of SK could be used to parameterize the model. However, although better values for the Stern layer thickness and ion size and better molecular surface definitions could improve the model's predictions of the numbers of ions around biomolecules and SK, ΔGel itself is more sensitive to parameters, such as the interior dielectric constant, which in turn do not significantly affect the distributions of ions around biomolecules. Therefore, improved estimates of the ion size and Stern layer thickness to use in the SMPBE will not necessarily improve the model's predictions of ΔGel.
A simple differential steady-state method to measure the thermal conductivity of solid bulk materials with high accuracy
Authors: Kraemer D. , Chen G.
Published: February 2014

Accurate measurements of thermal conductivity are of great importance for materials research and development. Steady-state methods determine thermal conductivity directly from the proportionality between heat flow and an applied temperature difference (Fourier Law). Although theoretically simple, in practice, achieving high accuracies with steady-state methods is challenging and requires rather complex experimental setups due to temperature sensor uncertainties and parasitic heat loss. We developed a simple differential steady-state method in which the sample is mounted between an electric heater and a temperature-controlled heat sink. Our method calibrates for parasitic heat losses from the electric heater during the measurement by maintaining a constant heater temperature close to the environmental temperature while varying the heat sink temperature. This enables a large signal-to-noise ratio which permits accurate measurements of samples with small thermal conductance values without an additional heater calibration measurement or sophisticated heater guards to eliminate parasitic heater losses. Additionally, the differential nature of the method largely eliminates the uncertainties of the temperature sensors, permitting measurements with small temperature differences, which is advantageous for samples with high thermal conductance values and/or with strongly temperature-dependent thermal conductivities. In order to accelerate measurements of more than one sample, the proposed method allows for measuring several samples consecutively at each temperature measurement point without adding significant error. We demonstrate the method by performing thermal conductivity measurements on commercial bulk thermoelectric Bi2Te3 samples in the temperature range of 30–150 °C with an error below 3%.
Acoustic study of a linear low-density polyethylene film after modification of the crystalline structure by heating
Authors: Tohmyoh Hironori , Sakamoto Yuhei
Published: February 2014

We report on a hybrid microscopy technique that enables us to measure the acoustic properties of a thin polymer film together with an optical microscope image of the corresponding area. Linear low-density polyethylene films are heated to various temperatures and examined by the technique. Density of the film is increased by heating and its sound velocity is decreased compared with a film without heating. Also, spherulites can clearly be seen in the optical microscope image, supporting the thermal shrinkage of the film which can be detected by the present technique.
Local and global bifurcations in an economic growth model with endogenous labour supply and multiplicative external habits
Authors: Gori Luca , Sodini Mauro
Published: February 2014

This paper analyses the mathematical properties of an economic growth model with overlapping generations, endogenous labour supply, and multiplicative external habits. The dynamics of the economy is characterised by a two-dimensional map describing the time evolution of capital and labour supply. We show that if the relative importance of external habits in the utility function is sufficiently high, multiple (determinate or indeterminate) fixed points and poverty traps can exist. In addition, periodic or quasiperiodic behaviour and/or coexistence of attractors may occur.
A multi-functional testing instrument for heat assisted magnetic recording media
Authors: Yang H. Z. , Chen Y. J. , Leong S. H. , An C. W. , Ye K. D. , Yin M. J. , Hu J. F.
Published: February 2014

With recent developments in heat assisted magnetic recording (HAMR), characterization of HAMR media is becoming very important. We present a multi-functional instrument for testing HAMR media, which integrates HAMR writing, reading, and a micro-magneto-optic Kerr effect (μ-MOKE) testing function. A potential application of the present instrument is to make temperature dependent magnetic property measurement using a pump-probe configuration. In the measurement, the media is heated up by a heating (intense) beam while a testing (weak) beam is overlapped with the heating beam for MOKE measurement. By heating the media with different heating beam power, magnetic measurements by MOKE at different temperatures can be performed. Compared to traditional existing tools such as the vibrating sample magnetometer, the present instrument provides localized and efficient heating at the measurement spot. The integration of HAMR writing and μ-MOKE system can also facilitate a localized full investigation of the magnetic media by potential correlation of HAMR head independent write/read performance to localized magnetic properties.
Influence of surface plasmon resonances of silver nanoparticles on optical and electrical properties of textured silicon solar cell
Authors: Sardana Sanjay K. , Chava Venkata S. N. , Thouti Eshwar , Chander Nikhil , Kumar Sanjai , Reddy S. R. , Komarala Vamsi K.
Published: February 2014

Here, we report average reflectance reduction of ∼8% in wavelength range of 300–1100 nm after coupling surface plasmon resonances (SPRs) of silver nanoparticles (NPs) to textured silicon (T-Si) surface. The enhancement of photocurrent from T-Si solar cell in off-resonant SPR region observed due to better radiative efficiency of NPs leading to outflow of scattered far-field into silicon maximized power generating electrons. Improvement in series resistance, fill factor, and open-circuit voltage (insensitive NPs size and morphology) are also observed with NPs along with photocurrent enhancement (sensitive to NPs sizes), which resulted cell efficiency enhancement from 4.49% to 6.42% for large area of 12.24 cm2.
Casimir and hydrodynamic force influence on microelectromechanical system actuation in ambient conditions
Authors: Sedighi Mehdi , Palasantzas George
Published: February 2014

Casimir and hydrodynamic dissipation forces can strongly influence the actuation of microelectromechanical systems in ambient conditions. The dissipative and stiction dynamics of an actuating system is shown to depend on surface physical processes related to fluid slip and the size of the actuating components. Using phase change materials the Casimir force magnitude can be modulated via amorphous-crystalline phase transitions. The dissipative motion between amorphous coated phase change material components can be changed towards stiction upon crystallization and suitable choice of restoring spring constants. By contrast, amorphization can augment switching from stiction to dissipative dynamics.
Direct imaging of light elements by annular dark-field aberration-corrected scanning transmission electron microscopy
Authors: Lotnyk Andriy , Poppitz David , Gerlach Jürgen W. , Rauschenbach Bernd
Published: February 2014

In this report, we show that an annular dark-field detector in an aberration-corrected scanning transmission electron microscope allows the direct observation of light element columns in crystalline lattices. At specific imaging conditions, an enhancement of the intensities of light element columns in the presence of heavy element columns is observed. Experimental results are presented for imaging the nitrogen and carbon atomic columns at the GaN-SiC interface and within the GaN and SiC compounds. The crystal polarity of GaN at the interface is identified. The obtained findings are discussed and are well supported by image simulations.
Ga gradients in Cu(In,Ga)Se2: Formation, characterization, and consequences
Authors: Klinkert T. , Jubault M. , Donsanti F. , Lincot D. , Guillemoles J.-F.
Published: February 2014

We report on the influence of the substrate temperature during the 2nd and 3rd stage of the Cu(In,Ga)Se2 3-stage co-evaporation process on the in-depth Ga and In concentrations and correlate these with the solar cell parameters and external quantum efficiency of soda-lime glass/Mo/CIGS/CdS/i-ZnO/ZnO:Al devices. An increased homogenization of the [Ga]/[III] fraction ([III] refers to the total concentration of the group 3 elements Ga and In) with temperature is found. In the investigated temperature range, the highest efficiency was measured for the lowest temperature and the steepest Ga-profile. The tendency of the short-circuit current density matches well with the notch-deepness. Surprisingly, the open-circuit voltage decreases for higher substrate temperatures, even though the Ga-concentration in the space-charge region increases. We propose back-grading variations and reduced back-interface recombination to explain this observation. For the highest of the tested temperatures of 540 °C, a homogenization of the Ga and In concentrations close to the surface is found. We explain this by the appearance of a liquid Cu2-xSe phase at the end of stage 2 for this high temperature. Break-off experiments at this point are conducted and reveal morphological and compositional lateral inhomogeneities for Tsub < 540 °C.
Dual-band high-temperature superconducting metamaterial structure based on multimode split ring resonator
Authors: Liu Haiwen , Li Shen , Guan Xuehui , Ren Baoping , Zhang Zhichong , Wang Yan , Ma Zhewang
Published: February 2014

In this Letter, a dual-band superconducting metamaterial structure with improved performance based on the proposed multimode split ring resonator (SRR) is proposed, which is constructed by two dual-mode SRRs and a high-impedance transmission line component. Also, its properties and equivalent circuit models are investigated by even- and odd-mode analysis. The mechanism producing four transmission zeros is discussed. To verify this design methodology, the dual-band superconducting metamaterial structure is designed and fabricated with a compact size of 10.6 mm × 13.75 mm. The insertion losses at each passband are 0.1 dB and 0.09 dB, respectively. Finally, measured results have a good agreement with simulations.
Behavior of a hollow core photonic crystal fiber under high radial pressure for downhole application
Authors: Sadeghi J. , Latifi H. , Santos J. L. , Chenari Z. , Ziaee F.
Published: February 2014

Pressure fiber sensors play an important role in downhole high pressure measurements to withstand long term operation. The purpose of this paper is to present an application of hollow core photonic crystal fiber (HC-PCF) as a high pressure sensor head for downhole application based on dispersion variation. We used a high pressure stainless steel unit to exert pressure on the sensor. The experimental results show that different wavelengths based on sagnac loop interferometer have additive sensitivities from 5 × 10−5 nm/psi at 1480 nm to 1.3 × 10−3 nm/psi at 1680 nm. We developed a simulation to understand the reason for difference in sensitivity of wavelengths and also the relationship between deformation of HC-PCF and dispersion variation under pressure. For this purpose, by using the finite element method, we investigated the effect of structural variation of HC-PCF on spectral transformation of two linear polarizations under 1000 psi pressure. The simulation and experimental results show exponential decay behavior of dispersion variation from −3.4 × 10−6 1/psi to −1.3 × 10−6 1/psi and from −5 × 10−6 1/psi to −1.8 × 10−6 1/psi, respectively, which were in a good accordance with each other.
Imprinted nonoxidized graphene sheets as an efficient hole transport layer in polymer light-emitting diodes
Authors: Huang Chun-Yuan , Peter Chen I-Wen , Chen Chih-Jung , Chiang Ray-Kuang , Vu Hoang-Tuan
Published: February 2014

Nonoxidized graphene sheets (NGSs) with single- and multilayered structures were generated by direct exfoliation of highly oriented pyrolytic graphite in a water-ethanol mixture with the assistances of pyridinium salt (Py+Br3–) and sonication. Raman spectrum exhibited a low intensity ratio (0.055) of D and G bands, indicating that the NGSs were nearly defect-free. Their application for the fabrication of polymer light-emitting diodes (PLEDs) was also demonstrated. The PLEDs that used an imprinted NGS film as a hole transport layer show a luminance exceeding 13000 cd/m2, which was comparable to that of devices using the typical hole transport material: poly(3,4-ethylenedioxythiophene)-polystyrenesulfonic acid.
GLTSCR2/PICT1 links mitochondrial stress and Myc signaling
Authors: Yoon John C. , Ling Alvin J. Y. , Isik Meltem , Lee Dong-Young Donna , Steinbaugh Michael J. , Sack Laura M. , Boduch Abigail N. , Blackwell T. Keith , Sinclair David A. , Elledge Stephen J.
Published: February 2014

Significance

Mitochondria play a vital role in cellular life. Understanding how mitochondria are regulated may uncover new ways to restore mitochondrial function in disease states. Here we use an unbiased, pooled ORFeome library screening strategy to identify 94 candidate mitochondrial regulator genes. We show that one of the candidate genes, glioma tumor-suppressor candidate region gene 2 (GLTSCR2), controls mitochondrial function in cultured cells and in
Caenorhabditis elegans
. The transcription factor Myc is a key downstream mediator of GLTSCR2 signaling. Furthermore, GLTSCR2 is itself induced by mitochondrial stress, pointing to a novel mitochondrial signaling pathway.
The dative alternation in South Asian English(es)
Authors: Bernaisch Tobias , Gries Stefan Th. , Mukherjee Joybrato
Published: February 2014

The present paper focuses on the modelling of cross-varietal differences and similarities in South Asian English(es) and British English at the level of verb complementation. Specifically, we analyse the dative alternation with GIVE, i.e. the alternation between the double-object construction (John gave Mary a book) and the prepositional dative (John gave a book to Mary) as well as their passivised constructions with regard to the factors that potentially exert an influence on this alternation in seven varieties of English. The South Asian varieties under scrutiny are Bangladeshi English, Indian English, Maldivian English, Nepali English, Pakistani English and Sri Lankan English, while British English serves as the reference variety. The patterns of GIVE are annotated according to the following parameters including potential predictors of the dative alternation: syntactic pattern and semantic class of GIVE; syntactic complexity, animacy, discourse accessibility and pronominality of constituents (cf. Gries 2003b; Bresnan and Hay 2008). The choices of complementation patterns are then statistically modelled using conditional inference trees and a random-forest analysis.

The results indicate that many of the predictors found to be relevant in British English are at play in the South Asian varieties, too. The syntactic pattern of GIVE is, in descending order, uniformly influenced by the predictors pronominality of recipient, length of recipient, semantic class of GIVE and length of patient. Interestingly, the predictor country is marginal in accounting for the dative alternation of GIVE across the varieties at hand. Based on this observation, we derive variety-independent protostructions, i.e. abstract combinations of (cross-varietally stable) features with high predictive power for a particular syntactic pattern, which we argue to be part of the lexicogrammatical “common core” (Quirket al. 1985: 16) of English.

The implications of the present paper are twofold. While the order of the predictors regarding their influence on the dative alternation is clearly compatible with earlier studies (cf. e.g. Green 1974; Ransom 1979; Hawkins 1994; Gries 2003b), the stability of the order across varieties of English calls for a) a more fine-grained gradation of linguistic forms and structures at the lexis-grammar interface as indicators of structural nativisation and b) a revision of earlier verb-complementational findings specific to individual or groups of varieties of South Asian English.
Causative verbs in the grammar of Spanish heritage speakers
Authors: Zyzik Eve
Published: February 2014

This study examines argument structure overgeneralizations among heritage speakers of Spanish who exhibit varying degrees of proficiency in the heritage language. Two questions motivated the design of the study: (1) Do heritage speakers differ from native speakers in their acceptance of causative errors? And if so, (2) which classes of verbs are most susceptible to this overgeneralization? A sentence acceptability task targeting two verb classes (unaccusatives and unergatives) was administered to 58 heritage speakers and a comparison group (n = 22) of monolingually-raised native speakers of Spanish. The results confirm that heritage speakers, in contrast to native speakers, accept causative errors with a variety of intransitive verbs. Unaccusative verbs are more readily accepted in transitive frames than unergatives for all groups. Acceptance rates for individual verbs are a function of the particular verb’s compatibility with external causation as well as the possibility of being transitive in English.
Dialect density in bilingual Puerto Rican Spanish-English speaking children
Authors: Fabiano-Smith Leah , Shuriff Rebecca , Barlow Jessica A. , Brian A. Goldstein
Published: February 2014

It is still largely unknown how the two phonological systems of bilingual children interact. In this exploratory study, we examine children’s use of dialect features to determine how their speech sound systems interact. Six monolingual Puerto Rican Spanish-speaking children and six bilingual Puerto Rican Spanish-English speaking children, ages 5–7 years, were included in the current study. Children’s single word productions were analyzed for (1) dialect density and (2) frequency of occurrence of dialect features (after Oetting & McDonald, 2002). Nonparametric statistical analyses were used to examine differences within and across language groups. Results indicated that monolinguals and bilinguals exhibited similar dialect density, but differed on the types of dialect features used. Findings are discussed within the theoretical framework of the Dual Systems Model (Paradis, 2001) of language acquisition in bilingual children.
American White Pelican Predation on Cui-ui in Pyramid Lake, Nevada
Authors: Scoppettone G. Gary , Rissler Peter H. , Fabes Mark C. , Withers Donna
Published: February 2014

Anthropogenic changes to the Pyramid Lake–Truckee River ecosystem in Nevada are suspected to have altered the predator–prey balance between American white pelican Pelecanus erythrorhynchos and Cui-ui Chasmistes cujus. We estimated the loss of the adult Cui-ui population to pelican predation over a 13-year period by netting and tagging Cui-uis as they aggregated at the mouth of the Truckee River prior to their spawning migration into the Truckee River. Cui-ui access to the Truckee River typically required traversing a shallow delta (a foraging advantage for these American white pelicans). Dams and greater frequency of low stream flows also contributed to American white pelican foraging success. We used tag recoveries from Pyramid Lake's nesting colony of American white pelicans along with an experiment to estimate the chance of tag recovery within the colony to calculate the number of tagged fish taken by American white pelicans. We also used numbered tags to test whether there was a size preference for Cui-uis taken. Our results showed that the primary source of adult Cui-ui mortality was from American white pelican predation in the Truckee River. Within a 13-year period American white pelicans had taken 90% of the tags deployed during the first 7 years of the interval. There was no preference for the size of Cui-uis taken. A better understanding of the effects of heavy cropping by American white pelicans on Cui-ui population dynamics is still needed.

Received March 26, 2013; accepted October 8, 2013

Published online January 24, 2014
Foreign rule? Transnational, national, and local perspectives on Venice and Venetia within the ‘multinational’ empire
Authors: Laven David , Parker Laura
Published: February 2014

The history of the Habsburg Empire in the post-Napoleonic era is frequently approached from the perspective of its various component nationalities. These were traditionally portrayed in the historiography as engaged in more-or-less open struggle with control from Vienna. This article argues that the over-privileging of such national categories can distort the picture. By looking at a number of case studies – the naming of Lombardy-Venetia, theBiblioteca italiana,the Panteon veneto – the relationship between Venice (and its Terraferma) and Habsburg rule during the second Austrian domination is examined. It will be argued that it is more profitable to see Venetian identities (municipal, local, Italian, and as part of a wider transnational European culture) as capable of working for as well as against the empire, and that Habsburg policy was as often concerned with managing potential local rivalries (notably between Lombards and Venetians) as with controlling a perceived Italian threat. It is also suggested that, while cultivation of local identity was often used to reinforce the national, the Austrian authorities were also happy to annex both to further imperial interests.
The uniform box product
Authors: Bell Jocelyn
Published: February 2014

The uniform box product problem is a weakening of the well-known box product problem, which asks whether box products of certain compact spaces are normal or even paracompact. Using uniformities, a new topology on products is defined between the box and Tychonov topologies. This new product, called the uniform box product, is an extension of the sup metric to powers of compact spaces. We investigate a certain non-metrizable compact space whose uniform box product, in ZFC, is normal, countably paracompact, and collectionwise Hausdorff.
Uniruledness of orthogonal modular varieties
Authors: Gritsenko V. , Hulek K.
Published: February 2014

A strongly reflective modular form with respect to an orthogonal group of signature

(
2
,
n
)

(2,n)

determines a Lorentzian Kac–Moody algebra. We find a new geometric application of such modular forms: we prove that if the weight is larger than

n
n

, then the corresponding modular variety is uniruled. We also construct new reflective modular forms and thus provide new examples of uniruled moduli spaces of lattice polarised

K
3

\mathrm {K3}

surfaces. Finally, we prove that the moduli space of Kummer surfaces associated to

(
1
,
21
)

(1,21)

-polarised abelian surfaces is uniruled.
Mantra 2.0: an online collaborative resource for drug mode of action and repurposing by network analysis
Authors: Carrella Diego , Napolitano Francesco , Rispoli Rossella , Miglietta Mario , Carissimo Annamaria , Cutillo Luisa , Sirci Francesco , Gregoretti Francesco , Di Bernardo Diego
Published: February 2014

Summary: Elucidation of molecular targets of a compound [mode of action (MoA)] and its off-targets is a crucial step in drug development. We developed an online collaborative resource (MANTRA 2.0) that supports this process by exploiting similarities between drug-induced transcriptional profiles. Drugs are organized in a network of nodes (drugs) and edges (similarities) highlighting ‘communities’ of drugs sharing a similar MoA. A user can upload gene expression profiles before and after drug treatment in one or multiple cell types. An automated processing pipeline transforms the gene expression profiles into a unique drug ‘node’ embedded in the drug-network. Visual inspection of the neighbouring drugs and communities helps in revealing its MoA and to suggest new applications of known drugs (drug repurposing). MANTRA 2.0 allows storing and sharing user-generated network nodes, thus making MANTRA 2.0 a collaborative ever-growing resource.

Availability and implementation: The web tool is freely available for academic use at http://mantra.tigem.it.

Contact:  dibernardo@tigem.it
MRHMMs: Multivariate Regression Hidden Markov Models and the variantS
Authors: Lee Yeonok , Ghosh Debashis , Hardison Ross C. , Zhang Yu
Published: February 2014

Summary: Hidden Markov models (HMMs) are flexible and widely used in scientific studies. Particularly in genomics and genetics, there are multiple distinct regimes in the genome within each of which the relationships among multivariate features are distinct. Examples include differential gene regulation depending on gene functions and experimental conditions, and varying combinatorial patterns of multiple transcription factors. We developed a software package called MRHMMs (Multivariate Regression Hidden Markov Models and the variantS) that accommodates a variety of HMMs that can be flexibly applied to many biological studies and beyond. MRHMMs supplements existing HMM software packages in two aspects. First, MRHMMs provides a diverse set of emission probability structures, including mixture of multivariate normal distributions and (logistic) regression models. Second, MRHMMs is computationally efficient for analyzing large data-sets generated in current genome-wide studies. Especially, the software is written in C for the speed advantage and further amenable to implement alternative models to meet users’ own purposes.

Availability and implementation: http://sourceforge.net/projects/mrhmms/

Contact:  ghoshd@psu.edu or yuzhang@stat.psu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Dynamics of filopodium-like protrusion and endothelial cellular motility on one-dimensional extracellular matrix fibrils
Authors: Xue Niannan , Bertulli Cristina , Sadok Amine , Huang Yan Yan Shery
Published: February 2014

Endothelial filopodia play key roles in guiding the tubular sprouting during angiogenesis. However, their dynamic morphological characteristics, with the associated implications in cell motility, have been subjected to limited investigations. In this work, the interaction between endothelial cells and extracellular matrix fibrils was recapitulated
in vitro
, where a specific focus was paid to derive the key morphological parameters to define the dynamics of filopodium-like protrusion during cell motility. Based on one-dimensional gelatin fibrils patterned by near-field electrospinning (NFES), we study the response of endothelial cells (EA.hy926) under normal culture or ROCK inhibition. It is shown that the behaviour of temporal protrusion length versus cell motility can be divided into distinct modes. Persistent migration was found to be one of the modes which permitted cell displacement for over 300 µm at a speed of approximately 1 µm min
−1
. ROCK inhibition resulted in abnormally long protrusions and diminished the persistent migration, but dramatically increased the speeds of protrusion extension and retraction. Finally, we also report the breakage of protrusion during cell motility, and examine its phenotypic behaviours.
A hybrid characterization framework to determine the visco-hyperelastic properties of a porcine zona pellucida
Authors: Boccaccio A. , Lamberti L. , Papi M. , De Spirito M. , Douet C. , Goudet G. , Pappalettere C.
Published: February 2014

The zona pellucida (ZP) is a specialized extracellular matrix surrounding the developing oocyte. This thick matrix consists of various types of glycoprotein that play different roles in the fertilization process. Nowadays, several techniques are available for assessing ZP's mechanical response. The basic assumption behind these methods is that the ZP behaves like an elastic body: hence, dissipative forces are neglected and Young's modulus remains unaffected by probe dynamics. However, dissipative forces are strongly regulated by the slippage of ZP chains past one another while reaction forces related to elastic deformations (driven by the ability of each chain to stretch) depend on the ZP structure (i.e. number of cross-links and distances between knots). Although viscous reaction forces generated by the ZP are one of the main factors regulating sperm transit, their peculiar behaviour along the ZP structure remains poorly understood and rarely investigated. In order to overcome this limitation, a novel visco-hyperelastic model describing the porcine ZP reaction forces generated by nanoindentations at different probe rates is developed and verified in this study. Visco-hyperelastic parameters of porcine ZP membranes are determined by means of a hybrid characterization framework combining atomic force microscopy nanoindentation measurements, nonlinear finite-element analysis and nonlinear optimization. Remarkably, it is possible to separate the contributions of hyperelastic and viscous terms to ZP mechanical response and evaluate the error made in the determination of ZP mechanical properties if viscous effects were not considered.
Thermococcus
nautili sp. nov., a hyperthermophilic archaeon isolated from a hydrothermal deep-sea vent
Authors: Gorlas Aurore , Croce Olivier , Oberto Jacques , Gauliard Emilie , Forterre Patrick , Marguet Evelyne
Published: February 2014

Thermococcus nautili, strain 30-1T (formerly reported as Thermococcus nautilus), was isolated from a hydrothermal chimney sample collected from the East Pacific Rise at a depth of 2633 m on the ‘La chainette PP57’ area. Cells were motile, irregular cocci with a polar tuft of flagella (0.8–1.5 µm) and divided by constriction. The micro-organism grew optimally at 87.5 °C (range 55–95 °C), at pH 7 (range pH 4–9) and with 2 % NaCl (range 1–4 %). Doubling time was 64 min in Zillig’s broth medium under optimal conditions. Growth was strictly anaerobic. It grew preferentially in the presence of elemental sulfur or cystine, which are reduced to H2S, on complex organic substrates such as yeast extract, tryptone, peptone, Casamino acids and casein. Slow growth was observed on starch and pyruvate. Strain 30-1T was resistant to chloramphenicol and tetracyclin (at 100 µg ml−1) but sensitive to kanamycin and rifampicin. The G+C content of the genomic DNA was 54 mol%. Strain 30-1T harboured three plasmids named pTN1, pTN2 and pTN3 and produced membrane vesicles that incorporate pTN1 and pTN3. As determined by 16S rRNA gene sequence analysis, strain 30-1T is related most closely to Thermococcus sp. AM4 (99.3 % similarity) and

Thermococcus gammatolerans

DSM 15229T (99.2 %). DNA–DNA hybridization values (in silico) with these two closest relatives were below the threshold value of 70 % (33 % with Thermococcus sp. AM4 and 32 % with

T. gammatolerans

DSM 15229T) and confirmed that strain 30-1 represents a novel species. On the basis of the data presented, strain 30-1T is considered to represent a novel species of the genus

Thermococcus

, for which the name Thermococcus nautili sp. nov. is proposed. The type strain is 30-1T ( = CNCM 4275 = JCM 19601).
Genomic and phylogenetic characterization of viruses included in the Manzanilla and Oropouche species complexes of the genus Orthobunyavirus, family Bunyaviridae
Authors: Ladner Jason T. , Savji Nazir , Lofts Loreen , Travassos da Rosa Amelia , Wiley Michael R. , Gestole Marie C. , Rosen Gail E. , Guzman Hilda , Vasconcelos Pedro F. C. , Nunes Marcio R. T. , J. Kochel Tadeusz , Lipkin W. Ian , Tesh Robert B. , Palacios Gustavo
Published: February 2014

A thorough characterization of the genetic diversity of viruses present in vector and vertebrate host populations is essential for the early detection of and response to emerging pathogenic viruses, yet genetic characterization of many important viral groups remains incomplete. The Simbu serogroup of the genus Orthobunyavirus, family Bunyaviridae, is an example. The Simbu serogroup currently consists of a highly diverse group of related arboviruses that infect both humans and economically important livestock species. Here, we report complete genome sequences for 11 viruses within this group, with a focus on the large and poorly characterized Manzanilla and Oropouche species complexes. Phylogenetic and pairwise divergence analyses indicated the presence of high levels of genetic diversity within these two species complexes, on a par with that seen among the five other species complexes in the Simbu serogroup. Based on previously reported divergence thresholds between species, the data suggested that these two complexes should actually be divided into at least five species. Together these five species formed a distinct phylogenetic clade apart from the rest of the Simbu serogroup. Pairwise sequence divergences among viruses of this clade and viruses in other Simbu serogroup species complexes were similar to levels of divergence among the other orthobunyavirus serogroups. The genetic data also suggested relatively high levels of natural reassortment, with three potential reassortment events present, including two well-supported events involving viruses known to infect humans.
An experimentally determined evolutionary model dramatically improves phylogenetic fit
Authors: Bloom Jesse D.
Published: February 2014

All modern approaches to molecular phylogenetics require a quantitative model for how genes evolve. Unfortunately, existing evolutionary models do not realistically represent the site-heterogeneous selection that governs actual sequence change. Attempts to remedy this problem have involved augmenting these models with a burgeoning number of free parameters. Here I demonstrate an alternative: experimental determination of a parameter-free evolutionary model via mutagenesis, functional selection, and deep sequencing. Using this strategy, I create an evolutionary model for influenza nucleoprotein that describes the gene phylogeny far better than existing models with dozens or even hundreds of free parameters. Emerging high-throughput experimental strategies such as the one employed here provide fundamentally new information that has the potential to transform the sensitivity of phylogenetic and genetic analyses.
Genome methylation in D. melanogaster is found at specific short motifs and is independent of DNMT2 activity
Authors: Takayama Sachiko , Dhahbi Joseph , Roberts Adam , Mao Guanxiong , Heo Seok-Jin , Pachter Lior , Martin David I.K. , Boffelli Dario
Published: February 2014

Cytosine methylation in the genome of Drosophila melanogaster has been elusive and controversial: Its location and function have not been established. We have used a novel and highly sensitive genomewide cytosine methylation assay to detect and map genome methylation in stage 5 Drosophila embryos. The methylation we observe with this method is highly localized and strand asymmetrical, limited to regions covering ∼1% of the genome, dynamic in early embryogenesis, and concentrated in specific 5-base sequence motifs that are CA- and CT-rich but depleted of guanine. Gene body methylation is associated with lower expression, and many genes containing methylated regions have developmental or transcriptional functions. The only known DNA methyltransferase in Drosophila is the DNMT2 homolog MT2, but lines deficient for MT2 retain genomic methylation, implying the presence of a novel methyltransferase. The association of methylation with a lower expression of specific developmental genes at stage 5 raises the possibility that it participates in controlling gene expression during the maternal-zygotic transition.
Structural insights into the novel ARM-repeat protein CTNNBL1 and its association with the hPrp19–CDC5L complex
Authors: Ahn Jae-Woo , Kim Sangwoo , Kim Eun-Jung , Kim Yeo-Jin , Kim Kyung-Jin
Published: February 2014

The hPrp19–CDC5L complex plays a crucial role during human pre-mRNA splicing by catalytic activation of the spliceosome. In order to elucidate the molecular architecture of the hPrp19–CDC5L complex, the crystal structure of CTNNBL1, one of the major components of this complex, was determined. Unlike canonical ARM-repeat proteins such as β-catenin and importin-α, CTNNBL1 was found to contain a twisted and extended ARM-repeat structure at the C-terminal domain and, more importantly, the protein formed a stable dimer. A highly negatively charged patch formed in the N-terminal ARM-repeat domain of CTNNBL1 provides a binding site for CDC5L, a binding partner of the protein in the hPrp19–CDC5L complex, and these two proteins form a complex with a stoichiometry of 2:2. These findings not only present the crystal structure of a novel ARM-repeat protein, CTNNBL1, but also provide insights into the detailed molecular architecture of the hPrp19–CDC5L complex.
Structural and functional analyses of a glutaminyl cyclase from Ixodes scapularis reveal metal-independent catalysis and inhibitor binding
Authors: Huang Kai-Fa , Hsu Hui-Ling , Karim Shahid , Wang Andrew H.-J.
Published: February 2014

Glutaminyl cyclases (QCs) from mammals and Drosophila are zinc-dependent enzymes that catalyze N-terminal pyroglutamate formation of numerous proteins and peptides. These enzymes have been found to be critical for the oviposition and embryogenesis of ticks, implying that they are possible physiological targets for tick control. Here, 1.10–1.15 Å resolution structures of a metal-independent QC from the black-legged tick Ixodes scapularis (Is-QC) are reported. The structures exhibit the typical scaffold of mammalian QCs but have two extra disulfide bridges that stabilize the central β-sheet, resulting in an increased thermal stability. Is-QC contains ∼0.5 stoichiometric zinc ions, which could be removed by 1 mM EDTA. Compared with the Zn-bound form, apo-Is-QC has a nearly identical active-site structure and stability, but unexpectedly possesses significantly increased QC activities towards both synthetic and physiological substrates. Enzyme-kinetic analysis revealed that apo-Is-QC has a stronger substrate-binding affinity, suggesting that bound zinc interferes with substrate binding during catalysis. The structures of Is-QC bound to the inhibitor PBD150 revealed similar binding modes to both forms of Is-QC, with the exception of the inhibitor imidazole ring, which is consistent with the comparable inhibition activities of the inhibitor towards both forms of Is-QC. These findings have implications for the design of new QC inhibitors.