bluuebunny/crossref_metadata_2025 huggingface dataset:
The influence of quantum dot size on the sub-bandgap intraband photocurrent in intermediate band solar cells
Authors: Mellor Alexander , Luque Antonio , Tobías Ignacio , Martí Antonio
Published: October 2012

The effect of quantum dot (QD) size on the performance of quantum dot intermediate band solar cells is investigated. A numerical model is used to calculate the bound state energy levels and the absorption coefficient of transitions from the ground state to all other states in the conduction band. Comparing with the current state of the art, strong absorption enhancements are found for smaller quantum dots, as well as a better positioning of the energy levels, which is expected to reduce thermal carrier escape. It is concluded that reducing the quantum dot size can increase sub-bandgap photocurrent and improve voltage preservation.
Electronic and magnetic structure of Fe3O4/BiFeO3 multiferroic superlattices: First principles calculations
Authors: Yang H. , Jin C. , Mi W. B. , Bai H. L. , Chen G. F.
Published: October 2012

Fe3O4/BiFeO3(001) superlattices comprising multiferroic BiFeO3 and ferrimagnetic half-metallic Fe3O4 have been investigated using first principles calculations. Two models were simulated: Model (a) contains the interfaces of Fe(A)−BiO and Fe2O4(B)−FeO2; Model (b) contains the interfaces of Fe(A)−FeO2 and Fe2O4(B)−BiO. The magnetization enhances 13% and 8% for models (a) and (b) due to the interfacial bonding between Fe(A)/Fe(B) and Bi atoms, respectively. The much larger enhancement in model (a) is ascribed to the facts that the Fe(A) atoms are surrounded by relatively less O atoms than Fe(B) in model (b), which increases the hybridization between Fe(A) and Bi atoms. The calculated results suggest that the number of oxygen atoms at the interfaces plays an important role on determining the interfacial coupling strength. Meanwhile, the interfacial bonding also affects the spin polarization of the Fe3O4 at the interface.
Dynamic response of exchange bias in graphene nanoribbons
Authors: Narayana Jammalamadaka S. , Rao S. S. , Vanacken J. , Moshchalkov V. V. , Lu Wei , Tour J. M.
Published: October 2012

The dynamics of magnetic hysteresis, including the training effect and the field sweep rate dependence of the exchange bias, is experimentally investigated in exchange-coupled potassium split graphene nanoribbons (GNRs). We find that, at low field sweep rate, the pronounced absolute training effect is present over a large number of cycles. This is reflected in a gradual decrease of the exchange bias with the sequential field cycling. However, at high field sweep rate above 0.5 T/min, the training effect is not prominent. With the increase in field sweep rate, the average value of exchange bias field grows and is found to follow power-law behavior. The response of the exchange bias field to the field sweep rate variation is linked to the difference in the time it takes to perform a hysteresis loop measurement compared with the relaxation time of the anti-ferromagnetically aligned spins. The present results may broaden our current understanding of magnetism of GNRs and would be helpful in establishing the GNRs-based spintronic devices.
Control of normal and abnormal bipolar resistive switching by interface junction on In/Nb:SrTiO3 interface
Authors: Sun J. , Jia C. H. , Li G. Q. , Zhang W. F.
Published: October 2012

The resistive switching behaviors of indium (In)/Nb:SrTiO3 (NSTO) with different metal/semiconductor contacts are investigated. The In electrodes with the Schottky contacts are fabricated on NSTO surface using direct current reactive magnetron sputtering, and the fresh In is directly pressed to form the Ohmic contact. The device with one Schottky barrier displays a normal bipolar resistive switching (BRS) behavior, while the device with two Schottky barriers shows an abnormal BRS behavior. The results demonstrate that the injection and trapping or detrapping of carriers near the interface between the metal electrode and semiconductor are closely related to the resistive switching performance.
Top-gate staggered poly(3,3″′-dialkyl-quarterthiophene) organic thin-film transistors with reverse-offset-printed silver source/drain electrodes
Authors: Kim Minseok , Bon Koo Jae , Baeg Kang-Jun , Jung Soon-Won , Ju Byeong-Kwon , You In-Kyu
Published: October 2012

Here, we report on high-performance top-gated poly(3,3″′-dialkyl-quarterthiophene) (PQT-12) organic thin-film transistors (OTFTs) with reverse-offset-printed (ROP) silver (Ag) source/drain (S/D) electrodes. OTFT devices with ROP S/D electrodes using Ag nanopaste show higher performance (∼0.01 cm2/Vs) than those fabricated by vacuum electron beam evaporation with conventional photolithography and a standard lift-off process (∼1 × 10−3 cm2/Vs). This dissimilarity is attributed to the higher work function (−4.9 eV) of the ROP Ag electrode due to AgO formation on the Ag surface during thermal annealing. This results in a low interfacial hole injection energy barrier between the S/D electrodes and the PQT-12 semiconductor.
Fabrication and performance optimization of the magneto-optical (Tb1−xRx)3Al5O12 (R = Y, Ce) transparent ceramics
Authors: Chen Chong , Zhou Shengming , Lin Hui , Yi Qing
Published: October 2012

(Tb1−xRx)3Al5O12 (R = Y, Ce) magneto-optical transparent ceramics were synthesized by solid state reaction and vacuum sintering. The two-step sintering method was also applied to investigate the properties of the Y3+ doped Tb3Al5O12 samples. The Verdet constant of the Y3+ doped Tb3Al5O12 transparent ceramic measured at 632.8 nm was −108.79 rad · T−1 · m−1, which was smaller than that of the Tb3Al5O12 transparent ceramics. However, the magneto-optical property of the Ce3+ doped Tb3Al5O12 samples was improved a lot. The Verdet constant measured at 632.8 nm was −199.55 rad · T−1 · m−1, which was about 16% larger than that of Tb3Al5O12.
Formation and cell translocation of carbon nanotube-fibrinogen protein corona
Authors: Chen Ran , Radic Slaven , Choudhary Poonam , Ledwell Kimberley G. , Huang George , Brown Jared M. , Chun Ke Pu
Published: October 2012

The binding of plasma fibrinogen with both single-walled and multi-walled carbon nanotubes (SWNTs and MWNTs) has been examined. Specifically, our absorbance study indicated that MWNTs were coated with multi-layers of fibrinogen to render a “hard protein corona,” while SWNTs were adsorbed with thin layers of the protein to precipitate out of the aqueous phase. In addition, static quenching as a result of energy transfer from fluorescently labeled fibrinogen to their nanotube substrates was revealed by Stern-Volmer analysis. When exposed to HT-29 cells, the nanotubes and fibrinogen could readily dissociate, possibly stemming from their differential affinities for the amphiphilic membrane bilayer.
Strong light-extraction enhancement in GaInN light-emitting diodes patterned with TiO2 micro-pillars with tapered sidewalls
Authors: Ma Ming , Cho Jaehee , Fred Schubert E. , Park Yongjo , Bum Kim Gi , Sone Cheolsoo
Published: October 2012

An effective method to enhance the light extraction for GaInN light-emitting diodes (LEDs) is reported. The method employs TiO2 micro-pillars with tapered sidewalls, which are refractive-index-matched to the underlying GaN. The tapered micro-pillars are fabricated by using reflowed photoresist as mask during CHF3-based dry etch, with O2 added in order to precisely control the taper angle. LEDs patterned with TiO2 micro-pillars with tapered sidewalls show a 100% enhancement in light-output power over planar reference LEDs. The measured results are in good agreement with ray-tracing simulations, showing strong potential of optical surfaces that are controlled in terms of refractive index and lateral structure.
Front contact layer of multiphase silicon-carbon in thin film silicon solar cell
Authors: Ho Kim Sun , Joo You Dong , Hee Park Jin , Eun Lee Sung , Lee Heon-Min , Kim Donghwan
Published: October 2012

In order to increase the quantum efficiency as well as conversion efficiency, we propose the boron doped hydrogenated multiphase silicon-carbon (called as “multiphase silicon-carbon”) as the front contact layer in thin film silicon solar cells. The multiphase silicon-carbon consists of amorphous carbon, amorphous silicon, and crystalline silicon-like clustering phase. We achieved a high conductivity and a low optical absorptance of multiphase silicon-carbon and compared it with the existing boron doped microcrystalline silicon. Applying this layer between transparent conductive oxide and the p layer, the amorphous silicon and silicon-germanium (a-Si/a-SiGe) double junction cell showed an increase of quantum efficiency in short wavelength and an improvement of the conversion efficiency by about 0.6% in 1 cm2 area.
Direct current pulse train actuation to enhance droplet control in digital microfluidics
Authors: Murran Miguel A. , Najjaran Homayoun
Published: October 2012

The effective operation of a digital microfluidic (DMF) device depends on its ability to actuate droplets. Pulse width modulation of actuating signals (DC pulse train actuation) is proposed as a practical digital implementation and enhanced droplet manipulation technique. Experimental and simulation results demonstrate the efficacy of droplet incremental displacement and velocity control by modulating the width of each actuation pulse. This will in turn enable the control of the non-linear droplet transport dynamics to minimize droplet position overshoot, deformation, and fragmentation. As a result, DCPT actuation offers unparalleled control over droplet position and speed in DMF devices.
Electric field assisted sputtering of Fe3O4 thin films and reduction in anti-phase boundaries
Authors: Kumar Ankit , Pandya Dinesh K. , Chaudhary Sujeet
Published: October 2012

Fe3O4 thin films have been prepared by a new approach of in-situ electric field assisted sputtering. Raman shift, ρ(T), and M(T) measurements reveal a reduction in anti-phase boundaries (APBs), which is explained by the electric field induced surface diffusion favouring [111] oriented growth with lesser defects. Early magnetization saturation (4 kOe) and its higher value (441 emu/cm3), low electron phonon coupling constant (0.48), sharp Verwey transition ΔTV = 12 K, Arrhenius law of conduction via delocalized states above TV and lower value of localization radius (1.5 nm) below TV compared to that observed in un-assisted films confirmed that the electric field assisted grown films are nearly free from anti-phase boundaries.
Control of ion density distribution by magnetic traps for plasma electrons
Authors: Baranov Oleg , Romanov Maxim , Fang Jinghua , Cvelbar Uros , (Ken) Ostrikov Kostya
Published: October 2012

The effect of a magnetic field of two magnetic coils on the ion current density distribution in the setup for low-temperature plasma deposition is investigated. The substrate of 400 mm diameter is placed at a distance of 325 mm from the plasma duct exit, with the two magnetic coils mounted symmetrically under the substrate at a distance of 140 mm relative to the substrate centre. A planar probe is used to measure the ion current density distribution along the plasma flux cross-sections at distances of 150, 230, and 325 mm from the plasma duct exit. It is shown that the magnetic field strongly affects the ion current density distribution. Transparent plastic films are used to investigate qualitatively the ion density distribution profiles and the effect of the magnetic field. A theoretical model is developed to describe the interaction of the ion fluxes with the negative space charge regions associated with the magnetic trapping of the plasma electrons. Theoretical results are compared with the experimental measurements, and a reasonable agreement is demonstrated.
GeSn p-i-n detectors integrated on Si with up to 4% Sn
Authors: Oehme M. , Schmid M. , Kaschel M. , Gollhofer M. , Widmann D. , Kasper E. , Schulze J.
Published: October 2012

GeSn heterojunction photodetectors on Si substrates were grown with Sn concentration up to 4%, fabricated for vertical light incidence, and characterized. The complete layer structure was grown by means of ultra low temperature (100 °C) molecular beam epitaxy. The Sn content shifts the responsivity into the infrared, about 310 nm for the 4% Sn sample. An increase of the optical responsivity for wavelengths higher than 1550 nm can be observed with increasing Sn content. At 1600 nm, the optical responsivity is increased by more than a factor of 10 for the GeSn diode with 4% Sn in comparison to the Ge reference diode.
Intrinsic threshold mechanism of phase-change memory cells by pulsed current–voltage characterization
Authors: Chen W. , Li Z. , Peng J. H. , Deng Y. F. , Miao X. S.
Published: October 2012

A short pulsed current–voltage (I-V) measurement method is proposed for phase-change random access memory (PCRAM) to investigate the self-heating behavior. The pulse widths and periods are indispensable parameters to describe pulsed I-V characteristics of PCRAM cells. By comparing the difference between direct current I-V curves and pulsed I-V curves, the threshold voltages of pulsed I-V are much higher. It implies the existence of self-heating and energy accumulation. Assume that the heating of the active region causes the change of the electronic barrier and the electronic activity, the physical model dominated by the self-heating in PCRAM cells is proposed.
Exotic chimera dynamics glimpsed in experiments
Authors: Smart Ashley G.
Published: October 2012

In such a state, synchrony and asynchrony coexist among coupled oscillators.
Serial verbs in English
Authors: Roberts John R.
Published: October 2012

Serial verb constructions (SVCs) are found in Creole languages and in the languages of West Africa, Southeast Asia, Amazonia, Oceania, and New Guinea. In this article we examine catenative verb constructions (CVCs) in English from a Role and Reference Grammar perspective and compare them with SVCs. More specifically, based on the set of syntactic and semantic properties of SVCs proposed by Kroeger (2004: 229–230), it will be demonstrated that CVCs in English have all of the characteristic syntactic and semantic properties of SVCs.
Postmodifying verb-second clauses in spoken German
Authors: Weinert Regina
Published: October 2012

This usage-based and corpus-based study examines the use of verb-second clauses as restrictive postmodifiers of noun phrases in spoken German (ich kenn leute die haben immer pech ‘I know people they are always unlucky’) in relation to verb-final relative clauses. Previous accounts largely work with de-contextualised and constructed data and stop short of accounting for the discourse function of verb-second postmodifying structures. The ratio of verb-final relative clauses to postmodifying verb-second clauses does not indicate a shift towards main clause syntax. Rather, the verb-second clauses form part of a set of existential or presentational and ascriptive copular constructions which serve to highlight properties of entities and/or introduce discourse topics. Relative clauses can be used for such functions, but this is not as common. The syntactic and semantic features associated with postmodifying verb-second clauses can be seen as a direct result of their discourse function, which only a corpus analysis could reveal. The paper also comments on the wider related aspects of verb position, clause combining and pronoun use in spoken German from the perspective of a usage-based language model.
A Reconnaissance Survey of the Effects of Sediment Traps on Michigan Streams
Authors: Zorn Troy G. , Wills Todd C.
Published: October 2012

Excess sand bedload can significantly degrade salmonid habitat and populations. Successful use of sediment traps to restore habitat and salmonid populations on two Michigan streams in the early 1980s led to application of traps at well over 100 coldwater streams in Michigan and rivers throughout the USA within a decade. Unfortunately, little quantitative evaluation has occurred other than anecdotal observations for some traps. We conducted a broad-scale survey of 65 Michigan stream reaches with sediment traps by collecting data along transects upstream and downstream of the traps to assess downstream changes in substrate composition, channel depth, and channel stability in response to sediment traps. We found that recent applications of sediment traps (usually as stand-alone instream habitat treatments) had no significant effect on substrate, thalweg depth, or bank stability conditions in the reaches studied. Using reach-based estimates of specific stream power at the 10% annual exceedence flow, we identified areas where sediment traps could potentially destabilize channels. Specific stream power estimates were positively correlated with the preponderance of gravel and coarser substrate in stream reaches. Our study and previous assessments of sediment traps suggest that managers carefully consider their river and all potential management options when deciding if sediment traps will provide the best return on their investment.

Received April 12, 2012; accepted July 4, 2012
Cytoskeleton key
Authors: Leslie Mitch
Published: October 2012

Study uncovers mechanism for integrating microtubules and actin.
Cortical dynein is critical for proper spindle positioning in human cells
Authors: Kotak Sachin , Busso Coralie , Gönczy Pierre
Published: October 2012

Correct spindle positioning is fundamental for proper cell division during development and in stem cell lineages. Dynein and an evolutionarily conserved ternary complex (nuclear mitotic apparatus protein [NuMA]–LGN–Gα in human cells and LIN-5–GPR-1/2–Gα in Caenorhabditis elegans) are required for correct spindle positioning, but their relationship remains incompletely understood. By analyzing fixed specimens and conducting live-imaging experiments, we uncovered that appropriate levels of ternary complex components are critical for dynein-dependent spindle positioning in HeLa cells and C. elegans embryos. Moreover, using mutant versions of Gα in both systems, we established that dynein acts at the membrane to direct spindle positioning. Importantly, we identified a region within NuMA that mediates association with dynein. By using this region to target dynein to the plasma membrane, we demonstrated that the mere presence of dynein at that location is sufficient to direct spindle positioning in HeLa cells. Overall, we propose a model in which the ternary complex serves to anchor dynein at the plasma membrane to ensure correct spindle positioning.
Differentiation-associated microRNAs antagonize the Rb–E2F pathway to restrict proliferation
Authors: Marzi Matteo J. , Puggioni Eleonora M. R. , Dall'Olio Valentina , Bucci Gabriele , Bernard Loris , Bianchi Fabrizio , Crescenzi Marco , Di Fiore Pier Paolo , Nicassio Francesco
Published: October 2012

The cancer-associated loss of microRNA (miRNA) expression leads to a proliferative advantage and aggressive behavior through largely unknown mechanisms. Here, we exploit a model system that recapitulates physiological terminal differentiation and its reversal upon oncogene expression to analyze coordinated mRNA/miRNA responses. The cell cycle reentry of myotubes, forced by the E1A oncogene, was associated with a pattern of mRNA/miRNA modulation that was largely reciprocal to that induced during the differentiation of myoblasts into myotubes. The E1A-induced mRNA response was preponderantly Retinoblastoma protein (Rb)-dependent. Conversely, the miRNA response was mostly Rb-independent and exerted through tissue-specific factors and Myc. A subset of these miRNAs (miR-1, miR-34, miR-22, miR-365, miR-29, miR-145, and Let-7) was shown to coordinately target Rb-dependent cell cycle and DNA replication mRNAs. Thus, a dual level of regulation—transcriptional regulation via Rb–E2F and posttranscriptional regulation via miRNAs—confers robustness to cell cycle control and provides a molecular basis to understand the role of miRNA subversion in cancer.
Effect of reviewer's origin on peer review: China vs. non‐China
Authors: ZHANG Xiangyi
Published: October 2012

Peer review is important in ensuring quality. As science and technology develops in China, the number of scientific papers is increasing, and it is interesting to discover whether there are differences between reviewers from China and those from other countries when they review manuscripts submitted by Chinese authors. This study was based on an environmental academic Chinese (English language) journal. The peer review of 157 manuscripts from Chinese authors was analyzed. There are significant differences in whether a potential reviewer accepts an invitation to review; however, the outcome of peer review is almost unaffected by the reviewer's geographical origin.
Giant texturing effect in multiferroic MnWO4 polycrystals
Authors: Jana Somnath , Nag Abhishek , Ray Sugata
Published: October 2012

Different methods of texturing polycrystalline materials have been developed over the years to use/probe anisotropic material properties with relative ease, where complicated and expensive single crystal growth processes could be avoided. In this paper, particle morphology assisted texturing in multiferroic MnWO4 has been discussed. Detailed powder x-ray diffraction vis-a-vis scanning electron microscopic studies on differently annealed and processed samples have been employed to probe the giant texturing effect in polycrystalline MnWO4. A quantitative measure of the texturing has been carried out by means of the Rietveld analysis technique. Qualitative presentation of magnetic and dielectric data on textured pellet demonstrated the development of clear anisotropic physical properties in polycrystalline pellets. Finally, we established that the highly anisotropic plate-like particles are formed due to easy cleavage of the significantly large crystalline grains.
Determining the nonparabolicity factor of the CdO conduction band using indium doping and the Drude theory
Authors: Mendelsberg Rueben J , Zhu Yuankun , Anders André
Published: October 2012

Due to their high intrinsic electron mobility, CdO-based materials are gaining interest as transparent conductive oxides. By creating model dielectric functions based on the Drude theory, accurate fits to the measured transmittance and reflectance of CdO and CdO : In thin films were achieved without using a frequency dependent Drude damping parameter. Difference in the model between undoped and In-doped CdO showed that the Burstein–Moss shift is not the only mechanism which improves the transparency in In-doped samples. Comparing the Drude analysis with Hall measurements revealed a nonlinear relationship between the free-electron effective mass and the carrier concentration, an effect which is caused by the nonparabolicity of the CdO conduction band. Analysis of 50 CdO : In thin films grown by pulsed filtered cathodic arc showed the nonparabolicity factor was C = (0.5 ± 0.2) eV−1 and the band-edge effective mass was (0.16 ± 0.05)m
e. Knowledge of the effective mass allows for optical measurements of carrier mobility, which was less than or equal to the measured Hall mobility in these films due to the large electron mean free path compared with the grain size.
Decay rates and global existence for semilinear dissipative Timoshenko systems
Authors: Racke Reinhard , Said-Houari Belkacem
Published: October 2012

We prove new decay estimates for the dissipative Timoshenko system in the one-dimensional whole space, and a global existence theorem for semilinear systems. More precisely, if we restrict the initial data

(
(

φ

0

,

ψ
0

)
,
(

φ

1

,

ψ
1

)
)

( (\varphi _{0},\psi _0),(\varphi _{1},\psi _1))

<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="element-of left-parenthesis upper H Superscript s plus 1 Baseline left-parenthesis double-struck upper R Superscript upper N Baseline right-parenthesis intersection upper L Superscript 1 comma gamma Baseline left-parenthesis double-struck upper R Superscript upper N Baseline right-parenthesis right-parenthesis times left-parenthesis upper H Superscript s Baseline left-parenthesis double-struck upper R Superscript upper N Baseline right-parenthesis right-parenthesis intersection upper L Superscript 1 comma gamma Baseline left-parenthesis double-struck upper R Superscript upper N Baseline right-parenthesis right-parenthesis">

∈

(

H

s
+
1

(

R

N

)
∩

L

1
,
γ

(

R

N

)

)

×

(

H

s

(

R

N

)

)

∩

L

1
,
γ

(

R

N

)

)

\in \Big ( H^{s+1}( \mathbb {R}^{N}) \cap L^{1,\gamma }( \mathbb {R}^{N}) \Big ) \times \Big ( H^{s}( \mathbb {R}^{N})\Big ) \cap L^{1,\gamma }( \mathbb {R}^{N}) \Big )

with

γ
∈

[
0
,
1
]

\gamma \in \left [ 0,1\right ]

, then we can derive faster decay estimates than those given by Ide, Haramoto and Kawashima. In addition, we use these decay estimates of the linear problem combined with the weighted energy method introduced by Todorova and Yordanov with the special weight given by Ikehata and Inoue to solve a semilinear problem with low regularity.
Adding unaligned sequences into an existing alignment using MAFFT and LAST
Authors: Katoh Kazutaka , Frith Martin C.
Published: October 2012

Two methods to add unaligned sequences into an existing multiple sequence alignment have been implemented as the ‘–add’ and ‘–addfragments’ options in the MAFFT package. The former option is a basic one and applicable only to full-length sequences, whereas the latter option is applicable even when the unaligned sequences are short and fragmentary. These methods internally infer the phylogenetic relationship among the sequences in the existing alignment and the phylogenetic positions of unaligned sequences. Benchmarks based on two independent simulations consistently suggest that the “–addfragments” option outperforms recent methods, PaPaRa and PAGAN, in accuracy for difficult problems and that these three methods appropriately handle easy problems.

Availability:  http://mafft.cbrc.jp/alignment/software/

Contact:  katoh@ifrec.osaka-u.ac.jp

Supplementary information:  Supplementary data are available at Bioinformatics online
SEQUENTIAL OPTICAL COHERENCE TOMOGRAPHY IMAGES OF RETINAL NECROSIS IN ACUTE OCULAR TOXOPLASMOSIS
Authors: Alwassia Ahmad A. , Cho Hyung , Adhi Mehreen , Duker Jay S. , Baumal Caroline R.
Published: October 2012

Purpose:

To describe the features of sequential spectral-domain optical coherence tomography (OCT) images in an eye with acute primary toxoplasmosis.

Methods:

Case report of an individual diagnosed with acute primary toxoplasmic retinochoroiditis. Initial and follow-up spectral-domain OCT findings are described.

Results:

This patient developed retinitis as a result of an acute infection consistent with Toxoplasma gondii suggested by toxoplasma-specific IgM serology and the response to therapy. The retinitis appeared initially as a hyperreflective region on spectral-domain OCT. An intraretinal cyst consistent with T. gondii parasitic infection was identified. Subsequent OCT images demonstrated progression to full-thickness retinal necrosis with the development of cystic spaces in the retina.

Conclusion:

Optical coherence tomography may be useful in characterizing the features, extent, and location of retinitis caused by T. gondii. Specific OCT features may indicate whether the infection is acute phase or becoming quiescent.
Inferring population-level contact heterogeneity from common epidemic data
Authors: Stack J. Conrad , Bansal Shweta , Kumar V. S. Anil , Grenfell Bryan
Published: October 2012

Models of infectious disease spread that incorporate contact heterogeneity through contact networks are an important tool for epidemiologists studying disease dynamics and assessing intervention strategies. One of the challenges of contact network epidemiology has been the difficulty of collecting individual and population-level data needed to develop an accurate representation of the underlying host population's contact structure. In this study, we evaluate the utility of common epidemiological measures (
R
0
, epidemic peak size, duration and final size) for inferring the degree of heterogeneity in a population's unobserved contact structure through a Bayesian approach. We test the method using ground truth data and find that some of these epidemiological metrics are effective at classifying contact heterogeneity. The classification is also consistent across pathogen transmission probabilities, and so can be applied even when this characteristic is unknown. In particular, the reproductive number,
R
0
, turns out to be a poor classifier of the degree heterogeneity, while, unexpectedly, final epidemic size is a powerful predictor of network structure across the range of heterogeneity. We also evaluate our framework on empirical epidemiological data from past and recent outbreaks to demonstrate its application in practice and to gather insights about the relevance of particular contact structures for both specific systems and general classes of infectious disease. We thus introduce a simple approach that can shed light on the unobserved connectivity of a host population given epidemic data. Our study has the potential to inform future data-collection efforts and study design by driving our understanding of germane epidemic measures, and highlights a general inferential approach to learning about host contact structure in contemporary or historic populations of humans and animals.
Inferring subjective states through the observation of actions
Authors: Patel D. , Fleming S. M. , Kilner J. M.
Published: October 2012

Estimating another person's subjective confidence is crucial for social interaction, but how this inference is achieved is unknown. Previous research has demonstrated that the speed at which people make decisions is correlated with their confidence in their decision. Here, we show that (i) subjects are able to infer the subjective confidence of another person simply through the observation of their actions and (ii) this inference is dependent upon the performance of each subject when executing the action. Crucially, the latter result supports a model in which motor simulation of an observed action mediates the successful understanding of other minds. We conclude that kinematic understanding allows access to the higher-order cognitive processes of others, and that this access plays a central role in social interactions.
Visible transitions from ground state H
3
+
measured with high-sensitivity action spectroscopy
Authors: Berg Max , Wolf Andreas , Petrignani Annemieke
Published: October 2012

We report on the recent observation of new spectral lines of cold H

ions lying well in the visible spectral region. Transitions from the two lowest ro–vibrational levels to final levels up to 16 700 cm
−1
, almost half way to the dissociation limit, have been measured, involving up to eight vibrational quanta. The observed transitions are more than six orders of magnitude less intense than the

fundamental band and yet another order of magnitude weaker than reached by previous sensitive action spectroscopy in the near-infrared region. The measurements were carried out in a cryogenic 22-pole ion trap with H

ions cooled to their lowest rotational levels by helium buffer gas. Laser-induced chemical reactions lead to the formation of ArH
+
ions detected with single-ion sensitivity. These visible measurements, together with the previous near-infrared measurements, have helped to further develop empirically corrected calculations and have provided essential benchmarks for new
ab initio
calculations that now reach a spectroscopic accuracy of 0.1 cm
−1
on average up to the highest observed transition. Highly sensitive action spectroscopy and the attained high-accuracy predictions will enable us to find and measure transitions even further into the visible region of H

, paving the way towards the dissociation limit.
Binary recombination of para- and ortho-H
3
+
with electrons at low temperatures
Authors: Dohnal P. , Hejduk M. , Varju J. , Rubovič P. , Roučka Š. , Kotrík T. , Plašil R. , Johnsen R. , Glosík J.
Published: October 2012

Results of an experimental study of binary recombination of para- and ortho-

ions with electrons are presented. Near-infrared cavity-ring-down absorption spectroscopy was used to probe the lowest rotational states of

ions in the temperature range of 77–200 K in an

-dominated afterglow plasma. By changing the para/ortho abundance ratio, we were able to obtain the binary recombination rate coefficients for pure

and

. The results are in good agreement with previous theoretical predictions.
Progress in calculating the potential energy surface of H
3
+
Authors: Adamowicz Ludwik , Pavanello Michele
Published: October 2012

The most accurate electronic structure calculations are performed using wave function expansions in terms of basis functions explicitly dependent on the inter-electron distances. In our recent work, we use such basis functions to calculate a highly accurate potential energy surface (PES) for the H

ion. The functions are explicitly correlated Gaussians, which include inter-electron distances in the exponent. Key to obtaining the high accuracy in the calculations has been the use of the analytical energy gradient determined with respect to the Gaussian exponential parameters in the minimization of the Rayleigh–Ritz variational energy functional. The effective elimination of linear dependences between the basis functions and the automatic adjustment of the positions of the Gaussian centres to the changing molecular geometry of the system are the keys to the success of the computational procedure. After adiabatic and relativistic corrections are added to the PES and with an effective accounting of the non-adiabatic effects in the calculation of the rotational/vibrational states, the experimental H

rovibrational spectrum is reproduced at the 0.1 cm
−1
accuracy level up to 16 600 cm
−1
above the ground state.
Transfer of a proton between H
2
and O
2
Authors: Kluge Lars , Gärtner Sabrina , Brünken Sandra , Asvany Oskar , Gerlich Dieter , Schlemmer Stephan
Published: October 2012

The proton affinities of hydrogen and oxygen are very similar. Therefore, it has been discussed that the proton transfer from the omnipresent H

to molecular oxygen in the near thermoneutral reaction

effectively binds the interstellar oxygen in O
2
H
+
. In this work, the proton transfer reaction has been investigated in a low-temperature 22-pole ion trap from almost room temperature (280 K) down to the lowest possible temperature limited by freeze out of oxygen gas (about 40 K at a low pressure). The Arrhenius behaviour of the rate coefficient for the forward reaction shows that it is subject to an activation energy of
E
A
/
k
=113 K. Thus, the forward reaction can proceed only in higher temperature molecular clouds. Applying laser-induced reactions to the given reaction (in the backward direction), a preliminary search for spectroscopic signatures of O
2
H
+
in the infrared was unsuccessful, whereas the forward reaction has been successfully used to probe the population of the lowest ortho and para levels of H

.
Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes
Authors: Gorkin David U. , Lee Dongwon , Reed Xylena , Fletez-Brant Christopher , Bessling Seneca L. , Loftus Stacie K. , Beer Michael A. , Pavan William J. , McCallion Andrew S.
Published: October 2012

We take a comprehensive approach to the study of regulatory control of gene expression in melanocytes that proceeds from large-scale enhancer discovery facilitated by ChIP-seq; to rigorous validation in silico, in vitro, and in vivo; and finally to the use of machine learning to elucidate a regulatory vocabulary with genome-wide predictive power. We identify 2489 putative melanocyte enhancer loci in the mouse genome by ChIP-seq for EP300 and H3K4me1. We demonstrate that these putative enhancers are evolutionarily constrained, enriched for sequence motifs predicted to bind key melanocyte transcription factors, located near genes relevant to melanocyte biology, and capable of driving reporter gene expression in melanocytes in culture (86%; 43/50) and in transgenic zebrafish (70%; 7/10). Next, using the sequences of these putative enhancers as a training set for a supervised machine learning algorithm, we develop a vocabulary of 6-mers predictive of melanocyte enhancer function. Lastly, we demonstrate that this vocabulary has genome-wide predictive power in both the mouse and human genomes. This study provides deep insight into the regulation of gene expression in melanocytes and demonstrates a powerful approach to the investigation of regulatory sequences that can be applied to other cell types.
Mammary Fat Pad Chamber Preparation in Mice
Authors: Jain Rakesh K. , Munn Lance L. , Fukumura Dai
Published: October 2012

This protocol describes a procedure to implant mammary fat pad chambers in mice. These chambers can then be used for studying breast cancer. In comparison to the classical mammary fat pad flap model, the chamber described here has the advantage of allowing multiple observation time points in the same animal with simple anesthesia.
Verticillium Infection Triggers VASCULAR-RELATED NAC DOMAIN7–Dependent de Novo Xylem Formation and Enhances Drought Tolerance in Arabidopsis
Authors: Reusche Michael , Thole Karin , Janz Dennis , Truskina Jekaterina , Rindfleisch Sören , Drübert Christine , Polle Andrea , Lipka Volker , Teichmann Thomas
Published: October 2012

The soilborne fungal plant pathogen Verticillium longisporum invades the roots of its Brassicaceae hosts and proliferates in the plant vascular system. Typical aboveground symptoms of Verticillium infection on Brassica napus and Arabidopsis thaliana are stunted growth, vein clearing, and leaf chloroses. Here, we provide evidence that vein clearing is caused by pathogen-induced transdifferentiation of chloroplast-containing bundle sheath cells to functional xylem elements. In addition, our findings suggest that reinitiation of cambial activity and transdifferentiation of xylem parenchyma cells results in xylem hyperplasia within the vasculature of Arabidopsis leaves, hypocotyls, and roots. The observed de novo xylem formation correlates with Verticillium-induced expression of the VASCULAR-RELATED NAC DOMAIN (VND) transcription factor gene VND7. Transgenic Arabidopsis plants expressing the chimeric repressor VND7-SRDX under control of a Verticillium infection-responsive promoter exhibit reduced de novo xylem formation. Interestingly, infected Arabidopsis wild-type plants show higher drought stress tolerance compared with noninfected plants, whereas this effect is attenuated by suppression of VND7 activity. Together, our results suggest that V. longisporum triggers a tissue-specific developmental plant program that compensates for compromised water transport and enhances the water storage capacity of infected Brassicaceae host plants. In conclusion, we provide evidence that this natural plant–fungus pathosystem has conditionally mutualistic features.
Common mechanisms for calorie restriction and adenylyl cyclase type 5 knockout models of longevity
Authors: Yan Lin , Park Ji Yeon , Dillinger Jean‐Guillaume , De Lorenzo Mariana S. , Yuan Chujun , Lai Lo , Wang Chunbo , Ho David , Tian Bin , Stanley William C. , Auwerx Johan , Vatner Dorothy E. , Vatner Stephen F.
Published: October 2012

Adenylyl cyclase type 5 knockout mice (AC5 KO) live longer and are stress resistant, similar to calorie restriction (CR). AC5 KO mice eat more, but actually weigh less and accumulate less fat compared with WT mice. CR applied to AC5 KO results in rapid decrease in body weight, metabolic deterioration, and death. These data suggest that despite restricted food intake in CR, but augmented food intake in AC5 KO, the two models affect longevity and metabolism similarly. To determine shared molecular mechanisms, mRNA expression was examined genome‐wide for brain, heart, skeletal muscle, and liver. Significantly more genes were regulated commonly rather than oppositely in all the tissues in both models, indicating commonality between AC5 KO and CR. Gene ontology analysis identified many significantly regulated, tissue‐specific pathways shared by the two models, including sensory perception in heart and brain, muscle function in skeletal muscle, and lipid metabolism in liver. Moreover, when comparing gene expression changes in the heart under stress, the glutathione regulatory pathway was consistently upregulated in the longevity models but downregulated with stress. In addition, AC5 and CR shared changes in genes and proteins involved in the regulation of longevity and stress resistance, including Sirt1, ApoD, and olfactory receptors in both young‐ and intermediate‐age mice. Thus, the similarly regulated genes and pathways in AC5 KO and CR mice, particularly related to the metabolic phenotype, suggest a unified theory for longevity and stress resistance.
Short‐term prophylaxis in hereditary angioedema due to deficiency of the C1‐inhibitor – a long‐term survey
Authors: Farkas H. , Zotter Z. , Csuka D. , Szabó E. , Nébenfűhrer Z. , Temesszentandrási G. , Jakab L. , Varga L. , Harmat G. , Karádi I.
Published: October 2012

Background

Hereditary angioedema is a potentially life‐threatening disorder, because edema occurring in the mucosa of the upper airways can lead to suffocation. The management of HAE consists of avoiding the triggering factors, prophylaxis, and the acute treatment of edematous episodes. Medical procedures can also provoke edematous attacks, and therefore, short‐term prophylaxis (STP) is recommended before such interventions. Our aim was to evaluate the efficacy and safety of STP administered before medical procedures.

Methods

We conducted a retrospective analysis before and a prospective survey after establishing the diagnosis in a group of 137 (60 males, 77 females; 20 pediatric and 117 adult) patients with HAE. Both were implemented using questionnaires, patient diaries and hospital charts focusing on medical interventions provoking edematous attack, and the medicinal products (C1‐INH concentrate, tranexamic acid, and danazol) administered for STP.

Results

Comparing surgical interventions performed without pre‐event STP (in 39/89 patients before HAE was diagnosed), or after STP (in 3/55 cases after diagnosis), we found a significant (P < 0.0001, Fisher's exact test) reduction in the number of edematous episodes. Evaluating the efficacy of the drugs administered for STP revealed that C1‐INH concentrate (Berinert®, CSL Behring, Marburg, Germany) was significantly (P = 0.0096, Fisher's exact test) superior to orally administered drugs in reducing the instances of postprocedural edema. None of the medicinal products caused adverse events potentially related to STP.

Conclusions

STP reduces the number of postprocedural edematous episodes. C1‐INH concentrate is safe and effective for prophylaxis. When this agent is not available, danazol is a potential alternative for prophylaxis before elective medical interventions.
A meta‐analysis of magnesium for tetanus
Authors: Rodrigo C. , Samarakoon L. , Fernando S. D. , Rajapakse S.
Published: October 2012

Uncontrolled studies suggest that magnesium sulphate controls spasms in patients with established tetanus. We performed a meta‐analysis of controlled trials that compared magnesium sulphate with placebo or diazepam for the treatment of patients with tetanus. We searched PubMed, Scopus, Embase and the Cochrane clinical trials registry. Three studies met the inclusion criteria, containing 275 participants (199 male patients, 72.4%). Magnesium sulphate did not reduce mortality, relative risk (95% CI): vs placebo, 0.80 (0.41–1.58); vs diazepam, 1.11 (0.70–1.75). The data on duration of total intensive care unit stay, total hospital stay and the need for ventilatory support were conflicting and pooling of results could not be done due to methodological differences of individual trials. More controlled trials are needed to assess the effect of magnesium sulphate on reducing autonomic instability, spasms, duration of intensive care and hospital stays and the need for mechanical ventilation.
Essential role of transient receptor potential vanilloid type 1 in evodiamine‐mediated protection against atherosclerosis
Authors: Wei J. , Ching L.‐C. , Zhao J.‐F. , Shyue S.‐K. , Lee H.‐F. , Kou Y. R. , Lee T.‐S.
Published: October 2012

Aim

We investigated whether transient receptor potential vanilloid type 1 (TRPV1) was involved in the therapeutic effect of evodiamine, a main bioactive component in the fruit of Evodiae rutaecarpa, on the development of atherosclerosis in apolipoprotein E‐deficient (ApoE−/−) mice and ApoE−/−TRPV1−/− mice.

Methods

Histopathology was examined by haematoxylin and eosin staining, levels of cytokines and mediators were evaluated by ELISA kits, and protein expression was determined by Western blotting.

Results

Chronic administration with evodiamine (10 mg kg−1 body weight) reduced the size of atherosclerotic lesions and alleviated the hyperlipidaemia and systemic inflammation, as well as hepatic macrovesicular steatosis, in ApoE−/− mice. Treating ApoE−/− mice with evodiamine enhanced hepatic cholesterol clearance, as revealed by upregulation of hepatic low‐density lipoprotein receptor and ATP‐binding cassette (ABC) transporters ABCG5, ABCG8 and cholesterol 7α‐hydrolase. Genetic deletion of TRPV1 in ApoE−/− mice promoted the progression of atherosclerosis; elevated the serum levels of cholesterol, cytokines and chemokines; and exacerbated hepatic macrovesicular steatosis. Moreover, genetic deletion of TRPV1 abrogated the evodiamine‐evoked atheroprotection but not anti‐obesity effect in ApoE−/− mice.

Conclusion

Evodiamine may confer novel TRPV1‐dependent atheroprotection and TRPV1‐independent anti‐obesity action.
Social cognition in bipolar disorder versus schizophrenia: comparability in mental state decoding deficits
Authors: Donohoe Gary , Duignan Aoife , Hargreaves April , Morris Derek W , Rose Emma , Robertson Deirdre , Cummings Elizabeth , Moore Susan , Gill Michael , Corvin Aiden
Published: October 2012

Donohoe G, Duignan A, Hargreaves A, Morris DW, Rose E, Robertson D, Cummings E, Moore S, Gill M, Corvin A. Social cognition in bipolar disorder versus schizophrenia: comparability in mental state decoding deficits. Bipolar Disord 2012: 14: 743–748. © 2012 The Authors. Journal compilation © 2012 John Wiley & Sons A/S.

Objectives:  Neuropsychological studies comparing patients with bipolar disorder (BD) to patients with schizophrenia (SZ) suggest milder cognitive deficits in BD patients and across a smaller range of functions. The present study investigated whether this pattern is also true for social cognition – a range of socially relevant abilities, including emotion perception and recognition, theory of mind, and social attributions – by comparing performance on measures of social cognition in patients with BD, SZ, and healthy participants.

Methods:  One hundred and two patients with BD, 208 patients with SZ, and 132 healthy participants were assessed using a battery of tasks measuring basic neuropsychological and social cognition.

Results:  We observed significant differences between patients with BD and healthy participants in a test of mental state decoding (‘eyes task’) that was at a level comparable to deficits seen in patients with SZ. By comparison, BD patients showed more subtle deficits in mental state reasoning (‘hinting task’) than those shown by patients with SZ.

Conclusions:  Mental state decoding difficulties are significant in BD. An important direction for further research will be to establish to what extent these deficits affect social and occupational functioning as a potential target for therapeutic intervention.