bluuebunny/crossref_metadata_2025 huggingface dataset:
Nanoparticle generation and transport resulting from femtosecond laser ablation of ultrathin metal films: Time-resolved measurements and molecular dynamics simulations
Authors: Rouleau C. M. , Shih C.-Y. , Wu C. , Zhigilei L. V. , Puretzky A. A. , Geohegan D. B.
Published: May 2014

The synthesis of metal nanoparticles by ultrafast laser ablation of nanometers-thick metal films has been studied experimentally and computationally. Near-threshold backside laser ablation of 2–20 nm-thick Pt films deposited on fused silica substrates was found to produce nanoparticles with size distributions that were bimodal for the thicker films, but collapsed into a single mode distribution for the thinnest film. Time-resolved imaging of blackbody emission from the Pt nanoparticles was used to reveal the nanoparticle propagation dynamics and estimate their temperatures. The observed nanoparticle plume was compact and highly forward-directed with a well-defined collective velocity that permitted multiple rebounds with substrates to be revealed. Large-scale molecular dynamics simulations were used to understand the evolution of compressive and tensile stresses in the thicker melted liquid films that lead to their breakup and ejection of two groups of nanoparticles with different velocity and size distributions. Ultrafast laser irradiation of ultrathin (few nm) metal films avoids the splitting of the film and appears to be a method well-suited to cleanly synthesize and deposit nanoparticles from semitransparent thin film targets in highly directed beams.
Terahertz radiation in alkali vapor plasmas
Authors: Sun Xuan , Zhang X.-C.
Published: May 2014

By taking advantage of low ionization potentials of alkali atoms, we demonstrate terahertz wave generation from cesium and rubidium vapor plasmas with an amplitude nearly one order of magnitude larger than that from nitrogen gas at low pressure (0.02–0.5 Torr). The observed phenomena are explained by the numerical modeling based upon electron tunneling ionization.
Observation of multi-scale turbulence and non-local transport in LHD plasmas
Authors: Tokuzawa T. , Inagaki S. , Ida K. , Itoh K. , Ido T. , Shimizu A. , Takahashi H. , Kitajima S. , Tamura N. , Yoshinuma M. , Tsuchiya H. , Yamada I. , Tanaka K. , Akiyama T. , Nagayama Y. , Kawahata K. , Watanabe K. Y. , Yamada H. ,   LHD Experiment Group
Published: May 2014

We have studied two types of spatio-temporal turbulence dynamics in plasmas in the Large Helical Device, based on turbulence measurements with high spatial and temporal resolution. Applying conditional ensemble-averaging to a plasma with Edge-Localized Modes (ELMs), fast radial inward propagation of a micro-scale turbulence front is observed just after ELM event, and the propagation speed is evaluated as ∼100 m/s. A self-organized radial electric field structure is observed in an electrode biasing experiment, and it is found to realize a multi-valued state. The curvature of the radial electric field is found to play an important role for turbulence reduction.
Highly deformable actuators made of dielectric elastomers clamped by rigid rings
Authors: Lu Tongqing , Chiang Foo Choon , Huang Jiangshui , Zhu Jian , Suo Zhigang
Published: May 2014

In the nascent field of soft machines, soft materials are used to create devices that actuate robots, sense environment, monitor health, and harvest energy. The soft materials undergo large deformation in response to external stimuli, often leading to instability that is usually undesirable but sometimes useful. Here, we study a dielectric elastomer membrane sandwiched between two soft conductors, rolled into a hollow tube, pre-stretched in the hoop direction, and fixed at the ends of the tube to two rigid rings. This structure functions as an electromechanical transducer when the two rings are subject to a mechanical force and the two conductors are subject to an electrical voltage. We formulate a computational model by using a variational principle and calculate the large and inhomogeneous deformation by solving a nonlinear boundary-value problem. We demonstrate that large actuation strains are achievable when the height-to-radius ratio of the tube is small and the hoop pre-stretch is large. The model provides a tool to analyze various modes of instability and optimize the electromechanical performance.
Effective imaging systems based on periodic lattices
Authors: Gennarelli Gianluca , Persico Raffaele , Soldovieri Francesco
Published: May 2014

A crucial question in imaging problems from diffracted wavefields is the evaluation of the information content of data and the related reconstruction performance in terms of spatial resolution. It is well-known that full-view tomographic reconstructions are characterized by resolution limits of the order of one half propagated wavelength. These limits are further deteriorated when a truncated measurement domain is exploited for the imaging. In this Letter, we show that when the imaging system comprises a periodic layer located between a linear array of probes and the investigated domain, the resolution limits are substantially improved compared to the case of a homogenous scenario. This intriguing result is a consequence of the multiscattering effects arising from the periodicity of the structure. The study provides physical insight supported by mathematical arguments paving the way to the development of effective imaging systems requiring few radiating elements.
Defect levels in Cu2ZnSn(SxSe1−x)4 solar cells probed by current-mode deep level transient spectroscopy
Authors: Das Sandip , Chaudhuri Sandeep K. , Bhattacharya Raghu N. , Mandal Krishna C.
Published: May 2014

Defect levels in kesterite Cu2ZnSn(S,Se)4 (CZTSSe) solar cells have been investigated by current-mode deep level transient spectroscopy. Experiments were carried out on two CZTSSe cells with photoconversion efficiencies of 4.1% and 7.1% measured under AM 1.5 illumination. The absorber layer of the 4.1% efficiency cell was prepared by annealing evaporated ZnS/Cu/Sn stacked precursor under S/Se vapor, while the absorber of the 7.1% efficiency cell was prepared by co-evaporation of the constituent elements. The 4.1% efficiency CZTSSe cell with a S/(S + Se) ratio of 0.58 exhibited two dominant deep acceptor levels at Ev + 0.12 eV, and Ev + 0.32 eV identified as CuZn(-/0) and CuSn(2-/-) antisite defects, respectively. The 7.1% efficiency cell with purely Se composition S/(S + Se) = 0 showed only one shallow level at Ev + 0.03 eV corresponding to Cu-vacancy (VCu). Our results revealed that VCu is the primary defect center in the high-efficiency kesterite solar cell in contrast to the detrimental CuZn and CuSn antisites found in the low efficiency CZTSSe cells limiting the device performance.
Electromagnetic gyrokinetic turbulence in finite-beta helical plasmas
Authors: Ishizawa A. , Watanabe T.-H. , Sugama H. , Maeyama S. , Nakajima N.
Published: May 2014

A saturation mechanism for microturbulence in a regime of weak zonal flow generation is investigated by means of electromagnetic gyrokinetic simulations. The study identifies a new saturation process of the kinetic ballooning mode (KBM) turbulence originating from the spatial structure of the KBM instabilities in a finite-beta Large Helical Device (LHD) plasma. Specifically, the most unstable KBM in LHD has an inclined mode structure with respect to the mid-plane of a torus, i.e., it has a finite radial wave-number in flux tube coordinates, in contrast to KBMs in tokamaks as well as ion-temperature gradient modes in tokamaks and helical systems. The simulations reveal that the growth of KBMs in LHD is saturated by nonlinear interactions of oppositely inclined convection cells through mutual shearing as well as by the zonal flow. The saturation mechanism is quantitatively investigated by analysis of the nonlinear entropy transfer that shows not only the mutual shearing but also a self-interaction with an elongated mode structure along the magnetic field line.
Enhanced performance of solar cells with optimized surface recombination and efficient photon capturing via anisotropic-etching of black silicon
Authors: Chen H. Y. , Yuan G. D. , Peng Y. , Hong M. , Zhang Y. B. , Zhang Y. , Liu Z. Q. , Wang J. X. , Cai Bin , Zhu Y. M. , Li J. M.
Published: May 2014

We report an enhanced conversion efficiency of femtosecond-laser treated silicon solar cells by surface modification of anisotropic-etching. The etching improves minority carrier lifetime inside modified black silicon area substantially; moreover, after the etching, an inverted pyramids/upright pyramids mixed texture surface is obtained, which shows better photon capturing capability than that of conventional pyramid texture. Combing of these two merits, the reformed solar cells show higher conversion efficiency than that of conventional pyramid textured cells. This work presents a way for fabricating high performance silicon solar cells, which can be easily applied to mass-production.
Topology optimization for locally resonant sonic materials
Authors: Matsuki T. , Yamada T. , Izui K. , Nishiwaki S.
Published: May 2014

This Letter presents an optimal design method for locally resonant sonic materials using topology optimization incorporating a level-set method. Examples demonstrate that this method provides optimal configurations that exhibit roughly hundred-fold acoustic attenuation at desired frequencies, evaluated using frequency analyses of displacements at the output side of the design domain. We also explore the effects on the acoustic response of combining two optimal configurations. Our results indicate that the proposed method can be applied for the design of locally resonant sonic materials that have multiple attenuation peaks in a combined configuration. Additionally, we analyze eight configuration combinations, one consisting of eight identical configurations and the other of eight slightly different unit cells. The results show the combination of eight slightly different optimal configurations achieves a wider frequency range of attenuation.
Self-organized arrays of graphene and few-layer graphene quantum dots in fluorographene matrix: Charge transient spectroscopy
Authors: Antonova Irina V. , Nebogatikova Nadezhda A. , Prinz Victor Ya.
Published: May 2014

Arrays of graphene or few-layer graphene quantum dots (QDs) embedded in a partially fluorinated graphene matrix were created by chemical functionalization of layers. Charge transient spectroscopy employed for investigation of obtained QD systems (size 20–70 nm) has allowed us to examine the QD energy spectra and the time of carrier emission (or charge relaxation) from QDs as a function of film thickness. It was found that the characteristic time of carrier emission from QDs decreased markedly (by about four orders of magnitude) on increasing the QD thickness from one graphene monolayer to 3 nm. Daylight-assisted measurements also demonstrate a strong decrease of the carrier emission time.
Regular ripples at the surfaces of heteroepitaxially grown Ag(111) ultra-thin films on Si(111) √3 × √3-B substrates
Authors: Yoshiike Yusaku , Fukumoto Hiroyuki , Kokubo Ikuya , Aoki Yuki , Nakatsuji Kan , Hirayama Hiroyuki
Published: May 2014

Faint ripples were observed at the flat surfaces of 10-monolayer-thick Ag films grown on Si(111)√3 × √3-B substrates using scanning tunneling microscopy. The ripples have the 3 × 3 periodicity and showed no dependence on the bias voltage. The ripples are considered to reflect the Ag(111)1 × 1 and Si(111)√3 × √3-B lattice commensuration at the buried interface, which propagates to the upper layers and causes the geometric corrugation at the Ag film surface.
Fullerene film on metal surface: Diffusion of metal atoms and interface model
Authors: Li Wen-jie , Wang Peng , Wang Xiao-Xiong , Wang Jia-Ou , Wu Rui , Qian Hai-Jie , Ibrahim Kurash , Li Hai-Yang , Li Hong-Nian
Published: May 2014

We try to understand the fact that fullerene film behaves as n-type semiconductor in electronic devices and establish a model describing the energy level alignment at fullerene/metal interfaces. The C60/Ag(100) system was taken as a prototype and studied with photoemission measurements. The photoemission spectra revealed that the Ag atoms of the substrate diffused far into C60 film and donated electrons to the molecules. So the C60 film became n-type semiconductor with the Ag atoms acting as dopants. The C60/Ag(100) interface should be understood as two sub-interfaces on both sides of the molecular layer directly contacting with the substrate. One sub-interface is Fermi level alignment, and the other is vacuum level alignment.
Strong exciton-photon coupling in open semiconductor microcavities
Authors: Dufferwiel S. , Fras F. , Trichet A. , Walker P. M. , Li F. , Giriunas L. , Makhonin M. N. , Wilson L. R. , Smith J. M. , Clarke E. , Skolnick M. S. , Krizhanovskii D. N.
Published: May 2014

We present a method to implement 3-dimensional polariton confinement with in-situ spectral tuning of the cavity mode. Our tunable microcavity is a hybrid system consisting of a bottom semiconductor distributed Bragg reflector (DBR) with a cavity containing quantum wells (QWs) grown on top and a dielectric concave DBR separated by a micrometer sized gap. Nanopositioners allow independent positioning of the two mirrors and the cavity mode energy can be tuned by controlling the distance between them. When close to resonance, we observe a characteristic anticrossing between the cavity modes and the QW exciton demonstrating strong coupling. For the smallest radii of curvature concave mirrors of 5.6 μm and 7.5 μm, real-space polariton imaging reveals submicron polariton confinement due to the hemispherical cavity geometry.
Trifluoromethylphenylcarbenes. Carbene-Carbene Interconversion on the Singlet Energy Surface and Rearrangement to Trifluorobenzocyclobutene, Trifluorostyrene, and Trifluoromethylfulvenallenes
Authors: Blanch Rodney J. , Wentrup Curt
Published: May 2014

The four isomeric α-, ortho-, meta-, and para-trifluoromethylphenylcarbenes were generated by photolysis of the corresponding 3-phenyl-3-trifluoromethyldiazirene 1 or the four isomeric trifluoromethylphenyldiazomethanes 2 and 4–6. The four corresponding triplet trifluoromethylphenylcarbenes 3 and 7–9 were observed by electron spin resonance (ESR) spectroscopy in Ar matrices at 14 K. The α- and ortho-carbenes 3 and 7 and the ortho- and para-carbenes 7 and 9 interconvert partially when generated by short-wavelength photolysis (350 nm) before intersystem crossing to the triplet states. The triplet states do not undergo further Carbene-Carbene interconversion. The interconversions are assumed to take place via the meta-trifluoromethylphenylcarbene 8. When the ortho- and para-carbenes are generated by long-wavelength photolysis (>450 nm), the discrete, non-interconverting triplet carbenes are observed in the ESR spectra. Flash vacuum thermolysis of the diazirene 1 at 500°C afforded a mixture of bis(trifluoromethyl)heptafulvalenes 11, bis(trifluoromethyl)stilbenes 12, and bis(trifluoromethyl)anthracenes 13, and the presence of their likely precursor(s), trifluoromethylcycloheptatetraene(s), was confirmed by a peak at 1830 cm–1 in the Ar matrix IR spectrum. In addition, at 700°C, four monomeric carbene rearrangement products were isolated and characterised, viz. 1,1,2-trifluorobenzocyclobutene 14, 1′,2′,2′-trifluorostyrene 15, and 1- and 2-trifluoromethylfulvenallenes 16 and 17.
Carnivore distributions across chaparral habitats exposed to wildfire and rural housing in southern California
Authors: Schuette P. A. , Diffendorfer J. E. , Deutschman D. H. , Tremor S. , Spencer W.
Published: May 2014

Chaparral and coastal sage scrub habitats in southern California support biologically diverse plant and animal communities. However, native plant and animal species within these shrubland systems are increasingly exposed to human-caused wildfires and an expansion of the human–wildland interface. Few data exist to evaluate the effects of fire and anthropogenic pressures on plant and animal communities found in these environments. This is particularly true for carnivore communities. To address this knowledge gap, we collected detection–non-detection data with motion-sensor cameras and track plots to measure carnivore occupancy patterns following a large, human-caused wildfire (1134km2) in eastern San Diego County, California, USA, in 2003. Our focal species set included coyote (Canis latrans), gray fox (Urocyon cinereoargenteus), bobcat (Lynx rufus) and striped skunk (Mephitis mephitis). We evaluated the influence on species occupancies of the burned environment (burn edge, burn interior and unburned areas), proximity of rural homes, distance to riparian area and elevation. Gray fox occupancies were the highest overall, followed by striped skunk, coyote and bobcat. The three species considered as habitat and foraging generalists (gray fox, coyote, striped skunk) were common in all conditions. Occupancy patterns were consistent through time for all species except coyote, whose occupancies increased through time. In addition, environmental and anthropogenic variables had weak effects on all four species, and these responses were species-specific. Our results helped to describe a carnivore community exposed to frequent fire and rural human residences, and provide baseline data to inform fire management policy and wildlife management strategies in similar fire-prone ecosystems.
A methodology for determining operational priorities for prevention and suppression of wildland fires
Authors: Rodríguez y Silva Francisco , Molina Martínez Juan Ramón , González-Cabán Armando
Published: May 2014

Traditional uses of the forest (timber, forage) have been giving way to other uses more in demand (recreation, ecosystem services). An observable consequence of this process of forest land use conversion is an increase in more difficult and extreme wildfires. Wildland forest management and protection program budgets are limited, and managers are requesting help in finding ways to objectively assign their limited protection resources based on the intrinsic environmental characteristics of a site and the site’s interrelationship with available firefighting resources and existing infrastructure. A Fire Suppression Priority Index, integrating information on both the potential fire behaviour risk (Potential Fire Behaviour Index) and the fire suppression difficulty (Suppression Difficulty Index), provides managers with fundamental information for strategic planning and development of tactical operations to protect the natural environment. Results in the Córdoba Province, Andalusia’s autonomous region, Spain, showed a statistically significant relationship between wildfire size and all three indices, demonstrating the utility of the methodology to identify and prioritise forest areas for strategic and tactical fire management operations. In addition, the methodology was tested and validated by trained and qualified wildfire management personnel in Chile and Israel, obtaining similar results as in Spain.
Cost shared wildfire risk mitigation in Log Hill Mesa, Colorado: survey evidence on participation and willingness to pay
Authors: Meldrum James R. , Champ Patricia A. , Warziniack Travis , Brenkert-Smith Hannah , Barth Christopher M. , Falk Lilia C.
Published: May 2014

Wildland–urban interface (WUI) homeowners who do not mitigate the wildfire risk on their properties impose a negative externality on society. To reduce the social costs of wildfire and incentivise homeowners to take action, cost sharing programs seek to reduce the barriers that impede wildfire risk mitigation. Using survey data from a WUI community in western Colorado and a two-stage decision framework, we examine residents’ willingness to participate in a cost sharing program for removing vegetation on their properties and the amount they are willing to contribute to the cost of that removal. We find that different factors motivate decisions about participation and about how much to pay. Willingness to participate correlates with both financial and non-monetary considerations, including informational barriers and wildfire risk perceptions, but not with concerns about effectiveness or visual impacts. Residents of properties with higher wildfire risk levels are less likely to participate in the cost sharing than those with lower levels of wildfire risk. We find widespread, positive willingness to pay for vegetation removal, with the amount associated negatively with property size and positively with respondent income. These results can inform the development of cost sharing programs to encourage wildfire risk mitigation on private property.
Bacterial RNA:DNA hybrids are activators of the NLRP3 inflammasome
Authors: Kailasan Vanaja Sivapriya , Rathinam Vijay A. K. , Atianand Maninjay K. , Kalantari Parisa , Skehan Brian , Fitzgerald Katherine A. , Leong John M.
Published: May 2014

Significance

The nucleotide-binding domain and leucine rich repeat containing family, pyrin domain containing 3 (NLRP3) inflammasome regulates capase-1-dependent maturation of interleukin-1β during infection with Gram-negative bacterial pathogens such as enterohemorrhagic
Escherichia coli
. Here we identified bacterial RNA:DNA hybrids as well as RNA as critical mediators of these responses. RNA:DNA hybrids and RNA gained access to the cytosol from phagolysosomal compartments during infection, leading to the assembly of NLRP3 inflammasome complex. Delivery of synthetic RNA:DNA hybrids into the cytosol triggered NLRP3-dependent responses, whereas introduction of RNase H, which degrades hybrids, abolished inflammasome activation. Notably, an
E. coli rnhA
mutant, incapable of producing RNase H, induced elevated levels of NLRP3-dependent inflammasome activation. Collectively, these studies define bacterial RNA:DNA hybrids as a new microbe-associated molecular pattern with innate immune stimulatory activity during microbial infections.
Polarized deposition of basement membrane proteins depends on Phosphatidylinositol synthase and the levels of Phosphatidylinositol 4,5-bisphosphate
Authors: Devergne Olivier , Tsung Karen , Barcelo Gail , Schüpbach Trudi
Published: May 2014

Significance

The cellular functions of epithelia rely on their polarized architecture. Loss of their polarity is often associated with carcinoma progression and tumor metastasis. The basement membrane (BM), a specialized sheet of the extracellular matrix, secreted basally by most epithelia, plays an important role in the establishment and maintenance of epithelial cell polarity. However, the process of BM-polarized secretion is not well understood. In this study, we show that a significant decrease of the phospholipid phosphatidylinositol 4,5-bisphosphate (PIP2) results in BM protein secretion on both the apical and the basal side of the epithelium. Together, our data indicate a specific role for PIP2 in the organization of epithelial architecture by restricting the deposition of BM proteins to the basal side.
A new compound from the mushroom Tricholoma flavovirens
Authors: Qiu Weitao , Kobori Hajime , Suzuki Tomohiro , Choi Jae-Hoon , Deo Vipin Kumar , Hirai Hirofumi , Kawagishi Hirokazu
Published: May 2014

A novel compound (1) and a known one (2) were isolated from the fruiting bodies of Tricholoma flavovirens. Their structures were determined by the interpretation of spectroscopic data. Both compounds showed inhibition effects on the growth of hypocotyl of lettuce with significant differences. In addition, compound 1 showed a promotion effect on the growth of root with significant differences and 2 had the similar tendency to promote the growth.
Identification and evaluation of anti-inflammatory compounds fromKaempferia parviflora
Authors: Horigome Satoru , Yoshida Izumi , Tsuda Aiko , Harada Teppei , Yamaguchi Akihiro , Yamazaki Kumiko , Inohana Shuichi , Isagawa Satoshi , Kibune Nobuyuki , Satoyama Toshiya , Katsuda Shin-ichi , Suzuki Shinobu , Watai Masatoshi , Hirose Naoto , Mitsue Takahiro , Shirakawa Hitoshi , Komai Michio
Published: May 2014

The rhizome of Kaempferia parviflora has been used in traditional Thai medicine. In this study, we identified and compared specific compounds from the hexane extract of K. parviflora with those from other Zingiberaceous plants by using gas chromatography–mass spectrometry. We identified 5,7-dimethoxyflavone (DMF), 5-hydroxy-3,7,3′,4′-tetramethoxyflavone (TMF), estimated 3,5,7-trimethoxyflavone, 5-hydroxy-7,4′-dimethoxyflavone, 3,5,7,4′-tetramethoxyflavone, and investigated their anti-inflammatory effects in rat basophilic leukemia (RBL-2H3) cells stimulated with an IgE antigen or a calcium ionophore. We found that DMF and TMF more potently inhibited antigen-induced degranulation than did nobiletin, a well-known anti-inflammatory agent. In addition, compared to RBL-2H3 cells stimulated with a calcium ionophore, those treated with DMF and TMF showed more marked inhibition of the degranulation and the production and mRNA expression of inflammatory mediators. These results suggest that DMF and TMF inhibit an early step in the high-affinity IgE receptor signaling cascade rather than intracellular calcium release and protein kinase C activation.
De novo assembly and analysis of Cassia obtusifolia seed transcriptome to identify genes involved in the biosynthesis of active metabolites
Authors: Liu Zubi , Song Tao , Zhu Qiankun , Wang Wanjun , Zhou Jiayu , Liao Hai
Published: May 2014

A cDNA library generated from seeds of Cassia obtusifolia was sequenced using Illumina/Solexa platform. More than 12,968,231 high quality reads were generated, and have been deposited in NCBI SRA (SRR 1012912). A total of 40,102 unigenes (>200 bp) were obtained with an average sequence length of 681 bp by de novo assembly. About 34,089 (85%) unique sequences were annotated and 8694 of the unique sequences were assigned to specific metabolic pathways by the Kyoto Encyclopedia of Genes and Genomes. Among them, 131 unigenes, which are involved in the biosynthesis and (or) regulation of anthraquinone, carotenoid, flavonoid, and lipid, the 4 best known active metabolites, were identified from cDNA library. In addition, three lipid transfer proteins were obtained, which may contribute to the lipid molecules transporting between biological membranes. Meanwhile, 30 cytochrome P450, 12 SAM-dependent methyltransferases, and 12 UDP-glucosyltransferase unigenes were identified, which could also be responsible for the biosynthesis of active metabolites.
Pueraria mirifica leaves, an alternative potential isoflavonoid source
Authors: Jungsukcharoen Jutarmas , Dhiani Binar Asrining , Cherdshewasart Wichai , Vinayavekhin Nawaporn , Sangvanich Polkit , Boonchird Chuenchit
Published: May 2014

We investigated the major leaf isoflavonoid contents of Pueraria mirifica from three different cultivars (PM-III, PM-IV, and PM-V) using reverse RP-HPLC analysis. The proportions and net levels of puerarin, daidzin, genistin, and daidzein in P. mirifica leaves were found to depend on the plant cultivar and to correlate with cultivation temperature and rainfall amount. The crude leaf-extracts were tested using the Yeast Estrogen Screen (YES) assay with both human estrogen receptors (hERα and hERβ). Their estrogenic activity was higher when determined by the YES system containing hERβ than that with hERα and was also higher when the Δsnq2 than the wildtype yeast was employed. The results open the possibility of selecting and cultivating certain P. mirifica cultivars at a farm scale to produce a sufficient supply of leaf material to act as a starting source for the commercial scale extraction of these major isoflavonoids.
Attentional Bias Induced by Solving Simple and Complex Addition and Subtraction Problems
Authors: Masson Nicolas , Pesenti Mauro
Published: May 2014

The processing of numbers has been shown to induce shifts of spatial attention in simple probe detection tasks, with small numbers orienting attention to the left and large numbers to the right side of space. Recently, the investigation of this spatial–numerical association has been extended to mental arithmetic with the hypothesis that solving addition or subtraction problems may induce attentional displacements (to the right and to the left, respectively) along a mental number line onto which the magnitude of the numbers would range from left to right, from small to large numbers. Here we investigated such attentional shifts using a target detection task primed by arithmetic problems in healthy participants. The constituents of the addition and subtraction problems (first operand; operator; second operand) were flashed sequentially in the centre of a screen, then followed by a target on the left or the right side of the screen, which the participants had to detect. This paradigm was employed with arithmetic facts (Experiment 1) and with more complex arithmetic problems (Experiment 2) in order to assess the effects of the operation, the magnitude of the operands, the magnitude of the results, and the presence or absence of a requirement for the participants to carry or borrow numbers. The results showed that arithmetic operations induce some spatial shifts of attention, possibly through a semantic link between the operation and space.
Control of Simultaneous Outbreaks of Carbapenemase-Producing Enterobacteriaceae and Extensively Drug-ResistantAcinetobacter baumanniiInfection in an Intensive Care Unit Using Interventions Promoted in the Centers for Disease Control and Prevention 2012 Carbapenemase-Resistant Enterobacteriaceae Toolkit
Authors: Enfield Kyle B. , Huq Nujhat N. , Gosseling Megan F. , Low Darla J. , Hazen Kevin C. , Toney Denise M. , Slitt Gavin , Zapata Heidi J. , Cox Heather L. , Lewis Jessica D. , Kundzins John R. , Mathers Amy J. , Sifri Costi D.
Published: May 2014

Objective

We describe the efficacy of enhanced infection control measures, including those recommended in the Centers for Disease Control and Prevention’s 2012 carbapenem-resistant Enterobacteriaceae (CRE) toolkit, to control concurrent outbreaks of carbapenemase-producing Enterobacteriaceae (CPE) and extensively drug-resistantAcinetobacter baumannii(XDR-AB).

Design

Before-after intervention study.

Setting

Fifteen-bed surgical trauma intensive care unit (ICU).

Methods

We investigated the impact of enhanced infection control measures in response to clusters of CPE and XDR-AB infections in an ICU from April 2009 to March 2010. Polymerase chain reaction was used to detect the presence ofblaKPCand resistance plasmids in CRE. Pulsed-field gel electrophoresis was performed to assess XDR-AB clonality. Enhanced infection-control measures were implemented in response to ongoing transmission of CPE and a new outbreak of XDR-AB. Efficacy was evaluated by comparing the incidence rate (IR) of CPE and XDR-AB before and after the implementation of these measures.

Results

The IR of CPE for the 12 months before the implementation of enhanced measures was 7.77 cases per 1,000 patient-days, whereas the IR of XDR-AB for the 3 months before implementation was 6.79 cases per 1,000 patient-days. All examined CPE shared endemicblaKPCresistance plasmids, and 6 of the 7 XDR-AB isolates were clonal. Following institution of enhanced infection control measures, the CPE IR decreased to 1.22 cases per 1,000 patient-days (P= .001), and no more cases of XDR-AB were identified.

Conclusions

Use of infection control measures described in the Centers for Disease Control and Prevention’s 2012 CRE toolkit was associated with a reduction in the IR of CPE and an interruption in XDR-AB transmission.
Survey of Infection Prevention Informatics Use and Practitioner Satisfaction in US Hospitals
Authors: Masnick Max , Morgan Daniel J. , Wright Marc-Oliver , Lin Michael Y. , Pineles Lisa , Harris Anthony D. ,   SHEA Research Network
Published: May 2014

We surveyed hospital epidemiologists and infection preventionists on their usage of and satisfaction with infection prevention–specific software supplementing their institution’s electronic medical record. Respondents with supplemental software were more satisfied with their software’s infection prevention and antimicrobial stewardship capabilities than those without. Infection preventionists were more satisfied than hospital epidemiologists.

Infect Control Hosp Epidemiol 2014;35(7):891–893
Resolution of telomere associations by TRF1 cleavage in mouse embryonic stem cells
Authors: Lisaingo Kathleen , Uringa Evert-Jan , Lansdorp Peter M.
Published: May 2014

Telomere associations have been observed during key cellular processes such as mitosis, meiosis, and carcinogenesis and must be resolved before cell division to prevent genome instability. Here we establish that telomeric repeat-binding factor 1 (TRF1), a core component of the telomere protein complex, is a mediator of telomere associations in mammalian cells. Using live-cell imaging, we show that expression of TRF1 or yellow fluorescent protein (YFP)-TRF1 fusion protein above endogenous levels prevents proper telomere resolution during mitosis. TRF1 overexpression results in telomere anaphase bridges and aggregates containing TRF1 protein and telomeric DNA. Site-specific protein cleavage of YFP-TRF1 by tobacco etch virus protease resolves telomere aggregates, indicating that telomere associations are mediated by TRF1. This study provides novel insight into the formation and resolution of telomere associations.
kmacs: the
k
-mismatch average common substring approach to alignment-free sequence comparison
Authors: Leimeister Chris-Andre , Morgenstern Burkhard
Published: May 2014

Motivation: Alignment-based methods for sequence analysis have various limitations if large datasets are to be analysed. Therefore, alignment-free approaches have become popular in recent years. One of the best known alignment-free methods is the average common substring approach that defines a distance measure on sequences based on the average length of longest common words between them. Herein, we generalize this approach by considering longest common substrings with k mismatches. We present a greedy heuristic to approximate the length of such k -mismatch substrings, and we describe kmacs , an efficient implementation of this idea based on generalized enhanced suffix arrays.

Results: To evaluate the performance of our approach, we applied it to phylogeny reconstruction using a large number of DNA and protein sequence sets. In most cases, phylogenetic trees calculated with kmacs were more accurate than trees produced with established alignment-free methods that are based on exact word matches. Especially on protein sequences, our method seems to be superior. On simulated protein families, kmacs even outperformed a classical approach to phylogeny reconstruction using multiple alignment and maximum likelihood.

Availability and implementation:  kmacs is implemented in C++, and the source code is freely available at http://kmacs.gobics.de/

Contact:  chris.leimeister@stud.uni-goettingen.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Entropy meters and the entropy of non-extensive systems
Authors: Lieb Elliott H. , Yngvason Jakob
Published: May 2014

In our derivation of the second law of thermodynamics from the relation of adiabatic accessibility of equilibrium states, we stressed the importance of being able to scale a system's size without changing its intrinsic properties. This leaves open the question of defining the entropy of macroscopic, but unscalable systems, such as gravitating bodies or systems where surface effects are important. We show here how the problem can be overcome, in principle, with the aid of an ‘entropy meter’. An entropy meter can also be used to determine entropy functions for non-equilibrium states and mesoscopic systems.
Chryseomicrobium aureum sp. nov., a bacterium isolated from activated sludge
Authors: Deng Shi-Kai , Ye Xiao-Mei , Chu Cui-Wei , Jiang Jin , He Jian , Zhang Jun , Li Shun-Peng
Published: May 2014

A Gram-stain-positive, rod-shaped, non-motile, non-spore-forming, aerobic bacterial strain, designated BUT-2T, was isolated from activated sludge of one herbicide-manufacturing wastewater-treatment facility in Kunshan, Jiangsu province, China, and subjected to polyphasic taxonomic studies. Analysis of the 16S rRNA gene sequence indicated that strain BUT-2Tshared the highest similarity withChryseomicrobium amylolyticum(98.98 %), followed byChryseomicrobium imtechense(98.88 %), with less than 96 % similarlity to members of the generaPaenisporosarcina,Planococcus,SporosarcinaandPlanomicrobium. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain BUT-2Tclustered withC. amylolyticumJC16TandC. imtechenseMW10T, occupying a distinct phylogenetic position. The major fatty acid (>10 % of total fatty acids) type of strain BUT-2Twas iso-C15 : 0.The quinone system comprised menaquinone MK-7 (77.8 %), MK-6 (11.9 %) and MK-8 (10.3 %). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and some unidentified phospholipids. The cell-wall peptidoglycan type of strain BUT-2Twasl-Orn-d-Glu. The genomic DNA G+C content of strain BUT-2Twas 48.5 mol%. Furthermore, the DNA–DNA relatedness in hybridization experiments against the reference strain was lower than 70 %, confirming that strain BUT-2Tdid not belong to previously described species of the genusChryseomicrobium. On the basis of its morphological, physiological and chemotaxonomic characteristics as well as phylogenetic analysis, strain BUT-2Tis considered to represent a novel species of the genusChryseomicrobium, for which the nameChryseomicrobiumaureumsp. nov. is proposed. The type strain is BUT-2T( = CCTCC AB2013082T = KACC 17219T).
A new regulator of pathogenicity (bvlR) is required for full virulence and tight microcolony formation in Pseudomonas aeruginosa
Authors: McCarthy Ronan R. , Mooij Marlies J. , Reen F. Jerry , Lesouhaitier Olivier , O’Gara Fergal
Published: May 2014

LysR-type transcriptional regulators (LTTRs) are the most common family of transcriptional regulators found in the opportunistic pathogenPseudomonas aeruginosa. They are known to regulate a wide variety of virulence determinants and have emerged recently as positive global regulators of pathogenicity in a broad spectrum of important bacterial pathogens. However, in spite of their key role in modulating expression of key virulence determinants underpinning pathogenic traits associated with the process of infection, surprisingly few are found to be transcriptionally altered by contact with host cells. BvlR (PA14_26880) an LTTR of previously unknown function, has been shown to be induced in response to host cell contact, and was therefore investigated for its potential role in virulence. BvlR expression was found to play a pivotal role in the regulation of acute virulence determinants such as type III secretion system and exotoxin A production. BvlR also played a key role inP. aeruginosapathogenicity within theCaenorhabditis elegansacute model of infection. Loss of BvlR led to an inability to form tight microcolonies, a key step in biofilm formation in the cystic fibrosis lung, although surface attachment was increased. Unusually for LTTRs, BvlR was shown to exert its influence through the transcriptional repression of many genes, including the virulence-associatedcupAandalggenes. This highlights the importance of BvlR as a new virulence regulator inP. aeruginosawith a central role in modulating key events in the pathogen–host interactome.
NSs protein of Schmallenberg virus counteracts the antiviral response of the cell by inhibiting its transcriptional machinery
Authors: Barry Gerald , Varela Mariana , Ratinier Maxime , Blomström Anne-Lie , Caporale Marco , Seehusen Frauke , Hahn Kerstin , Schnettler Esther , Baumgärtner Wolfgang , Kohl Alain , Palmarini Massimo
Published: May 2014

Bunyaviruses have evolved a variety of strategies to counteract the antiviral defence systems of mammalian cells. Here we show that the NSs protein of Schmallenberg virus (SBV) induces the degradation of the RPB1 subunit of RNA polymerase II and consequently inhibits global cellular protein synthesis and the antiviral response. In addition, we show that the SBV NSs protein enhances apoptosis in vitro and possibly in vivo, suggesting that this protein could be involved in SBV pathogenesis in different ways.
qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots
Authors: Turner Stephen D.
Published: May 2014

Genome-wide association studies (GWAS) have identified thousands of human trait-associated single nucleotide polymorphisms. Here, I describe a freely available R package for visualizing GWAS results using Q-Q and manhattan plots. Theqqmanpackage enables the flexible creation of manhattan plots, both genome-wide and for single chromosomes, with optional highlighting of SNPs of interest.

Availability

qqmanis released under the GNU General Public License, and is freely available on the Comprehensive R Archive Network (http://cran.r-project.org/package=qqman). The source code is available on GitHub (https://github.com/stephenturner/qqman).

Contact

turner@virginia.edu
Metabolomic Characterization of Knockout Mutants in Arabidopsis: Development of a Metabolite Profiling Database for Knockout Mutants in Arabidopsis
Authors: Fukushima Atsushi , Kusano Miyako , Mejia Ramon Francisco , Iwasa Mami , Kobayashi Makoto , Hayashi Naomi , Watanabe-Takahashi Akiko , Narisawa Tomoko , Tohge Takayuki , Hur Manhoi , Wurtele Eve Syrkin , Nikolau Basil J. , Saito Kazuki
Published: May 2014

Despite recent intensive research efforts in functional genomics, the functions of only a limited number of Arabidopsis (Arabidopsis thaliana) genes have been determined experimentally, and improving gene annotation remains a major challenge in plant science. As metabolite profiling can characterize the metabolomic phenotype of a genetic perturbation in the plant metabolism, it provides clues to the function(s) of genes of interest. We chose 50 Arabidopsis mutants, including a set of characterized and uncharacterized mutants, that resemble wild-type plants. We performed metabolite profiling of the plants using gas chromatography-mass spectrometry. To make the data set available as an efficient public functional genomics tool for hypothesis generation, we developed the Metabolite Profiling Database for Knock-Out Mutants in Arabidopsis (MeKO). It allows the evaluation of whether a mutation affects metabolism during normal plant growth and contains images of mutants, data on differences in metabolite accumulation, and interactive analysis tools. Nonprocessed data, including chromatograms, mass spectra, and experimental metadata, follow the guidelines set by the Metabolomics Standards Initiative and are freely downloadable. Proof-of-concept analysis suggests that MeKO is highly useful for the generation of hypotheses for genes of interest and for improving gene annotation. MeKO is publicly available at http://prime.psc.riken.jp/meko/.
Efficacy and safety of infliximab in treating patients with ulcerative colitis: Experiences from a single medical center in southern China
Authors: Zhou You Lian , Xie Shan , Wang Pu , Zhang Ting , Lin Min Yi , Tan Jia Sheng , Zhi Fa Chao , Jiang Bo , Chen Ye
Published: May 2014

Objective

This study aimed to evaluate the efficacy including the patients' response rates to infliximab (IFX) therapy, relapse rates after IFX‐induced clinical remission, and the safety of IFX in Chinese patients with ulcerative colitis (UC) from a single center in southern China and to identify the risk factors associated with disease relapse.

Methods

Medical records of Chinese UC patients who were diagnosed and received at least two infusions of IFX at Nanfang Hospital, Southern Medical University from July 2010 to February 2013 were retrospectively reviewed. Primary outcomes were regarded as the clinical response and relapse rates during 30 weeks after the initiation of the therapy. Overall adverse events and relapse‐related risk factors were also evaluated.

Results

A total of 24 UC patients was finally included. The clinical response and remission rates were 83.3% and 50.0% at week 2, 91.3% and 73.9% at week 6 and 84.6% and 61.5% by week 30. Relapse after IFX‐induced clinical remission was initiated at the fourth infusion. The relapse rate was 29.4% at week 14, 25.0% at week 22 and 20.0% at week 30, respectively. After 30 weeks only 33.3% remained on maintenance therapy. IFX‐associated adverse events occurred in 29.2% of patients, with most being mild and transient. Patients with distal or extensive colitis were at a higher risk of relapse than those with ulcerative proctitis.

Conclusions

IFX is effective and safe in treating Chinese UC patients, although long‐term remission is hard to achieve. Distal or extensive colitis may be an independent predictor of disease relapse.
Granulocyte‐colony stimulating factor (G‐CSF) producing malignant pleural mesothelioma: Report of a case
Authors: Fujiwara Ayako , Higashiyama Masahiko , Kanou Takashi , Okami Jiro , Tokunaga Toshiteru , Tomita Yasuhiko , Kodama Ken
Published: May 2014

This report presents a case of malignant pleural mesothelioma (MPM) producing granulocyte colony‐stimulating factor (G‐CSF) that was treated by tumor resection. A 76‐year‐old male presented with a huge right‐side chest wall tumor, along with a slight fever and chest wall pain. Laboratory findings showed an increased white blood cell count (64600 cells/μL) and C‐reactive protein level (20.57 mg/dL). The patient underwent surgical removal of the tumor along with tissue from the chest wall and histopathological analysis led to a diagnosis of sarcomatous type of MPM. Immunohistochemical findings for both anti‐human G‐CSF and interleukin‐6 monoclonal antibodies were positive. Although the general condition of the patient quickly improved after surgery, local recurrence occurred two months later and he died of respiratory failure seven months after the operation, though surgery provided symptom relief. G‐CSF‐producing MPMs usually show a poor prognosis, though less‐invasive surgery may be considered for relief of symptoms.
Efficacy of simulation‐based trauma team training of non‐technical skills. A systematic review
Authors: GJERAA K. , MØLLER T. P. , ØSTERGAARD D.
Published: May 2014

Trauma resuscitation is a complex situation, and most organisations have multi‐professional trauma teams. Non‐technical skills are challenged during trauma resuscitation, and they play an important role in the prevention of critical incidents. Simulation‐based training of these is recommended. Our research question was: Does simulation‐based trauma team training of non‐technical skills have effect on reaction, learning, behaviour or patient outcome?

The authors searched PubMed, EMBASE and the Cochrane Library and found 13 studies eligible for analysis. We described and compared the educational interventions and the evaluations of effect according to the four Kirkpatrick levels: reaction, learning (knowledge, skills, attitudes), behaviour (in a clinical setting) and patient outcome.

No studies were randomised, controlled and blinded, resulting in a moderate to high risk of bias. The multi‐professional trauma teams had positive reactions to simulation‐based training of non‐technical skills. Knowledge and skills improved in all studies evaluating the effect on learning. Three studies found improvements in team performance (behaviour) in the clinical setting. One of these found difficulties in maintaining these skills. Two studies evaluated on patient outcome, of which none showed improvements in mortality, complication rate or duration of hospitalisation.

A significant effect on learning was found after simulation‐based training of the multi‐professional trauma team in non‐technical skills. Three studies demonstrated significantly increased clinical team performance. No effect on patient outcome was found. All studies had a moderate to high risk of bias. More comprehensive randomised studies are needed to evaluate the effect on patient outcome.