bluuebunny/crossref_metadata_2025 huggingface dataset:
Hydrothermal synthesis and infrared emissivity property of flower-like SnO2 particles
Authors: Tian J. X. , Zhang Z. Y. , Yan J. F. , Ruan X. F. , Yun J. N. , Zhao W. , Zhai C. X.
Published: April 2014

The flower-like SnO2 particles are synthesized through a simple hydrothermal process. The microstructure, morphology and the infrared emissivity property of the as-prepared products are characterized by x-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscope (TEM), and infrared spectroradio meter (ISM) respectively. The results show that the as-prepared SnO2 products are all indexed to tetragonal cassiterite phase of SnO2. The different molarity ratios of the OH− concentration to Sn4+ concentration ([OH−]:[Sn4+]) and the polyacrylamide (PAM) lead to the different morphological structures of SnO2, which indicates that both the [OH−]:[Sn4+] and the PAM play an important role in the morphological evolution respectively. The infrared emissivities of the as-prepared SnO2 products are discussed.
Dimensionality-induced insulator-metal crossover in layered nickelates Lan+1NinO2n+2 (n = 2, 3, and ∞)
Authors: Liu Ting , Wu Hua , Jia Ting , Zhang Xiaoli , Zeng Zhi , Lin H. Q. , Li X. G.
Published: April 2014

Low-valence layered nickelates are a structural analog to the superconducting cuprates and possess interesting properties. In this work, we have systematically studied the electronic structure of Lan+1NinO2n+2 using first-principles calculations. Our results reveal that the Ni-3d 3z2 − r2 orbital state is active and evolves from discrete molecular levels to a continuous solid band and its filling varies as the dimensionality (or n) increases. The two-dimensional (2D) La3Ni2O6 and La4Ni3O8 are thus found to have a molecular insulating state. In contrast, the 3D LaNiO2 is metallic and its 3z2 − r2 band surprisingly becomes 3D due to the Ni-La hybridization, and the La-5d xy orbital also forms a 2D metallic band. Therefore, Lan+1NinO2n+2 is a dimensionality-controlled insulator-metal crossover system.
Chemically strengthened protection glasses for the applications of space solar cells
Authors: Wang H. F. , Xing G. Z. , Wang X. Y. , Zhang L. L. , Zhang L. , Li S.
Published: April 2014

The effects of chemically strengthened processing and the ion beam irradiation on the mechanical characteristics of space solar cell protection glasses are investigated using dynamic mechanical analysis and micro hardness instrument; also the corresponding optical properties were analyzed by utilizing the UV/visible spectrophotometer. The results suggest that the flexural strength, fracture toughness and surface characteristics are enhanced via the chemical strengthening process. Importantly, such process has a trivial influence with ∼0.2% degradation on the transparency of chemically strengthened glasses in the band range of 350 ∼ 1000 nm, while exhibits an excellent resistance on radiation damage by ion beams bombardment, demonstrating an outstanding durability in the space radiation environment.
Thermal conductivity of mesoporous films measured by Raman spectroscopy
Authors: Stoib B. , Filser S. , Petermann N. , Wiggers H. , Stutzmann M. , Brandt M. S.
Published: April 2014

We measure the in-plane thermal conductance of mesoporous Ge and SiGe thin films using the Raman-shift method and, based on a finite differences simulation accounting for the geometry of the sample, extract the in-plane thermal conductivity. For a suspended thin film of laser-sintered SiGe nanoparticles doped with phosphorus, we find an effective in-plane thermal conductivity of 0.05 W/m K in vacuum for a temperature difference of 400 K and a mean temperature of 500 K. Under similar conditions, the effective in-plane thermal conductivity of a laser-sintered undoped Ge nanoparticle film is 0.5 W/m K. Accounting for a porosity of approximately 50%, the normalized thermal conductivities are 0.1 W/m K and 1 W/m K, respectively. The thermoelectric performance is discussed, considering that the electrical in-plane conductivity is also affected by the mesoporosity.
Electromagnetic energy harvesting using complementary split-ring resonators
Authors: Alavikia Babak , Almoneef Thamer S. , Ramahi Omar M.
Published: April 2014

This work introduces a class of electrically small resonators composed of a complementary split-ring resonator backed by a ground plane. The proposed structure has low profile, efficient for wide range of illumination angles and can be placed on metallic surfaces. An example unit cell was designed, optimized, and fabricated to resonate at around 5.8 GHz. It is shown through numerical simulations and laboratory measurements that the complementary split-ring resonator can efficiently deliver the incident power carried by an electromagnetic wave to a resistive load.
Franz-Keldysh effect in GeSn pin photodetectors
Authors: Oehme M. , Kostecki K. , Schmid M. , Kaschel M. , Gollhofer M. , Ye K. , Widmann D. , Koerner R. , Bechler S. , Kasper E. , Schulze J.
Published: April 2014

The optical properties and the Franz-Keldysh effect at the direct band gap of GeSn alloys with Sn concentrations up to 4.2% at room temperature were investigated. The GeSn material was embedded in the intrinsic region of a Ge heterojunction photodetector on Si substrates. The layer structure was grown by means of ultra-low temperature molecular beam epitaxy. The absorption coefficient as function of photon energy and the direct bandgap energies were determined. In all investigated samples, the Franz-Keldysh effect can be observed. A maximum absorption ratio of 1.5 was determined for 2% Sn for a voltage swing of 3 V.
Tuning photoluminescence of reduced graphene oxide quantum dots from blue to purple
Authors: Liu Fuchi , Tang Tao , Feng Qian , Li Ming , Liu Yuan , Tang Nujiang , Zhong Wei , Du Youwei
Published: April 2014

Reduced graphene oxide quantum dots (rGOQDs) were synthesized by annealing GOQDs in H2 atmosphere. The photoluminescence (PL) properties of GOQDs and the rGOQDs samples were investigated. The results showed that compared to GOQDs, a blue to purple tunable PL of rGOQDs can be obtained by regulating the annealing temperature. The increase fraction of the newly formed isolated sp2 clusters may be responsible for the observed tunable PL.
Land-Use Planning and the Urban Heat Island
Authors: Kim Jun-Pill , Guldmann Jean-Michel
Published: April 2014

Local-climate changes due to urbanization are epitomiz ed by the urban heat island (UHI), which is characterized by temperature differences between urban and rural areas. The UHI is a critical factor for energy consumption and air quality, resulting in higher peak electricity demand in summer because of air conditioning, increased emissions of primary pollutants associated with power production, and increased generation of ozone. However, planners need a better understanding of the relationship between the UHI and land-use patterns in order to reduce the UHI and promote more sustainable urban development. This research develops statistical models of local surface temperatures, using Landsat-5 satellite remote-sensing data, whereby the temperature at any location and for any land use is modeled as a function of the pattern of land uses around this location. Normalized Difference Vegetation Index (NDVI) and area land-use variables are used as inputs to these models, which are estimated with data for the Columbus, Ohio, metropolitan area. The results confirm the effects of neighboring land uses on local temperatures. The applicability of these models for land-use planning is illustrated by simulating hypothetical land-use changes, and computing the resulting temperature effects. The results demonstrate that it is possible to reduce temperatures in residential and urban areas through judicious siting of green areas.
Breaking Barriers to Transit-Oriented Development: Insights from the Serious Game SPRINTCITY
Authors: Duffhues Jan , Mayer Igor S , Nefs Merten , van der Vliet Mirte
Published: April 2014

The authors discuss and analyse the complex interplay between rail transport and urban development around railway stations in the Netherlands. Although this interrelationship, known as transit-oriented development (TOD), has been theorised and studied in the academic literature, the complex and dynamic underlying mechanisms and the appropriate planning and management responses have yet to be understood sufficiently. This is particularly relevant for local, regional, and national policy makers in the various planning subsystems. In order to improve the understanding and management of the dynamic relationship between rail transport and urban development, a conceptual model of TOD was developed. Actors validate and learn from this model in the serious game SPRINTCITY, in which a rail corridor is developed over a period of twenty years. It is hypothesised that playing SPRINTCITY helps actors to understand factors, other actors, and potential barriers related to TOD. Research data were collected through debriefings, questionnaires, and model output from more than thirty sessions conducted between 2010 and 2012. The authors conclude that the combined and iterative use of modelling and gaming was effective from the perspectives of design (development of the TOD model), research (insight acquired on TOD), and policy (policy-oriented learning and analysis).
Academic Entrepreneurship in the Creative Arts
Authors: Abreu Maria , Grinevich Vadim
Published: April 2014

The extensive literature on academic entrepreneurship has focused almost entirely on science and engineering, while little is known about the extent of it in other disciplines, most notably the creative arts. We analyse the context, motivations, and variety of academic entrepreneurship in the creative arts using a recently completed survey of UK academics, providing microdata on 1108 academics. The data are complemented using institutional data taken from the Higher Education–Business and Community Interaction Survey, and data on individual submissions to the Research Assessment Exercise 2008. We highlight four characteristics of academic environment in the creative arts that strongly influence the nature of the entrepreneurship in the field: the practice-based nature of the research; the role of networks, particularly networks linked to teaching; the importance on nonmonetary rewards; and the role of geography. Our results indicate that academic entrepreneurship in the creative arts is varied and extensive, and that it could be better supported by policy.
A model for the generation and transmission of variations in evolution
Authors: Rivoire Olivier , Leibler Stanislas
Published: April 2014

Significance

Few things are excluded in biology if they are not physically impossible, but some have been advocated to be, for instance, the absence of reverse flow of information from phenotype to genotype, often assimilated to Lamarckism. Regardless of the question of whether this prohibition is universally true or not, could any such prohibition logically result from natural selection? We introduce a mathematical model to examine this question and, more generally, the conditions under which various mechanisms for generating and transmitting variations in evolving populations may be favored or suppressed by natural selection.
Charge gradient microscopy
Authors: Hong Seungbum , Tong Sheng , Park Woon Ik , Hiranaga Yoshiomi , Cho Yasuo , Roelofs Andreas
Published: April 2014

Significance

Polarization charges of ferroelectric materials are screened by an equal amount of surface charges with opposite polarity in ambient condition. Here we show that scraping, collecting, and quantifying the surface screen charges reveals the underlying polarization domain structure at high speed, a technique we call charge gradient microscopy. The scraped charge, measured as a current that scales with scraping rate, induces a charge gradient which leads to the immediate relocation or refill of the screen charges from the vicinity of the probe, making this method a reliable tool to study the complex dynamics of domain nucleation and growth induced by a biased tip in the absence of surface screen charges.
Semantic effects in word recognition are moderated by body-object interaction
Authors: Havermaet Lisa R. Van , Wurm Lee H.
Published: April 2014

A potential embodied influence in the semantic effects of Danger and Usefulness is investigated using Body-Object Interaction (BOI). Lexical decision times are influenced by ratings of Danger and Usefulness. In a frequently-found interaction, thought to be produced by activated approach-withdraw motor responses, increasing Danger ratings produce faster responses for items with lower Usefulness ratings while producing slower responses for items with higher Usefulness ratings. BOI is used to test the embodied explanation of this interaction. The same 102 words were presented in two lexical decision experiments. In both auditory and visual lexical decision, the effects of Danger and Usefulness were found to be diminished for items with higher BOI ratings. BOI moderates Danger and Usefulness effects in both auditory and visual lexical decision, in a way that suggests BOI is either the stronger or the temporally earlier effect.
Estimating second language productive vocabulary size
Authors: Williams Joy , Segalowitz Norman , Leclair Tatsiana
Published: April 2014

This study provides validity evidence for the Capture-Recapture (CR) method, borrowed from ecology, as a measure of second language (L2) productive vocabulary size (PVS). Two separate “captures” of productive vocabulary were taken using written word association tasks (WAT). At Time 1, 47 bilinguals provided at least 4 associates to each of 30 high-frequency stimulus words in English, their first language (L1), and in French, their L2. A few days later (Time 2), this procedure was repeated with a different set of stimulus words in each language. Since the WAT was used, both Lex30 and CR PVS scores were calculated in each language. Participants also completed an animacy judgment task assessing the speed and efficiency of lexical access.
Results indicated that, in both languages, CR and Lex30 scores were significantly positively correlated (evidence of convergent validity). CR scores were also significantly larger in the L1, and correlated significantly with the speed of lexical access in the L2 (evidence of construct validity). These results point to the validity of the technique for estimating relative L2 PVS. However, CR scores are not a direct indication of absolute vocabulary size. A discussion of the method’s underlying assumptions and their implications for interpretation are provided.
Relational diversity affects ease of processing even for opaque English compounds
Authors: Spalding Thomas L. , Gagné Christina L.
Published: April 2014

Recent research has indicated that understanding compound words involves an attempt at semantic composition of the constituent words, and that this meaning construction process involves an attempt to identify a relation linking the constituents. Research with novel compounds, where a meaning construction process is necessary, has shown that relational interpretations compete to be selected during comprehension, and that increased competition leads to increased processing difficulty. The current project investigates relational competition during the processing of transparent and opaque English compounds. The results show that the diversity of possible relational interpretations affects the ease with which participants can make a lexical decision for a compound. This is true even for opaque compounds, where the identification of the meaning of the compound cannot, by definition, be the result of the meaning construction process. This suggests that initiation of the meaning construction process is obligatory during compound processing.
The chronological I
Authors: Blomberg Helena , Börjesson Mats
Published: April 2014

The aim of the article is to problematise and discuss the usefulness of thechronological Ias a new analytical approach for studying the doing of identity in storytelling. The chronological I can be both a rhetorical resource for narrators and a new analytical tool for studying the process of doing identity. The article suggests that the chronological I adds a new analytical dimension to different types of narrative analysis. The article takes its point of departure in the understanding of the narrator as using time as a rhetorical resource for telling or doing identity in ongoing interactions. In this discursive narrative approach, narratives are viewed as socially situated actions in a context in which the narrator has to relate to culturally accepted agreements about responsibility and agency. The data for this article is based on interviews with twelve individuals exposed to workplace bullying. As this topic is sensitive, there is a need for narrators to manage their accountability when asked to account for their agency or non agency in the reported events.
Creating a test corpus for term extractors through term annotation
Authors: Bernier-Colborne Gabriel , Drouin Patrick
Published: April 2014

In this paper, we describe a methodology used to create a test corpus for the evaluation of term extractors. This methodology relies on term annotation: terms in a corpus on automotive engineering are selected based on specific criteria pertaining to the terminological setting as well as linguistic and formal properties of terms and term variations. The test corpus accounts for the variety of ways in which terms are realized in running text, and provides a means of automatically evaluating the relevance of term candidate lists produced by term extractors. Due to the XML annotation scheme used, the corpus can be customized, e.g. by filtering out some of the annotated terms based on the type of term or term variation, or frequency. In this paper, we focus on the methodological aspects of this work.
Substance Abuse/Dependence Treatment: A European Perspective
Authors: Metz Verena E. , Brandt Laura , Unger Annemarie , Fischer Gabriele
Published: April 2014

During the past decade, substantial progress has been made in the field of addiction medicine in Europe, particularly regarding the development of new treatment interventions, resulting in a wide range of therapeutic options for patients with substance use disorders. However, not all interventions are evidence based. Patients with cannabis and cocaine/amphetamine use disorders and special patient populations especially lack evidence-based treatment recommendations. Many patients undergo treatment that has not been scientifically evaluated for quality and efficacy. Moreover, there are large disparities regarding availability and treatment access across Europe, with the new member states of the European Union (EU) reporting long waiting lists and low treatment coverage. Even in Austria, which ranks among the countries with relatively high treatment coverage and good diversification of treatment in opioid maintenance therapy due to the availability of methadone, buprenorphine, and slow-release oral morphine (SROM), a considerable population of untreated or inadequately treated patients exists. Treatment for substance use disorders in Europe still has scope for improvement in terms of treatment availability and access, which is ideally provided by further development and implementation of evidence-based interventions.
Where are all the female participants in Sports and Exercise Medicine research?
Authors: Costello Joseph T. , Bieuzen Francois , Bleakley Chris M.
Published: April 2014

The aim of this study is to estimate the ratio of male and female participants in Sports and Exercise Medicine research. Original research articles published in three major Sports and Exercise Medicine journals (Medicine and Science in Sports and Exercise, British Journal of Sports Medicine and American Journal of Sports Medicine) over a three‐year period were examined. Each article was screened to determine the following: total number of participants, the number of female participants and the number of male participants. The percentage of females and males per article in each of the journals was also calculated. Cross tabulations and Chi‐square analysis were used to compare the gender representation of participants within each of the journals. Data were extracted from 1382 articles involving a total of 6,076,580 participants. A total of 2,366,968 (39%) participants were female and 3,709,612 (61%) were male. The average percentage of female participants per article across the journals ranged from 35% to 37%. Females were significantly under‐represented across all of the journals (χ2 = 23,566, df = 2, p < 0.00001). In conclusion, Sports and Exercise Medicine practitioners should be cognisant of sexual dimorphism and gender disparity in the current literature.
Use of Pulmonary Arterial Hypertension–Specific Therapy in Overweight or Obese Patients with Obstructive Sleep Apnea and Pulmonary Hypertension
Authors: Shujaat Adil , Bellardini Jason , Girdhar Ankur , Bajwa Abubakr A.
Published: April 2014

Pulmonary hypertension (PH) in overweight or obese patients with obstructive sleep apnea (OSA) may be multifactorial. The effect of pulmonary artery hypertension (PAH)‐specific drugs on PH and exercise capacity in such patients is unknown. We performed a retrospective review of overweight or obese patients with OSA and PH who were treated with PAH‐specific therapy in our PH clinic. We identified 9 female and 2 male patients. The mean age ± SD was 54.9 ± 9.3 years. The mean pulmonary artery pressure at the time of diagnosis of PH was 39.8 ± 16.1 mmHg. The right atrial pressure was 11.1 ± 4.5 mmHg, the pulmonary artery wedge pressure was 14.1 ± 2.9 mmHg, the cardiac index was 2.6 ± 0.5 L/min/m2, and the pulmonary vascular resistance index was 10.6 ± 7.1 Wood units/m2. The indications for use of PAH‐specific therapy were dyspnea in association with right heart failure (n = 4), persistent PH despite compliance with nocturnal positive airway pressure (PAP) therapy (n = 4), or inability to tolerate PAP therapy (n = 3). PH was treated with an endothelin receptor antagonist (n = 8) or a phosphodiesterase‐5 inhibitor (n = 3). The 6‐minute walk distance (6MWD) improved significantly, from 234 ± 49.7 to 258 ± 54.6 m (24 m [95% confidence interval (CI): 6.5–341.5 m]; P = 0.014) over a period of 4.4 ± 1.8 months (n = 8) and from 241.7 ± 48.5 to 289.9 ± 91 m (48 m [95% CI: 5.5–90.8 m]; P = 0.033) in those with a longer follow‐up period of 12.1 ± 6.4 months (n = 7). The systolic pulmonary artery pressure dropped significantly, from 64 ± 25.2 to 42 ± 10.4 mmHg (22 mmHg [95% CI: 4–40 mmHg]; P = 0.024) over a period of 6.1 ± 4.1 months (n = 7). In conclusion, PAH‐specific therapy resulted in significant improvement in both PH and 6MWD.
Circular RNAs are depleted of polymorphisms at microRNA binding sites
Authors: Thomas Laurent F. , Sætrom Pål
Published: April 2014

Motivation: Circular RNAs (circRNAs) are an abundant class of highly stable RNAs that can affect gene regulation by binding and preventing microRNAs (miRNAs) from regulating their messenger RNA (mRNA) targets. Mammals have thousands of circRNAs with predicted miRNA binding sites, but only two circRNAs have been verified as being actual miRNA sponges. As it is unclear whether these thousands of predicted miRNA binding sites are functional, we investigated whether miRNA seed sites within human circRNAs are under selective pressure.

Results: Using SNP data from the 1000 Genomes Project, we found a significant decrease in SNP density at miRNA seed sites compared with flanking sequences and random sites. This decrease was similar to that of miRNA seed sites in 3' untranslated regions, suggesting that many of the predicted miRNA binding sites in circRNAs are functional and under similar selective pressure as miRNA binding sites in mRNAs.

Contact:  pal.satrom@ntnu.no

Supplementary information:  Supplementary Data are available at Bioinformatics online.
kdetrees: non-parametric estimation of phylogenetic tree distributions
Authors: Weyenberg Grady , Huggins Peter M. , Schardl Christopher L. , Howe Daniel K. , Yoshida Ruriko
Published: April 2014

Motivation: Although the majority of gene histories found in a clade of organisms are expected to be generated by a common process (e.g. the coalescent process), it is well known that numerous other coexisting processes (e.g. horizontal gene transfers, gene duplication and subsequent neofunctionalization) will cause some genes to exhibit a history distinct from those of the majority of genes. Such ‘outlying’ gene trees are considered to be biologically interesting, and identifying these genes has become an important problem in phylogenetics.

Results: We propose and implement kdetrees, a non-parametric method for estimating distributions of phylogenetic trees, with the goal of identifying trees that are significantly different from the rest of the trees in the sample. Our method compares favorably with a similar recently published method, featuring an improvement of one polynomial order of computational complexity (to quadratic in the number of trees analyzed), with simulation studies suggesting only a small penalty to classification accuracy. Application of kdetrees to a set of Apicomplexa genes identified several unreliable sequence alignments that had escaped previous detection, as well as a gene independently reported as a possible case of horizontal gene transfer. We also analyze a set of Epichloë genes, fungi symbiotic with grasses, successfully identifying a contrived instance of paralogy.

Availability and implementation: Our method for estimating tree distributions and identifying outlying trees is implemented as the R package kdetrees and is available for download from CRAN.

Contact:  ruriko.yoshida@uky.edu

Supplementary information:  Supplementary Data are available at Bioinformatics online.
Source and processing effects on noise correlations
Authors: Fichtner Andreas
Published: April 2014

We quantify the effects of spatially heterogeneous noise sources and seismic processing on noise correlation measurements and their sensitivity to Earth structure. Using numerical wavefield simulations and adjoint techniques, we calculate interstation correlations and sensitivity kernels for arbitrarily distributed noise sources where—as in the real Earth—different frequencies are generated in different locations. While both heterogeneous noise sources and processing can have profound effects on noise correlation waveforms, narrow-band traveltime measurements are less affected, in accord with previous analytical studies. Sensitivities to Earth structure depend strongly on the source distribution and the processing scheme, and they reveal exotic frequency dependencies that go beyond the well-known frequency scaling of the Fresnel zone width. Our results indicate that modern full waveform inversion applied to noise correlations is not possible unless one of the following measures is taken: (1) properly account for noise source distribution and processing, or (2) limit measurements to phase or time shifts in narrow frequency bands. Failure to do so can lead to erroneous misfits, tomographic artefacts, and reduced resolution.
QoI-Resistance Stability in Relation to Pathogenic and Saprophytic Fitness Components of Alternaria alternata from Citrus
Authors: Vega Byron , Dewdney Megan M.
Published: April 2014

The phenotypic stability, fitness components, and ability to cause disease of isolates of the Alternaria alternata tangerine pathotype resistant to quinone-outside inhibitors (QoIs) were studied. Stability of resistance to azoxystrobin (AZ) and pyraclostrobin (PYR) was determined after consecutive transfers on potato dextrose agar (PDA). The sensitivity to QoIs did not change significantly after 10 transfers on PDA compared with the initial sensitivity of all isolates tested. Fitness components evaluated in vitro were mycelial growth, conidial germination, and conidial production. Incubation period, number of lesions per leaf area, and virulence were determined with detached leaf assays using four cultivars: Dancy, Minneola, Murcott, and Sunburst. Variability in fitness components was observed among isolates within the same sensitivity group. As a group, no significant differences in the mean values of these fitness components were observed between resistant and sensitive phenotypes, except for virulence. Resistant isolates were significantly (P < 0.05) more virulent than the sensitive isolates on Dancy, Minneola, and Sunburst but not on Murcott (P = 0.3506). There was no significant correlation between individual fitness components and the level of sensitivity to AZ and PYR. Preventive applications of Abound (commercial formulation of AZ) at full field rates failed to control disease caused by QoI-resistant isolates under greenhouse conditions. Our results suggest that QoI resistance in A. alternata tangerine pathotype is stable in the absence of QoI selection pressure and that resistance development did not affect the fitness of resistant isolates.
Reproduction of Didymella bryoniae on Nine Species of Cucurbits Under Field Conditions
Authors: Keinath Anthony P.
Published: April 2014

Eighteen cucurbit cultivars representing 5 genera, 9 species, and 11 taxa susceptible to gummy stem blight were inoculated with Didymella bryoniae in field plots in Charleston, SC, in autumn 2008, autumn 2009, and spring 2011 to determine the suitability of the hosts and various plant parts for formation of sexual and asexual fruiting bodies of the pathogen. In 1, 2, or 3 years, D. bryoniae reproduced on all 18 cultivars, on leaves, and on all plant parts examined—pedicles, peduncles, petioles, tendrils, and vines. Watermelon and citron (both Citrullus lanatus) and melon (Cucumis melo) had significantly more leaves with fruiting bodies than cucumber (Cucumis sativus), bottle gourd (Lagenaria siceraria), and eight cultivars of squash and pumpkin (Cucurbita maxima, C. moschata, and C. pepo). On plant parts other than leaves, melon had the greatest proportions of tissue pieces with fruiting bodies, and citron had the least. Fruiting bodies were observed on 86% of plant parts examined in autumn 2009 but on only 28% in spring 2011, when environmental conditions were hot and dry. In 2009, pseudothecia and pycnidia were found in equal proportions on leaves, but pseudothecia were found more frequently than pycnidia on leaves in 2011 and on other plant parts in 2009 and 2011.
Epigenetic state network approach for describing cell phenotypic transitions
Authors: Wang Ping , Song Chaoming , Zhang Hang , Wu Zhanghan , Tian Xiao-Jun , Xing Jianhua
Published: April 2014

Recent breakthroughs of cell phenotype reprogramming impose theoretical challenges on unravelling the complexity of large circuits maintaining cell phenotypes coupled at many different epigenetic and gene regulation levels, and quantitatively describing the phenotypic transition dynamics. A popular picture proposed by Waddington views cell differentiation as a ball sliding down a landscape with valleys corresponding to different cell types separated by ridges. Based on theories of dynamical systems, we establish a novel ‘epigenetic state network’ framework that captures the global architecture of cell phenotypes, which allows us to translate the metaphorical low-dimensional Waddington epigenetic landscape concept into a simple-yet-predictive rigorous mathematical framework of cell phenotypic transitions. Specifically, we simplify a high-dimensional epigenetic landscape into a collection of discrete states corresponding to stable cell phenotypes connected by optimal transition pathways among them. We then apply the approach to the phenotypic transition processes among fibroblasts (FBs), pluripotent stem cells (PSCs) and cardiomyocytes (CMs). The epigenetic state network for this case predicts three major transition pathways connecting FBs and CMs. One goes by way of PSCs. The other two pathways involve transdifferentiation either indirectly through cardiac progenitor cells or directly from FB to CM. The predicted pathways and multiple intermediate states are supported by existing microarray data and other experiments. Our approach provides a theoretical framework for studying cell phenotypic transitions. Future studies at single-cell levels can directly test the model predictions.
Acetobacter sicerae sp. nov., isolated from cider and kefir, and identification of species of the genus Acetobacter by dnaK, groEL and rpoB sequence analysis
Authors: Li Leilei , Wieme Anneleen , Spitaels Freek , Balzarini Tom , Nunes Olga C. , Manaia Célia M. , Van Landschoot Anita , De Vuyst Luc , Cleenwerck Ilse , Vandamme Peter
Published: April 2014

Five acetic acid bacteria isolates, awK9_3, awK9_4 ( = LMG 27543), awK9_5 ( = LMG 28092), awK9_6 and awK9_9, obtained during a study of micro-organisms present in traditionally produced kefir, were grouped on the basis of their MALDI-TOF MS profile with LMG 1530 and LMG 1531T, two strains currently classified as members of the genusAcetobacter. Phylogenetic analysis based on nearly complete 16S rRNA gene sequences as well as on concatenated partial sequences of the housekeeping genesdnaK,groELandrpoBindicated that these isolates were representatives of a single novel species together with LMG 1530 and LMG 1531Tin the genusAcetobacter, withAcetobacter aceti,Acetobacter nitrogenifigens,Acetobacter oeniandAcetobacter estunensisas nearest phylogenetic neighbours. Pairwise similarity of 16S rRNA gene sequences between LMG 1531Tand the type strains of the above-mentioned species were 99.7 %, 99.1 %, 98.4 % and 98.2 %, respectively. DNA–DNA hybridizations confirmed that status, while amplified fragment length polymorphism (AFLP) and random amplified polymorphic DNA (RAPD) data indicated that LMG 1531T, LMG 1530, LMG 27543 and LMG 28092 represent at least two different strains of the novel species. The major fatty acid of LMG 1531Tand LMG 27543 was C18 : 1ω7c. The major ubiquinone present was Q-9 and the DNA G+C contents of LMG 1531Tand LMG 27543 were 58.3 and 56.7 mol%, respectively. The strains were able to grow ond-fructose andd-sorbitol as a single carbon source. They were also able to grow on yeast extract with 30 %d-glucose and on standard medium with pH 3.6 or containing 1 % NaCl. They had a weak ability to produce acid fromd-arabinose. These features enabled their differentiation from their nearest phylogenetic neighbours. The nameAcetobacter siceraesp. nov. is proposed with LMG 1531T( = NCIMB 8941T) as the type strain.
Morphological and molecular characterization of Parafurgasonia zhangi spec. nov. and Chilodonella acuta Kahl, 1931 (Protozoa, Ciliophora), from a soil habitat of Saudi Arabia
Authors: Fan Xinpeng , Ma Rui , Al-Farraj Saleh A. , Gu Fukang
Published: April 2014

The morphology and infraciliature of two soil ciliates,Parafurgasonia zhangispec. nov. andChilodonella acutaKahl, 1931, collected from Saudi Arabia, were investigated by observations of both living cells and specimens after standard staining methods.P. zhangidiffers from its congeners by the combination of the following features: excretory pore quite near posterior end of paroral membrane, 16 or 17 somatic kineties with about 11 kinetids in each one on dorsal side, paroral membrane gently curved and composed of about 15 dikinetids, and hypostomial organelle composed of four or five files of kinetids with four monokinetids each. The diagnosis ofChilodonella acutawas renewed to include characteristics revealed by the silver impregnation method: cellsin vivomeasuring 33–45×18–26 µm, dorsal hump and tail-like podite present, two contractile vacuoles, seven left and five right kineties, 9–11 nematodesmal rods, and dorsal brush containing about 11 basal bodies. Phylogenetic analyses based on small-subunit rRNA gene sequences showed thatP. zhangiwas closer to species of the Colpodidiidae rather than the Furgasoniidae represented byFurgasonia blochmanni, andChilodonella acutaclustered with its congenerChilodonella uncinatabut was a well-outlined species of the genus.
An alternative to the adenovirus inverted terminal repeat sequence increases the viral genome replication rate and provides a selective advantage in vitro
Authors: Wunderlich Kerstin , van der Helm Esmeralda , Spek Dirk , Vermeulen Mark , Gecgel Adile , Pau Maria Grazia , Vellinga Jort , Custers Jerome
Published: April 2014

During the development of human adenovirus 35-derived replication-incompetent (rAd35) vaccine vectors for prevention of infectious diseases, we detected mutations in the terminal 8 nt of the inverted terminal repeats (ITRs) of rAd35. The switch from the plasmid-encoded sequence 5′-CATCATCA-3′ to the alternative sequence 5′-CTATCTAT-3′ in the ITRs was found to be a generalin vitropropagation phenomenon, as shown for several vectors carrying different transgenes or being derived from different adenovirus serotypes. In each tested case, the plasmid-encoded ITR sequence changed to exactly the same alternative ITR sequence, 5′-CTATCTAT-3′. The outgrowth of this alternative ITR version should result from a growth advantage conferred by the alternative ITR sequence. Indeed, replication kinetics studies of rAd35 harbouring either the original or alternative ITR sequence confirmed an increase in replication speed for rAd35 vectors with the alternative ITR sequence. These findings can be applied to generate recombinant adenoviral vectors harbouring the alternative ITR sequence, which will facilitate the generation of genetically homogeneous seed virus batches. Moreover, vector production may be accelerated by taking advantage of the observed improved replication kinetics associated with the alternative ITR sequence.
Predicting evolutionary site variability from structure in viral proteins: buriedness, packing, flexibility, and design
Authors: Shahmoradi Amir , Sydykova Dariya K. , Spielman Stephanie J. , Jackson Eleisha L. , Dawson Eric T. , Meyer Austin G. , Wilke Claus O.
Published: April 2014

Several recent works have shown that protein structure can predict site-specific evolutionary sequence variation. In particular, sites that are buried and/or have many contacts with other sites in a structure have been shown to evolve more slowly, on average, than surface sites with few contacts. Here, we present a comprehensive study of the extent to which numerous structural properties can predict sequence variation. The quantities we considered include buriedness (as measured by relative solvent accessibility), packing density (as measured by contact number), structural flexibility (as measured by B factors, root-mean-square fluctuations, and variation in dihedral angles), and variability in designed structures. We obtained structural flexibility measures both from molecular dynamics simulations performed on 9 non-homologous viral protein structures and from variation in homologous variants of those proteins, where available. We obtained measures of variability in designed structures from flexible-backbone design in the Rosetta software. We found that most of the structural properties correlate with site variation in the majority of structures, though the correlations are generally weak (correlation coefficients of 0.1 to 0.4). Moreover, we found that buriedness and packing density were better predictors of evolutionary variation than was structural flexibility. Finally, variability in designed structures was a weaker predictor of evolutionary variability than was buriedness or packing density, but it was comparable in its predictive power to the best structural flexibility measures. We conclude that simple measures of buriedness and packing density are better predictors of evolutionary variation than are more complicated predictors obtained from dynamic simulations, ensembles of homologous structures, or computational protein design.
In vivo generation of DNA sequence diversity for cellular barcoding
Authors: Peikon Ian , Gizatullina Diana , Zador Anthony
Published: April 2014

Heterogeneity is a ubiquitous feature of biological systems. A complete understanding of such systems requires a method for uniquely identifying and tracking individual components and their interactions with each other. We have developed a novel method of uniquely tagging individual cells in vivo with a genetic 'barcode' that can be recovered by DNA sequencing. We demonstrate the feasibility of this technique in bacterial cells. This method should prove useful in tracking interactions of cells within a network, and/or heterogeneity within complex biological samples.
Crowdsourced analysis of ash and ash dieback through the Open Ash Dieback project: A year 1 report on datasets and analyses contributed by a self-organising community
Authors: Saunders Diane , Yoshida Kentaro , Sambles Christine , Glover Rachel , Clavijo Bernardo , Corpas Manuel , Bunting Daniel , Dong Suomeng , Rallapalli Ghanasyam , Clark Matthew D. , Swarbreck David , Ayling Sarah , Bashton Matthew , Collin Steve , Hosoya Tsuyoshi , Edwards Anne , Crossman Lisa , Etherington Graham , Win Joe , Cano Liliana , Studholme David J. , Downie J. Allan , Caccamo Mario , Kamoun Sophien , MacLean Dan
Published: April 2014

Ash dieback is a fungal disease of ash trees caused by Hymenoscyphus pseudoalbidus that has swept across Europe in the last two decades and is a significant threat to the ash population. This emergent pathogen has been relatively poorly studied and little is known about its genetic make-up. In response to the arrival of this dangerous pathogen in the UK we took the unusual step of providing an open access database and initial sequence datasets to the scientific community for analysis prior to performing an analysis of our own. Our goal was to crowdsource genomic and other analyses and create a community analysing this pathogen. In this report on the evolution of the community and data and analysis obtained in the first year of this activity, we describe the nature and the volume of the contributions and reveal some preliminary insights into the genome and biology of H. pseudoalbidus that emerged. In particular our nascent community generated a first-pass genome assembly containing abundant collapsed AT-rich repeats indicating a typically complex genome structure. Our open science and crowdsourcing effort has brought a wealth of new knowledge about this emergent pathogen within a short time-frame. Our community endeavour highlights the positive impact that open, collaborative approaches can have on fast, responsive modern science.
A slow-forming isopeptide bond in the structure of the major pilin SpaD fromCorynebacterium diphtheriaehas implications for pilus assembly
Authors: Kang Hae Joo , Paterson Neil G. , Kim Chae Un , Middleditch Martin , Chang Chungyu , Ton-That Hung , Baker Edward N.
Published: April 2014

The Gram-positive organismCorynebacterium diphtheriae, the cause of diphtheria in humans, expresses pili on its surface which it uses for adhesion and colonization of its host. These pili are covalent protein polymers composed of three types of pilin subunit that are assembled by specific sortase enzymes. A structural analysis of the major pilin SpaD, which forms the polymeric backbone of one of the three types of pilus expressed byC. diphtheriae, is reported. Mass-spectral and crystallographic analysis shows that SpaD contains three internal Lys–Asn isopeptide bonds. One of these, shown by mass spectrometry to be located in the N-terminal D1 domain of the protein, only forms slowly, implying an energy barrier to bond formation. Two crystal structures, of the full-length three-domain protein at 2.5 Å resolution and of a two-domain (D2-D3) construct at 1.87 Å resolution, show that each of the three Ig-like domains contains a single Lys–Asn isopeptide-bond cross-link, assumed to give mechanical stability as in other such pili. Additional stabilizing features include a disulfide bond in the D3 domain and a calcium-binding loop in D2. The N-terminal D1 domain is more flexible than the others and, by analogy with other major pilins of this type, the slow formation of its isopeptide bond can be attributed to its location adjacent to the lysine used in sortase-mediated polymerization during pilus assembly.
An improved integration method in serial femtosecond crystallography
Authors: Qu Kun , Zhou Liang , Dong Yu-Hui
Published: April 2014

Recent experiments in serial femtosecond crystallography (SFX) have demonstrated the feasibility of obtaining structural information from nanoscale crystals using X-ray free-electron lasers (XFELs). However, millions of crystals are required to determine one reliable structure. Here, an improved integration algorithm for SFX data processing is reported. By evaluating the dimensions of each crystal and correcting for the geometric factors of single patterns, the effective diffraction intensities, as opposed to the directly measured single-shot pattern diffraction intensities, can be merged to acquire more accurate integrated intensities which can be used for structure determination. This improvement enhances the quality of electron-density maps and decreases the number of diffraction patterns that are needed to solve the crystal structure in SFX experiments.
Poly[(μ3-3,5-diisopropyl-4H-1,2,4-triazolato-κ3N:N′:N′′)silver(I)]
Authors: Cui Guo-Gen , Yang Xiao-Xi , Yang Jian-Ping , Jiang Xiang
Published: April 2014

In the polymeric title compound, [Ag(C8H14N3)]n, the AgIcation is coordinated by three N atoms from three 3,5-diisopropyl-1,2,4-triazolate anions in a T-shaped geometry. The AgIcation deviates from the coordination plane by 0.014 (1) Å and the N—Ag—N bond angles are 96.85 (11), 97.72 (10) and 165.39 (12)°. The triazolate anion bridges three AgIcations, forming a three-dimensional polymeric network.
2-Amino-6-methylpyridinium 4-methylbenzenesulfonate
Authors: Babu K. Syed Suresh , Dhavamurthy M. , NizamMohideen M. , Peramaiyan G. , Mohan R.
Published: April 2014

In the asymmetric unit of the title salt, C6H9N2+·C7H7O3S−, there are two independent 2-amino-6-methylpyridinium cations and two independent 4-methylbenzenesulfonate anions. Both cations are protonated at their pyridine N atoms and their geometries reveal amine–imine tautomerism. In the 4-methylbenzenesulfonate anions, the carboxylate groups are twisted out of the benzene ring planes by 88.4 (1) and 86.2 (2)°. In the crystal, the sulfonate O atoms of an anion interact with the protonated N atoms and the 2-amino groups of a cationviaa pair of N—H...O hydrogen bonds, forming anR22(8) ring motif. These motifs are connectedviaN—H...O hydrogen bonds, forming chains running along thea-axis direction. Within the chains there are weak C—H...O hydrogen bonds present. In addition, aromatic π–π stacking interactions [centroid–centroid distances = 3.771 (2), 3.599 (2), 3.599 (2) and 3.497 (2) Å] involving neighbouring chains are also observed.
(1S,2R,3S,6S,7R)-3,7,11,11-Tetramethyl-6,7-epoxybicyclo[5.4.0]undecane-2-ol
Authors: Loubidi Mohamed , Benharref Ahmed , El Ammari Lahcen , Saadi Mohamed , Berraho Moha
Published: April 2014

The title compound, C15H26O2, was synthesized from β-himachalene (3,5,5,9-tetramethyl-2,4a,5,6,7,8-hexahydro-1H-benzocycloheptene), which was isolated from the Atlas cedar (cedrus atlantica). The molecule is built up from a seven-membered ring to which a six- and a three-membered ring are fused. The seven- and six-membered rings each have a twist-boat conformation. In the crystal, O—H...O hydrogen bonds link the molecules into zigzag chains running along theb-axis direction.
5-Cyclopentyl-2-methyl-3-(4-methylphenylsulfonyl)-1-benzofuran
Authors: Choi Hong Dae , Seo Pil Ja , Lee Uk
Published: April 2014

In the title compound, C21H22O3S, the cyclopentyl ring adopts a twist conformation. The dihedral angle between the mean planes of the benzofuran and 4-methylphenyl rings is 72.38 (6)°. In the crystal, molecules are linked by C—H...O and C—H...π interactions, forming a three-dimensional supramolecular network.