bluuebunny/crossref_metadata_2025 huggingface dataset:
Tunable Fano resonance in hybrid graphene-metal gratings
Authors: Chen Zhao-xian , Chen Jin-hui , Wu Zi-jian , Hu Wei , Zhang Xue-jin , Lu Yan-qing
Published: April 2014

Hybrid graphene-metal gratings with tunable Fano resonance are proposed and theoretically investigated in THz band. The grating contains alternately aligned metal and graphene stripes, which could be viewed as the superposition of two kinds of gratings with the same period. Due to different material properties, the resonance coupling between the metal and graphene parts forms typical Fano-type transmitting spectra. The related physical mechanism is studied by inspecting the induced dipole moment and local surface charge distributions at different wavelengths. Both of the resonance amplitude and frequency of the structure thus are adjustable by tuning graphene's Fermi energy and the grating's geometrical parameters. Furthermore, the Fano-type spectra are also quite sensitive to environmental indices, which supply another kind of tunability. All these features should have promising applications in tunable THz filters, switches, and modulators.
Generation and coherent control of pure spin currents via terahertz pulses
Authors: Schüler Michael , Berakdar Jamal
Published: April 2014

We inspect the time and spin-dependent, inelastic tunneling in engineered semiconductor-based double quantum well driven by time-structured terahertz pulses. An essential ingredient is an embedded spin-active structure with vibrational modes that scatter the pulse driven carriers. Due to the different time scales of the charge and spin dynamics, the spin-dependent electron-vibron coupling may result in pure net spin current (with negligible charge current). Heating the vibrational site may affect the resulting spin current. Furthermore, by controlling the charge dynamics, the spin dynamics and the generated spin current can be manipulated and switched on and off coherently.
Discrimination of equi-sized nanoparticles by surface charge state using low-aspect-ratio pore sensors
Authors: Arima Akihide , Tsutsui Makusu , Taniguchi Masateru
Published: April 2014

In the field of nanopore sensing, it is difficult to distinguish particles of similar sizes by the ionic current signatures. In contrast, here, we demonstrated discrimination of equi-sized polystyrene (PS) particles by utilizing a low thickness-to-diameter aspect-ratio nanopore. We found distinct changes of the ionic current through the pore associated with translocation of PS particles modified with different functional groups. Comparing results about different size of nanopore can lead to discrimination of their surface charge densities. This discrimination technique may be useful in the development of low-aspect-ratio nanopore sensors for bioanalysis.
Graphene—A rather ordinary nonlinear optical material
Authors: Khurgin J. B.
Published: April 2014

An analytical expression for the nonlinear refractive index of graphene has been derived and used to obtain the performance metrics of third order nonlinear devices using graphene as a nonlinear medium. None of the metrics is found to be superior to the existing nonlinear optical materials.
Magnetic collimation of relativistic positrons and electrons from high intensity laser–matter interactions
Authors: Chen Hui , Fiksel G. , Barnak D. , Chang P.-Y. , Heeter R. F. , Link A. , Meyerhofer D. D.
Published: April 2014

Collimation of positrons produced by laser-solid interactions has been observed using an externally applied axial magnetic field. The collimation leads to a narrow divergence positron beam, with an equivalent full width at half maximum beam divergence angle of 4° vs the un-collimated divergence of about 20°. A fraction of the laser-produced relativistic electrons with energies close to those of the positrons is collimated, so the charge imbalance ratio (ne−/ne+) in the co-propagating collimated electron-positron jet is reduced from ∼100 (no collimation) to ∼2.5 (with collimation). The positron density in the collimated beam increased from 5 × 107 cm−3 to 1.9 × 109 cm−3, measured at the 0.6 m from the source. This is a significant step towards the grand challenge of making a charge neutral electron-positron pair plasma jet in the laboratory.
Investigations on residual strains and the cathodoluminescence and electron beam induced current signal of grain boundaries in silicon
Authors: Nacke M. , Allardt M. , Chekhonin P. , Hieckmann E. , Skrotzki W. , Weber J.
Published: April 2014

Cathodoluminescence (CL) and electron beam induced current (EBIC) measurements were used to investigate the optical behavior and electrical activity of grain boundaries (GBs) in coarsely grained silicon. Electron backscatter diffraction (EBSD) was applied for a comprehensive characterization of the structural properties of the high angle and low angle GBs (HAGBs and LAGBs) in the sample. It was found that not only the EBIC but also the panchromatic (pan) CL contrast of Σ3 HAGBs strongly depends on the hkl-type of the boundary plane. At room temperature coherent Σ3 GBs exhibit no significant contrast in the CL or EBIC images, whereas at low temperatures the pan-CL contrast is strong. For incoherent Σ3 GBs, a strong pan-CL and EBIC contrast was observed in the entire temperature range. Only on a LAGB (misorientation angle 4.5°) CL investigations at low temperatures revealed a line with peak position at about (0.82 ± 0.01) eV, usually related to the dislocation associated D1 transition. Cross-correlation EBSD was applied to analyze the strain fields of Σ3 HAGBs as well as of the LAGB. All the components of the local strain tensors were quantitatively determined. The relationship between the extension of the strain field at the LAGB and the spatial D1 intensity distribution is discussed.
A multi-objective optimization for energy management in a renewable micro-grid system: A data mining approach
Authors: Parvizimosaed Mehdi , Farmani Farid , Rahimi-Kian Ashkan , Monsef Hassan
Published: April 2014

To make renewable Micro-Grid (MG) systems work as a sustainable set, one confronts a multi-objective, multi-constraint problem. To optimally operate these hybrid energy systems, one should consider the problems due to huge amount of raw data achieved through several measuring systems in different sections in a MG. In this paper, a new Smart Energy Management System (SEMS) is proposed and tested via simulation studies. The proposed SEMS performs some critical tasks such as data acquisition, data processing, and determining control signals for the MG. Two objective functions are defined for the SEMS to minimize the total operating cost and the net emission of the fossil fueled Distributed Generators with respect to some technical and reliability (Expected Energy Not Supplied index) constraints for the MG. The simulation results show a promising performance of the proposed SEMS for smart micro-grids.
The Sicilian Baroque: Reconciling Postquake Tensions
Authors: Puleo Thomas J
Published: April 2014

Building upon discourses on trauma, art, and architecture, this work examines how the design and construction of buildings mediate the cultural, social, and political changes that occur after a catastrophe. It takes as its case study the reconstruction of Sicily's Val di Noto following an earthquake in 1693 and the role that the Baroque architectural style played in it. In this study, Sicilian Baroque building decoration emerges as a medium that facilitated the reconciliation of tensions that inhered among survivors of the earthquake and their social and material milieus.
A Phenomenological Approach to Water in the City: Towards a Policy of Letting Water Appear
Authors: Dicks Henry
Published: April 2014

Ivan Illich and Jamie Linton have both argued that our current technological relation to water constitutes an abstraction. Developing this insight in the context of phenomenology, I draw on Michel Haar's French translation of Gestell—the essence of technology, according to Heidegger—as ‘consommation’ (consumption), to put forward a criticism of the abstract status of water in postindustrial, consumer societies. I propose in its place a concrete, phenomenological approach, according to which a policy of ‘letting water appear’ can not only play a significant role in the unconcealment of poiēsis— Heidegger's response to the question concerning technology—but also form the basis of a renewed urban water policy. Four key examples of letting water appear are examined: Daylighting urban rivers and streams; harvesting local rain and ground water; treating wastewater on-site using ‘living machines’; and attuning demand to local water flows. I conclude by suggesting that urban water policy cannot be reduced to integrated water resource management, for the transition to sustainability also requires a fuller understanding of the phenomenological issue of ‘letting appear’ (poiēsis).
Peroxisome proliferator-activated receptor δ promotes colonic inflammation and tumor growth
Authors: Wang Dingzhi , Fu Lingchen , Ning Wei , Guo Lixia , Sun Xiaofei , Dey Sudhansu K. , Chaturvedi Rupesh , Wilson Keith T. , DuBois Raymond N.
Published: April 2014

Significance

Our study not only reveals a novel role of peroxisome proliferator-activated receptor δ (PPARδ) in colonic inflammation and colitis-associated tumorigenesis, but also provides some rationale for development of PPARδ antagonists as new therapeutic agents in the treatment of inflammatory bowel disease and colitis-associated colorectal cancer. Moreover, our findings indicate that prostaglandin E
2
generated by chronic inflammation is a crucial mediator connecting chronic inflammation and colorectal carcinogenesis.
Perfectivity and grounding in Mandarin Chinese
Authors: Li Wendan
Published: April 2014

This paper analyses the encoding of perfectivity in Chinese, focusing on its form, interpretation, and grounding functions. Three major points are made based on examinations of narrative text. First, perfectivity is indicated not only by the perfective marker -le, but also by an array of “bounding expressions” that explicitly designate the endpoint of events. Second, Chinese perfective clauses as currently defined vary in grounding roles. They may present bounded dynamic events and play a foregrounding role or denote stative situations and have a backgrounding function. The different grounding functions are determined not by the verb form but by the transitivity features of the clauses and the context in which they occur. Third, the flexibility is closely related to the nature and semantics of perfectivity and the structural components of the Chinese perfective constructions. The study adds unique features of an isolating language to our existing knowledge of grounding.
A novel dichotomy of the Korean adverb nemwu in opinion classification
Authors: Nam Jeesun
Published: April 2014

While the adverb nemwu, roughly equivalent to the intensifier too in English, has been considered an adverb that intensifies gradable predicates in excess, thereby provoking a negative interpretation, it can also be used to emphasize a positive evaluation in online subjective texts. Moreover, even in the sentences conveying a negative evaluation, only some of the occurrences of nemwu are used as a polarity reversing valence shifter. This paper proposes a novel dichotomy for the usages of nemwu, consisting of ‘Intensifying Adverbs’ (IAs) and ‘Opinion Introducers’ (OIs), and examines the necessary contexts for determining the function of the adverb.
Knee extension fatigue attenuates repeated force production of the elbow flexors
Authors: Halperin Israel , Aboodarda Saied J. , Behm David G.
Published: April 2014

Non‐local muscle fatigue has been demonstrated with unilateral activities, where fatiguing one limb alters opposite limb forces. Fewer studies have examined if non‐local fatigue occurs with unrelated muscles. The purpose of this study was to investigate if knee extensors fatigue alters elbow flexors force and electromyography (EMG) activity. Eighteen males completed a control and fatiguing session (randomised). Blood lactate was initially sampled followed by three maximal voluntary contractions (MVC) with the elbow flexors and two with the knee extensors. Thereafter, subjects either sat (control) or performed five sets of bilateral dynamic knee extensions to exhaustion using a load equal to the dominant limb MVC (1‐min rest between sets). Immediately afterwards, subjects were assessed for blood lactate and unilateral knee extensors MVC, and after 1 min performed a single unilateral elbow flexor MVC. Two minutes later, subjects performed 12 unilateral elbow flexor MVCs (5 s contraction/10 s rest) followed by a third blood lactate test. Compared to control, knee extensor force dropped by 35% (p < 0.001; ES = 1.6) and blood lactate increased by 18% (p < 0.001; ES = 2.8). Elbow flexor forces were lower after the fatiguing protocol only during the last five MVCs (p < 0.05; ES = ∼0.58; ∼5%). No changes occurred between conditions in EMG. Elbow flexor forces significantly decreased after knee extensors fatigue. The effect was revealed during the later stages of the repeated MVCs protocol, demonstrating that non‐local fatigue may have a stronger effect on repeated rather than on single attempts of maximal force production.
Priming word order by thematic roles: No evidence for an additional involvement of phrase structure
Authors: Pappert Sandra , Pechmann Thomas
Published: April 2014

Three experiments are reported that studied the priming of word order in German. Experiment 1 demonstrated priming of the order of case-marked verb arguments. However, order of noun phrases and order of thematic roles were confounded. In Experiment 2, we therefore aimed at disentangling the impact of these two possible factors. By using primes that differed from targets in phrase structure but were parallel with regard to the order of thematic roles, we nevertheless found priming demonstrating the critical impact of thematic roles. Experiment 3 replicated the priming effects from Experiments 1 and 2 within participants and revealed no evidence for a modulation of priming by phrase structure. Consequently, our findings suggest that word order priming crucially depends on the structural outline of thematic roles rather than on the linearization of phrases.
Energy, Backstop Endogeneity, and the Optimal Use of Groundwater
Authors: Roumasset James , Wada Christopher A.
Published: April 2014

To meet the growing demand for freshwater, many regions have increased groundwater pumping in recent years, resulting in declining groundwater levels worldwide. A promising development to address these declines is technical change regarding groundwater substitutes such as desalination and wastewater recycling. However, because these technologies are energy intensive, optimal implementation also depends on future energy price trends. We provide an operational model for the case of reverse‐osmosis seawater desalination. In an application to the Pearl Harbor Aquifer in Hawaii, we find that allowing the cost of desalination to increase at an average annual rate of 2.4% over the next century results in a substantially steeper efficiency price path for water. The higher prices decrease optimal groundwater extraction and induce a slower head drawdown over a longer period of time, thereby delaying the transition to desalination by over 30 years. Because the rise in energy costs exacerbates efficiency losses from under‐pricing, any delay in implementing efficiency pricing will cause either a greater future increase in prices or the need for rationing. Reforming prices sooner rather than later may be more politically feasible, given that consumers may be more amenable to a gradual rise in prices today than a sudden doubling or tripling of prices ten years from now. Using this as a foundation, we outline a research agenda for extending the framework to other groundwater substitutes and for adapting to climate change.
GenCLiP 2.0: a web server for functional clustering of genes and construction of molecular networks based on free terms
Authors: Wang Jia-Hong , Zhao Ling-Feng , Lin Pei , Su Xiao-Rong , Chen Shi-Jun , Huang Li-Qiang , Wang Hua-Feng , Zhang Hai , Hu Zhen-Fu , Yao Kai-Tai , Huang Zhong-Xi
Published: April 2014

Summary: Identifying biological functions and molecular networks in a gene list and how the genes may relate to various topics is of considerable value to biomedical researchers. Here, we present a web-based text-mining server, GenCLiP 2.0, which can analyze human genes with enriched keywords and molecular interactions. Compared with other similar tools, GenCLiP 2.0 offers two unique features: (i) analysis of gene functions with free terms (i.e. any terms in the literature) generated by literature mining or provided by the user and (ii) accurate identification and integration of comprehensive molecular interactions from Medline abstracts, to construct molecular networks and subnetworks related to the free terms.

Availability and implementation:  http://ci.smu.edu.cn.

Contact:  zxhuang@smu.edu.cn

Supplementary information:  Supplementary Data are available at Bioinformatics online.
Standard error estimation using the EM algorithm for the joint modeling of survival and longitudinal data
Authors: Xu Cong , Baines Paul D. , Wang Jane-Ling
Published: April 2014

Joint modeling of survival and longitudinal data has been studied extensively in the recent literature. The likelihood approach is one of the most popular estimation methods employed within the joint modeling framework. Typically, the parameters are estimated using maximum likelihood, with computation performed by the expectation maximization (EM) algorithm. However, one drawback of this approach is that standard error (SE) estimates are not automatically produced when using the EM algorithm. Many different procedures have been proposed to obtain the asymptotic covariance matrix for the parameters when the number of parameters is typically small. In the joint modeling context, however, there may be an infinite-dimensional parameter, the baseline hazard function, which greatly complicates the problem, so that the existing methods cannot be readily applied. The profile likelihood and the bootstrap methods overcome the difficulty to some extent; however, they can be computationally intensive. In this paper, we propose two new methods for SE estimation using the EM algorithm that allow for more efficient computation of the SE of a subset of parametric components in a semiparametric or high-dimensional parametric model. The precision and computation time are evaluated through a thorough simulation study. We conclude with an application of our SE estimation method to analyze an HIV clinical trial dataset.
Cohort resonance: a significant component of fluctuations in recruitment, egg production, and catch of fished populations
Authors: Botsford Louis W. , Holland Matthew D. , Field John C. , Hastings Alan
Published: April 2014

Hjort (1914. Fluctuations in the great fisheries of northern Europe. Rapport et Procès-Verbaux des Réunions du Conseil Permanent International pour l'exploration de la Mer, XX: 1–228) identified two important aspects of the early life of fish as being important determinants of fluctuations in year-class strength: changes in nutrition and transport. He dismissed a third possible influence, changes in the abundance of the reproductive stock. Here, we describe how a recently discovered characteristic behaviour of age-structured populations termed cohort resonance, which does involve changes in adult abundance, can have a substantial effect on fluctuations in fished populations. Cohort resonance involves selectively greater sensitivity of age-structured populations to generational frequencies and to very low frequencies in the environmental signal influencing a population. This frequency-dependent selectivity has been shown to increase with fishing, as do the total amounts of variability in recruitment, egg production, and catch. Cohort resonance differs from other recent model mechanisms proposed to explain the observed increase in variability with fishing in that it does not require over-compensatory density-dependence. It stems from the compensatory ascending limb of the egg–recruit relationship, and is a characteristic of a stable population driven by a random environment. We demonstrate the differences in frequency selectivity and increases in variability with fishing among three different Pacific coast species with different longevity: coho salmon (Oncorhynchus kisutch; ∼3 years), Pacific hake (Merluccius productus; ∼25 years), and Pacific Ocean perch (Sebastes alutus; ∼90 years). The shortest lived, coho salmon is the most sensitive to environmental variability, but variability in egg production and catch both increase more rapidly with fishing in the longer-lived species. Understanding cohort resonance will aid in anticipation of predicted potential changes in the frequency content of the physical environment with changing climate (e.g. more frequent El Niños), and it provides a warning regarding the possible confounding of increasing sensitivity to slow change due to fishing with actual slow change of population parameters due to climate change. Our understanding of the role of cohort resonance in population variability will be enhanced by further identification of empirical examples. We describe some of the challenges in this effort.
Efficacy of Fungicide Applications During and After Anthesis Against Fusarium Head Blight and Deoxynivalenol in Soft Red Winter Wheat
Authors: D'Angelo D. L. , Bradley C. A. , Ames K. A. , Willyerd K. T. , Madden L. V. , Paul P. A.
Published: April 2014

Seven field experiments were conducted in Ohio and Illinois between 2011 and 2013 to evaluate postanthesis applications of prothioconazole + tebuconazole and metconazole for Fusarium head blight and deoxynivalenol (DON) control in soft red winter wheat. Treatments consisted of an untreated check and fungicide applications made at early anthesis (A), 2 (A+2), 4 (A+4), 5 (A+5), or 6 (A+6) days after anthesis. Six of the seven experiments were augmented with artificial Fusarium graminearum inoculum, and the other was naturally infected. FHB index (IND), Fusarium damaged kernels (FDK), and DON concentration of grain were quantified. All application timings led to significantly lower mean arcsine-square-root-transformed IND and FDK (arcIND and arcFDK) and log-transformed (logDON) than in the untreated check; however, arcIND, arcFDK, and logDON for the postanthesis applications were generally not significantly different from those for the anthesis applications. Relative to the check, A+2 resulted in the highest percent control for both IND and DON, 69 and 54%, respectively, followed by A+4 (62 and 52%), A+6 (62 and 48%), and A (56 and 50%). A+2 and A+6 significantly reduced IND by 30 and 14%, respectively, relative to the anthesis application. Postanthesis applications did not, however, reduce DON relative to the anthesis application. These results suggest that applications made up to 6 days following anthesis may be just as effective as, and sometimes more effective than, anthesis applications at reducing FHB and DON.
Efficacy and Economics of Integrating In-Field and Harvesting Strategies to Manage Fusarium Head Blight of Wheat
Authors: Salgado Jorge David , Madden Laurence V. , Paul Pierce A.
Published: April 2014

Fusarium head blight (FHB), a fungal disease of wheat caused by Fusarium graminearum, and its associated toxins, particularly deoxynivalenol (DON), are best managed by integrating multiple strategies. Experiments were established in 2011 and 2013 to evaluate the effects of integrating cultivar resistance, fungicide application, and grain harvesting strategy on FHB index (IND; field severity), DON, grain yield (YLD), and grain test weight (TW; weight per unit volume). Plots of two moderately resistant and two susceptible cultivars were either treated with 19% tebuconazole + 19% prothioconazole or left untreated, and then inoculated with F. graminearum. IND was rated as the mean percentage of diseased spikelets per spike. Separate subsets of the plots of each cultivar–treatment combination were harvested with one of two combine harvester configuration: C1 (the default, set at a fan speed of 1,375 rpm and a shutter opening of 70 mm) and C4 (modified, with the same fan speeds but a wider shutter opening of 90 mm). YLD and TW data were collected, and grain samples were rated for percent Fusarium-damaged kernels (FDK) and tested for DON. Results from linear mixed-model analyses showed that the cultivar–treatment interaction was significant for all FHB-related responses, with the magnitude of the difference in mean arcsine-square-root-transformed IND and FDK (arcIND and arcFDK) and log-transformed DON (logDON) between treated and untreated being higher for susceptible than moderately resistant cultivars. Plots harvested with the C4 combine configuration had significantly higher mean TW than those harvested with C1. Treated plots had significantly higher YLD and TW than untreated plots, regardless of cultivar and configuration. Relative to the reference management program (untreated, susceptible cultivar, harvested with C1), the greatest percent reduction in FDK and DON and increase in YLD was observed for programs that included moderate resistance and fungicide treatment. The greatest percent increase in TW relative to the reference was observed when C4 adjusted combine setting was integrated with resistance and fungicide. Overall, the most effective management programs all included fungicide treatment, two included moderate resistance, and two included C4 combine setting. Relative to the reference management program, these programs resulted in 30 to 51% reduction in total estimated price discount, $127 to 312 ha−1 increase in gross cash income, and economic benefit of $31 to 272 ha−1, depending on the level of FHB IND (5 to 15%), grain price ($118 to 276 metric ton−1), and fungicide application cost ($40 to 96 ha−1).
Suppression of Cucumber Powdery Mildew by Supplemental UV-B Radiation in Greenhouses Can be Augmented or Reduced by Background Radiation Quality
Authors: Suthaparan A. , Stensvand A. , Solhaug K. A. , Torre S. , Telfer K. H. , Ruud A. K. , Mortensen L. M. , Gadoury D. M. , Seem R. C. , Gislerød H. R.
Published: April 2014

This study demonstrates that the spectral quality of radiation sources applied with ultraviolet-B (UV-B; background radiation) affects the suppression of cucumber powdery mildew (Podosphaera xanthii) by UV-B. Suppression provided by daily UV-B exposure of 1 W/m2 for 10 min was greatest in the presence of red light or by a complete lack of background light, and powdery mildew suppression was least in the presence of ultraviolet-A (UV-A) or blue radiation compared with plants exposed only to 16 h of daily natural light supplemented with high-pressure sodium lamps that supply broad-spectrum radiation with peaks in the yellow-orange region. Exposure of powdery mildew-inoculated plants to supplemental red light without UV-B, beginning at the end of the daylight period, also reduced disease severity; however, supplemental blue light applied in the same fashion had no effect. Daily application of UV-B at 1 W/m2 beginning on the day of inoculation significantly reduced the severity of powdery mildew to 15% compared with 100% severity on control plants. Maximum suppression of powdery mildew was observed following 15 min of exposure to UV-B (1.1% severity compared with 100% severity on control plants) but exposure time had to be limited to 5 to 10 min to reduce phytotoxicity. There was no additional disease suppression when plants were exposed to UV-B beginning 2 days prior to inoculation compared with plants exposed to UV-B beginning on the day of inoculation. UV-B inhibited germination, infection, colony expansion, and sporulation of P. xanthii. The results suggest that efficacy of UV-B treatments, alone or in combination with red light, against P. xanthii can be enhanced by exposure of inoculated plants to these wavelengths of radiation during the night, thereby circumventing the counteracting effects of blue light and UV-A radiation. The effect of UV-B on powdery mildew seemed to be directly upon the pathogen, rather than induced resistance of the host. Night exposure of plants to 5 to 10 min of UV-B at 1 W/m2 and inexpensive, spectral-specific, light-emitting diodes may provide additional tools to suppress powdery mildews of diverse greenhouse crops.
First Report of Peanut mottle virus Infecting Soybean in South Korea
Authors: Lim S. , Lee Y.-H. , Igori D. , Zhao F. , Yoo R. H. , Lee S.-H. , Baek I. Y. , Moon J. S.
Published: April 2014

In July 2013, soybean (Glycine max) plants at the research field in Daegu, South Korea, showed virus-like symptoms, such as mosaic, mottle, yellowing, and stunting. Overall, there were approximately 1% of soybean plants that showed these symptoms. Sixteen soybean samples were collected based on visual symptoms and subjected to laboratory characterization. Total RNA was extracted from each sample with the Tri Reagent (Molecular Research Center, Cincinnati, OH) and cDNA was synthesized using random N25 primer with RevertAid Reverse Transcriptase (Thermo Scientific, Waltham, MA), according to the manufacturers' instructions. All samples were tested by PCR with Prime Taq Premix (2X) (GeNet Bio, Daejeon, Korea) and primer sets specific to Soybean mosaic virus (SMV; 5′-CATATCAGTTTGTTGGGCA-3′ and 5′-TGCCTATACCCTCAACAT-3′), Peanut stunt virus (PSV; 5′-TGACCGCGTGCCAGTAGGAT-3′ and 5′-AGGTDGCTTTCTWTTGRATTTA-3′), Soybean yellow mottle mosaic virus (SYMMV; 5′-CAACCCTCAGCCACATTCAACTAT-3′ and 5′-TCTAACCACCCCACCCGAAGGATT-3′), and Soybean yellow common mosaic virus (SYCMV; 5′-TTGGCTGAGAGGAGTGGCTT-3′ and 5′-TGCGGTCGTGTAGTCAGTG-3′). Among 16 samples tested, five were positive for SMV and two for SYMMV. Three samples were found infected by both SMV and SYMMV and four by both SMV and PSV. Since two of the symptomatic samples were not infected by viruses described above, a pair of primers specific to Peanut mottle virus (PeMoV; 5′-GCTGTGAATTGTTGTTGAGAA-3′ and 5′-ACAATGATGAAGTTCGTTAC-3′) was tested (1). All 16 samples were subjected to RT-PCR with primers specific to PeMoV. Four were found positive for PeMoV. Two of them were already found infected with SYMMV. In order to identify the complete nucleotide sequences of PeMoV coat protein (CP), another primer set (5′-TGAGCAGGAAAGAATTGTTTC-3′ and 5′-GGAAGCGATATACACACCAAC-3′) was used. RT-PCR product was cloned into RBC TA Cloning Vector (RBC Bioscience, Taipei, Taiwan) and the nucleotide sequence of the insert was determined by Macrogen (Seoul, Korea). CP gene of the PeMoV (GenBank Accession No. KJ664838) showed the highest nucleotide sequence identity with PeMoV isolate Habin (KF977830; 99% identity), and the highest amino acid identity with GenBank Accession No. ABI97347 (100% identity). In order to fulfill Koch's postulates, several G. max cv. Williams 82 were inoculated with the extracts of PeMoV-infected leaf tissue. At 14 days post-inoculation, plants showed systemic mottle symptoms. These symptomatic plants were subjected to RT-PCR, and the nucleotide sequences of the PCR product were found identical to that of the virus in the inoculum. To our knowledge, this is the first report of soybean-infecting PeMoV, a member of the genus Potyvirus in the family Potyviridae, in South Korea.

Reference: (1) R. G. Dietzgen et al. Plant Dis. 85:989, 2001.
First Report of Clover yellow vein virus on Glycine max in Korea
Authors: Shin J.-C. , Kim M.-K. , Kwak H.-R. , Choi H.-S. , Kim J.-S. , Park C.-Y. , Cha B. J.
Published: April 2014

Glycine max (Soybean) is the most important edible crop in Korea. In Korea, eight viruses have been reported to infect soybean, including Alfalfa mosaic virus (AMV), Cowpea mosaic virus (CPMV), Cucumber mosaic virus (CMV), Soybean dwarf virus (SbDV), Soybean mosaic virus (SMV), Soybean yellow common mosaic virus (SYCMV), Soybean yellow mottle virus (SYMMV), and Peanut stunt virus (PSV) (1). In 2012, Glycine max were observed in Daegu, South Korea, with mosaic and mottling symptoms on leaves. Samples with virus-like symptoms (n = 151) were collected from Daegu including legume genetic resource field. Virus particles were filamentous rod shaped, average length 760 nm, and were analyzed by RT-PCR using specific primers for several Potyviruses and previously reported viruses infecting soybean. Only two samples showing mosaic and mottling symptoms were identified as Clover yellow vein virus (ClYVV) based on RT-PCR using primers specific for ClYVV (5′-GTTGGCTTGGTTGACACTGA-3′ and 5′-CTTCGATCATGGATGCACA-3′). The sequences of amplified fragments were 97 to 98% similar with ClYVV. ClYVV is a distinct species in the genus Potyvirus and family Potyviridae. ClYVV is transmitted by several species of aphids and by mechanical inoculation (2). ClYVV was first reported on Gentiana scabra, and the disease has never been reported in soybean fields in Korea. The biological properties and full genome sequence of the selected ClYVV isolate of apparent virus symptoms between two samples were analyzed. The ClYVV isolate was inoculated to local lesion plants, re-isolated from local lesions three times, and propagated in Nicotiana benthamiana, and then named ClYVV-Gm. The ClYVV-Gm induced local lesions on inoculated leaves of N. tabacum cv. Xanthi-nc, Tetragonia expansa, and systemic symptoms on upper leaves of Chenopodium amaranticolor, C. quinoa, and N. clevelandii. The ClYVV-Gm caused mosaic and mottling symptoms on Glycine max cv. Kwangan and Phaseolus vulgaris. The genome of ClYVV-Gm was determined to be 9,584 nucleotides in length (GenBank Accession No. KF975894), and it shared 83% to 97% nucleotide identity with the sequences of 27 previously reported ClYVV isolates including Vicia fava and Pisum sativum. Despite low occurrence of ClYVV in Glycine max, ClYVV has a broad host range including tobacco, weed species, and soybean, which can lead to spreading of the virus. Our results indicate that emergence of ClYVV could become a problem to Leguminosae in Korea. To our knowledge, this is the first biological and molecular report of ClYVV infecting Glycine max in Korea.

References: (1) Y. H. Lee et al. Korea Soybean Digest 29:7, 2012. (2) T. Sasaya et al. Phytopathology 87:1014, 1997.
Quantitative implementation of the endogenous molecular–cellular network hypothesis in hepatocellular carcinoma
Authors: Wang Gaowei , Zhu Xiaomei , Gu Jianren , Ao Ping
Published: April 2014

A quantitative hypothesis for cancer genesis and progression—the endogenous molecular–cellular network hypothesis, intended to include both genetic and epigenetic causes of cancer—has been proposed recently. Using this hypothesis, here we address the molecular basis for maintaining normal liver and hepatocellular carcinoma (HCC), and the potential strategy to cure or relieve HCC. First, we elaborate the basic assumptions of the hypothesis and establish a core working network of HCC according to the hypothesis. Second, we quantify the working network by a nonlinear dynamical system. We show that the working network reproduces the main known features of normal liver and HCC at both the modular and molecular levels. Lastly, the validated working network reveals that (i) specific positive feedback loops are responsible for the maintenance of normal liver and HCC; (ii) inhibiting proliferation and inflammation-related positive feedback loops and simultaneously inducing a liver-specific positive feedback loop is predicated as a potential strategy to cure or relieve HCC; and (iii) the genesis and regression of HCC are asymmetric. In light of the characteristic properties of the nonlinear dynamical system, we demonstrate that positive feedback loops must exist as a simple and general molecular basis for the maintenance of heritable phenotypes, such as normal liver and HCC, and regulating the positive feedback loops directly or indirectly provides potential strategies to cure or relieve HCC.
Modelling chromosome dynamics in mitosis: a historical perspective on models of metaphase and anaphase in eukaryotic cells
Authors: Civelekoglu-Scholey Gul , Cimini Daniela
Published: April 2014

Mitosis is the process by which the genome is segregated to form two identical daughter cells during cell division. The process of cell division is essential to the maintenance of every form of life. However, a detailed quantitative understanding of mitosis has been difficult owing to the complexity of the process. Indeed, it has been long recognized that, because of the complexity of the molecules involved, their dynamics and their properties, the mitotic events that mediate the segregation of the genome into daughter nuclei cannot be fully understood without the contribution of mathematical/quantitative modelling. Here, we provide an overview of mitosis and describe the dynamic and mechanical properties of the mitotic apparatus. We then discuss several quantitative models that emerged in the past decades and made an impact on our understanding of specific aspects of mitosis, including the motility of the chromosomes within the mitotic spindle during metaphase and anaphase, the maintenance of spindle length during metaphase and the switch to spindle elongation that occurs during anaphase.
Using 2k + 2 bubble searches to find SNPs in k-mer graphs
Authors: Younsi Reda , MacLean Dan
Published: April 2014

Single Nucleotide Polymorphism (SNP) discovery is an important preliminary for understanding genetic variation. With current sequencing methods we can sample genomes comprehensively. SNPs are found by aligning sequence reads against longer assembled references. De Bruijn graphs are efficient data structures that can deal with the vast amount of data from modern technologies. Recent work has shown that the topology of these graphs captures enough information to allow the detection and characterisation of genetic variants, offering an alternative to alignment-based methods. Such methods rely on depth-first walks of the graph to identify closing bifurcations. These methods are conservative or generate many false-positive results, particularly when traversing highly inter-connected (complex) regions of the graph or in regions of very high coverage. We devised an algorithm that calls SNPs in converted De Bruijn graphs by enumerating 2k + 2 cycles. We evaluated the accuracy of predicted SNPs by comparison with SNP lists from alignment based methods. We tested accuracy of the SNP calling using sequence data from sixteen ecotypes of Arabidopsis thaliana and found that accuracy was high. We found that SNP calling was even across the genome and genomic feature types. Using sequence based attributes of the graph to train a decision tree allowed us to increase accuracy of SNP calls further. Together these results indicate that our algorithm is capable of finding SNPs accurately in complex sub-graphs and potentially comprehensively from whole genome graphs. The source code for a C++ implementation of our algorithm is available under the GNU Public Licence v3 at: https://github.com/redayounsi/2kplus2
Detecting patterns of species diversification in the presence of both rate shifts and mass extinctions
Authors: Laurent Sacha , Robinson-Rechavi Marc , Salamin Nicolas
Published: April 2014

ABSTRACT

Recent methodological advances are enabling better examination of speciation and extinction processes and patterns. A major open question is the origin of large discrepancies in species number between groups of the same age. Existing frameworks to model this diversity either focus on changes between lineages, neglecting global effects such as mass extinctions, or focus on changes over time which would affect all lineages. Yet it seems probable that both lineages differences and mass extinctions affect the same groups. Here we used simulations to test the performance of two widely used methods, under complex scenarios. We report good performances, although with a tendency to over-predict events when increasing the complexity of the scenario. Overall, we find that lineage shifts are better detected than mass extinctions. This work has significance for assessing the methods currently used for estimating changes in diversification using phylogenies and developing new tests.
Photobody Localization of Phytochrome B Is Tightly Correlated with Prolonged and Light-Dependent Inhibition of Hypocotyl Elongation in the Dark
Authors: Van Buskirk Elise K. , Reddy Amit K. , Nagatani Akira , Chen Meng
Published: April 2014

Photobody localization of Arabidopsis (Arabidopsis thaliana) phytochrome B (phyB) fused to green fluorescent protein (PBG) correlates closely with the photoinhibition of hypocotyl elongation. However, the amino-terminal half of phyB fused to green fluorescent protein (NGB) is hypersensitive to light despite its inability to localize to photobodies. Therefore, the significance of photobodies in regulating hypocotyl growth remains debatable. Accumulating evidence indicates that under diurnal conditions, photoactivated phyB persists into darkness to inhibit hypocotyl elongation. Here, we examine whether photobodies are involved in inhibiting hypocotyl growth in darkness by comparing the PBG and NGB lines after the red light-to-dark transition. Surprisingly, after the transition from 10 μmol m−2 s−1 red light to darkness, PBG inhibits hypocotyl elongation three times longer than NGB. The disassembly of photobodies in PBG hypocotyl nuclei correlates tightly with the accumulation of the growth-promoting transcription factor PHYTOCHROME-INTERACTING FACTOR3 (PIF3). Destabilizing photobodies by either decreasing the light intensity or adding monochromatic far-red light treatment before the light-to-dark transition leads to faster PIF3 accumulation and a dramatic reduction in the capacity for hypocotyl growth inhibition in PBG. In contrast, NGB is defective in PIF3 degradation, and its hypocotyl growth in the dark is nearly unresponsive to changes in light conditions. Together, our results support the model that photobodies are required for the prolonged, light-dependent inhibition of hypocotyl elongation in the dark by repressing PIF3 accumulation and by stabilizing the far-red light-absorbing form of phyB. Our study suggests that photobody localization patterns of phyB could serve as instructive cues that control light-dependent photomorphogenetic responses in the dark.
Hitting the target: fragment screening with acousticin situco-crystallization of proteins plus fragment libraries on pin-mounted data-collection micromeshes
Authors: Yin Xingyu , Scalia Alexander , Leroy Ludmila , Cuttitta Christina M. , Polizzo Gina M. , Ericson Daniel L. , Roessler Christian G. , Campos Olven , Ma Millie Y. , Agarwal Rakhi , Jackimowicz Rick , Allaire Marc , Orville Allen M. , Sweet Robert M. , Soares Alexei S.
Published: April 2014

Acoustic droplet ejection (ADE) is a powerful technology that supports crystallographic applications such as growing, improving and manipulating protein crystals. A fragment-screening strategy is described that uses ADE to co-crystallize proteins with fragment libraries directly on MiTeGen MicroMeshes. Co-crystallization trials can be prepared rapidly and economically. The high speed of specimen preparation and the low consumption of fragment and protein allow the use of individual rather than pooled fragments. The Echo 550 liquid-handling instrument (Labcyte Inc., Sunnyvale, California, USA) generates droplets with accurate trajectories, which allows multiple co-crystallization experiments to be discretely positioned on a single data-collection micromesh. This accuracy also allows all components to be transferred through small apertures. Consequently, the crystallization tray is in equilibrium with the reservoir before, during and after the transfer of protein, precipitant and fragment to the micromesh on which crystallization will occur. This strict control of the specimen environment means that the crystallography experiments remain identical as the working volumes are decreased from the few microlitres level to the few nanolitres level. Using this system, lysozyme, thermolysin, trypsin and stachydrine demethylase crystals were co-crystallized with a small 33-compound mini-library to search for fragment hits. This technology pushes towards a much faster, more automated and more flexible strategy for structure-based drug discovery using as little as 2.5 nl of each major component.
(2E)-2-Benzylidene-N-phenylhydrazinecarboxamide
Authors: Layana S. R. , Sithambaresan M. , Siji V. L. , Sudarsanakumar M. R. , Suma S.
Published: April 2014

The molecule of the title compound, C14H13N3O, adopts anEconformation with respect to the azomethine C=N bond, and is roughly planar, with an r.m.s. deviation of the non-H atoms from the least-squares plane of 0.100 (2) Å and a dihedral angle between the terminal benzene rings of 5.74 (12)°. An intramolecular N—H...N hydrogen bond closes anS(6) ring. In the crystal, molecules are linked by the pairs of N—H...O hydrogen bonds into centrosymmetric dimers. Dimers related by translation along [010] form slanted stacks, the shortest C...C intermolecular distance within the stack being 3.283 (3) Å. Weak C—H...π interactions link the stacks into a three-dimensional structure.
(1E,4E)-1,5-Bis[4-(diethylamino)phenyl]penta-1,4-dien-3-one
Authors: Ruanwas Pumsak , Chantrapromma Suchada , Ghabbour Hazem A. , Fun Hoong-Kun
Published: April 2014

There are two crystallograpically independent molecules in the asymmetric unit of the title bischalcone derivative, C25H32N2O. Both molecules are twisted with a dihedral angle between the two substituted benzene rings of 11.19 (16)° in one molecule and 14.40 (15)° in the other. The central penta-1,4-dien-3-one fragments make dihedral angles of 8.49 (17) and 4.26 (17)° with the two adjacent benzene rings in one molecule, whereas the corresponding values are 8.42 (16) and 6.18 (16)° in the other. In the crystal, molecules are arranged into chains along thec-axis direction. Adjacent chains are inter-linked by weak intermolecular C—H...O interactions. The crystal is further stabilized by C—H...π interactions.
(E)-4-Chloro-2-{[4-(dimethylamino)benzylidene]amino}phenol
Authors: Ghichi Nadir , Benaouida Mohamed Amine , Benosmane Ali , Benboudiaf Ali , Merazig Hocine
Published: April 2014

In the title aromatic Schiff base compound, C15H15ClN2O, the molecule exists in atransconformation with respect to the C=N bond. The dihedral angle between the benzene rings is 14.49 (6)°. In the crystal, weak C—H...π interactions link molecules into supramolecular chains propagated along thea-axis direction.
N-(2-Nitrophenyl)thiophene-2-carboxamide
Authors: Moreno-Fuquen Rodolfo , Azcárate Alexis , Kennedy Alan R.
Published: April 2014

The title compound, C11H8N2O3S, shows two molecules per asymmetric unit, with the dihedral angles between the benzene and thiophene rings of 13.53 (6) and 8.50 (5)° being a notable difference between them. An intramolecular N—H...O hydrogen-bond in each molecule generates anS(6) ring motif. The crystal packing shows no classical hydrogen bonds with the molecules being packed to form weak C—H...O and C—H...S interactions leading toR22(9) andR44(25) rings which are edge-shared, giving layers parallel to (010).