bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dislocation-free Ge Nano-crystals via Pattern Independent Selective Ge Heteroepitaxy on Si Nano-Tip Wafers
Authors: Niu Gang , Capellini Giovanni , Schubert Markus Andreas , Niermann Tore , Zaumseil Peter , Katzer Jens , Krause Hans-Michael , Skibitzki Oliver , Lehmann Michael , Xie Ya-Hong , von Känel Hans , Schroeder Thomas 
Published: March 2016

AbstractThe integration of dislocation-free Ge nano-islands was realized via selective molecular beam epitaxy on Si nano-tip patterned substrates. The Si-tip wafers feature a rectangular array of nanometer sized Si tips with (001) facet exposed among a SiO2 matrix. These wafers were fabricated by complementary metal-oxide-semiconductor (CMOS) compatible nanotechnology. Calculations based on nucleation theory predict that the selective growth occurs close to thermodynamic equilibrium, where condensation of Ge adatoms on SiO2 is disfavored due to the extremely short re-evaporation time and diffusion length. The growth selectivity is ensured by the desorption-limited growth regime leading to the observed pattern independence, i.e. the absence of loading effect commonly encountered in chemical vapor deposition. The growth condition of high temperature and low deposition rate is responsible for the observed high crystalline quality of the Ge islands which is also associated with negligible Si-Ge intermixing owing to geometric hindrance by the Si nano-tip approach. Single island as well as area-averaged characterization methods demonstrate that Ge islands are dislocation-free and heteroepitaxial strain is fully relaxed. Such well-ordered high quality Ge islands present a step towards the achievement of materials suitable for optical applications.
HoxD expression in the fin-fold compartment of basal gnathostomes and implications for paired appendage evolution
Authors: Tulenko Frank J. , Augustus Gaius J. , Massey James L. , Sims Seth E. , Mazan Sylvie , Davis Marcus C. 
Published: March 2016

AbstractThe role of Homeobox transcription factors during fin and limb development have been the focus of recent work investigating the evolutionary origin of limb-specific morphologies. Here we characterize the expression of HoxD genes, as well as the cluster-associated genes Evx2 and LNP, in the paddlefish Polyodon spathula, a basal ray-finned fish. Our results demonstrate a collinear pattern of nesting in early fin buds that includes HoxD14, a gene previously thought to be isolated from global Hox regulation. We also show that in both Polyodon and the catshark Scyliorhinus canicula (a representative chondrichthyan) late phase HoxD transcripts are present in cells of the fin-fold and co-localize with And1, a component of the dermal skeleton. These new data support an ancestral role for HoxD genes in patterning the fin-folds of jawed vertebrates, and fuel new hypotheses about the evolution of cluster regulation and the potential downstream differentiation outcomes of distinct HoxD-regulated compartments.
Discontinuous nature of the repulsive-to-attractive colloidal glass transition
Authors: van de Laar T. , Higler R. , Schroën K. , Sprakel J. 
Published: March 2016

AbstractIn purely repulsive colloidal systems a glass transition can be reached by increasing the particle volume fraction beyond a certain threshold. The resulting glassy state is governed by configurational cages which confine particles and restrict their motion. A colloidal glass may also be formed by inducing attractive interactions between the particles. When attraction is turned on in a repulsive colloidal glass a re-entrant solidification ensues. Initially, the repulsive glass melts as free volume in the system increases. As the attraction strength is increased further, this weakened configurational glass gives way to an attractive glass in which motion is hindered by the formation of physical bonds between neighboring particles. In this paper, we study the transition from repulsive-to-attractive glasses using three-dimensional imaging at the single-particle level. We show how the onset of cage weakening and bond formation is signalled by subtle changes in local structure. We then demonstrate the discontinuous nature of the solid-solid transition, which is marked by a critical onset at a threshold bonding energy. Finally, we highlight how the interplay between bonding and caging leads to complex and heterogeneous dynamics at the microscale.
Virus infection mediates the effects of elevated CO2 on plants and vectors
Authors: Trębicki Piotr , Vandegeer Rebecca K. , Bosque-Pérez Nilsa A. , Powell Kevin S. , Dader Beatriz , Freeman Angela J. , Yen Alan L. , Fitzgerald Glenn J. , Luck Jo E. 
Published: March 2016

AbstractAtmospheric carbon dioxide (CO2) concentration has increased significantly and is projected to double by 2100. To increase current food production levels, understanding how pests and diseases respond to future climate driven by increasing CO2is imperative. We investigated the effects of elevated CO2(eCO2) on the interactions among wheat (cv. Yitpi),Barley yellow dwarf virusand an important pest and virus vector, the bird cherry-oat aphid (Rhopalosiphum padi), by examining aphid life history, feeding behavior and plant physiology and biochemistry. Our results showed for the first time that virus infection can mediate effects of eCO2on plants and pathogen vectors. Changes in plant N concentration influenced aphid life history and behavior and N concentration was affected by virus infection under eCO2. We observed a reduction in aphid population size and increased feeding damage on noninfected plants under eCO2but no changes to population and feeding on virus-infected plants irrespective of CO2treatment. We expect potentially lower future aphid populations on noninfected plants but no change or increased aphid populations on virus-infected plants therefore subsequent virus spread. Our findings underscore the complexity of interactions between plants, insects and viruses under future climate with implications for plant disease epidemiology and crop production.
Investigation of multilayer planar hybrid plasmonic waveguide and bends
Authors: Sharma P. , Kumar V.D. 
Published: March 2016

Hybrid metal insulator metal plasmonic waveguide has been investigated at 1550 nm wavelength using frequency‐domain electromagnetic solver of computer simulation technology microwave studio. This waveguide overcomes the limitations of conventional plasmonic metal insulator metal waveguide and provides good balance between propagation length and confinement. Propagation length up to 2.5 mm and confinement factor more than 80% have been observed. Waveguide bends such as 90° and S‐shaped, based on the presented waveguide have been examined; these bends exhibit more than 90% transmission efficiency in a confinement area of 40 × 200 nm2. The application of these structures in the design of chip scale integrated circuitry is motivated.
Wearable antenna with tripolarisation diversity for WBAN communications
Authors: Yan S. , Vandenbosch G.A.E. 
Published: March 2016

A wearable antenna with tripolarisation diversity is designed for wireless body area networks (WBANs). The antenna is fabricated with flexible materials. Three polarisations are realised by combining an inductive loaded circular monopolar patch antenna with a microstrip annular ring antenna. Simulated and measured results show that the antenna has sufficient bandwidth for a WBAN. The port isolation reaches 13.5 dB, and the correlation coefficients show a good diversity performance.
Inhibitory effect ofPterocarpus indicusWilld water extract on IgE/Ag-induced mast cell and atopic dermatitis-like mouse models
Authors: Cha Hae-Sim , Kim Wan-Joong , Lee Myung-Hun , Kim Sun-Young , Kim Seo Ho , Lee Kwang-Ho , Kim Tack-Joong 
Published: March 2016

AbstractPterocarpus indicus Willd has been widely used as a traditional medicine to treat edema, cancer, and hyperlipidemia, but its antiallergic properties and underlying mechanisms have not yet been studied. The purpose of this study was to evaluate the antiallergic activity of Pterocarpus indicus Willd water extract (PIW) using activated mast cells and an atopic dermatitis (AD)-like mouse model. PIW decreased IgE/Ag-induced mast cell degranulation and the phosphorylation of Syk and downstream signaling molecules such as PLC-γ, Akt, Erk 1/2, JNK compared to stimulated mast cells. In DNCB-induced AD-like mice, PIW reduced IgE level in serum, as well as AD-associated scratching behavior and skin severity score. These results indicate that PIW inhibits the allergic response by reducing mast cell activation and may have clinical potential as an antiallergic agent for disorders such as AD.
MetaKTSP: a meta-analytic top scoring pair method for robust cross-study validation of omics prediction analysis
Authors: Kim SungHwan , Lin Chien-Wei , Tseng George. C. 
Published: March 2016

AbstractMotivation: Supervised machine learning is widely applied to transcriptomic data to predict disease diagnosis, prognosis or survival. Robust and interpretable classifiers with high accuracy are usually favored for their clinical and translational potential. The top scoring pair (TSP) algorithm is an example that applies a simple rank-based algorithm to identify rank-altered gene pairs for classifier construction. Although many classification methods perform well in cross-validation of single expression profile, the performance usually greatly reduces in cross-study validation (i.e. the prediction model is established in the training study and applied to an independent test study) for all machine learning methods, including TSP. The failure of cross-study validation has largely diminished the potential translational and clinical values of the models. The purpose of this article is to develop a meta-analytic top scoring pair (MetaKTSP) framework that combines multiple transcriptomic studies and generates a robust prediction model applicable to independent test studies.Results: We proposed two frameworks, by averaging TSP scores or by combining P-values from individual studies, to select the top gene pairs for model construction. We applied the proposed methods in simulated data sets and three large-scale real applications in breast cancer, idiopathic pulmonary fibrosis and pan-cancer methylation. The result showed superior performance of cross-study validation accuracy and biomarker selection for the new meta-analytic framework. In conclusion, combining multiple omics data sets in the public domain increases robustness and accuracy of the classification model that will ultimately improve disease understanding and clinical treatment decisions to benefit patients.Availability and Implementation: An R package MetaKTSP is available online. (http://tsenglab.biostat.pitt.edu/software.htm).Contact: ctseng@pitt.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Assortative mating can impede or facilitate fixation of underdominant alleles
Authors: Newberry Mitchell G , McCandlish David M , Plotkin Joshua B 
Published: March 2016

ABSTRACTAlthough underdominant mutations have undoubtedly fixed between divergent species, classical models of population genetics suggest underdominant alleles should be purged quickly, except in small or subdivided populations. Here we study the fixation of underdominant alleles at loci that also influence mate choice, such as loci encoding coloration patterns visible to mates and predators alike. We analyze a mechanistic model of positive assortative mating in which individuals havenchances to sample compatible mates. This one-parameter model naturally spans the two classical extremes of random mating (n= 1) and complete assortment (n→ ∞), and yet it produces a complex form of sexual selection that depends non-monotonically on the number of mating opportunities,n. The resulting interaction between viability selection and sexual selection can either inhibit or facilitate fixation of underdominant alleles, compared to random mating. As the number of mating opportunities increases, underdominant alleles can fix at rates that even approach the neutral substitution rate. This result is counterintuitive because sexual selection and underdominance each suppress rare alleles in this model, and yet in combination they can promote the fixation of rare alleles. This phenomenon constitutes a new mechanism for the fixation of underdominant alleles in large populations, and it illustrates how incorporating life history characteristics can alter the predictions of population-genetic models for evolutionary change.
Establishing elements of a synthetic biology platform for Vaccinia virus production: BioBrick™ design, serum-free virus production and microcarrier-based cultivation of CV-1 cells
Authors: Liu Shuchang , Ruban Ludmila , Wang Yaohe , Zhou Yuhong , Nesbeth Darren N. 
Published: March 2016

AbstractVaccinia virus (VACV) is an established tool for vaccination and is beginning to prove effective as an oncolytic agent. Industrial production of VACV stands to benefit in future from advances made by synthetic biology in genome engineering and standardisation. As a step toward realising these benefits we analysed the Lister Vaccinia virus genome with respect to refactoring options and propose a VACV genome engineering BioBrick™. We then used the CV-1 cell line to produce a conventional recombinant Lister strain VACV, VACVL-15 RFP in a serum-free process. CV-1 cells grown in 5% foetal bovine serum (FBS) Dulbecco’s Modified Eagle Medium (DMEM) were adapted to growth in OptiPRO and VP-SFM brands of serum-free media. Specific growth rates of 0.047 h−1and 0.044 h−1were observed for cells adapted to OptiPRO and VP-SFM respectively, compared to 0.035 h−1in 5% FBS DMEM. Cells adapted to OptiPRO and to 5% FBS DMEM achieved recovery ratios of over 96%, an indication of their robustness to cryopreservation. Cells adapted to VP-SFM showed a recovery ratio of 82%. VACV production in static culture, measured as plaque forming units (PFU) per propagator cell, was 75 PFU/cell for cells in 5% FBS DMEM. VP-SFM and OptiPRO adaptation increased VACV production to 150 PFU/cell and 350 PFU/cell respectively. Boosted PFU/cell from OptiPRO-adapted cells persisted when 5% FBS DMEM or OptiPRO medium was present during the infection step and when titre was measured using cells adapted to 5% FBS DMEM or OptiPRO medium. Finally, OptiPRO-adapted CV-1 cells were successfully cultivated using Cytodex-1 microcarriers to inform future scale up studies.
RNA-guided endonuclease-driven mutagenesis in tobacco followed by efficient fixation of mutated sequences in doubled haploid plants
Authors: Schedel Sindy , Pencs Stefanie , Hensel Göetz , Müller Andrea , Kumlehn Jochen 
Published: March 2016

AbstractBackgroundCustomizable endonucleases are providing an effective tool for genome engineering. The resulting primary transgenic individuals are typically heterozygous and/or chimeric with respect to any mutations induced. To generate genetically fixed mutants, they are conventionally allowed to self-pollinate, a procedure which segregates individuals into mutant heterozygotes/homozygotes and wild types. The chances of recovering homozygous mutants among the progeny depends not only on meiotic segregation but also on the frequency of mutated germline cells in the chimeric mother plant.ResultsRNA-guided endonuclease-mediated mutagenesis was targeted to the green fluorescent protein gene (gfp) harboured by a transgenic tobacco line. Upon retransformation using agfp-specific endonuclease construct, the T0plants were allowed to either self-pollinate, or were propagated via regeneration fromin vitrocultured embryogenic pollen which give rise to haploid/doubled haploid plants or from leaf explants that form plants vegetatively. Single or multiple mutations were detected in 80% of the T0plants. The majority of these mutations proved heritable by each of the three propagation systems used. Regeneration fromin vitrocultured embryogenic pollen allowed for homozygous mutants to be produced more efficiently than via sexual reproduction. The recovery of mutations that were not found among sexually produced progeny was shown to be achievable through vegetative plant propagationin vitro. In addition, a number of mutations not detected in the primary gRNA/Cas9-expressing plants were uncovered in the progeny, irrespective of the mode of propagation.ConclusionRegeneration from embryogenic pollen culture provides a convenient method to rapidly generate a variety of genetically fixed mutants following site-directed mutagenesis. Induced mutations that are not sexually transmitted can be recovered through vegetative plant regeneration from somatic tissue.
The roles of LINEs, LTRs and SINEs in lineage-specific gene family expansions in the human and mouse genomes
Authors: Janoušek Václav , Laukaitis Christina M. , Yanchukov Alexey , Karn Robert C. 
Published: March 2016

ABSTRACTWe explored genome-wide patterns of RT content surrounding lineage-specific gene family expansions in the human and mouse genomes. Our results suggest that the size of a gene family is an important predictor of the RT distribution in close proximity to the family members. The distribution differs considerably between the three most common RT classes (LINEs, LTRs and SINEs). LINEs and LTRs tend to be more abundant around genes of multi-copy gene families, whereas SINEs tend to be depleted around such genes. Detailed analysis of the distribution and diversity of LINEs and LTRs with respect to gene family size suggests that each has a distinct involvement in gene family expansion. LTRs are associated with open chromatin sites surrounding the gene families, supporting their involvement in gene regulation, whereas LINEs may play a structural role, promoting gene duplication. This suggests that gene family expansions, especially in the mouse genome, might undergo two phases, the first is characterized by elevated deposition of LTRs and their utilization in reshaping gene regulatory networks. The second phase is characterized by rapid gene family expansion due to continuous accumulation of LINEs and it appears that, in some instances at least, this could become a runaway process. We provide an example in which this has happened and we present a simulation supporting the possibility of the runaway process. Our observations also suggest that specific differences exist in this gene family expansion process between human and mouse genomes.
Transposable Element Evolution in the AllotetraploidCapsella bursa-pastoris
Authors: Ågren J. Arvid , Huang Hui-Run , Wright Stephen I. 
Published: March 2016

AbstractPremise of the studyShifts in ploidy affect the evolutionary dynamics of genomes in a myriad of ways. Population genetic theory predicts that transposable element (TE) proliferation may follow because the genome wide efficacy of selection should be reduced and the increase in gene copies may mask the deleterious effects of TE insertions. Moreover, in allopolyploids TEs may further accumulate because of hybrid breakdown of TE silencing. However, to date the evidence of TE proliferation following an increase in ploidy is mixed, and the relative importance of relaxed selection vs. silencing breakdown remains unclear.MethodsWe used high-coverage whole genome sequence data to evaluate the abundance, genomic distribution, and population frequencies of TEs in the self-fertilizing recent allotetraploidCapsella bursa-pastoris(Brassicaceae). We then compared theC. bursa-pastorisTE profile with that of its two parental diploid species, outcrossingC. grandifloraand self-fertilizingC. orientalis.Key resultsWe found no evidence thatC. bursa-pastorishas experienced a large genome wide proliferation of TEs relative to its parental species. However, when centromeric regions are excluded, we find evidence of significantly higher abundance of retrotransposons inC. bursa-pastorisalong the gene-rich chromosome arms, compared to C.grandifloraandC. orientalis.ConclusionsThe lack of a genome-wide effect of allopolyploidy on TE abundance, combined with the increases TE abundance in gene-rich regions suggest that relaxed selection rather than hybrid breakdown of host silencing explains the TE accumulation inC. bursa-pastoris
Dynamics and Control of Phloem Loading of Indoleacetic Acid in Seedling Cotyledons ofRicinus CommunisDuring Germination
Authors: Tamas Imre A , Davies Peter J 
Published: March 2016

AbstractDuring seed germination sugars and auxin are produced from stored precursors or conjugates respectively and transported to the seedling axis. To elucidate the mode of travel of IAA into the phloem a solution of [3H]indoleacetic acid (IAA), together with [14C]sucrose, was injected in the endosperm cavity harboring the cotyledons of germinating seedlings ofRicinus communis. Phloem exudate from the cut hypocotyl was collected and the radioactivity recorded. Sucrose loading in the phloem was inhibited at higher IAA levels, and the rate of filling of the transient pool(s) was reduced by IAA. IAA was detected within 10 minutes, with the concentration increasing over 30 min and reaching a steady-state by 60 min. The kinetics indicated that phloem loading of IAA involving both an active, carrier-based, and a passive, diffusion-based component, with IAA traveling along a pathway containing an intermediary pool, possibly the protoplasts of mesophyll cells. Phloem loading of IAA was altered by sucrose, K+and a range of non-specific and IAA-specific analogues and inhibitors in a manner that showed that IAA moves into the phloem from the extra cotyledonary solution by multiple pathways, with a carrier mediated pathway playing a principal role.Summary StatementIndoleacetic acid is transported from the peri-cotyledonary space into the phloem of germinatingRicinusseedlings by both trans-membrane carriers and diffusive pathways, with the cells of the cotyledons forming an intermediate reservoir.
A day in the life of a peer support worker: endings
Authors: Watson Emma 
Published: March 2016

Purpose
– The purpose of this paper is to describe the experiences of a day in the life of a peer support worker based within an NHS trust and to use these experiences as a basis for reflection on key issues in recovery focused practice and peer support.

Design/methodology/approach
– A reflective approach is used to consider the experience of ending peer support relationships and the emotion which this creates for both parties.

Findings
– Reflections are offered relating to boundaires, grieving and the experience of endings within peer support and other contexts.

Originality/value
– As a narrative account of the experience of a peer support worker, this paper adds to the small number of reflective pieces in this area.