bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural Color Painting by Rubbing Particle Powder
Authors: Park ChooJin , Koh Kunsuk , Jeong Unyong 
Published: February 2015

AbstractStructural colors originate from purely physical structures. Scientists have been inspired to mimic the structures found in nature, the realization of these structures still presents a great challenge. We have recently introduced unidirectional rubbing of a dry particle powder on a rubbery surface as a quick, highly reproducible means to fabricate a single crystal monolayer assembly of particles over an unlimited area. This study extends the particle-rubbing process to a novel fine-art painting, structural color painting (SCP). SCP is based on structural coloring with varying iridescence according to the crystal orientation, as controlled by the rubbing direction. This painting technique can be applied on curved surfaces, which enriches the objects to be painted and helps the painter mimic the structures found in nature. It also allows for quick fabrication of complicated particle-assembly patterns, which enables replication of paintings.
Calcium-dependent protein kinases responsible for the phosphorylation of a bZIP transcription factor FD crucial for the florigen complex formation
Authors: Kawamoto Nozomi , Sasabe Michiko , Endo Motomu , Machida Yasunori , Araki Takashi 
Published: February 2015

AbstractAppropriate timing of flowering is critical for reproductive success and necessarily involves complex genetic regulatory networks. A mobile floral signal, called florigen, is a key molecule in this process and FLOWERING LOCUS T (FT) protein is its major component in Arabidopsis. FT is produced in leaves, but promotes the floral transition in the shoot apex, where it forms a complex with a basic region/leucine-zipper (bZIP) transcription factor, FD. Formation of the florigen complex depends on the supposed phosphorylation of FD; hitherto, however, the responsible protein kinase(s) have not been identified. In this study, we prepared protein extracts from shoot apices of plants around the floral transition and detected a protein kinase activity that phosphorylates a threonine residue at position 282 of FD (FD T282), which is a crucial residue for the complex formation with FT via 14-3-3. The kinase activity was calcium-dependent. Subsequent biochemical, cellular and genetic analyses showed that three calcium-dependent protein kinases (CDPKs) efficiently phosphorylate FD T282. Two of them (CPK6 and CPK33) are expressed in shoot apical meristem and directly interact with FD, suggesting they have redundant functions. The loss of function of one CDPK (CPK33) resulted in a weak but significant late-flowering phenotype.
Enhanced targeted integration mediated by translocated I-SceI during the Agrobacterium mediated transformation of yeast
Authors: Rolloos Martijn , Hooykaas Paul J. J. , van der Zaal Bert J. 
Published: February 2015

AbstractAgrobacterium mediated transformation (AMT) has been embraced by biotechnologists as the technology of choice to introduce or alter genetic traits of plants. However, in plants it is virtually impossible to predetermine the integration site of the transferred T-strand unless one is able to generate a double stranded break (DSB) in the DNA at the site of interest. In this study, we used the model organism Saccharomyces cerevisiae to investigate whether the Agrobacterium mediated translocation of site-specific endonucleases via the type IV secretion system (T4SS), concomitantly with T-DNA transfer is possible and whether this can improve the gene targeting efficiency. In addition to that, the effect of different chromatin states on targeted integration, was investigated. It was found that Agrobacterium mediated translocation of the homing endonuclease I-SceI has a positive effect on the integration of T-DNA via the homologous repair (HR) pathway. Furthermore, we obtained evidence that nucleosome removal has a positive effect on I-SceI facilitated T-DNA integration by HR. Reversely; inducing nucleosome formation at the site of integration removes the positive effect of translocated I-SceI on T-DNA integration.
Constraints on changes in the proton–electron mass ratio using methanol lines
Authors: Kanekar N. , Ubachs W. , Menten K. M. , Bagdonaite J. , Brunthaler A. , Henkel C. , Muller S. , Bethlem H. L. , Daprà M. 
Published: February 2015

Abstract
We report Karl G. Jansky Very Large Array (VLA) absorption spectroscopy in four methanol (CH3OH) lines in the z = 0.885 82 gravitational lens towards PKS1830−211. Three of the four lines have very different sensitivity coefficients Kμ to changes in the proton–electron mass ratio μ; a comparison between the line redshifts thus allows us to test for temporal evolution in μ. We obtain a stringent statistical constraint on changes in μ by comparing the redshifted 12.179 and 60.531 GHz lines, [Δμ/μ] ≤ 1.1 × 10−7 (2σ) over 0 &lt; z ≤ 0.885 82, a factor of ≈2.5 more sensitive than the best earlier results. However, the higher signal-to-noise ratio (by a factor of ≈2) of the VLA spectrum in the 12.179 GHz transition also indicates that this line has a different shape from that of the other three CH3OH lines (at &gt;4σ significance). The sensitivity of the above result, and that of all earlier CH3OH studies, is thus likely to be limited by unknown systematic errors, probably arising due to the frequency-dependent structure of PKS1830−211. A robust result is obtained by combining the three lines at similar frequencies, 48.372, 48.377 and 60.531 GHz, whose line profiles are found to be in good agreement. This yields the 2σ constraint [Δμ/μ] ≲ 4 × 10−7, the most stringent current constraint on changes in μ. We thus find no evidence for changes in the proton–electron mass ratio over a lookback time of ≈7.5 Gyr.
Retrieval-extinction within the memory reconsolidation window does not influence appetitive choice
Authors: Bakkour Akram , Schonberg Tom , Hover Ashleigh M. , Poldrack Russell A. 
Published: February 2015

AbstractInfluencing choice behavior is key to achieving behavioral change. Traditional means to influence choice behavior rely on effortful self control, which is known to be fragile under several circumstances, rendering these methods ineffectual in maintaining any change in behavior over time. Behavioral maintenance efforts are likely more effective over the long term if they target more automatic processes such as attention or memory. Memories are not set in stone and are vulnerable to change and updating under certain circumstances when retrieved. It is possible to target specific memories for updating. In two studies, we sought to update the memory for an appetitive choice by way of reversal learning following retrieval of the targeted choice behavior. We found that targeting memories of a choice behavior for updating shortly after a reminder did not significantly attenuate the renewal of the targeted choice under extinction conditions. Possible explanations and suggested future directions are discussed.
A population density and moment-based approach to modeling domain Ca2+-mediated inactivation of L-type Ca2+channels
Authors: Wang Xiao , Hardcastle Kiah , Weinberg Seth H. , Smith Gregory D. 
Published: February 2015

AbstractWe present a population density and moment-based description of the stochastic dynamics of domain Ca2+-mediated inactivation of L-type Ca2+channels. Our approach accounts for the effect of heterogeneity of local Ca2+signals on whole cell Ca2+currents; however, in contrast with prior work, e.g., Sherman et al. (1990), we do not assume that Ca2+domain formation and collapse are fast compared to channel gating. We demonstrate the population density and moment-based modeling approaches using a 12-state Markov chain model of an L-type Ca2+channel introduced by Greenstein and Winslow (2002). Simulated whole cell voltage clamp responses yield an inactivation function for the whole cell Ca2+current that agrees with the traditional approach when domain dynamics are fast. We analyze the voltage-dependence of Ca2+inactivation that may occur via slow heterogeneous domains. Next, we find that when channel permeability is held constant, Ca2+-mediated inactivation of L-type channel increases as the domain time constant increases, because a slow domain collapse rate leads to increased mean domain [Ca2+] near open channels; conversely, when the maximum domain [Ca2+] is held constant, inactivation decreases as the domain time constant increases. Comparison of simulation results using population densities and moment equations confirms the computational efficiency of the moment-based approach, and enables the validation of two distinct methods of truncating and closing the open system of moment equations. In general, a slow domain time constant requires higher order moment truncation for agreement between moment-based and population density simulations.
Sincell:Bioconductor package for the statistical assessment of cell-state hierarchies from single-cell RNA-seq data
Authors: Juliá Miguel , Telenti Amalio , Rausell Antonio 
Published: February 2015

ABSTRACTSummaryCell differentiation processes are achieved through a continuum of hierarchical intermediate cell-states that might be captured by single-cell RNA seq. Existing computational approaches for the assessment of cell-state hierarchies from single-cell data might be formalized under a general framework composed of i) a metric to assess cell-to-cell similarities (combined or not with a dimensionality reduction step), and ii) a graph-building algorithm (optionally making use of a cells-clustering step).SincellR package implements a methodological toolbox allowing flexible workflows under such framework. Furthermore,Sincellcontributes new algorithms to provide cell-state hierarchies with statistical support while accounting for stochastic factors in single-cell RNA seq. Graphical representations and functional association tests are provided to interpret hierarchies.Sincellfunctionalities are illustrated in a real case study where its ability to discriminate noisy from stable cell-state hierarchies is demonstrated.Availability and implementationSincellis an open-source R/Bioconductor package available athttp://bioconductor.org/packages/3.1/bioc/html/sincell.html. A detailed manual and vignette describing functions and workflows is provided with the package.Contact:antonio.rausell@isb-sib.ch
A unique HMG-box domain of mouse Maelstrom binds structured RNA but not double stranded DNA
Authors: Genzor Pavol , Bortvin Alex 
Published: February 2015

AbstractPiwi-interacting piRNAs are a major and essential class of small RNAs in the animal germ cells with a prominent role in transposon control. Efficient piRNA biogenesis and function require a cohort of proteins conserved throughout the animal kingdom. Here we studied Maelstrom (MAEL), which is essential for piRNA biogenesis and germ cell differentiation in flies and mice. MAEL contains a high mobility group (HMG)-box domain and a Maelstrom-specific domain with a presumptive RNase H-fold. We employed a combination of sequence analyses, structural and biochemical approaches to evaluate and compare nucleic acid binding of mouse MAEL HMG-box to that of canonical HMG-box domain proteins (SRY and HMGB1a). MAEL HMG-box failed to bind double-stranded (ds)DNA but bound to structured RNA. We also identified important roles of a novel cluster of arginine residues in MAEL HMG-box in these interactions. Cumulatively, our results suggest that the MAEL HMG-box domain may contribute to MAEL function in selective processing of retrotransposon RNA into piRNAs. In this regard, a cellular role of MAEL HMG-box domain is reminiscent of that of HMGB1 as a sentinel of immunogenic nucleic acids in the innate immune response.
Community stability and selective extinction during Earth’s greatest mass extinction
Authors: Roopnarine Peter D. , Angielczyk Kenneth D. 
Published: February 2015

AbstractWe modelled the resilience and transient dynamics of terrestrial paleocommunities from the Karoo Basin, South Africa, around the Permian-Triassic mass extinction. Using recently refined biostratigraphic data that suggest two pulses of extinction leading up to the Permian-Triassic boundary, we show that during times of low extinction, paleocommunities were no more stable than randomly assembled communities, but they became stable during the mass extinction. Modelled food webs before and after the mass extinction have lower resilience and less stable transient dynamics compared to random food webs lacking in functional structure but of equal species richness. They are, however, more stable than random food webs of equal richness but with randomized functional structure. In contrast, models become increasingly more resilient and have more stable transient dynamics, relative to the random models, as the mass extinction progressed. The increased stability of the community that resulted from the first pulse of extinction was driven by significant selective extinction against small-bodied amniotes, and significantly greater probabilities of survival of large-bodied amniotes. These results point to a positive relationship between evolved patterns of functional diversity and emergent community dynamics, with observed patterns being more stable than alternative possibilities.SignificanceAnthropogenic impacts on modern ecosystems have no precedents in human history. The fossil record does contain episodes of severe biodiversity crises, but incomplete preservation and low temporal resolution make it difficult to equate fossil data to modern ecological processes. We examined terrestrial paleocommunities from Earth’s most severe mass extinction, the Permian-Triassic mass extinction (PTME), and modelled their dynamic stabilities. We show that during times of low extinction, paleocommunities were no more stable than randomly assembled communities, but they became more stable during the mass extinction. Increased stability resulted mostly from selective extinction and survival based on vertebrate body size. Whether modern communities will behave similarly depends on the similarity between human drivers and those of the PTME.
Natural Selection Shapes the Mosaic Ancestry of theDrosophilaGenetic Reference Panel and theD. melanogasterReference Genome
Authors: Pool John E. 
Published: February 2015

ABSTRACTNorth American populations ofDrosophila melanogasterare thought to derive from both European and African source populations, but despite their importance for genetic research, patterns of admixture along their genomes are essentially undocumented. Here, I infer geographic ancestry along genomes of theDrosophilaGenetic Reference Panel (DGRP) and theD. melanogasterreference genome. Overall, the proportion of African ancestry was estimated to be 20% for the DGRP and 9% for the reference genome. Based on the size of admixture tracts and the approximate timing of admixture, I estimate that the DGRP population underwent roughly 13.9 generations per year. Notably, ancestry levels varied strikingly among genomic regions, with significantly less African introgression on the X chromosome, in regions of high recombination, and at genes involved in specific processes such as circadian rhythm. An important role for natural selection during the admixture process was further supported by a genome-wide signal of ancestry disequilibrium, in that many between-chromosome pairs of loci showed a deficiency of Africa-Europe allele combinations. These results support the hypothesis that admixture between partially genetically isolatedDrosophilapopulations led to natural selection against incompatible genetic variants, and that this process is ongoing. The ancestry blocks inferred here may be relevant for the performance of reference alignment in this species, and may bolster the design and interpretation of many population genetic and association mapping studies.
Discovery and characterization ofAlurepeat sequences via precise local read assembly
Authors: Wildschutte Julia H , Baron Alayna , Diroff Nicolette M , Kidd Jeffrey M 
Published: February 2015

ABSTRACTAluinsertions have contributed to >11% of the human genome and ~30–35Alusubfamilies remain actively mobile, yet the characterization of polymorphicAluinsertions from short-read data remains a challenge. We build on existing computational methods to combineAludetection andde novoassembly of WGS data as a means to reconstruct the full sequence of insertion events from Illumina paired end reads. Comparison with published calls obtained using PacBio long-reads indicates a false discovery rate below 5%, at the cost of reduced sensitivity due to the colocation of reference and non-reference repeats. We generate a highly accurate call set of 1,614 completely assembledAluvariants from 53 samples from the Human Genome Diversity Project panel. We utilize the reconstructed alternative insertion haplotypes to genotype 1,010 fully assembled insertions, obtaining >99% agreement with genotypes obtained by PCR. In our assembled sequences, we find evidence of premature insertion mechanisms and observe 5’ truncation in 16% ofAluYa5 andAluYb8 insertions. The sites of truncation coincide with stem-loop structures and SRP9/14 binding sites in theAluRNA, implicating L1 ORF2p pausing in the generation of 5’ truncations. Additionally, we identified variableAluJ andAluS elements that likely arose due to non-retrotransposition mechanisms.
Entrepreneurship and innovation
Authors: Maritz Alex , Donovan Jerome 
Published: February 2015

Purpose– The purpose of this paper is to explore the synergies, similarities and differences between entrepreneurship and innovation education and training programs, with the aim of challenging the context of such programs.Design/methodology/approach– This study utilises an extensive review of extant literature in the fields of innovation, entrepreneurship and education. The literature, propositions and discussion are intended to provide a bridge between entrepreneurship and innovation education and training programs and seek to address the scientific legitimacy of these education and training disciplines as separate, yet integrated disciplines.Findings– Identifies a need to reconsider the diversity and relationship between innovation and entrepreneurship education and training, primarily from contextual, theoretical, measurement, distinctiveness, content, pedagogical and typology points of view. The range of multiple teaching models and learning processes to embrace in various contexts.Research limitations/implications– The propositions allow for the combination of teaching initiatives in a theory-driven framework and their applicability to specific entrepreneurship and innovation education and training situations.Practical implications– The authors’ contribution identifies the synergies and differences between entrepreneurship education and training programs. The propositions highlight areas of contextualisation and practice-based view application, to adopt specific learning initiatives between constructs.Originality/value– The authors address a gap in the literature regarding the delineation of entrepreneurship and innovation education and training, which has thus far remained sparsely addressed in the education and training literature. The authors provide a practice-based view of propositions, developed for future testing.
The impact of gender perceptions and professional values on women’s careers in nursing
Authors: McIntosh Bryan , McQuaid Ronald , Munro Anne 
Published: February 2015

Purpose
– This purpose of this paper is to engage two enduring sets of assumptions within nursing: firstly, that woman with children should prioritise the care of children; and secondly, that nursing standards require nurses to put their profession above other priorities. Commitment is linked to full-time working which contrasts sharply with the reality for many women with children who need to work part-time and are not able to change or extend working hours

Design/methodology/approach
– This qualitative research involved the use of 32 in-depth interviews with 32 female registered nurses with children and without children. They were employed in “acute” nursing, aged between 25 and 60 years, and in registered grades “D” to “senior nurse manager”. They worked or had worked on a variety of employment conditions, some, but not all, had taken career breaks. The rationale for exclusively selecting women was based on the need to identify and describe organisational, situational and individual factors related to women and the associations and barriers which affected their careers.

Findings
– In a female-dominated profession, we find the profession resisting attempts to make the profession more accessible to women with young children. The career progression of women with children is inhibited, and this is driven in part by a determination to maintain “traditional” employment practices.

Originality/value
– This paper develops Heilman’s argument that gender perceptions, by both males and females, can be biased against women, and these produce gender inequalities in employment. These findings are relevant across many areas of employment, and they are significant in relation to broadening the debate around equal opportunities for women.
Multimedia Super Corridor, Malaysia
Authors: Yigitcanlar Tan , Sarimin Muna 
Published: February 2015

Purpose– This paper aims to investigate and provide insights on knowledge-based urban development (KBUD) in the context of emerging economies. KBUD has been an effective strategy and an opportunity for emerging economies for catching up with the developed economies.Design/methodology/approach– The paper scrutinizes the Multimedia Super Corridor (MSC) of Malaysia by focusing on the planning, development and orchestration of the knowledge corridor.Findings– The paper reveals a number of lessons and insights drawn from the development of MSC as the largest manifestation of the KBUD initiative in Malaysia.Originality/value– The paper provides lessons and recommendations on the planning, development and management of KBUD for emerging economies that are seeking a prosperous development.