bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Proteolytic Landscape of an Arabidopsis Separase-Deficient Mutant Reveals Novel Substrates Associated With Plant Development
Authors: Liu Chen , Stael Simon , Gevaert Kris , Van Breusegem Frank , Bozhkov Peter V , Moschou Panagiotis N 
Published: May 2017

AbstractDigestive proteolysis executed by the proteasome plays an important role in plant development. Yet, the role of limited proteolysis in this process is still obscured due to the absence of studies. Previously, we showed that limited proteolysis by the caspase-related protease separase (EXTRA SPINDLE POLES [ESP]) modulates development in plants through the cleavage of unknown substrates. Here we used a modified version of the positional proteomics method COmbined FRActional DIagonal Chromatography (COFRADIC) to survey the proteolytic landscape of wild-type and separase mutantRADIALLY SWOLLEN 4(rsw4) root tip cells, as an attempt to identify targets of separase. We have discovered that proteins involved in the establishment of pH homeostasis and sensing, and lipid signalling in wild-type cells, suggesting novel potential roles for separase. We also observed significant accumulation of the protease PRX34 inrsw4which negatively impacts growth. Furthermore, we observed an increased acetylation of N-termini ofrsw4proteins which usually comprise degrons identified by the ubiquitin-proteasome system, suggesting that separase intersects with additional proteolytic networks. Our results hint to potential pathways by which separase could regulate development suggesting also novel proteolytic functions.
Image Memorability in the Eye of the Beholder: Tracking the Decay of Visual Scene Representations
Authors: Võ Melissa Le-Hoa , Bylinskii Zoya , Oliva Aude 
Published: May 2017

ABSTRACTSome images stick in your mind for days or even years, while others seem to vanish quickly from memory. We tested whether differences in image memorability 1) are already evident immediately after encoding, 2) produce different rates of forgetting, and 3) whether the retrieval of images with different memorability scores affords differential degrees of cognitive load, mirrored by graded pupillary and blink rate responses. We monitored participants’ eye activity while they viewed a sequence of >1200 images in a repetition detection paradigm. 240 target images from 3 non-overlapping memorability classes were repeated at 4 different lags. Overall, performance decreased log-linearly with time. Differences in memorability were already visible at the shortest lag (~ 20 sec) and became more pronounced as time passed on. The rate of forgetting was steepest for low memorable images. We found that pupils dilated significantly more to correctly identified targets than correctly rejected distractors. Importantly, this “pupil old/new effect” increased with increasing number of lags and decreasing image memorability. A similar modulation of blink rates corroborated these findings. These results suggest that during memory retrieval of scenes, image inherent characteristics pose differential degrees of cognitive load on observers as seen in their eyes.
Cancer progression models and fitness landscapes: a many-to-many relationship
Authors: Diaz-Uriarte Ramon 
Published: May 2017

AbstractThe identification of constraints, due to gene interactions, in the order of accumulation of mutations during cancer progression can allow us to single out therapeutic targets. Cancer progression models (CPMs) use genotype frequency data from cross-sectional samples to try to identify these constraints, and return Directed Acyclic Graphs (DAGs) of genes. On the other hand, fitness landscapes, which map genotypes to fitness, contain all possible paths of tumor progression. Thus, we expect a correspondence between DAGs from CPMs and the fitness landscapes where evolution happened. But many fitness landscapes —e.g., those with reciprocal sign epistasis— cannot be represented by CPMs. Using simulated data under 500 fitness landscapes, I show that CPMs’ performance (prediction of genotypes that can exist) degrades with reciprocal sign epistasis. There is large variability in the DAGs inferred from each landscape, which is also affected by mutation rate, detection regime, and fitness landscape features, in ways that depend on CPM method. And the same DAG is often observed in very different landscapes, which differ in more than 50% of their accessible genotypes. Using a pancreatic data set, I show that this many-to-many relationship affects the analysis of empirical data. Fitness landscapes that are widely different from each other can, when evolutionary processes run repeatedly on them, both produce data similar to the empirically observed one, and lead to DAGs that are very different among themselves. Because reciprocal sign epistasis can be common in cancer, these results question the use and interpretation of CPMs.
Coordinated shifts in allocation among reproductive tissues across 14 coexisting plant species
Authors: Wenk E. H. , Abramowicz K. , Westoby M. , Falster D. S. 
Published: May 2017

AbstractPlant species differ in the amounts of energy allocated to different reproductive tissues, driving differences in their ecology and energy flows within ecosystems. While it is widely agreed that energy allocation is key to reproductive outcomes, few studies have estimated how reproductive effort (RE) is partitioned among different pools, for multiple species in a community. In plants, RE can be partitioned in several meaningful ways: seed versus non-seed tissues; into flowers that form seeds and those that fail to develop; into pre-versus post-pollination tissues, and into successful versus aborted ovules. Evolutionary theory suggests several hypotheses about how these tissues should be coordinated across species. To quantify variation in allocation to different reproductive tissues, we collected detailed RE measurements for a year from 14 perennial species in a recurrent-fire coastal heath community in eastern Australia. Overall we found that total accessory costs – the proportion of RE not directly invested in provisioning the seed – were very large, varying from 95.8% to 99.8% across the study species. These results suggest that studies using seed or fruit production as measures of RE may underestimate it by 10-to 500-fold. We propose a suitable alternative that well-approximates true RE. When comparing species, we found strong support for three evolutionary trade-offs that are predicted to arise when a given energy pool is divided into different tissue masses and counts across species: 1) between successful pollen-attraction costs and mature ovule count, 2) between total reproductive costs and seed count, and 3) between seedset and relative investment in pollen-attraction costs. As a result of these trade-offs, species were also predicted to show coordinated shifts in the amounts invested in floral construction, in seedset and seed size. These shifts in investment were indeed observed, with the amount allocated to discarded tissues increasing with seed size and the amount allocated to pollen-attraction decreasing with seed size. It is already well-established that the seed size axis aligns with the colonization-competition life history spectrum; here we show that relative construction costs of pollen-attraction versus provisioning tissues and seedset are also part of this trajectory, expanding our understanding of the relatives sizes of floral and fruiting structures observed across angiosperms.
Stratification of TAD boundaries identified in reproducible Hi-C contact matrices reveals preferential insulation of super-enhancers by strong boundaries
Authors: Gong Yixiao , Lazaris Charalampos , Sakellaropoulos Theodore , Lozano Aurelie , Kambadur Prabhanjan , Ntziachristos Panagiotis , Aifantis Iannis , Tsirigos Aristotelis 
Published: May 2017

ABSTRACTThe metazoan genome is compartmentalized in megabase-scale areas of highly interacting chromatin known as topologically associating domains (TADs), typically identified by computational analyses of Hi-C sequencing data. TADs are demarcated by boundaries that are largely conserved across cell types and even across species, although, increasing evidence suggests that the seemingly invariant TAD boundaries may exhibit plasticity and their insulating strength can vary. However, a genome-wide characterization of TAD boundary strength in mammals is still lacking. A systematic classification and characterization of TAD boundaries may generate new insights into their function. In this study, we first use fused two-dimensional lasso as a machine learning method to improve Hi-C contact matrix reproducibility, and, subsequently, we categorize TAD boundaries based on their insulation score. We demonstrate that higher TAD boundary insulation scores are associated with elevated CTCF levels and that they may differ across cell types. Intriguingly, we observe that super-enhancer elements are preferentially insulated by strong boundaries, i.e. boundaries of higher insulation score. Furthermore, we perform a pan-cancer analysis to demonstrate that strong TAD boundaries and super-enhancer elements are frequently co-duplicated in cancer patients. Taken together, our findings suggest that super-enhancers insulated by strong TAD boundaries may be exploited, as a functional unit, by cancer cells to promote oncogenesis.
Natural mismatch repair mutations mediate phenotypic diversity and drug resistance inCryptococcus deuterogattii
Authors: Billmyre R. Blake , Clancey Shelly Applen , Heitman Joseph 
Published: May 2017

AbstractPathogenic microbes confront a constant evolutionary conflict between the pressure to maintain genome stability and the need to adapt to mounting external stresses. Prokaryotes often respond with elevated mutation rates, but to date little evidence exists of stable eukaryotic hypermutators in nature. Whole genome resequencing of the human fungal pathogenCryptococcus deuterogattiiidentified an outbreak lineage characterized by a nonsense mutation inMSH2. This defect in mismatch repair results in a moderate mutation rate increase in typical genes, and a larger increase in genes containing homopolymer runs. This allows facile inactivation of genes with coding homopolymer runs includingFRR1, which encodes the target of the immunosuppresive antifungal drugs FK506 and rapamycin. Our study identifies a eukaryotic hypermutator lineage spread over two continents and suggests that pathogenic eukaryotic microbes may experience similar selection pressures on mutation rate as bacterial pathogens, particularly during long periods of clonal growth or while expanding into new environments.
Genome-wide SNP discovery in field and laboratory colonies of AustralianPlutellaspecies
Authors: Perry K.D. , Pederson S.M. , Baxter S.W. 
Published: May 2017

ABSTRACTUnderstanding dispersal and gene flow is an important focus of evolutionary biology, conservation biology and pest management. The diamondback moth,Plutella xylostella, is a worldwide pest ofBrassicavegetable and oilseed cropping systems. This insect has high dispersal ability, which has important consequences for population dynamics and the potential spread of insecticide resistance genes. Population genetic studies of the diamondback moth have found little evidence of population structure, suggesting that frequent intermixing occurs within regions, however the patterns of local and regional dispersal remain to be identified. For this and many other pest species, understanding dispersal is crucial for developing integrated management tactics such as forecasting systems and insecticide resistance management plans. In recent years, next generation sequencing (NGS) methods have provided previously unparalleled resolution for population genetic studies in a wide range of species. Here, we assessed the potential of NGS-derived molecular markers to provide new insights about population structure in the diamondback moth. We use restriction-site-associated DNA sequencing (RAD-Seq) to discover hundreds to thousands of single nucleotide polymorphism (SNP) markers in nine field and laboratory-reared populations collected from Australia. Genotypic data from RAD-Seq markers identified a cryptic species,P. australiana, among individuals collected from a wild host,Diplotaxissp., indicating strong divergence in the nuclear genomes of two AustralianPlutellalineages. Significant genetic differentiation was detected among populations ofP. xylostellaused in our study, however this could be explained by reduced heterozogosity and genetic drift in laboratory-reared populations founded by relatively few individuals. This study demonstrates that RAD-Seq is a powerful method for generating SNP markers for population genetic studies in this species.
The peach RGF/GLV signalling peptide pCTG134 is involved in a regulatory circuit that sustains auxin and ethylene actions
Authors: Busatto Nicola , Salvagnin Umberto , Resentini Francesca , Quaresimin Silvia , Navazio Lorella , Marin Oriano , Pellegrini Maria , Costa Fabrizio , Mierke Dale F. , Trainotti Livio 
Published: May 2017

AbstractPeach is a climacteric species whose ripening is regulated by the plant hormone ethylene. A crosstalk mechanism with auxin is necessary to support climacteric ethylene synthesis. The homeostasis control of auxin is regulated also by the activity of peptide hormones (PHs), acting both as short and long distant ligands. In this work, we investigated the role ofCTG134, a peach gene encoding a GOLVEN-like PH isolated in mesocarp at the onset of ripening.In peach fruit,CTG134was expressed during the climacteric transition and its mRNA level was induced by auxin and 1-methylcyclopropene (1-MCP) treatments, whereas it was minimally affected by ethylene. To better elucidate its function,CTG134was overexpressed inArabidopsisand tobacco, which showed abnormal root hair growth, similar to wild-type plants treated with a synthetic form of the peptide. Molecular surveys demonstrated an impaired hormonal crosstalk, resulting in a re-modulated expression of a set of genes involved in both ethylene and auxin domains. In addition, the promoter of pCTG134 fused with GUS reporter highlighted gene activity in plant organs in which the auxin-ethylene interplay is known to occur. These data support the role of pCTG134 as mediator in an auxin-ethylene regulatory circuit.HighlightThe role of the peach RGF/GLV peptide during root hair formation inArabidopsisand tobacco supports its involvement in a cross-hormonal auxin-ethylene regulatory circuit.
Cross-cultural effects on ensemble coding of emotion in facial crowds
Authors: Im Hee Yeon , Chong Sang Chul , Sun Jisoo , Steiner Troy G. , Albohn Daniel N. , Adams Reginald B. , Kveraga Kestutis 
Published: May 2017

AbstractIn many social situations, we make a snap judgment about crowds of people relying on their overall mood (termed “crowd emotion”). Although reading crowd emotion is critical for interpersonal dynamics, the sociocultural aspects of this process have not been explored. The current study examined how culture modulates the processing of crowd emotion in Korean and American observers. Korean and American participants were briefly presented with two groups of faces that were individually varying in emotional expressions and asked to choose which group between the two they would rather avoid. We found that Korean participants were more accurate than American participants overall, in line with the framework on cultural viewpoints: Holistic versus analytic processing in East Asians versus Westerners. Moreover, we found a speed advantage for other-race crowds in both cultural groups. Finally, we found different hemispheric lateralization patterns: American participants were more accurate for angry crowds presented in the left visual field and happy crowds presented in the right visual field, replicating previous studies, whereas Korean participants did not show an interaction between emotional valence and visual field. This work suggests that culture plays a role in modulating our crowd emotion perception of groups of faces and responses to them.
A kinetically-driven free exchange mechanism of EmrE antiport sacrifices coupling efficiency in favor of promiscuity
Authors: Robinson Anne E. , Thomas Nathan E. , Morrison Emma A. , Balthazor Bryan , Henzler-Wildman Katherine A. 
Published: May 2017

ABSTRACTEmrE is a small multidrug resistance transporter found inE. colithat confers resistance to toxic polyaromatic cations due to its proton-coupled antiport of these substrates. Here we show that EmrE breaks the rules generally deemed essential for coupled antiport. NMR spectra reveal that EmrE can simultaneously bind and cotransport proton and drug. The functional consequence of this finding is an exceptionally promiscuous transporter: Not only can EmrE export diverse drug substrates, it can couple antiport of a drug to either one or two protons, performing both electrogenic and electroneutral transport of a single substrate. We present a new kinetically-driven free exchange model for EmrE antiport that is consistent with these results and recapitulates ΔpH-driven concentrative drug uptake. Our results suggest that EmrE sacrifices coupling efficiency for initial transport speed and multidrug specificity.SIGNIFICANCEEmrE facilitatesE. colimultidrug resistance by coupling drug efflux to proton import. This antiport mechanism has been thought to occur via a pure exchange model which achieves coupled antiport by restricting when the single binding pocket can alternate access between opposite sides of the membrane. We test this model using NMR titrations and transport assays and find it cannot account for EmrE antiport activity. We propose a new kinetically-driven free exchange model of antiport with fewer restrictions that better accounts for the highly promiscuous nature of EmrE drug efflux. This model expands our understanding of coupled antiport and has implications for transporter design and drug development.
Many si/shRNAs can kill cancer cells by targeting multiple survival genes through an off-target mechanism
Authors: Putzbach William , Gao Quan Q. , Patel Monal , van Dongen Stijn , Haluck-Kangas Ashley , Sarshad Aishe A. , Bartom Elizabeth , Kim Kwang-Youn A. , Scholtens Denise M. , Hafner Markus , Zhao Jonathan C. , Murmann Andrea E. , Peter Marcus E. 
Published: May 2017

AbstractOver 80% of multiple tested siRNAs and shRNAs targeting CD95 or CD95 ligand (CD95L) induce a form of cell death characterized by simultaneous activation of multiple cell death pathways preferentially killing transformed and cancer stem cells. We now show these si/shRNAs kill cancer cells through canonical RNAi by targeting the 3’UTR of critical survival genes in a unique form of off-target effect we call DISE (death induced by survival gene elimination). Drosha and Dicer deficient cells, devoid of most miRNAs, are hypersensitive to DISE, suggesting cellular miRNAs protect cells from this form of cell death. By testing 4666 shRNAs derived from the CD95 and CD95L mRNA sequences and an unrelated control gene, Venus, we have identified many toxic sequences - most of them located in the open reading frame of CD95L. We propose that using specific toxic RNAi-active sequences present in the genome can kill cancer cells.
Establishment path and management innovation of mutually beneficial nonprofit organization (MBNPO)
Authors: Shin Kwang-yong , Ge Fa-quan , Qin Peng-fei 
Published: May 2017

PurposeResearch about the modern mutually beneficial nonprofit organizations (MBNPOs) has great value because of the increasingly important role that the MBNPO plays in society. The establishment and management of MBNPOs are critical for its development.Design/methodology/approachIntegrated marketing communications (IMC) theory is applied to the research on establishment and management innovation. The establishment of MBNPOs needs four sequential steps: identifying the target group, providing services to meet the demand of stakeholders, designing appropriate communication tactics and deploying proper organizational structure to accomplish efficient communication.FindingsThree types of approach enable traditional enterprises to transform into MBNPOs: product innovation, operational innovation and synergetic development. The application of IMC theory accomplishes management innovation of MBNPOs in three aspects: leading market-orientation specific to stakeholder-orientation, making management innovation systematic in MBNPOs and clarifying targets of management innovation in MBNPOs.Originality/valueThis is one of the first examinations of establishment path and management innovation of MBNPO based on IMC theory.
Nation image and its dynamic changes in Wikipedia
Authors: Lee Youngwhan , Chun Heuiju 
Published: May 2017

Purpose
In this volatile and increasingly fast-revolving world, it has become crucially important to monitor, measure and manage nation image and its dynamic changes in real time. However, few studies have been conducted on a model to measure the image and/or its changes. The purpose of this paper is to find an economically affordable methodology to measure nation image and its changes online in real time.

Design/methodology/approach
The study took an approach to build dynamic ontology that may reflect to change nation image in real-time. With it, the authors attempted to measure nation image in real time.

Findings
Among many social media, the authors found that Wikipedia is particularly suitable for the purpose of measuring nation image. An ontology of nation image was built from the keywords collected from the pages directly related to the big three exporting countries in East Asia, i.e. Korea, Japan and China. The click views on the pages of the countries in two different language editions of Wikipedia, Vietnamese and Indonesian were counted.

Originality/value
The study confirms the objective: the data from a social media service, Wikipedia, may work very well as an economically affordable real-time supplement to offline nation image indices that are currently used.
The contribution of environmental regulation to technological innovation and quality competitiveness
Authors: Cao Yuhong , You Jianxin 
Published: May 2017

Purpose
This paper aims to explore the relationship between environmental regulation, technological innovation and manufacturing quality competitiveness to provide some references for emission reduction activities and improvements in manufacturing quality competitiveness to achieve environmental protection targets and economic development as part of a win–win situation.

Design/methodology/approach
Based on the structure-behavior-performance paradigm and Grabowski’s research, a new empirical model was provided. The software, EViews 6.0, was used for econometric analysis. Regression analysis was adopted to explore the three indicators’ relationships.

Findings
First, environmental regulation can promote technological innovation effectively. Second, compared with wasted gas and wasted solids, investment in wasted water control promotes Chinese technological innovation most. Third, the impact of research and development investment, induced by environmental regulation, on manufacturing quality competitiveness is greater than that induced by non-environmental regulation. Fourth, the impact of lagged two-phase environmental regulation on manufacturing quality competitiveness is similar to that of lagged one-phase regulation.

Practical implications
The issue that Chinese manufacturing is facing is how to manage the trade-off between pollution control investment and improved quality competitiveness. This study enables managers to understand how to better implement environmental regulation initiatives while achieving environmental protection and quality competitiveness as part of a win–win situation.

Originality/value
This paper analyzes the relationships between environmental regulation, technological innovation and manufacturing quality competitiveness for the first time and provides the basic argument for integrating Chinese environmental regulation with quality competitiveness to reveal the uniqueness of the circumstances determining China’s economic development.