bluuebunny/crossref_metadata_2025_split huggingface dataset:
RING E3 mechanism for ubiquitin ligation to a disordered substrate visualized for human anaphase-promoting complex
Authors: Brown Nicholas G. , VanderLinden Ryan , Watson Edmond R. , Qiao Renping , Grace Christy R. R. , Yamaguchi Masaya , Weissmann Florian , Frye Jeremiah J. , Dube Prakash , Ei Cho Shein , Actis Marcelo L. , Rodrigues Patrick , Fujii Naoaki , Peters Jan-Michael , Stark Holger , Schulman Brenda A. 
Published: April 2015

Significance
The anaphase-promoting complex/cyclosome (APC) is a multisubunit RING E3 ubiquitin (Ub) ligase that regulates mitosis, meiosis, and numerous facets of neurobiology by targeting key regulatory proteins for Ub-mediated degradation. Despite great importance, it remains unclear how APC, or most of the other 600 RING E3s in humans, targets Ub to lysines in disordered substrates. Here, we report the structural and molecular basis for substrate ubiquitination by APC and its partner E2, UBCH10. UBCH10 is recruited to APC, activated for ubiquitination, and positioned for substrate targeting through multisite interactions with the APC cullin–RING core. We propose that many RING E3–E2 assemblies work similarly, with multisite interactions establishing specificity, harnessing ubiquitination machineries to accelerate searching for target lysines, and facilitating regulation.
Cis and trans interactions between atlastin molecules during membrane fusion
Authors: Liu Tina Y. , Bian Xin , Romano Fabian B. , Shemesh Tom , Rapoport Tom A. , Hu Junjie 
Published: April 2015

Significance
The membrane-anchored GTPase atlastin (ATL) mediates the fusion of endoplasmic reticulum membranes into a network of tubules and sheets, but the mechanism of ATL function is still poorly understood. Here we show that vesicle fusion is preceded by GTP hydrolysis-dependent tethering, caused by the interaction of ATL molecules in opposing membranes. GTP hydrolysis also dissociates ATL dimers sitting in the same membrane (cis dimers), generating a pool of ATL monomers that can dimerize with molecules on a different (trans) membrane. Multiple rounds of GTP hydrolysis and the cooperation of several ATL molecules in each membrane are required for a successful fusion event. These results lead to a model of ATL-mediated fusion that also may have implications for SNARE-mediated fusion.
The circadian oscillator in
Synechococcus elongatus
controls metabolite partitioning during diurnal growth
Authors: Diamond Spencer , Jun Darae , Rubin Benjamin E. , Golden Susan S. 
Published: April 2015

Significance
Cyanobacteria are increasingly being considered for use in large-scale outdoor production of fuels and industrial chemicals. Cyanobacteria can anticipate daily changes in light availability using an internal circadian clock and rapidly alter their metabolic processes in response to changes light availability. Understanding how signals from the internal circadian clock and external light availability are integrated to control metabolic shifts will be important for engineering cyanobacteria for production in natural outdoor environments. This study has assessed how “knowing” the correct time of day, via the circadian clock, affects metabolic changes when a cyanobacterium goes through a dark-to-light transition. Our data show that the circadian clock plays an important role in inhibiting activation of the oxidative pentose phosphate pathway in the morning.
Clustering of mammalian
Hox
genes with other H3K27me3 targets within an active nuclear domain
Authors: Vieux-Rochas Maxence , Fabre Pierre J. , Leleu Marion , Duboule Denis , Noordermeer Daan 
Published: April 2015

Significance
The development of an embryo from a single fertilized cell is orchestrated by a large set of key regulatory genes whose activities need to be precisely controlled. Proteins from the Polycomb group (PcG) family maintain the inactive state of these genes by modifying the surrounding histone H3 tails. Here we report that these inactive genes contact other PcG-rich regions within otherwise active environments in the cell nucleus, suggesting the presence of repressive microenvironments. PcG positive genes interact independently from neighboring genes, depending on their linear distance and more global chromosome folding characteristics, with only moderate changes during embryonic development.
High dispersion spectroscopy of solar-type superflare stars. II. Stellar rotation, starspots, and chromospheric activities
Authors: Notsu Yuta , Honda Satoshi , Maehara Hiroyuki , Notsu Shota , Shibayama Takuya , Nogami Daisaku , Shibata Kazunari 
Published: April 2015

Abstract
We conducted high dispersion spectroscopic observations of 50 superflare stars with Subaru/HDS. These 50 stars were selected from the solar-type superflare stars that we had discovered from the Kepler data. More than half (34 stars) of these 50 target superflare stars show no evidence of binarity, and we estimated stellar parameters of these 34 stars in our previous study (Notsu et al. 2015, PASJ, 67, 32). According to our previous studies using Kepler data, superflare stars show quasi-periodic brightness variations whose amplitude (0.1%–10%) is much larger than that of the solar brightness variations (0.01%–0.1%) caused by the existence of sunspots on the rotating solar surface. In this study, we investigated whether these quasi-periodic brightness variations of superflare stars are explained by the rotation of a star with fairly large starspots, by using stellar parameters derived in Paper I. First, we confirmed that the value of the projected rotational velocity, v sin i, is consistent with the rotational velocity estimated from the period of the brightness variation. Next, we measured the intensity of Ca ii infrared triplet lines and Hα line, good indicators of the stellar chromospheric activity, and compared them with other stellar properties. The intensity of Ca ii infrared triplet lines indicates that the mean magnetic field strength (〈fB〉) of the target superflare stars can be higher than that of the Sun. A correlation between the amplitude of the brightness variation and the intensity of Ca ii triplet line was found. All the targets expected to have large starspots because of their large amplitude of the brightness variation show high chromospheric activities compared to the Sun. These results support the idea that the brightness variation of superflare stars is due to the rotation with large starspots.
An emergence of a new polarized emission region in blazar Mrk 421 associated with an X-ray flare
Authors: Itoh Ryosuke , Fukazawa Yasushi , Tanaka Yasuyuki T. , Kawabata Koji S. , Takaki Katsutoshi , Hayashi Kazuma , Uemura Makoto , Ui Takahiro , Sasada Mahito , Yamanaka Masayuki , Yoshida Michitoshi 
Published: April 2015

Abstract
We report on long-term multi-wavelength monitoring of blazar Mrk 421 from 2010 to 2011. The source exhibited extreme X-ray flares in 2010. Our research group performed optical photopolarimetric follow-up observations using the Kanata telescope. In 2010, the variability in the X-ray band was significant, while the optical and ultraviolet (UV) flux decreased gradually. Polarization properties also exhibited unique variability in 2010, suggesting the presence of a systematic component of polarization and magnetic field alignment for the emergence of a new polarized emission region. In contrast, in 2011 the variability in the X-ray band was smaller, and the variability in the optical and UV bands was larger, than in 2010. To explore the reasons for these differences, spectral fitting analysis was performed via simple synchrotron self-Compton modeling; the results revealed different behaviors in terms of spectral evolution between these periods, suggesting different variability mechanisms between 2010 and 2011. In 2010, the radiation was likely the result of energy injection into the emitting regions with an aligned magnetic field. In contrast, in 2011 the superposition of different emission regions may have contributed to the low degree of observed polarization. It also implies that high-energy electrons which were not accelerated to ultra-relativistic velocities were injected in 2011.
Novel APC-like properties of human NK cells directly regulate T cell activation
Authors: Hanna Jacob , Mandelboim Ofer 
Published: April 2015

AbstractInitiation of the adaptive immune response is dependent on the priming of naive T cells by APCs. Proteomic analysis of unactivated and activated human NK cell membrane–enriched fractions demonstrated that activated NK cells can efficiently stimulate T cells, since they upregulate MHC class II molecules and multiple ligands for TCR costimulatory molecules. Furthermore, by manipulating antigen administration, we show that NK cells possess multiple independent unique pathways for antigen uptake. These results highlight NK cell–mediated cytotoxicity and specific ligand recognition by cell surface–activating receptors on NK cells as unique mechanisms for antigen capturing and presentation. In addition, we analyzed the T cell–activating potential of human NK cells derived from different clinical conditions, such as inflamed tonsils and noninfected and CMV–infected uterine decidual samples, and from transporter-associated processing antigen 2–deficient patients. This in vivo analysis revealed that proinflammatory, but not immune-suppressive, microenvironmental requirements can selectively dictate upregulation of T cell–activating molecules on NK cells. Taken together, these observations offer new and unexpected insights into the direct interactions between NK and T cells and suggest novel APC-like activating functions for human NK cells.Nonstandard abbreviations usedANKactivated NKdNKdecidual NKHAhemagglutininImDCimmature DCMDCmature DCMFImean fluorescence intensityNCRnatural cytotoxicity receptorTAP2transporter-associated processing antigen 2UaNKunactivated NK
Processes driving nocturnal transpiration and implications for estimating land evapotranspiration
Authors: Resco de Dios Vίctor , Roy Jacques , Ferrio Juan Pedro , Alday Josu G. , Landais Damien , Milcu Alexandru , Gessler Arthur 
Published: April 2015

AbstractEvapotranspiration is a major component of the water cycle, yet only daytime transpiration is currently considered in Earth system and agricultural sciences. This contrasts with physiological studies where 25% or more of water losses have been reported to occur occurring overnight at leaf and plant scales. This gap probably arose from limitations in techniques to measure nocturnal water fluxes at ecosystem scales, a gap we bridge here by using lysimeters under controlled environmental conditions. The magnitude of the nocturnal water losses (12-23% of daytime water losses) in row-crop monocultures of bean (annual herb) and cotton (woody shrub) would be globally an order of magnitude higher than documented responses of global evapotranspiration to climate change (51-98vs.7-8 mm yr−1). Contrary to daytime responses and to conventional wisdom, nocturnal transpiration was not affected by previous radiation loads or carbon uptake, and showed a temporal pattern independent of vapour pressure deficit or temperature, because of endogenous controls on stomatal conductance via circadian regulation. Our results have important implications from large-scale ecosystem modelling to crop production: homeostatic water losses justify simple empirical predictive functions, and circadian controls show a fine-tune control that minimizes water loss while potentially increasing posterior carbon uptake.
Design of a Toolbox of RNA Thermometers
Authors: Sen Shaunak , Apurva Divyansh , Satija Rohit , Siegal Dan , Murray Richard M 
Published: April 2015

AbstractBiomolecular temperature sensors can be used for efficient control of large-volume bioreactors, for spatiotemporal control and imaging of gene expression, as well as to engineer robustness to temperature in biomolecular circuit design. While RNA-based sensors, called ‘thermometers’, have been investigated in natural and synthetic contexts, an important challenge is to design different responses to temperature, differing in sensitivities and thresholds. We address this issue using experimental measurements in cells and in cell-free biomolecular ‘breadboards’ in combination with computations of RNA thermodynamics. We designed a library of RNA thermometers, finding, computationally, that it could contain a multiplicity of responses to temperature. We constructed this library and found a wide range of responses to temperature, ranging from 3.5-fold to over 10-fold in the temperature range 29°C – 37°C. These were largely linear responses with over 10-fold difference in slopes. We correlated the measured responses with computational expectations, finding that while there was no strong correlation in the individual values, the overall trends were similar. These results present a toolbox of RNA-based circuit elements with varying temperature sensitivities.
Non-dichotomous inference using bootstrapped evidence
Authors: Schwarzkopf D. Samuel 
Published: April 2015

AbstractThe problems with classical frequentist statistics have recently received much attention, yet the enthusiasm of researchers to adopt alternatives like Bayesian inference remains modest. Here I present thebootstrapped evidence test, an objective resampling procedure that takes the precision with which both the experimental and null hypothesis can be estimated into account. Simulations and reanalysis of actual experimental data demonstrate that this test minimizes false positives while maintaining sensitivity. It is equally applicable to a wide range of situations and thus minimizes problems arising from analytical flexibility. Critically, it does not dichotomize the results based on an arbitrary significance level but instead quantifies how well the data support either the alternative or the null hypothesis. It is thus particularly useful in situations with considerable uncertainty about the expected effect size. Because it is non-parametric, it is also robust to severe violations of assumptions made by classical statistics.
Improving effect size estimation and statistical power with multi-echo fMRI and its impact on understanding the neural systems supporting mentalizing
Authors: Lombardo Michael V. , Auyeung Bonnie , Holt Rosemary J. , Waldman Jack , Ruigrok Amber N. V. , Mooney Natasha , Bullmore Edward T. , Baron-Cohen Simon , Kundu Prantik 
Published: April 2015

AbstractFunctional magnetic resonance imaging (fMRI) research is routinely criticized for being statistically underpowered due to characteristically small sample sizes and much larger sample sizes are being increasingly recommended. Additionally, various sources of artifact inherent in fMRI data can have detrimental impact on effect size estimates and statistical power. Here we show how specific removal of non-BOLD artifacts can improve effect size estimation and statistical power in task-fMRI contexts, with particular application to the social-cognitive domain of mentalizing/theory of mind. Non-BOLD variability identification and removal is achieved in a biophysical and statistically principled manner by combining multi-echo fMRI acquisition and independent components analysis (ME-ICA). Group-level effect size estimates on two different mentalizing tasks were enhanced by ME-ICA at a median rate of 24% in regions canonically associated with mentalizing, while much more substantial boosts (40-149%) were observed in non-canonical cerebellar areas. This effect size boosting is primarily a consequence of reduction of non-BOLD noise at the subject-level, which then translates into consequent reductions in between-subject variance at the group-level. Power simulations demonstrate that enhanced effect size enables highly-powered studies at traditional sample sizes. Cerebellar effects observed after applying ME-ICA may be unobservable with conventional imaging at traditional sample sizes. Thus, ME-ICA allows for principled design-agnostic non-BOLD artifact removal that can substantially improve effect size estimates and statistical power in task-fMRI contexts. ME-ICA could help issues regarding statistical power and non-BOLD noise and enable potential for novel discovery of aspects of brain organization that are currently under-appreciated and not well understood.
Natural Variation in Epigenetic Pathways Affects the Specification of Female Gamete Precursors in Arabidopsis
Authors: Rodríguez-Leal Daniel , León-Martínez Gloria , Abad-Vivero Ursula , Vielle-Calzada Jean-Philippe 
Published: April 2015

Abstract
In angiosperms, the transition to the female gametophytic phase relies on the specification of premeiotic gamete precursors from sporophytic cells in the ovule. In Arabidopsis thaliana, a single diploid cell is specified as the premeiotic female gamete precursor. Here, we show that ecotypes of Arabidopsis exhibit differences in megasporogenesis leading to phenotypes reminiscent of defects in dominant mutations that epigenetically affect the specification of female gamete precursors. Intraspecific hybridization and polyploidy exacerbate these defects, which segregate quantitatively in F2 populations derived from ecotypic hybrids, suggesting that multiple loci control cell specification at the onset of female meiosis. This variation in cell differentiation is influenced by the activity of ARGONAUTE9 (AGO9) and RNA-DEPENDENT RNA POLYMERASE6 (RDR6), two genes involved in epigenetic silencing that control the specification of female gamete precursors. The pattern of transcriptional regulation and localization of AGO9 varies among ecotypes, and abnormal gamete precursors in ovules defective for RDR6 share identity with ectopic gamete precursors found in selected ecotypes. Our results indicate that differences in the epigenetic control of cell specification lead to natural phenotypic variation during megasporogenesis. We propose that this mechanism could be implicated in the emergence and evolution of the reproductive alternatives that prevail in flowering plants.
Perceived managerial and leadership effectiveness in Colombia
Authors: Torres Luis Eduardo , Ruiz Carlos Enrique , Hamlin Bob , Velez-Calle Andres 
Published: April 2015

Purpose– The purpose of this study was to identify what Colombians perceive as effective and least effective/ineffective managerial behavior.Design/methodology/approach– This study was conducted following a qualitative methodology based on the philosophical assumptions of pragmatism and the “pragmatic approach” (Morgan, 2007). The critical incident technique was used to generate data from a purposive sample of 27 managers and non-managerial employees located in Medellin and Bogota, Colombia.Findings– The results of this study suggest that effective managers in Colombia are those who are supportive, caring, considerate, participative, understanding, communicative and flexible, and are also good problem solvers.Research limitations/implications– This study focused on the perceptions of Colombian managers and non-managerial employees only. Therefore, the description of effective and least effective/ineffective managers in Colombia could be highly value-laden from the national cultural perspective. Hence, it is recommended that further research should be carried out to explore the perceptions of international managers who have frequently interacted or worked with Colombian managers.Originality/value– The results of this study have practical implications for Colombian managers and international managers who manage the Colombian workforce. For Colombian managers, this study provides insight into what is considered effective or least effective/ineffective managerial and leadership behavior. The findings provide useful information on foreign multinational corporations (MNCs) that have operations in Colombia. MNCs can use the results of this study to create effective management development models for their expatriates in Colombia.
2050: New Zealand's sustainable future
Authors: Yeoman Ian , Andrade Amalina , Leguma Elisante , Wolf Natalie , Ezra Peter , Tan Rebecca , McMahon‐Beattie Una 
Published: April 2015

Purpose
The purpose of this paper is to portray the future of tourism in New Zealand based upon a philosophy of sustainability and cultural identity as a response to the present 2025 Tourism Strategy.

Design/methodology/approach
The research deployed a scenario planning methodology resulting in four portraits of the future.

Findings
Environmental issues and global migration are the key issues that will shape the future of New Zealand tourism. In order to address these issues four scenarios were constructed. New Zealand Wonderland portrays a future based upon a grounded international reputation for environmentalism driven by good governance, climate change targets and ecotourism. Indiana Jones and the Search for Cultural Identity position a future driven by rapid growth and unregulated air travel resulting in environmental degradation. A Peaceful Mixture is a balance of socio‐cultural and environmental dimensions of sustainability at the centre of a tourism product shaped upon Maori culture and economic prosperity. The final scenario, New Zealand in Depression, is the worst possible outcome for New Zealand's tourism industry as the three dimensions of economy, community, and environment are not at equilibrium. New Zealand would be over‐polluted with an uncontrolled number of migrants.

Research limitations/implications
The research was a social construction of ten experts’ views on the future of sustainable tourism.

Originality/value
New Zealand's present approach to the future of tourism is shaped by the 2025 Tourism Framework (http://tourism2025.org.nz/). This is derived from a business perspective and a neoliberal political philosophy and it is void of the words ecotourism and sustainability. This paper argues that the present strategy will fail because of community disengagement that proposes a range of alternative directions based upon a political discourse of sustainability and shaped by environmental credentials and cultural identity.
New Zealand's future: the potential for knitting tourism
Authors: Yeoman Ian , McMahon‐Beattie Una 
Published: April 2015

Purpose
The purpose of this paper is to gain an understanding of why the phenomena of knitting is important in society and an explanation of the underlying currents for tourism.

Design/methodology/approach
The paper presents a futurist's observations and reflections.

Findings
Why is knitting making a comeback? Consumers are shutting the door on the world and cocooning thus returning to the world of crafts and hobbies as a way to seek enjoyment. An interest in authenticity and the past as an escape from the present. Single people looking for something to do in an urban world, thus some consumers have turned to knitting. Today, the authors are seeing niche holiday providers offering knitting cruises, knitting escapes and knitting adventures. For New Zealand the home Merrino wool knitting tourism has the potential to be bigger than bungy jumping (some would say).

Originality/value
The trends paper provides an insight of the key trends from a societal perspective of what knitting means and its manifestation as a tourism experience. The value to operators is understanding those trends in context of why the phenomena is occurring.