bluuebunny/crossref_metadata_2025_split huggingface dataset:
Depletion Calculations Based on Perturbations. Application to the Study of a Rep-Like Assembly at Beginning of Cycle with TRIPOLI-4®.
Authors: Dieudonne Cyril , Dumonteil Eric , Malvagi Fausto , Diop Cheikh M’Backé 
Published: June 2014

For several years, Monte Carlo burnup/depletion codes have appeared, which couple Monte Carlo codes to simulate the neutron transport to deterministic methods, which handle the medium depletion due to the neutron flux. Solving Boltzmann and Bateman equations in such a way allows to track fine 3-dimensional effects and to get rid of multi-group hypotheses done by deterministic solvers. The counterpart is the prohibitive calculation time due to the Monte Carlo solver called at each time step.In this paper we present a methodology to avoid the repetitive and time-expensive Monte Carlo simulations, and to replace them by perturbation calculations: indeed the different burnup steps may be seen as perturbations of the isotopic concentration of an initial Monte Carlo simulation. In a first time we will present this method, and provide details on the perturbative technique used, namely the correlated sampling. In a second time the implementation of this method in the TRIPOLI-4®code will be discussed, as well as the precise calculation scheme a meme to bring important speed-up of the depletion calculation. Finally, this technique will be used to calculate the depletion of a REP-like assembly, studied at beginning of its cycle. After having validated the method with a reference calculation we will show that it can speed-up by nearly an order of magnitude standard Monte-Carlo depletion codes.
Calculation of ex-core physical quantities using the 3D importance functions
Authors: Trakas Christos , De Laubiere Xavier 
Published: June 2014

Diverse physical quantities are calculated in engineering studies with penalizing hypotheses to assure the required operation margins for each reactor. Today, these physical quantities are obtained by direct calculations from deterministic or Monte Carlo codes. The related states are critical or sub-critical.
The current physical quantities are for example: the SRD counting rates (source range detector) in the sub-critical state, the IRD (intermediary range detector) and PRD (power range detector) counting rates (neutron particles only), the deposited energy in the reflector (neutron + photon particles), the fluence or the DPA (displacement per atom) in the reactor vessel (neutron particles only).
The reliability of the proposed methodology is tested in the EPR reactor. The main advantage of the new methodology is the simplicity to obtain the physical quantities by an easy matrix calculation importance linked to nuclear power sources for all the cycles of the reactor. This method also allows to by-pass the direct calculations of the physical quantity of irradiated cores by Monte Carlo Codes, these calculations being impossible today (too many isotopic concentrations / MCNP5 limit).
This paper presents the first feasibility study for the physical quantities calculation outside of the core by the importance method instead of the direct calculations used currently by AREVA.
Withdrawn article – Performance Assessment of the Commercial CFD Software for the Prediction of the Reactor Internal Flow
Authors: Hee Lee Gong , Seok Bang Young , Woong Woo Sweng , Kim Do Hyeong , Ku Kang Min 
Published: June 2014

This paper published in SNA + MC 2013 has been formally withdrawn. It should not be cited or referred to in the future.
A corrected version replaces this article, see SNA + MC 2013, 05128 (2014), DOI: 10.1051/snamc/201405128.
Request approved by the Editors and the Publisher on July 22, 2014.
Usage of Simulated Response Matrices for the Scintillation Spectra Unfolding
Authors: Klusoň J. , Urban T. 
Published: June 2014

Response of the scintillation spectrometer to incident photons has complex character due to complex character of photon interaction processes. Experimental spectrum thus provide qualitative information given by the identifiable peaks positions, while extraction of the full, quantitative information (i.e. photon flux energy distribution) require spectra unfolding based on the spectrometer response (represented by the response matrix) knowledge. As experimental determination of response matrix is difficult or impossible in most cases, the Monte Carlo simulation is the proved solution. Usage of the unfolding for experimental spectra processing enable to determine dosimetric characteristics of the incident photon fields and/or characteristics of the sources, creating those photon fields.
The response matrices for scintillation spectrometers with different detectors (commonly used NaI, BGO and new LaBr) were calculated using Monte Carlo method. The response to the internal activity of the LaBr detector was also simulated and considered in spectra processing. Calculated matrices were used for unfolding of the experimental spectra from different applications to determine desired dosimetric quantities. Typical applications are environmental monitoring, monitoring of the working environment, accidental monitoring and contamination measurement, etc. Method is suitable also for the airborne monitoring or security applications. Results for individual detection systems are compared and discussed with aim to analyze potential advantages of the LaBr detector for considered applications.
Development of Safety Analysis Code System of Beam Transport and Core for Accelerator Driven System
Authors: Aizawa Naoto , Iwasaki Tomohiko 
Published: June 2014

Safety analysis code system of beam transport and core for accelerator driven system (ADS) is developed for the analyses of beam transients such as the change of the shape and position of incident beam. The code system consists of the beam transport analysis part and the core analysis part. TRACE 3-D is employed in the beam transport analysis part, and the shape and incident position of beam at the target are calculated. In the core analysis part, the neutronics, thermo-hydraulics and cladding failure analyses are performed by the use of ADS dynamic calculation code ADSE on the basis of the external source database calculated by PHITS and the cross section database calculated by SRAC, and the programs of the cladding failure analysis for thermoelastic and creep.
By the use of the code system, beam transient analyses are performed for the ADS proposed by Japan Atomic Energy Agency. As a result, the rapid increase of the cladding temperature happens and the plastic deformation is caused in several seconds. In addition, the cladding is evaluated to be failed by creep within a hundred seconds. These results have shown that the beam transients have caused a cladding failure.
An alcohol-sensing site in the calcium- and voltage-gated, large conductance potassium (BK) channel
Authors: Bukiya Anna N. , Kuntamallappanavar Guruprasad , Edwards Justin , Singh Aditya K. , Shivakumar Bangalore , Dopico Alex M. 
Published: June 2014

Significance
Alcohol (ethanol) is one of the most widely consumed psychoactive agents. Ethanol’s targets in the body include voltage/calcium-gated, large conductance potassium (BK) channels. Here we identified and characterized for the first time an alcohol-sensing site in BK channel-forming proteins. Our discovery opens new ground for rational design of tools to counteract the effects of ethanol intoxication that are mediated by BK channels. We anticipate that genetic or epigenetic modifications of the BK channel ethanol-recognition site could explain differential sensitivity to ethanol. Finally, since individuals with low sensitivity to ethanol are prone to developing heavy drinking habits, genetic, epigenetic or other mechanisms acting at the newly identified BK channel ethanol-recognition site might be considered as potential predictors for developing alcohol preference.
Sources and sinks of carbonyl sulfide in an agricultural field in the Southern Great Plains
Authors: Maseyk Kadmiel , Berry Joseph A. , Billesbach Dave , Campbell John Elliott , Torn Margaret S. , Zahniser Mark , Seibt Ulli 
Published: June 2014

SignificanceWe report observations of ecosystem carbonyl sulfide (COS) and CO2fluxes that resolve key gaps in an emerging framework for using concurrent COS and CO2measurements to quantify terrestrial gross primary productivity. We show for the first time that leaf relative uptake ratios of COS and CO2during photosynthesis measured in the field vary systematically with light. We established that nocturnal COS uptake by vegetation is a significant component of daily net ecosystem COS fluxes. We also quantified a close correlation of soil COS fluxes with soil temperature. The small soil contribution to net ecosystem fluxes confirms that vegetation uptake is the dominant ecosystem COS flux in the growing season, a prerequisite for COS-based flux partitioning approaches.
Oxytocin promotes social bonding in dogs
Authors: Romero Teresa , Nagasawa Miho , Mogi Kazutaka , Hasegawa Toshikazu , Kikusui Takefumi 
Published: June 2014

Significance
Although the positive impact of social bonds on individual’s fitness has recently been demonstrated, the mechanisms underlying the motivation to form long-term associations remain largely unknown. Current evidence shows that oxytocin modulates social behavior but evidence of its effects in bond maintenance remains scant, especially in nonreproductive contexts. We provide evidence that in the domestic dog oxytocin enhances social motivation to approach and affiliate with conspecifics and human partners, which constitutes the basis for the formation of any stable social bond. Furthermore, endogenous oxytocin levels increased after dogs engaged in affiliation with their dog partners, indicating a stimulation of the oxytocin system during social interactions. Our findings highlight the important role that oxytocin has in the expression of sociality in mammals.
High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource
Authors: Seaver Samuel M. D. , Gerdes Svetlana , Frelin Océane , Lerma-Ortiz Claudia , Bradbury Louis M. T. , Zallot Rémi , Hasnain Ghulam , Niehaus Thomas D. , El Yacoubi Basma , Pasternak Shiran , Olson Robert , Pusch Gordon , Overbeek Ross , Stevens Rick , de Crécy-Lagard Valérie , Ware Doreen , Hanson Andrew D. , Henry Christopher S. 
Published: June 2014

Significance
Genes must be annotated with their correct functions if genome data are to support hypothesis building and metabolic engineering. PlantSEED was developed to streamline the process of annotating plant genome sequences, to construct metabolic models based on genome annotations automatically, and to use models to test the annotation of these sequences, allowing the detection of gaps and errors in gene annotations and the prediction of new functions. PlantSEED is designed to grow in an iterative manner by including new plant genome sequences, new annotations harvested from the literature, and improved biochemical data, all of which are integrated in a consistent manner into the PlantSEED genomes and metabolic models.
Badger responses to small-scale culling may compromise targeted control of bovine tuberculosis
Authors: Bielby Jon , Donnelly Christl A. , Pope Lisa C. , Burke Terry , Woodroffe Rosie 
Published: June 2014

Significance
Bovine tuberculosis (TB) killed 1,500 people annually in 1930s Britain. TB control efforts still entail slaughtering many thousands of cattle annually, costing British farmers and taxpayers millions of dollars. Transmission from wild badgers impedes control of cattle TB, but nonselective badger culls confer limited benefits because culling changes badger behavior in ways that increase disease spread. A new plan to cull only test-positive badgers, and vaccinate test-negative badgers [termed test–vaccinate/remove (TVR)], is probably more publicly acceptable, and might be more effective if culling small numbers of badgers prompts no behavioral change. Unfortunately, this study shows that small-scale culling (such as TVR) changes badgers’ behavior in ways that risk increasing TB transmission among badgers and exacerbating cattle TB incidence rather than reducing it.
Targeting and in vivo imaging of non-small–cell lung cancer using nebulized multimodal contrast agents
Authors: Bianchi Andrea , Dufort Sandrine , Lux François , Fortin Pierre-Yves , Tassali Nawal , Tillement Olivier , Coll Jean-Luc , Crémillieux Yannick 
Published: June 2014

Significance
One of the main reasons for the dismal prognosis of lung cancer is related to late diagnosis of this pathology. In this work we show that the synergic employment of a properly chosen free-breathing MRI protocol and gadolinium-based nanoparticles allow early-stage accurate and noninvasive detection of millimetric-size lung tumor and of its contours. In addition, this work shows for the first time, to our knowledge, the advantages that can come from the choice of an orotracheal administration route instead of a more conventional systemic administration when studying pathomorphological changes due to lung cancers. Potential applications of this result may range from effective lung pathology detection and follow-up to pulmonary therapeutic applications of selected drugs.
Evolutionary developmental transcriptomics reveals a gene network module regulating interspecific diversity in plant leaf shape
Authors: Ichihashi Yasunori , Aguilar-Martínez José Antonio , Farhi Moran , Chitwood Daniel H. , Kumar Ravi , Millon Lee V. , Peng Jie , Maloof Julin N. , Sinha Neelima R. 
Published: June 2014

Significance
Ever since Darwin’s pioneering research, a major challenge in biology has been to understand the genetic basis of morphological evolution. Utilizing the natural variation in leaf morphology between tomato and two related wild species, we identified a gene network module that leads to a dynamic rewiring of interactions in the whole leaf developmental gene regulatory network. Our work experimentally validates the hypothesis that peripheral regions of network, rather than network hubs, are more likely to contribute to evolutionary innovations. Our data also suggest that, likely due to their bottleneck location in the network, the regulation in KNOX homeobox genes was repeatedly manipulated to generate natural variation in leaf shape.
Cofactor-dependent conformational heterogeneity of GAD65 and its role in autoimmunity and neurotransmitter homeostasis
Authors: Kass Itamar , Hoke David E. , Costa Mauricio G. S. , Reboul Cyril F. , Porebski Benjamin T. , Cowieson Nathan P. , Leh Hervé , Pennacchietti Eugenia , McCoey Julia , Kleifeld Oded , Borri Voltattorni Carla , Langley David , Roome Brendan , Mackay Ian R. , Christ Daniel , Perahia David , Buckle Malcolm , Paiardini Alessandro , De Biase Daniela , Buckle Ashley M. 
Published: June 2014

Significance
Autoimmune type 1 diabetes is characterized by the formation of self-reactive antibodies. A prevalent human autoantigen is glutamate decarboxylase (GAD)65, a highly predictive marker that can precede the emergence of disease by up to several years. Intriguingly, the closely related isoform GAD67 is not immunogenic. What are the determinants of the unique self-reactivity of GAD65 vs. GAD67? We show that, unlike GAD67, GAD65 is highly flexible and exists in multiple structural forms. We show that self-antibodies bind differentially to these GAD65 forms. These properties may be an undesirable consequence of conformational flexibility necessary for enzyme function. Our findings, thus, provide insights into how structural flexibility governs protein immunogenicity in autoimmune diabetes and have implications for therapeutic antibody and vaccine design.
Packing density of rigid aggregates is independent of scale
Authors: Zangmeister Christopher D. , Radney James G. , Dockery Lance T. , Young Jessica T. , Ma Xiaofei , You Rian , Zachariah Michael R. 
Published: June 2014

Significance
Particle aggregates are one of the most ubiquitous structural arrangements in the universe, making up large interstellar planetary seedlings and comets, microscale powdered pharmaceuticals, and nanoscale atmospheric particles. The packing of aggregates determines structure and, in many cases, chemical, physical, and mechanical properties. Here we show that packing in weakly compacted aggregated materials is scale invariant over many orders of magnitude. We demonstrate that the effective density of compacted soot aggregates and comets are equivalent, and conclude that the packing of aggregated materials appear to be remarkably independent of the aggregating forces, mechanisms, or initial conditions.
Economic scarcity alters the perception of race
Authors: Krosch Amy R. , Amodio David M. 
Published: June 2014

Significance
Racial disparities on socioeconomic indices expand dramatically during economic recession. Although prior explanations for this phenomenon have focused on institutional causes, our research reveals that perceived scarcity influences people’s visual representations of race in a way that may promote discrimination. Across four studies, scarce conditions led perceivers to view Black people as “darker” and “more stereotypically Black” in appearance, relative to control conditions, and this shift in perception under scarcity was sufficient to elicit reduced resource allocations to African American recipients. These findings introduce a “motivated perception” account for the proliferation of racial and ethnic discrimination during times of economic duress.
Evidence for elevated and spatially variable geothermal flux beneath the West Antarctic Ice Sheet
Authors: Schroeder Dustin M. , Blankenship Donald D. , Young Duncan A. , Quartini Enrica 
Published: June 2014

Significance
Thwaites Glacier is one of the West Antarctica's most prominent, rapidly evolving, and potentially unstable contributors to global sea level rise. Uncertainty in the amount and spatial pattern of geothermal flux and melting beneath this glacier is a major limitation in predicting its future behavior and sea level contribution. In this paper, a combination of radar sounding and subglacial water routing is used to show that large areas at the base of Thwaites Glacier are actively melting in response to geothermal flux consistent with rift-associated magma migration and volcanism. This supports the hypothesis that heterogeneous geothermal flux and local magmatic processes could be critical factors in determining the future behavior of the West Antarctic Ice Sheet.
An iron-regulated and glycosylation-dependent proteasomal degradation pathway for the plasma membrane metal transporter ZIP14
Authors: Zhao Ningning , Zhang An-Sheng , Worthen Christal , Knutson Mitchell D. , Enns Caroline A. 
Published: June 2014

Significance
The canonical degradation pathway for plasma membrane proteins is through endocytosis and targeting to lysosomes. In some cases, plasma membrane proteins undergo retrograde trafficking to the endoplasmic reticulum (ER) for extraction through an endoplasmic reticulum-associated degradation pathway. We identified a novel proteasome-mediated pathway for the degradation of a plasma membrane iron transporter, ZIP14. Extraction and degradation of ZIP14 occurred after endocytosis, but did not occur by retrograde trafficking to the ER. Both ubiquitination and deglycosylation of ZIP14 were identified prior to degradation. To our knowledge, ZIP14 is the first identified multispanning plasma membrane protein to undergo such a pathway. In addition, we showed that membrane extraction is regulated by cellular iron content, providing insight into the disorders of iron metabolism.
Plasticity of hydrogen bond networks regulates mechanochemistry of cell adhesion complexes
Authors: Chakrabarti Shaon , Hinczewski Michael , Thirumalai D. 
Published: June 2014

Significance
Selectins and integrins are receptor proteins on cell surfaces responsible for adhesion to extracellular biomolecules, a critical component of physiological processes like white blood cell localization at sites of inflammation. The bonds which the receptors form with their targets are regulated by mechanical forces (for example due to blood flow). The bond lifetimes before rupture increase with force before decreasing. Based on crystal structures of selectin and integrin, we created a general analytic theory which for the first time, to our knowledge, relates microscopic structural rearrangements at the receptor–ligand interface to macroscopic bond lifetimes. We quantitatively explain experimental data from diverse systems spanning four decades of lifetime scales, and also predict the outcome of mutations in specific residues.
Medically important differences in snake venom composition are dictated by distinct postgenomic mechanisms
Authors: Casewell Nicholas R. , Wagstaff Simon C. , Wüster Wolfgang , Cook Darren A. N. , Bolton Fiona M. S. , King Sarah I. , Pla Davinia , Sanz Libia , Calvete Juan J. , Harrison Robert A. 
Published: June 2014

Significance
The toxic composition of snake venom varies between species. Such variation can have major medical implications for the treatment of human snakebite victims. Venom variation is largely attributed to differences in toxin-encoding genes present in the genome or venom gland of snakes. Here, we demonstrate that mechanisms affecting the transcription, translation, and posttranslational modification of toxins also significantly contribute to the diversity of venom protein composition. Venom variation observed between related snake species is therefore the result of a complex interaction between a variety of genetic and postgenomic factors acting on toxin genes. Ultimately, this variation results in significant differences in venom-induced pathology and lethality and can undermine the efficacy of antivenom therapies used to treat human snakebite victims.
Structural and mechanistic studies of polymerase η bypass of phenanthriplatin DNA damage
Authors: Gregory Mark T. , Park Ga Young , Johnstone Timothy C. , Lee Young-Sam , Yang Wei , Lippard Stephen J. 
Published: June 2014

Significance
In this work we investigated the ability of phenanthriplatin, a novel, potent monofunctional platinum anticancer agent, to inhibit DNA replication. Biochemical assays using site-specifically platinated DNA probes revealed the ability of phenanthriplatin lesions to block DNA replication by all polymerases tested except for Pol η, which exhibited inefficient but high-fidelity lesion bypass. Crystallographic studies of Pol η stalled at different stages of translesion synthesis past phenanthriplatin-platinated DNA provided insight into the mechanism by which the lesion inhibits DNA polymerases to induce cellular toxicity. Cytotoxicity studies using cells derived from patients who do not express functional Pol η suggest that phenanthriplatin-based therapy will be useful to treat cancers resistant to cisplatin by upregulating Pol η expression.
Mechanism of staphylococcal multiresistance plasmid replication origin assembly by the RepA protein
Authors: Schumacher Maria A. , Tonthat Nam K. , Kwong Stephen M. , Chinnam Naga babu , Liu Michael A. , Skurray Ronald A. , Firth Neville 
Published: June 2014

Significance
The large staphylococcal multiresistance plasmids harbored in Gram-positive pathogens contribute significantly to the spread of multidrug-resistant bacteria and are typified by the presence of a highly conserved replication initiator protein, RepA, which is required for plasmid retention. RepA proteins contain N-terminal (NTD) and C-terminal (CTD) domains, which are both required for replication. We show that the RepA NTD and CTD show striking homology to the host primosome protein DnaD yet perform distinct functions; the NTD binds origin DNA in a novel manner and the CTD recruits the replicative helicase. Moreover, NTD–DNA structures reveal the first mechanism of origin handcuffing. Combined, the data unveil the minimal mechanism by which multiresistance plasmids mediate origin assembly via the highly conserved RepA protein.