bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhanced nitric oxide synthesis through nitrate supply improves drought tolerance of sugarcane plants
Authors: Pissolato Maria D. , Silveira Neidiquele M. , Prataviera Paula J. , Machado Eduardo C. , Seabra Amedea B. , Pelegrino Milena T. , Sodek Ladaslav , Ribeiro Rafael V. 
Published: December 2019

AbstractNitric oxide (NO) is an important signaling molecule associated with many biochemical and physiological processes in plants under stressful conditions. Nitrate reductase (NR) not only mediates the reduction of NO3− to NO2− but also reduces NO2− to NO, a relevant pathway for NO production in higher plants. Herein, we hypothesized that sugarcane plants supplied with more NO3− as a source of N would produce more NO under water deficit. Such NO would reduce oxidative damage and favor photosynthetic metabolism and growth under water limiting conditions. Sugarcane plants were grown in nutrient solution and received the same amount of nitrogen, with varying nitrate:ammonium ratios (100:0 and 70:30). Plants were then grown under well-watered or water deficit conditions, in which the osmotic potential of nutrient solution was −0.15 and −0.75 MPa, respectively. Under water deficit, plants exhibited higher root [NO3−] and [NO2−] when supplied with 100% NO3−. Accordingly, the same plants also showed higher root NR activity and root NO production. We also found higher photosynthetic rates and stomatal conductance in plants supplied with more NO3−, which improved root growth. ROS accumulation was reduced due to increases in the activity of catalase in leaves and superoxide dismutase and ascorbate peroxidase in roots of plants supplied with 100% NO3− and facing water deficit. Such positive responses to water deficit were offset when a NO scavenger was supplied to the plants, thus confirming that increases in leaf gas exchange and plant growth were induced by NO. Concluding, NO3− supply is an interesting strategy for alleviating the negative effects of water deficit on sugarcane plants, increasing drought tolerance through enhanced NO production. Our data also provide insights on how plant nutrition could improve crop tolerance against abiotic stresses, such as drought.HighlightsNitrate supply improves sugarcane growth under water deficit.Nitrate supply stimulated nitrate reductase activity and NO synthesis in sugarcane roots facing water deficit.Leaf gas exchange was increased by nitrate supply as well as root growth under water limiting conditions.Antioxidant responses were also improved in plants supplied exclusively with nitrate.Nitrogen management may be an interesting strategy for improving drought tolerance in sugarcane fields.
A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients
Authors: Bekker-Jensen Dorte B. , del Val Ana Martínez , Steigerwald Sophia , Rüther Patrick , Fort Kyle , Arrey Tabiwang N. , Harder Alexander , Makarov Alexander , Olsen Jesper V. 
Published: December 2019

ABSTRACTState-of-the-art proteomics-grade mass spectrometers can measure peptide precursors and their fragments with ppm mass accuracy at sequencing speeds of tens of peptides per second with attomolar sensitivity. Here we describe a compact and robust quadrupole-orbitrap mass spectrometer equipped with a front-end High Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) Interface. The performance of the Orbitrap Exploris 480 mass spectrometer is evaluated in data-dependent acquisition (DDA) and data-independent acquisition (DIA) modes in combination with FAIMS. We demonstrate that different compensation voltages (CVs) for FAIMS are optimal for DDA and DIA, respectively. Combining DIA with FAIMS using single CVs, the instrument surpasses 2500 unique peptides identified per minute. This enables quantification of >5000 proteins with short online LC gradients delivered by the Evosep One LC system allowing acquisition of 60 samples per day. The raw sensitivity of the instrument is evaluated by analyzing 5 ng of a HeLa digest from which >1000 proteins were reproducibly identified with 5 minute LC gradients using DIA-FAIMS. To demonstrate the versatility of the instrument we recorded an organ-wide map of proteome expression across 12 rat tissues quantified by tandem mass tags and label-free quantification using DIA with FAIMS to a depth of >10,000 proteins.
pSpatiocyte: a high-performance simulator for intracellular reaction-diffusion systems
Authors: Arjunan Satya N. V. , Miyauchi Atsushi , Iwamoto Kazunari , Takahashi Koichi 
Published: December 2019

ABSTRACTBackgroundStudies using quantitative experimental methods have shown that intracellular spatial distribution of molecules plays a central role in many cellular systems. Spatially resolved computer simulations can integrate quantitative data from these experiments to construct physically accurate models of the systems. Although computationally expensive, microscopic resolution reaction-diffusion simulators, such as Spatiocyte can directly capture intracellular effects comprising diffusion-limited reactions and volume exclusion from crowded molecules by explicitly representing individual diffusing molecules in space. To alleviate the steep computational cost typically associated with the simulation of large or crowded intracellular compartments, we present a parallelized Spatiocyte method called pSpatiocyte.ResultsThe new high-performance method employs unique parallelization schemes on hexagonal close-packed (HCP) lattice to efficiently exploit the resources of common workstations and large distributed memory parallel computers. We introduce a coordinate system for fast accesses to HCP lattice voxels, a parallelized event scheduler, a parallelized Gillespie’s direct-method for unimolecular reactions, and a parallelized event for diffusion and bimolecular reaction processes. We verified the correctness of pSpatiocyte reaction and diffusion processes by comparison to theory. To evaluate the performance of pSpatiocyte, we performed a series of parallelized diffusion runs on the RIKEN K computer. In the case of fine lattice discretization with low voxel occupancy, pSpatiocyte exhibited 74% parallel efficiency and achieved a speedup of 7686 times with 663552 cores compared to the runtime with 64 cores. In the weak scaling performance, pSpatiocyte obtained efficiencies of at least 60% with up to 663552 cores. When executing the Michaelis-Menten benchmark model on an eight-core workstation, pSpatiocyte required 45- and 55-fold shorter runtimes than Smoldyn and the parallel version of ReaDDy, respectively. As a high-performance application example, we study the dual phosphorylation-dephosphorylation cycle of the MAPK system, a typical reaction network motif in cell signaling pathways.ConclusionspSpatiocyte demonstrates good accuracies, fast runtimes and a significant performance advantage over well-known microscopic particle simulators for large-scale simulations of intracellular reaction-diffusion systems. The source code of pSpatiocyte is available at https://spatiocyte.org.
RNA-Seq Analysis Reveals Localization-Associated Alternative Splicing across 13 Cell Lines
Authors: Zeng Chao , Hamada Michiaki 
Published: December 2019

ABSTRACTAlternative splicing, a ubiquitous phenomenon in eukaryotes, is a regulatory mechanism for the biological diversity of individual genes. Most studies have focused on the effects of alternative splicing for protein synthesis. However, the transcriptome-wide influence of alternative splicing on RNA subcellular localization has rarely been studied. By analyzing RNA-seq data obtained from subcellular fractions across 13 human cell lines, we identified 8720 switching genes between the cytoplasm and the nucleus. Consistent with previous reports, intron retention was observed to be enriched in the nuclear transcript variants. Interestingly, we found that short and structurally stable introns were positively correlated with nuclear localization. Motif analysis reveals that fourteen RNA-binding protein (RBPs) are prone to be preferentially bound with such introns. To our knowledge, this is the first transcriptome-wide study to analyze and evaluate the effect of alternative splicing on RNA subcellular localization. Our findings reveal that alternative splicing plays a promising role in regulating RNA subcellular localization.
BoxCar Assisted MS Fragmentation (BAMF)
Authors: Jenkins Conor , Orsburn Ben 
Published: December 2019

AbstractA recent study described the utilization of complex quadrupole isolation schemes to reduce high abundance ion saturation in Orbitrap systems. The BoxCar technique effectively democratizes MS1 scans by restricting high abundance ions from consuming as much space in the trap. This restriction allows lower abundance ions more acquisition time and can increase the signal to noise by a full order of magnitude. While effective at the MS1 level, BoxCar does not show an improvement in MS/MS acquisition as ions selected for fragmentation must come from an additional MS1 full scan in the method. In this study we describe BoxCar Assisted MS Fragmentation (BAMF), wherein ions for fragmentation are selected directly from the BoxCar scans. When utilizing BAMF, we observe the identification of ions by MS/MS that are not at all detectable in the MS1 scans of identical concentrations of peptides analyzed by standard data dependent acquisition experiments.Abstract Graphic
Females don’t always sing in response to male song, but when they do, they sing to males with higher pitched songs
Authors: Kirschel Alexander N. G. , Zanti Zacharo , Harlow Zachary T. , Vallejo Edgar E. , Cody Martin L. , Taylor Charles E. 
Published: December 2019

AbstractThe long-held view that bird song is exclusively a male trait has been challenged recently by a number of studies and reviews highlighting the prevalence of female song. In spite of that, there remains a lack of knowledge on the function of female song, with most evidence thus far focusing on females performing duets with males in courtship displays, typically for joint territory defence or mate guarding purposes. Here we show in a tracheophone suboscine passerine Formicarius moniliger, a sexually monomorphic species in which both sexes sing, that females may participate in both intrasexual and intersexual territory defence. Females sing more in response to females than to males, suggesting they consider females more of a threat to their territory. Yet, females also demonstrate an unexpected pattern of singing back to playback of males singing higher frequency song than themselves. Unlike males, who respond indiscriminately to playback of any song performed by either sex, females appear to discern not only the sex, but perhaps also the size of the presumed intruder. There is a strong negative relationship between body mass and frequency, and females responding only to higher frequency male song suggests they will only engage in territory defence with males when they expect those males to be weaker than they are. While our results are consistent with expectations of a shared ancestral function of song in territory defence, they also suggest females may suffer greater costs in engaging in territorial disputes and thus limit their vocal contribution according to the perceived threat.
Melatonin reduces GSK3β expression and tau phosphorylation via Nrf2 nuclear translocation
Authors: Das Rashmi , Balmik Abhishek Ankur , Chinnathambi Subashchandrabose 
Published: December 2019

AbstractAlzheimer’s disease is a neuropathological condition with abnormal formation of extracellular Amyloid-β plaques and intracellular neurofibrillary tangles (NFTs) of Microtubule-associated protein Tau (Tau) in brain. In pathological condition, MAP-Tau can undergo various post-translational modifications such as hyperphosphorylation by the activity of cellular kinases which eventually leads to protein aggregation in neurons. Melatonin is a hormone which mainly secreted from pineal gland, functions to modulate cellular kinases. In our study, we elucidated that Melatonin has inhibited the Tau aggregates mediated cytotoxicity and membrane leakage by MTT and LDH assay respectively in neuro2A cells. Melatonin has found to reduce the GSK3β mRNA expression and protein level by western blot and immunofluorescence assay. Melatonin has also decreased phospho-Tau level (pThr181 and pThr212-pSer214) in neuron cell line upon OA induction as seen by microscopic analysis.. Melatonin treatment has associated with ROS quenching by DCFDA assay, reduced caspase 3 activity in neuronal cells. Further, Melatonin has increased Nrf2 level and nuclear translocation as oxidative stress response in Tauopathy. Together, these findings clearly signifies that Melatonin remediate the Tau-induced neuronal cytotoxicity and reduce Tau hyperphosphorylation via downregulating GSK3β expression. Melatonin can combat oxidative damage by Nrf2 activation and nuclear translocation in AD condition.
Effect of Melatonin on Tau aggregation and Tau-mediated cell surface morphology
Authors: Das Rashmi , Balmik Abhishek Ankur , Chinnathambi Subashchandrabose 
Published: December 2019

ABSTRACTTau is the major neuronal protein involved in the stabilization of microtubule assembly. In Alzheimer’s disease, Tau self assembles to form intracellular protein aggregates, which are toxic to cells. Various methods have been tried and tested to restrain the aggregation of Tau. Most of the agents tested for this purpose have limitations in their effectiveness and availability to neuronal cells. We tested melatonin against in vitro Tau aggregation and observed its effect on membrane topology, tubulin network and Tau phosphorylation in neuro2a and N9 cell lines. The aggregation and conformation of Tau was determined by ThT fluorescence and CD spectroscopy respectively. The morphology of Tau aggregates in presence and absence of melatonin was studied by transmission electron microscopy. Melatonin was found to reduce the formation of higher order oligomeric structures without affecting the overall aggregation kinetics of Tau. Melatonin also modulates and helps to maintain membrane topology as evidenced by FE-SEM analysis. Overall, melatonin administration shows mild anti-aggregation and cytoprotective effects.
Numerical investigation of the unsteady aerodynamics of NACA 0012 with suction surface protrusion
Authors: Bodavula Aslesha , Yadav Rajesh , Guven Ugur 
Published: December 2019

Purpose
The purpose of this paper is to investigate the effect of surface protrusions on the flow unsteadiness of NACA 0012 at a Reynolds number of 100,000.

Design/methodology/approach
Effect of protrusions is investigated through numerical simulation of two-dimensional Navier–Stokes equations using a finite volume solver. Turbulent stresses are resolved through the transition Shear stress transport (four-equation) turbulence model.

Findings
The small protrusion located at 0.05c and 0.1c significantly improve the lift coefficient by up to 36% in the post-stall regime. It also alleviates the leading edge stall. The larger protrusions increase the drag significantly along with significant degradation of lift characteristics in the pre-stall regime as well. The smaller protrusions also increase the frequency of the vortex shedding.

Originality/value
The effect of macroscopic protrusions or deposits in rarely investigated. The delay in stall shown by smaller protrusions can be beneficial to micro aerial vehicles. The smaller protrusions increase the frequency of the vortex shedding, and hence, can be used as a tool to enhance energy production for energy harvesters based on vortex-induced vibrations and oscillating wing philosophy.
Implementation of a new inlet protection system into HEMS fleet
Authors: Przybyła Bartosz Stanisław , Przysowa Radoslaw , Zapałowicz Zbigniew 
Published: December 2019

Purpose
EC-135P2+ helicopters operated by Polish Medical Air Rescue are highly exposed to environmental particles entering engines when performing helicopter emergency medical services. This paper aims to assess the effectiveness of inlet barrier filters installed to protect the engines, including their impact on maintenance.

Design/methodology/approach
The organisation adopted a comprehensive set of measures to predict and limit the impact of dust ingestion including visual inspections, health management and engine trend monitoring based on ground power checks’ (GPC) results. Three alternative particle separation solutions were considered. Finally, helicopter inlets were modified to allow the selected filter system to be installed, which reduced the number of particles ingested by the engine and prevented from premature overhauls.

Findings
The analyses carried out enabled not only the selection of the optimal filtration solution and its seamless implementation into the fleet but also confirmed its efficiency. After installing the filters, engines’ lifetime is extended from 500 to 4,500 flight hours while operating costs and the number of maintenance tasks was reduced significantly.

Originality/value
Lessons learned from operational experience show that a well-matched particle separation system can mitigate accelerated engine deterioration even if the platform is continuously exposed to environmental particles. The remaining useful life of engines can be predicted using performance models and data from GPC.
The determinants of accounting comparability around the world
Authors: Ross Jonathan , Shi Linna , Xie Hong 
Published: December 2019

PurposeThe purpose of this paper is to investigate country-level and firm-level determinants of within-country accounting comparability for 16 European Union countries plus the USA in the post-International Financial Reporting Standards adoption period.Design/methodology/approachThe authors use ordinary least squares regression to test the hypotheses with a correction for heteroscedasticity.FindingsThe authors find that firms in countries with rules-based accounting, higher quality public auditor work environments, stricter enforcement of accounting standards and more reliance on equity-market financing have higher within-country comparability with each other. At the firm-level, the authors find that firms which are larger, engage in less earnings management, and have lower return-on-asset volatility have higher within-country comparability with each other.Research limitations/implicationsThe authors use one measure of accounting comparability. Alternative measures of accounting comparability could test the hypotheses more completely.Practical implicationsThe findings of the paper may help the regulators make more efficient policies to establish an efficient financial market within their country.Originality/valueThe paper is the first, to the authors’ knowledge, to identify country-level and firm-level determinants of within-country accounting comparability. It contributes to the accounting literature by completing the theory of international accounting comparability from the within-country perspectives, as prior literature focuses on the cross-country perspective of international accounting comparability.
Does strategic orientation influence strategy formulation and organisational design in Italian food medium sized enterprises? The role of the family
Authors: Penco Lara , Torre Teresina , Scarsi Roberta 
Published: December 2019

PurposeThe purpose of this paper is to examine the impact of strategic orientation (defined using the Miles and Snow’s paradigm) on the processes of strategic decision-making and organisational design in medium-sized firms (MEs) operating in the Italian family food and beverage industry (F&B). It answers the following research questions: Does the orientation towards market development lead to different strategic formulation styles and developing innovative approaches towards organisational design?Design/methodology/approachThe study is based on five cases of Italian family MEs operating in the F&B industry with a focus on premium segments, following the Mediobanca and Unioncamere criteria.FindingsThe strategy formulation process and the organisational design are affected by strategic orientation, highlighting the relevance of the “prospector” orientation in modifying the behavioural models among the selected companies.Research limitations/implicationsThe limitations concern the number of examined case studies and the geographical location of firms.Practical implicationsThe attitude to plan and develop new organisational designs is required by a more “prospector” strategic orientation due to the increasing level of work complexity and the process of innovation to manage the market share. Thus, the emergence of a prospector attitude must be reinforced with specific managerial competencies and suggested as necessary support for development strategies.Originality/valueThis study focusses on strategic and organisational profiles of MEs operating in the F&B context, where literature is still fragmented. It explores the relationship between strategic orientation, strategic formulation and organisational design by analysing all constructs simultaneously, thereby bridging the theoretical gap in the existing literature.
Investigating young adults’ perceived effectiveness of textual information about food-related nudging
Authors: Djupegot Ingrid Laukeland 
Published: December 2019

PurposePerceived effectiveness of nudging has been established as one of the most reliable predictors of acceptance of nudging. The purpose of this paper is to investigate how source credibility and argument strength influence the perceived effectiveness of textual information about food-related nudging in order to provide a better understanding of how acceptance of nudging may be facilitated.Design/methodology/approachA 2 × 2 scenario-based between-subjects factorial experiment with source credibility (high vs low) and argument strength (high vs low) as factors was applied. Data on respondents’ level of involvement in food-related behaviour were also collected.FindingsArgument strength had a positive main effect on the perceived effectiveness of nudging, and there was a significant positive interaction effect of source credibility × argument strength on the perceived effectiveness of nudging.Practical implicationsThe findings of this paper provide policy makers and other decision makers with a better understanding of how information about nudging should be communicated to consumers in order to facilitate acceptance.Originality/valueThis paper is one of the first to investigate how information about nudging should be communicated to consumers in order for nudging to be perceived as an effective and thus acceptable measure to influence food-related behaviour.