bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expression, purification and crystal structure determination of a ferredoxin reductase from the actinobacteriumThermobifida fusca
Authors: Rodriguez Buitrago Jhon Alexander , Klünemann Thomas , Blankenfeldt Wulf , Schallmey Anett 
Published: March 2020

AbstractFerredoxin reductase FdR9 fromThermobifida fusca, a member of the oxygenase-coupled NADH-dependent ferredoxin reductase (FNR) family, catalyzes electron transfer from NADH to its physiological electron acceptor ferredoxin. It forms part of a three-component cytochrome P450 monooxygenase system inT. fusca. Here, FdR9 was overexpressed and purified and its crystal structure was determined at 1.8 Å resolution. The overall structure of FdR9 is similar to other members of the FNR family and is composed of an FAD-binding domain, an NAD-binding domain and a C-terminal domain. Activity measurements with FdR9 confirmed a strong preference for NADH as the cofactor. Comparison of the FAD- and NAD-binding domains of FdR9 with other ferredoxin reductases revealed the presence of conserved sequence motifs in the FAD-binding domain as well as several highly conserved residues involved in FAD and NAD cofactor binding. Moreover, the NAD-binding site of FdR9 contains a modified Rossmann fold motif, GxSxxS, instead of the classical GxGxxG motif.
Biological activity ofAjuga ivaextracts against the African cotton leafwormSpodoptera littoralis
Authors: Taha-Salaime Leena , Lebedev Galina , Abo-Nassar Jackline , Marzouk Sally , Inbar Moshe , Ghanim Murad , Aly Radi 
Published: March 2020

AbstractThe African cotton leafwormSpodoptera littoralis, a major crop pest worldwide, is controlled by chemical insecticides, leading to serious resistance problems.Ajugaplants contain phytoecdysteroids (analogs of arthropod steroid hormones that regulate metamorphoses) and clerodanes (diterpenoids exhibiting antifeedant activity). We analyzed phytoecdysteroids and clerodanes in leaf extracts of the IsraeliAjuga ivaby LC-TOF-MS and TLC, and their efficiency at reducingS. littoralisfitness. Castor bean leaves were smeared with an aqueous suspension of dried methanolic crude extract of phytoecdysteroid and clerodanes fromA. ivaleaves (50, 100 and 250 µg/µl). First and third instars ofS. littoralislarvae were fed with 1 treated leaf for 3 and 4 days, respectively. Mortality, larval weight gain, relative growth rate and survival were compared to feeding on control leaves. To evaluate and localizeA. ivacrude leaf extract activity in the insect gut, we used DAPI and phalloidin staining. Crude extract ofA. ivaleaves (50, 100 and 250 µg/µl) significantly increased mortality of first instarS. littoralislarvae (36%, 70% and 87%, respectively) compared to controls (6%). Third instar larval weight gain decreased significantly (by 52%, 44% and 30%, respectively), as did relative growth rate (–0.05 g/g day, compared to the relevant controls).S. littoralislarvae were further affected at later stages, with few survivors. Insect-gut staining showed that 250 µg/µl crude leaf extract reduces gut size, with relocation of nuclei and abnormal actin-filament organization. Our results demonstrate the potential ofA. ivaextract for alternative, environmentally safe insect-pest control.Key MessageInsects cause severe damage to numerous crops and their control relies on pesticides. Green control is becoming increasingly popular due to concerns about the negative impacts of pesticides on the environment. Phytoecdysteroids are found in Ajuga plants and affect a wide range of insects at very low concentrations. Here we demonstrate that crude extract fromAjuga ivaalters the development ofSpodoptera littoralis. Phytoecdysteroids may therefore be beneficial in IPM programs.
Year-to-year crop shifts promote weed diversity in tropical permanent rainfed cultivation
Authors: Neyret Margot , de Rouw Anneke , Colbach Nathalie , Robain Henri , Soulileuth Bounsamay , Valentin Christian 
Published: March 2020

AbstractIn the past decades, the expansion and modernisation of agriculture in the mountainous areas of Southeast Asia has had severe impacts on biodiversity, as the once species-rich forests were turned into homogeneous fields receiving ample external inputs. A common feature of permanent cropping with annual crops is the frequent change of crop choice, depending on market opportunities or other motives. However, the precise effect of crop shifts on weeds in tropical areas is largely unknown. In this study, we investigated the short-term effect of crop sequences on the diversity of weed communities in smallholder fields in Northern Thailand. Crop choices were upland rice, maize, fallow and young tree plantations with or without intercrop. We counted the number of crop shifts and the number of crops involved during a 3-years period preceding weed sampling. We showed that the number of crop shifts did not affect weed density and biomass. However, herbaceous species number and diversity (measured as Shannon index) increased by 36% and 46% respectively, while herbaceous species dominance decreased by 38%, in fields with yearly crop shifts compared to fields with no shifts in the previous three years. The effect of a particular crop on diversity, or the effect of intercropping with young trees, was weaker. It was likely due to the more variable resources (especially light) in fields with two crop shifts, allowing species with different niches to co-exist. Crop type and frequent crop shifts did not affect shrub and tree species number, diversity or dominance. Some species were strongly associated with fields with no crop shift in the sequence (e.g. the treeAntidesma velutinosum) or to fields with two crop shifts in the sequence (e.g. the herbCentella asiatica, the C4grassDigitaria radicosa). Overall, this study showed that in this agronomical system, maintaining yearly crop shifts does not significantly affect weed abundance, but supports in-field plant species diversity, which is likely to impact the services provisioned by tropical mountainous agro-ecosystemsHighlightsFrequent crop shifts in a crop sequence increased weed richness and diversity.Crop shifts had a stronger effect on weed richness and diversity than the current crop.The number of crop shifts did not affect weed biomass and density.Graphical abstract
Minimizing the number of optimizations for efficient community dynamic flux balance analysis
Authors: Brunner James D. , Chia Nicholas 
Published: March 2020

AbstractDynamic flux balance analysis uses a quasi-steady state assumption to calculate an organism’s metabolic activity at each time-step of a dynamic simulation, using the well-know technique of flux balance analysis. For microbial communities, this calculation is especially costly and involves solving a linear constrained optimization problem for each member of the community at each time step. However, this is unnecessary and inefficient, as prior solutions can be used to inform future time steps. Here, we show that a basis for the space of internal fluxes can be chosen for each microbe in a community and this basis can be used to simulate forward by solving a relatively inexpensive system of linear equations at most time steps, instead of the full optimization problem. Using our method, we can use this solution as long as the resulting metabolic activity remains within the optimization problem’s constraints (i.e. the solution remains feasible). As the solution becomes infeasible, it first becomes a feasible but degenerate solution to the optimization problem, and we can solve a different but related optimization problem to choose an appropriate basis to continue forward simulation. We show using an eight species community that this is an efficient and robust method for computing dynamic flux balance analysis simulations, and so is capable of simulating communities of organisms. We demonstrate that the method gives an approximately 85% speed-up per organism over the standard and widely used method. Our method has been implemented in thePythonlanguage and source code is available athttps://github.com/jdbrunner/surfin_fbaand in the Python Package Index (PyPI) assurfinFBA.Author summaryThe standard method in the field for dynamic flux balance analysis carries a prohibitively high computational cost because it requires solving a linear optimization problem at each time-step. We have developed a novel method for producing solutions to this dynamical system which greatly reduces the number of optimization problems that must be solved. We prove mathematically that we can solve the optimization problem once and simulate the system forward as an ordinary differential equation for some time interval, and solutions to this ODE provide solutions to the optimization problem. Eventually, the system reaches an easily checkable condition which implies that another optimization problem must be solved. We compare our method with the classical method to validate that it provides equivalent solutions in much lower computational time.
Landmark navigation in a mantis shrimp
Authors: Patel Rickesh N. , Cronin Thomas W. 
Published: March 2020

SummaryMantis shrimp are predatory crustaceans that commonly occupy burrows in shallow, tropical waters worldwide. Most of these animals inhabit structurally complex, benthic environments where many potential landmarks are available. Mantis shrimp of the speciesNeogonodactylus oerstediireturn to their burrows between foraging excursions using path integration, a vector-based navigational strategy that is prone to accumulated error. Here we show thatN. oerstediican navigate using landmarks in parallel with their path integration system, offseting error generated when navigating using solely path integration. We also report that when the path integration and landmark navigation systems are placed in conflict,N. oerstediiwill orient using either system or even switch systems enroute. How they make the decision to trust one navigational system over another is unclear. These findings add to our understanding of the refined navigational toolkitN. oerstediirelies upon to efficiently navigate back to its burrow, complementing its robust, yet error prone, path integration system with landmark guidance.
Age-Dependent Changes in the Progenitor Translatome Coordinated in part byTsc1Increase Perception of Signaling Inputs to End Nephrogenesis
Authors: Brunskill Eric , Jarmas Alison , Chaturvedi Praneet , Kopan Raphael 
Published: March 2020

AbstractMammalian nephron endowment is determined by the coordinated cessation of nephrogenesis in independent niches. Here we report that in young niches, cellular Wnt agonists are poorly translated, Fgf20 levels are high and R-spondin levels are low, resulting in a pro self-renewal environment. By contrast, older niches are low in Fgf20 and high in R-spondin, with increased cellular translation of Wnt agonists, including the signalosome-promoting Tmem59. This suggests a hypothesis that the tipping point for nephron progenitor exit from the niche is controlled by the gradual increase in stability and clustering of Wnt/Fzd complexes in individual cells, enhancing the response to ureteric bud-derived Wnt9b inputs and driving differentiation. We showTsc1hemizygosity differentially promoted translation of Wnt antagonists over agonists, expanding a transitional (Six2+, Cited1+, Wnt4+) state and delaying the tipping point. As predicted by these findings, reducing Rspo3 dosage in nephron progenitors or Tmem59 globally increased nephron numbersin vivo.
Protein dynamics enables phosphorylation of buried residues in Cdk2/Cyclin A-bound p27
Authors: Henriques João , Lindorff-Larsen Kresten 
Published: March 2020

AbstractProteins carry out a wide range of functions that are tightly regulated in space and time. Protein phosphorylation is the most common post-translation modification of proteins and plays key roles in the regulation of many biological processes. The finding that many phosphorylated residues are not solvent exposed in the unphosphorylated state opens several questions for understanding the mechanism that underlies phosphorylation and how phosphorylation may affect protein structures. First, since kinases need access to the phosphorylated residue, how do such buried residues become modified? Second, once phosphorylated, what are the structural effects of phosphorylation of buried residues and do they lead to changed conformational dynamics. We have used the ternary complex between p27, Cdk2 and Cyclin A to study these questions using enhanced sampling molecular dynamics simulations. In line with previous NMR and single-molecule fluorescence experiments we observe transient exposure of Tyr88 in p27, even in its unphosphorylated state. Once Tyr88 is phosphorylated, we observe a coupling to a second site, thus making Tyr74 more easily exposed, and thereby the target for a second phosphorylation step. Our observations provide atomic details on how protein dynamics plays a role in modulating multi-site phosphorylation in p27, thus supplementing previous experimental observations. More generally, we discuss how the observed phenomenon of transient exposure of buried residues may play a more general role in regulating protein function.Significance StatementProtein phosphorylation is a common post-translation modification and is carried out by kinases. While many phosphorylation sites are located in disordered regions of proteins or in loops, a surprisingly large number of modification sites are buried inside folded domains. This observation led us to ask the question of how kinases gain access to such buried residues. We used the complex between p27, a regulator of cell cycle progression, and Cyclin-dependent kinase 2/Cyclin A to study this problem. We hypothesized that transient exposure of buried tyrosines in p27 to the solvent would make them accessible to kinases, explaining how buried residues get modified. We provide an atomic-level description of these dynamic processes revealing how protein dynamics plays a role in regulation.
Quantifying redox heterogeneity in single-crystalline LiCoO2 cathode particles
Authors: Wei Chenxi , Hong Yanshuai , Tian Yangchao , Yu Xiqian , Liu Yijin , Pianetta Piero 
Published: March 2020

Active cathode particles are fundamental architectural units for the composite electrode of Li-ion batteries. The microstructure of the particles has a profound impact on their behavior and, consequently, on the cell-level electrochemical performance. LiCoO2 (LCO, a dominant cathode material) is often in the form of well-shaped particles, a few micrometres in size, with good crystallinity. In contrast to secondary particles (an agglomeration of many fine primary grains), which are the other common form of battery particles populated with structural and chemical defects, it is often anticipated that good particle crystallinity leads to superior mechanical robustness and suppressed charge heterogeneity. Yet, sub-particle level charge inhomogeneity in LCO particles has been widely reported in the literature, posing a frontier challenge in this field. Herein, this topic is revisited and it is demonstrated that X-ray absorption spectra on single-crystalline particles with highly anisotropic lattice structures are sensitive to the polarization configuration of the incident X-rays, causing some degree of ambiguity in analyzing the local spectroscopic fingerprint. To tackle this issue, a methodology is developed that extracts the white-line peak energy in the X-ray absorption near-edge structure spectra as a key data attribute for representing the local state of charge in the LCO crystal. This method demonstrates significantly improved accuracy and reveals the mesoscale chemical complexity in LCO particles with better fidelity. In addition to the implications on the importance of particle engineering for LCO cathodes, the method developed herein also has significant impact on spectro-microscopic studies of single-crystalline materials at synchrotron facilities, which is broadly applicable to a wide range of scientific disciplines well beyond battery research.
Developing a theoretical framework for intelligent contract acceptance
Authors: McNamara Alan J. , Sepasgozar Samad M.E. 
Published: March 2020

Purpose
This paper aims to develop a novel theoretical technology acceptance model, namely, for predicting acceptance of the trending technology of intelligent contracts (iContracts) in construction, which aims to integrate the data from emerging cyber-physical systems being introduced to the sector through the industry 4.0 revolution. This model includes main dimensions and critical contributing factors to assess the readiness for the iContract concept within the construction contract environment.

Design/methodology/approach
Through an extensive literature review, the structure of a unique theoretical technology acceptance model for iContract implementation, within construction, was developed iContract acceptance model (iCAM). Relevant themes were assessed through the lens of the technology acceptance model framework and the four accepted dimensions of the technology readiness index (TRI) concept. The main components of the model were examined with selected practitioners, with relevant experience and understanding of the iContract concept, with thematic mapping of the discussions correlated back to 12 specific iContract contributing constructs of the four adapted TRI dimensions.

Findings
The paper contributes to the body of knowledge by proposing a novel iCAM for a trending technology based on the specific requirements of iContract adoption. The interviews show that while the desire to digitalise the contractual environment exists, the readiness of the sector for such a disruptive change is unknown.

Practical implications
The findings and proposed conceptual iCAM offers a lens for the further development of the iContract concept by assisting practitioners to forecast digital readiness of the contract process in construction.

Originality/value
This study offers a unique and theoretical framework, in an embryonic field, for predicting the success of iContract implementation within construction organisations through the digital, industry 4.0 and revolution.
The strange case ofUSv.ZTE: a prosecution, a ban, a fine and a presidential intervention
Authors: Sutherland Ewan 
Published: March 2020

PurposeThe purpose of this paper is to review the prosecution by US authorities of Zhongxing Telecommunication Equipment (ZTE) Corporation for its violation of sanctions against the sale of systems to Iran and North Korea; the violation of the plea agreement; and, following presidential intervention, the imposition of a further fine and restructuring of its management.Design/methodology/approachAn analysis of the materials used in court proceedings and speeches by officials in the case against ZTEFindingsThe US president intervened in a quasi-judicial matter in which a foreign firm had violated US sanctions that he had supported to lessen the penalties it faced. The firm had also violated its plea agreement. This personal intervention weakened enforcement of US sanctions on human rights and weapons of mass destruction (WMD). However, it revealed the excessive reliance of Chinese manufacturers on US-domiciled suppliers of semiconductors and software.Research limitations/implicationsNeither was access to Chinese documents possible nor would it have been practicable to interview managers at ZTE.Practical implicationsEnforcement of US sanctions on the sale of telecommunications equipment have now been moved from strict enforcement on matters of human rights and WMD into political, trade and even personal negotiations with the US president.Originality/valueA first analysis of a telecommunications sanctions case.
Simulation of the temperature field for massive concrete structures using an interval finite element method
Authors: Xie Zhiqiang , Wang Lei , Zhu Zhengyang , Fu Zhi , Lv Xingdong 
Published: March 2020

Purpose
The purpose of this paper is to introduce an interval finite element method (IFEM) to simulate the temperature field of mass concrete under multiple influence uncertainties e.g. environmental temperature, material properties, pouring construction and pipe cooling.

Design/methodology/approach
Uncertainties of the significant factors such as the ambient temperature, the adiabatic temperature rise, the placing temperature and the pipe cooling are comprehensively studied and represented as the interval numbers. Then, an IFEM equation is derived and a method for obtaining interval results based on monotonicity is also presented. To verify the proposed method, a non-adiabatic temperature rise test was carried out and subsequently simulated with the method. An excellent agreement is achieved between the simulation results and the monitoring data.

Findings
An IFEM method is proposed and a non-adiabatic temperature rise test is simulated to verify the method. The interval results are discussed and compared with monitoring data. The proposed method is found to be feasible and effective.

Originality/value
Compared with the traditional finite element methods, the proposed method taking the uncertainty of various factors into account and it will be helpful for engineers to gain a better understanding of the real condition.
On modeling of responses generated by travel 2.0 implementation: fuzzy rule-based systems
Authors: Basaran Murat Alper , Dogan Seden , Kantarci Kemal 
Published: March 2020

Purpose
Web 2.0 applications enable travelers to evaluate several services and assessment attributes. Constructed websites in several languages trigger a new way of data collections resulting in data streams leading to the accumulation of vast amounts of data, called big data. The need for analysis is in high demand. This study aims to construct a model to investigate which single attribute or interrelated ones having an impact on the performances of hotels.

Design/methodology/approach
The total number of 1,137 observations collected from the website HolidayCheck.de are used from the hotels in the Bavaria region in 2016. Bavaria is a region where both domestic and foreign travelers mostly prefer to visit. Fuzzy rule-based systems, which is a combination of fuzzy set theory (FST) and fuzzy logic, are used. Although the FST is used to convert linguistically expressed perceptions by travelers into mathematically usable data, fuzzy logic is used to construct a model between service attributes and price-performance (PP) to attain the set of single and interrelated attributes on the assessment of PP.

Findings
No single attribute plays a key role in PP assessment. However, two or more interrelated combinations have different impacts on PP. For example, when “Food—Drink” and “Room” moves together from average to good level, PP reaches the highest level of assessment.

Research limitations/implications
Accessibility to too much data is difficult.

Practical implications
A model can be continuously run so that any changes can be observed during the incoming of data.

Social implications
As the consumer reviews and ratings are the crucial source of information for other travelers, hoteliers must monitor and respond them on time in order to deal with the complaints.

Originality/value
Travelers’ perceptions or evaluations are treated with a FST that measures the impression of human beings. New modeling enables researchers to observe not only any single attribute but also interrelated ones on the PP.