bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying the Feedback Between Rice Architecture, Physiology, and Microclimate Under Current and Future CO2 Conditions
Authors: Sikma M. , Ikawa H. , Heusinkveld B. G. , Yoshimoto M. , Hasegawa T. , Groot Haar L. T. , Anten N. P. R. , Nakamura H. , Vilà‐Guerau de Arellano J. , Sakai H. , Tokida T. , Usui Y. , Evers J. B. 
Published: January 2020

AbstractTo assess the micrometeorological consequences of rice variety choices in relation to rising CO2 associated to climate change, we quantified the interplay between rice architecture, physiology, and microclimate in current (~385 μmol mol−1) and future (~580 μmol mol−1) CO2 microenvironments. Two rice varieties contrasting in canopy structure and physiology were grown embedded in irrigated rice paddies, under elevated CO2 (using a Free‐Air CO2 Enrichment facility) and ambient CO2 conditions. The high‐yielding indica variety Takanari is more photosynthetically active and characterized by a more open canopy than a commonly cultivated variety Koshihikari. Our results show a strong diurnal interplay between solar angle, canopy structure, plant physiology, and the overlying atmosphere. Plant architecture was identified as a strong determinant of the relation between plant physiology and microclimate that in turn affects the surface forcing to the overlying atmosphere. Takanari was able to maintain lower canopy temperature both in current and future CO2 owing to the greater atmospheric mixing and stomatal conductance than Koshihikari. In the perspective of food security, a shift to such a higher‐yielding variety would have consequences on the regional surface energy balance, which subsequently might alter regional weather.
Consensus statement for stability assessment and reporting for perovskite photovoltaics based on ISOS procedures
Authors: Khenkin Mark V. , Katz Eugene A. , Abate Antonio , Bardizza Giorgio , Berry Joseph J. , Brabec Christoph , Brunetti Francesca , Bulović Vladimir , Burlingame Quinn , Di Carlo Aldo , Cheacharoen Rongrong , Cheng Yi-Bing , Colsmann Alexander , Cros Stephane , Domanski Konrad , Dusza Michał , Fell Christopher J. , Forrest Stephen R. , Galagan Yulia , Di Girolamo Diego , Grätzel Michael , Hagfeldt Anders , von Hauff Elizabeth , Hoppe Harald , Kettle Jeff , Köbler Hans , Leite Marina S. , Liu Shengzhong , Loo Yueh-Lin , Luther Joseph M. , Ma Chang-Qi , Madsen Morten , Manceau Matthieu , Matheron Muriel , McGehee Michael , Meitzner Rico , Nazeeruddin Mohammad Khaja , Nogueira Ana Flavia , Odabaşı Çağla , Osherov Anna , Park Nam-Gyu , Reese Matthew O. , De Rossi Francesca , Saliba Michael , Schubert Ulrich S. , Snaith Henry J. , Stranks Samuel D. , Tress Wolfgang , Troshin Pavel A. , Turkovic Vida , Veenstra Sjoerd , Visoly-Fisher Iris , Walsh Aron , Watson Trystan , Xie Haibing , Yıldırım Ramazan , Zakeeruddin Shaik Mohammed , Zhu Kai , Lira-Cantu Monica 
Published: January 2020

AbstractImproving the long-term stability of perovskite solar cells is critical to the deployment of this technology. Despite the great emphasis laid on stability-related investigations, publications lack consistency in experimental procedures and parameters reported. It is therefore challenging to reproduce and compare results and thereby develop a deep understanding of degradation mechanisms. Here, we report a consensus between researchers in the field on procedures for testing perovskite solar cell stability, which are based on the International Summit on Organic Photovoltaic Stability (ISOS) protocols. We propose additional procedures to account for properties specific to PSCs such as ion redistribution under electric fields, reversible degradation and to distinguish ambient-induced degradation from other stress factors. These protocols are not intended as a replacement of the existing qualification standards, but rather they aim to unify the stability assessment and to understand failure modes. Finally, we identify key procedural information which we suggest reporting in publications to improve reproducibility and enable large data set analysis.
Structural and dynamic origins of ESR lineshapes in spin-labeled GB1 domain: the insights from spin dynamics simulations based on long MD trajectories
Authors: Izmailov Sergei A. , Rabdano Sevastyan O. , Hasanbasri Zikri , Podkorytov Ivan S. , Saxena Sunil , Skrynnikov Nikolai R. 
Published: January 2020

AbstractSite-directed spin labeling (SDSL) ESR is a valuable tool to probe protein systems that are not amenable to characterization by x-ray crystallography, NMR or EM. While general principles that govern the shape of SDSL ESR spectra are known, its precise relationship with protein structure and dynamics is still not fully understood. To address this problem, we designed seven variants of GB1 domain bearing R1 spin label and recorded the corresponding MD trajectories (combined length 180 μs). The MD data were subsequently used to calculate time evolution of the relevant spin density matrix and thus predict the ESR spectra. The simulated spectra proved to be in good agreement with the experiment. Further analysis confirmed that the spectral shape primarily reflects the degree of steric confinement of the R1 tag and, for the well-folded protein such as GB1, offers little information on local backbone dynamics. The rotameric preferences of R1 side chain are determined by the type of the secondary structure at the attachment site. The rotameric jumps involving dihedral angles χ1 and χ2 are sufficiently fast to directly influence the ESR lineshapes. However, the jumps involving multiple dihedral angles tend to occur in (anti)correlated manner, causing smaller-than-expected movements of the R1 proxyl ring. Of interest, ESR spectra of GB1 domain with solvent-exposed spin label can be accurately reproduced by means of Redfield theory. In particular, the asymmetric character of the spectra is attributable to Redfield-type cross-correlations. We envisage that the current MD-based, experimentally validated approach should lead to a more definitive, accurate picture of SDSL ESR experiments.
Sea lice exposure to non-lethal levels of emamectin benzoate after treatments: a potential risk factor for drug resistance
Authors: Lam Chun Ting , Rosanowski Sarah M. , Walker Martin , St-Hilaire Sophie 
Published: January 2020

AbstractThe avermectin derivative emamectin benzoate (EMB) has been widely used by salmon industries around the world to control sea lice infestations. Resistance to this anti-parasitic drug is also commonly reported in these industries. The objective of this study was to quantify the number of sea lice potentially exposed to sub-lethal concentrations of EMB while fish clear the drug after treatments. We assessed juvenile sea lice abundance after 38 EMB treatments on six Atlantic salmon farms, in a small archipelago in British Colombia, Canada, between 2007 and 2018. We fitted a standard EMB pharmacokinetic curve to determine the time when fish treated with this product would have EMB tissue concentrations below the recommended target therapeutic level. During the study, we estimated that for each sea lice treatment there was, on average, an abundance of 0.12 juvenile sea lice per fish during the time period when the concentrations of EMB would have been lower than 60ppb, the recommended therapeutic treatment level for sea lice. The findings from this study on metaphylactic anti-parasitic treatments identify a potential driver for drug resistance in sea lice that should be further explored.
Study of Soil Seed Banks in Ex-closures for Restoration of Degraded Lands in the Central Rift Valley of Ethiopia
Authors: Mohammed Shemsedin Ahmed , Denboba Mekuria Argaw 
Published: January 2020

AbstractSoil seed banks (SSB) can be important components in the process of rehabilitating degraded lands. Thus, this study was aimed to evaluate the role of SSB to the restoration of degraded lands in six, fifteen and twenty-five year’s ex-closures and adjacent degraded open grazing land (DOGL). Totally, 160 samples of SSB from four soil layers (litter, 0–3 cm, 3–6 cm & 6–9 cm), four sites and ten in a composite of 5 (15 × 15 cm) were collected and tested for seed viability through seed extraction and seedling emergence methods. Species richness and diversity showed a significant difference between the SSB of the ex-closures and DOGL (P = 0.0148 and P = 0.0218 respectively). Seed densities also showed significant differences between the vertical layers of the soils in the ex-closures and DOGL (P = 0.0112) and the interaction effect of the land use type and the vertical soil layers (P = 0.0174). Ex-closures and DOGL scored highest seed densities in their litter and bottom layers of the soils respectively. Most of the woody species in the SSB of older ex-closures were represented in the aboveground flora. Thus, this study has verified that SSB has played a vital role in the restoration of woody species in degraded land through ex-closure practices.
Real-time monitoring of glutathione in living cells using genetically encoded FRET-based ratiometric nanosensor
Authors: Ahmad Mohammad , Anjum Naser A. , Asif Ambreen , Ahmad Altaf 
Published: January 2020

AbstractReduced glutathione (GSH) level inside the cell is a critical determinant for cell viability. The level of GSH varies across the cells, tissues and environmental conditions. However, our current understanding of physiological and pathological GSH changes at high spatial and temporal resolution is limited due to non-availability of practicable GSH-detection methods. In order to measure GSH at real-time, a ratiometric genetically encoded nanosensor was developed using fluorescent proteins and fluorescence resonance energy transfer (FRET) approach. The construction of the sensor involved the introduction of GSH binding protein (YliB) as a sensory domain between cyan fluorescent protein (CFP; FRET donor) and yellow fluorescent protein (YFP; FRET acceptor). The developed sensor, named as FLIP-G (Fluorescence Indicator Protein for Glutathione) was able to measure the GSH level under in vitro and in vivo conditions. When the purified FLIP-G was titrated with different concentrations of GSH, the FRET ratio increased with increase in GSH-concentration. The sensor was found to be specific for GSH and also stable to changes in pH. Moreover, in live bacterial cells, the constructed sensor enabled the real-time quantification of cytosolic GSH that is controlled by the oxidative stress level. When expressed in yeast cells, FRET ratio increased with the external supply of GSH to living cells. Therefore, as a valuable tool, the developed FLIP-G can monitor GSH level in living cells and also help in gaining new insights into GSH metabolism.
Epothilone D alters normal growth, viability and microtubule dependent intracellular functions of cortical neurons in vitro
Authors: Clark J. A. , Chuckowree J. A. , Dyer M. S. , Dickson T. C. , Blizzard C. A. 
Published: January 2020

AbstractBrain penetrant microtubule stabilising agents (MSAs) are being increasingly validated as potential therapeutic strategies for neurodegenerative diseases and traumatic injuries of the nervous system. MSAs are historically used to treat malignancies to great effect. However, this treatment strategy can also cause adverse off-target impacts, such as the generation of debilitating neuropathy and axonal loss. Understanding of the effects that individual MSAs have on neurons of the central nervous system is still incomplete. Previous research has revealed that aberrant microtubule stabilisation can perturb many neuronal functions, such as neuronal polarity, neurite outgrowth, microtubule dependant transport and overall neuronal viability. In the current study, we evaluate the dose dependant impact of epothilone D, a brain penetrant MSA, on both immature and relatively mature mouse cortical neurons in vitro. We show that epothilone D reduces the viability, growth and complexity of immature cortical neurons in a dose dependant manner. Furthermore, in relatively mature cortical neurons, we demonstrate that while cellularly lethal doses of epothilone D cause cellular demise, low sub lethal doses can also affect mitochondrial transport over time. Our results reveal an underappreciated mitochondrial disruption over a wide range of epothilone D doses and reiterate the importance of understanding the dosage, timing and intended outcome of MSAs, with particular emphasis on brain penetrant MSAs being considered to target neurons in disease and trauma.
Efficient whole-cell catalysis for 5-aminovalerate production from L-lysine by using engineered Escherichia coli with ethanol pretreatment
Authors: Cheng Jie , Luo Qing , Duan Huaichuan , Peng Hao , Zhang Yin , Hu Jianping , Lu Yao 
Published: January 2020

AbstractMicroorganisms can utilize biomass to produce valuable chemicals, showing sustainable, renewable and economic advantages compared with traditional chemical synthesis. As a potential five-carbon platform polymer monomer, 5-aminovalerate has been widely used in industrial fields such as clothes and disposable goods. Here we establish an efficient whole-cell catalysis for 5-aminovalerate production with ethanol pretreatment. In this study, the metabolic pathway from L-lysine to 5-aminovalerate was constructed at the cellular level by introducing L-lysine α-oxidase. The newly produced H2O2 and added ethanol both are toxic to the cells, obviously inhibiting their growth. Here, a promising strategy of whole-cell catalysis with ethanol pretreatment is proposed, which greatly improves the yield of 5-aminovalerate. Subsequently, the effects of ethanol pretreatment, substrate concentration, reaction temperature, pH value, metal ion additions and hydrogen peroxide addition on the whole-cell biocatalytic efficiency were investigated. Using 100 g/L of L-lysine hydrochloride as raw material, 50.62 g/L of 5-aminovalerate could be excellently produced via fed-batch bioconversion with the yield of 0.84 mol/mol. The results show that a fast, environmentally friendly and efficient production of 5-aminovalerate was established after introducing the engineered whole-cell biocatalysts. This strategy, combined with ethanol pretreatment, can not only greatly enhance the yield of 5-aminovalerate but also be applied to the biosynthesis of other valuable chemicals.
The plant natural product 2-methoxy-1,4-naphthoquinone stimulates therapeutic neural repair properties of olfactory ensheathing cells
Authors: Chen M. , Vial M. L. , Gee L. , Davis R. A. , St John J. A. , Ekberg J. A. K. 
Published: January 2020

AbstractOlfactory ensheathing cells (OECs) are crucial for promoting the regeneration of the primary olfactory nervous system that occurs throughout life. Transplantation of OECs has emerged as a promising therapy for nervous system injuries, in particular for spinal cord injury repair. Functional outcomes in both animals and humans are, however, highly variable, primarily because it is difficult to rapidly obtain enough OECs for transplantation. Compounds which can stimulate OEC proliferation without changing the phenotype of the cells are therefore highly sought after. Additionally, compounds which can stimulate favourable cell behaviours such as migration and phagocytic activity are desirable. We conducted a medium-throughput screen testing the Davis open access natural product-based library (472 compounds) and subsequently identified the known plant natural product 2-methoxy-1,4-naphthoquinone as a stimulant of OEC viability. We showed that 2-methoxy-1,4-naphthoquinone: (i) strongly stimulates proliferation over several weeks in culture whilst maintaining the OEC phenotype; (ii) stimulates the phagocytic activity of OECs, and (iii) modulates the cell cycle. We also identified the transcription factor Nrf2 as the compound’s potential molecular target. From these extensive investigations we conclude that 2-methoxy-1,4-naphthoquinone may enhance the therapeutic potential of OECs by stimulating proliferation prior to transplantation.
Astroglial changes in the zona incerta in response to motor cortex stimulation in a rat model of chronic neuropathy
Authors: Cha Myeounghoon , Lee Kyung Hee , Lee Bae Hwan 
Published: January 2020

AbstractAlthough astrocytes are known to regulate synaptic transmission and affect new memory formation by influencing long-term potentiation and functional synaptic plasticity, their role in pain modulation is poorly understood. Motor cortex stimulation (MCS) has been used to reduce neuropathic pain through the incertothalamic pathway, including the primary motor cortex (M1) and the zona incerta (ZI). However, there has been no in-depth study of these modulatory effects and region-specific changes in neural plasticity. In this study, we investigated the effects of MCS-induced pain modulation as well as the relationship between the ZI neuroplasticity and MCS-induced pain alleviation in neuropathic pain (NP). MCS-induced threshold changes were evaluated after daily MCS. Then, the morphological changes of glial cells were compared by tissue staining. In order to quantify the neuroplasticity, MAP2, PSD95, and synapsin in the ZI and M1 were measured and analyzed with western blot. In behavioral test, repetitive MCS reduced NP in nerve-injured rats. We also observed recovered GFAP expression in the NP with MCS rats. In the NP with sham MCS rats, increased CD68 level was observed. In the NP with MCS group, increased mGluR1 expression was observed. Analysis of synaptogenesis-related molecules in the M1 and ZI revealed that synaptic changes occured in the M1, and increased astrocytes in the ZI were more closely associated with pain alleviation after MCS. Our findings suggest that MCS may modulate the astrocyte activities in the ZI and synaptic changes in the M1. Our results may provide new insight into the important and numerous roles of astrocytes in the formation and function.
Nearest Neighbour Propensity Score Matching and Bootstrapping for Estimating Binary Patient Response in Oncology: A Monte Carlo Simulation
Authors: Geldof Tine , Popovic Dusan , Van Damme Nancy , Huys Isabelle , Van Dyck Walter 
Published: January 2020

AbstractNearest Neighbour (NN) propensity score (PS) matching methods are commonly used in pharmacoepidemiology to estimate treatment response using observational data. Unfortunately, there is limited evidence on the optimal approach for accurately estimating binary treatment response and, more so, to estimate its variance. Bootstrapping, although commonly used to accurately estimate variance, is rarely used together with PS matching. In this Monte Carlo simulation-based study, we examined the performance of bootstrapping used in conjunction with PS matching, as opposed to different NN matching techniques, on a simulated dataset exhibiting varying levels of real world complexity. Thus, an experimental design was set up that independently varied the proportion of patients treated, the proportion of outcomes censored and the amount of PS matches used. Simulation results were externally validated on a real observational dataset obtained from the Belgian Cancer Registry. We found all investigated PS methods to be stable and concordant, with k-NN matching to be optimally dealing with the censoring problem, typically present in chronic cancer-related datasets, whilst being the least computationally expensive. In contrast, bootstrapping used in conjunction with PS matching, being the most computationally expensive, only showed superior results in small patient populations with long-term largely unobserved treatment effects.
Offsetting anthropogenic carbon emissions from biomass waste and mineralised carbon dioxide
Authors: Tripathi Nimisha , Hills Colin D. , Singh Raj S. , Singh Jamuna S. 
Published: January 2020

AbstractThe present work investigates biomass wastes and their ashes for re-use in combination with mineralised CO2 in cement-bound construction products. A range of biomass residues (e.g., wood-derived, nut shells, fibres, and fruit peels) sourced in India, Africa and the UK were ashed and exposed to CO2 gas. These CO2-reactive ashes could mineralise CO2 gas and be used to cement ‘raw’ biomass in solid carbonated monolithic composites. The CO2 sequestered in ashes (125–414 g CO2/kg) and that emitted after incineration (400–500 g CO2/kg) was within the same range (w/w). The CO2-reactive ashes embodied significant amounts of CO2 (147–424 g equivalent CO2/kg ash). Selected ashes were combined with raw biomass and Portland Cement, CEM 1 and exposed to CO2. The use of CEM 1 in the carbonated products was offset by the CO2 mineralised (i.e. samples were ‘carbon negative’, even when 10% w/w CEM 1 was used); furthermore, biomass ashes were a suitable substitute for CEM 1 up to 50% w/w. The approach is conceptually simple, scalable, and can be applicable to a wide range of biomass ashes in a closed ‘emission-capture’ process ‘loop’. An extrapolation of potential for CO2 offset in Europe provides an estimate of CO2 sequestration potential to 2030.
Analyzing changes in the complexity of climate in the last four decades using MERRA-2 radiation data
Authors: Delgado-Bonal Alfonso , Marshak Alexander , Yang Yuekui , Holdaway Daniel 
Published: January 2020

AbstractThe energy balance of the Earth is controlled by the shortwave and longwave radiation emitted to space. Changes in the thermodynamic state of the system over time affect climate and are noticeable when viewing the system as a whole. In this paper, we study the changes in the complexity of climate in the last four decades using data from the Modern-Era Retrospective analysis for Research and Applications, Version 2 (MERRA-2). First, we study the complexity of the shortwave and longwave radiation fields independently using Approximate Entropy and Sample Entropy, observing that the rate of complexity change is faster for shortwave radiation. Then, we study the causality of those changes using Transfer Entropy to capture the non-linear dynamics of climate, showing that the changes are mainly driven by the variations in shortwave radiation. The observed behavior of climatic complexity could be explained by the changes in cloud amount, and we research that possibility by investigating its evolution from a complexity perspective using data from the International Satellite Cloud Climatology Project (ISCCP).