bluuebunny/crossref_metadata_2025_split huggingface dataset:
A first-principles analysis of the charge transfer in magnesium corrosion
Authors: Würger Tim , Feiler Christian , Vonbun-Feldbauer Gregor B. , Zheludkevich Mikhail L. , Meißner Robert H. 
Published: September 2020

AbstractMagnesium is the lightest structural engineering material and bears high potential to manufacture automotive components, medical implants and energy storage systems. However, the practical use of untreated magnesium alloys is restricted as they are prone to corrosion. An essential prerequisite for the control or prevention of the degradation process is a deeper understanding of the underlying corrosion mechanisms. Prior investigations of the formation of gaseous hydrogen during the corrosion of magnesium indicated that the predominant mechanism for this process follows the Volmer–Heyrovský rather than the previously assumed Volmer–Tafel pathway. However, the energetic and electronic states of both reaction paths as well as the charge state of dissolved magnesium have not been fully unraveled yet. In this study, density functional theory calculations were employed to determine these parameters for the Volmer, Tafel and Heyrovský steps to gain a comprehensive understanding of the major corrosion mechanisms responsible for the degradation of magnesium.
StoneMod: a database for kidney stone modulatory proteins with experimental evidence
Authors: Sassanarakkit Supatcha , Peerapen Paleerath , Thongboonkerd Visith 
Published: September 2020

AbstractBetter understanding of molecular mechanisms for kidney stone formation is required to improve management of kidney stone disease with better therapeutic outcome. Recent kidney stone research has indicated critical roles of a group of proteins, namely ‘stone modulators’, in promotion or inhibition of the stone formation. Nevertheless, such information is currently dispersed and difficult to obtain. Herein, we present the kidney stone modulator database (StoneMod), which is a curated resource by obtaining necessary information of such stone modulatory proteins, which can act as stone promoters or inhibitors, with experimental evidence from previously published studies. Currently, the StoneMod database contains 10, 16, 13, 8 modulatory proteins that affect calcium oxalate crystallization, crystal growth, crystal aggregation, and crystal adhesion on renal tubular cells, respectively. Informative details of each modulatory protein and PubMed links to the published articles are provided. Additionally, hyperlinks to other protein/gene databases (e.g., UniProtKB, Swiss-Prot, Human Protein Atlas, PeptideAtlas, and Ensembl) are made available for the users to obtain additional in-depth information of each protein. Moreover, this database provides a user-friendly web interface, in which the users can freely access to the information and/or submit their data to deposit or update. Database URL:https://www.stonemod.org.
Development of screening methods for functional characterization of UGTs from Stevia rebaudiana
Authors: Petit Eva , Berger Monique , Camborde Laurent , Vallejo Veronica , Daydé Jean , Jacques Alban 
Published: September 2020

AbstractGlycosylation is a key modification that contributes to determine bioactivity and bioavailability of plant natural products, including that of terpenoids and steviol glycosides (SVglys). It is mediated by uridine-diphosphate glycosyltransferases (UGTs), that achieve their activity by transferring sugars on small molecules. Thus, the diversity of SVglys is due to the number, the position and the nature of glycosylations on the hydroxyl groups in C-13 and C-19 of steviol. Despite the intense sweetener property of SVglys and the numerous studies conducted, the SVglys biosynthetic pathway remains largely unknown. More than 60 SVglys and 68 putative UGTs have been identified in Stevia rebaudiana. This study aims to provide methods to characterize UGTs putatively involved in SVglys biosynthesis. After agroinfiltration-based transient gene expression in Nicotiana benthamiana, functionality of the recombinant UGT can be tested simply and directly in plants expressing it or from a crude extract. The combined use of binary vectors from pGWBs series to produce expression vectors containing the stevia's UGT, enables functionality testing with many substrates as well as other applications for further analysis, including subcellular localization.
Computational mechanistic study of the unimolecular dissociation of ethyl hydroperoxide and its bimolecular reactions with atmospheric species
Authors: Almatarneh Mansour H. , Alnajajrah Asmaa , Altarawneh Mohammednoor , Zhao Yuming , Halim Mohammad A. 
Published: September 2020

AbstractA detailed computational study of the atmospheric reaction of the simplest Criegee intermediate CH2OO with methane has been performed using the density functional theory (DFT) method and high-level calculations. Solvation models were utilized to address the effect of water molecules on prominent reaction steps and their associated energies. The structures of all proposed mechanisms were optimized using B3LYP functional with several basis sets: 6-31G(d), 6-31G (2df,p), 6-311++G(3df,3pd) and at M06-2X/6-31G(d) and APFD/6-31G(d) levels of theory. Furthermore, all structures were optimized at the B3LYP/6-311++G(3df,3pd) level of theory. The intrinsic reaction coordinate (IRC) analysis was performed for characterizing the transition states on the potential energy surfaces. Fifteen different mechanistic pathways were studied for the reaction of Criegee intermediate with methane. Both thermodynamic functions (ΔH and ΔG), and activation parameters (activation energies Ea, enthalpies of activation ΔHǂ, and Gibbs energies of activation ΔGǂ) were calculated for all pathways investigated. The individual mechanisms for pathways A1, A2, B1, and B2, comprise two key steps: (i) the formation of ethyl hydroperoxide (EHP) accompanying with the hydrogen transfer from the alkanes to the terminal oxygen atom of CIs, and (ii) a following unimolecular dissociation of EHP. Pathways from C1 → H1 involve the bimolecular reaction of EHP with different atmospheric species. The photochemical reaction of methane with EHP (pathway E1) was found to be the most plausible reaction mechanism, exhibiting an overall activation energy of 7 kJ mol−1, which was estimated in vacuum at the B3LYP/6-311++G(3df,3pd) level of theory. All of the reactions were found to be strongly exothermic, expect the case of the sulfur dioxide-involved pathway that is predicted to be endothermic. The solvent effect plays an important role in the reaction of EHP with ammonia (pathway F1). Compared with the gas phase reaction, the overall activation energy for the solution phase reaction is decreased by 162 and 140 kJ mol−1 according to calculations done with the SMD and PCM solvation models, respectively.
In vivo assessment of mechanisms underlying the neurovascular basis of postictal amnesia
Authors: Farrell Jordan S. , Colangeli Roberto , Dudok Barna , Wolff Marshal D. , Nguyen Sarah L. , Jackson Jesse , Dickson Clayton T. , Soltesz Ivan , Teskey G. Campbell 
Published: September 2020

AbstractLong-lasting confusion and memory difficulties during the postictal state remain a major unmet problem in epilepsy that lacks pathophysiological explanation and treatment. We previously identified that long-lasting periods of severe postictal hypoperfusion/hypoxia, not seizures per se, are associated with memory impairment after temporal lobe seizures. While this observation suggests a key pathophysiological role for insufficient energy delivery, it is unclear how the networks that underlie episodic memory respond to vascular constraints that ultimately give rise to amnesia. Here, we focused on cellular/network level analyses in the CA1 of hippocampus in vivo to determine if neural activity, network oscillations, synaptic transmission, and/or synaptic plasticity are impaired following kindled seizures. Importantly, the induction of severe postictal hypoperfusion/hypoxia was prevented in animals treated by a COX-2 inhibitor, which experimentally separated seizures from their vascular consequences. We observed complete activation of CA1 pyramidal neurons during brief seizures, followed by a short period of reduced activity and flattening of the local field potential that resolved within minutes. During the postictal state, constituting tens of minutes to hours, we observed no changes in neural activity, network oscillations, and synaptic transmission. However, long-term potentiation of the temporoammonic pathway to CA1 was impaired in the postictal period, but only when severe local hypoxia occurred. Lastly, we tested the ability of rats to perform object-context discrimination, which has been proposed to require temporoammonic input to differentiate between sensory experience and the stored representation of the expected object-context pairing. Deficits in this task following seizures were reversed by COX-2 inhibition, which prevented severe postictal hypoxia. These results support a key role for hypoperfusion/hypoxia in postictal memory impairments and identify that many aspects of hippocampal network function are resilient during severe hypoxia except for long-term synaptic plasticity.
Seasonality of moisture supplies to precipitation over the Third Pole: a stable water isotopic perspective
Authors: Yang Xiaoxin , Yao Tandong 
Published: September 2020

AbstractThis study integrated isotopic composition in precipitation at 50 stations on and around the Tibetan Plateau (TP) and demonstrated the distinct seasonality of isotopic composition in precipitation across the study period. The potential effect of water vapor isotopes on precipitation isotopes is studied by comparing the station precipitation data with extensive isotopic patterns in atmospheric water vapor, revealing the close linkage between the two. The analysis of contemporary water vapor transport and potential helps confirm the different mechanisms behind precipitation isotopic compositions in different areas, as the southern TP is more closely related to large-scale atmospheric circulation such as local Hadley and summer monsoon circulations during other seasons than winter, while the northern TP is subject to the westerly prevalence and advective moisture supply and precipitation processes. The new data presented in this manuscript also enrich the current dataset for the study of precipitation isotopes in this region and together provide a valuable database for verification of the isotope-integrated general circulation model and explanation of related physical processes.
Viromers as carriers for mRNA-mediated expression of therapeutic molecules under inflammatory conditions
Authors: Jansig Edith , Geissler Stefanie , Rieckmann Vera , Kuenemund Anja , Hietel Benjamin , Schenk Mathias , Wussow Sebastian , Kreideweiss Patrick , Panzner Steffen , Reinsch Christian , Cynis Holger 
Published: September 2020

AbstractTherapeutic mRNA delivery has been described for several treatment options, such as vaccination and cancer immunotherapy. However, mRNA delivery has to be accompanied by the development and testing of suitable carrier materials due to the instability of mRNAs in human body fluids. In the present study, we investigated the ability of recently developed Viromers to deliver mRNAs in a classical inflammatory setting. We tested mRNAs coding for active components of preclinical (7ND) and approved (sTNF-RII) biologics, in vitro and in vivo. 7ND is an established blocker of the CCR2 axis, whereas sTNF-RII is the active component of the approved drug Etanercept. Viromer/mRNA complexes were transfected into murine macrophages in vitro. Protein expression was analysed using Luciferase reporter expression and mainly identified in spleen, blood and bone marrow in vivo. 7ND-mRNA delivery led to efficient blockage of monocytes infiltration in thioglycolate-induced peritonitis in mice, underlining the ability of Viromers to deliver a therapeutic mRNA cargo without overt toxicity. Therefore, we propose Viromer-based mRNA delivery as a suitable option for the treatment of inflammatory disorders beyond infusion of biological molecules.
Advantage of fat-derived CD73 positive cells from multiple human tissues, prospective isolated mesenchymal stromal cells
Authors: Suto Eriko G. , Mabuchi Yo , Toyota Saki , Taguchi Miyu , Naraoka Yuna , Itakura Natsumi , Matsuoka Yoh , Fujii Yasuhisa , Miyasaka Naoyuki , Akazawa Chihiro 
Published: September 2020

AbstractSomatic stem cells have been isolated from multiple human tissues for their potential usefulness in cell therapy. Currently, mesenchymal stromal cells (MSCs) are prepared after several passages requiring a few months of cell culture. In this study, we used a prospective isolation method of somatic stem cells from gestational or fat tissues, which were identified using CD73 antibody. CD73-positive population from various tissues existed individually in flowcytometric pattern, especially subcutaneous fat- and amniotic-derived cells showed the highest enrichment of CD73-positive cells. Moreover, the cell populations isolated with the prospective method showed higher proliferative capacity and stem cell marker expression, compared to the cell populations which isolated through several passages of culturing whole living cells: which we named “conventional method” in this paper. Furthermore, the therapeutic potential of CD73-positive cells was evaluated in vivo using a mouse model of pulmonary fibrosis. After intranasal administration, murine CD73-positive cells reduced macrophage infiltration and inhibited fibrosis development. These results suggest that further testing using CD73-positive cells may be beneficial to help establish the place in regenerative medicine use.
Spatial structure, parameter nonlinearity, and intelligent algorithms in constructing pedotransfer functions from large-scale soil legacy data
Authors: Chakraborty Poulamee , Das Bhabani S. , Vasava Hitesh B. , Panigrahi Niranjan , Santra Priyabrata 
Published: September 2020

AbstractPedotransfer function (PTF) approach is a convenient way for estimating difficult-to-measure soil properties from basic soil data. Typically, PTFs are developed using a large number of samples collected from small (regional) areas for training and testing a predictive model. National soil legacy databases offer an opportunity to provide soil data for developing PTFs although legacy data are sparsely distributed covering large areas. Here, we examined the Indian soil legacy (ISL) database to select a comprehensive training dataset for estimating cation exchange capacity (CEC) as a test case in the PTF approach. Geostatistical and correlation analyses showed that legacy data entail diverse spatial and correlation structure needed in building robust PTFs. Through non-linear correlation measures and intelligent predictive algorithms, we developed a methodology to extract an efficient training dataset from the ISL data for estimating CEC with high prediction accuracy. The selected training data had comparable spatial variation and nonlinearity in parameters for training and test datasets. Thus, we identified specific indicators for constructing robust PTFs from legacy data. Our results open a new avenue to use large volume of existing soil legacy data for developing region-specific PTFs without the need for collecting new soil data.
A data-driven typology of asthma medication adherence using cluster analysis
Authors: Tibble Holly , Chan Amy , Mitchell Edwin A. , Horne Elsie , Doudesis Dimitrios , Horne Rob , Mizani Mehrdad A. , Sheikh Aziz , Tsanas Athanasios 
Published: September 2020

AbstractAsthma preventer medication non-adherence is strongly associated with poor asthma control. One-dimensional measures of adherence may ignore clinically important patterns of medication-taking behavior. We sought to construct a data-driven multi-dimensional typology of medication non-adherence in children with asthma. We analyzed data from an intervention study of electronic inhaler monitoring devices, comprising 211 patients yielding 35,161 person-days of data. Five adherence measures were extracted: the percentage of doses taken, the percentage of days on which zero doses were taken, the percentage of days on which both doses were taken, the number of treatment intermissions per 100 study days, and the duration of treatment intermissions per 100 study days. We applied principal component analysis on the measures and subsequently applied k-means to determine cluster membership. Decision trees identified the measure that could predict cluster assignment with the highest accuracy, increasing interpretability and increasing clinical utility. We demonstrate the use of adherence measures towards a three-group categorization of medication non-adherence, which succinctly describes the diversity of patient medication taking patterns in asthma. The percentage of prescribed doses taken during the study contributed to the prediction of cluster assignment most accurately (84% in out-of-sample data).
Left hemispheric α band cerebral oscillatory changes correlate with verbal memory
Authors: Araki Toshihiko , Watanabe Yoshiyuki , Hirata Masayuki 
Published: September 2020

AbstractEvent-related synchronisation (ERS) and event-related desynchronisation (ERD) have been observed via magnetoencephalography (MEG) in the language-dominant hemisphere. However, the relationship between ERS/ERD and clinical language indices is unclear. Therefore, the present study evaluated brain activity utilising MEG during a verb generation task in 36 subjects and determined ERS/ERD power values in θ, α, β, low γ and high γ frequency bands. To measure clinical language indices, we adopted Wechsler Memory Scale-revised. We observed ERD in the α band from the bilateral occipital to the left central brain region, in the β band from the bilateral occipital to the left frontal region and in the low γ band a high-power signal in the left frontal region. We also observed ERS in the θ band in bilateral frontal region and in the high γ band in bilateral occipital region. Furthermore, we found a significant negative correlation between α-band ERD power at the left postcentral gyrus and medial superior frontal gyrus and verbal memory score (correlation coefficients =  − 0.574 and − 0.597, respectively). These results suggest that individuals with lower linguistic memory have less desynchronised α-band ERD power and α-band ERD power in the left hemisphere may be a neurophysiological biomarker for verbal memory.
Characterization of rare ABCC8 variants identified in Spanish pulmonary arterial hypertension patients
Authors: Lago-Docampo Mauro , Tenorio Jair , Hernández-González Ignacio , Pérez-Olivares Carmen , Escribano-Subías Pilar , Pousada Guillermo , Baloira Adolfo , Arenas Miguel , Lapunzina Pablo , Valverde Diana 
Published: September 2020

AbstractPulmonary Arterial Hypertension (PAH) is a rare and fatal disease where knowledge about its genetic basis continues to increase. In this study, we used targeted panel sequencing in a cohort of 624 adult and pediatric patients from the Spanish PAH registry. We identified 11 rare variants in the ATP-binding Cassette subfamily C member 8 (ABCC8) gene, most of them with splicing alteration predictions. One patient also carried another variant in SMAD1 gene (c.27delinsGTAAAG). We performed an ABCC8 in vitro biochemical analyses using hybrid minigenes to confirm the correct mRNA processing of 3 missense variants (c.211C > T p.His71Tyr, c.298G > A p.Glu100Lys and c.1429G > A p.Val477Met) and the skipping of exon 27 in the novel splicing variant c.3394G > A. Finally, we used structural protein information to further assess the pathogenicity of the variants. The results showed 11 novel changes in ABCC8 and 1 in SMAD1 present in PAH patients. After in silico and in vitro biochemical analyses, we classified 2 as pathogenic (c.3288_3289del and c.3394G > A), 6 as likely pathogenic (c.211C > T, c.1429G > A, c.1643C > T, c.2422C > A, c.2694 + 1G > A, c.3976G > A and SMAD1 c.27delinsGTAAAG) and 3 as Variants of Uncertain Significance (c.298G > A, c.2176G > A and c.3238G > A). In all, we show that coupling in silico tools with in vitro biochemical studies can improve the classification of genetic variants.
Flexible ZnO-mAb nanoplatforms for selective peripheral blood mononuclear cell immobilization
Authors: Babu K. Sowri , Pinheiro Pedro F. , Marques Cátia F. , Justino Gonçalo C. , Andrade Suzana M. , Alves Marta M. 
Published: September 2020

AbstractCancer is the second cause of death worldwide. This devastating disease requires specific, fast, and affordable solutions to mitigate and reverse this trend. A step towards cancer-fighting lies in the isolation of natural killer (NK) cells, a set of innate immune cells, that can either be used as biomarkers of tumorigenesis or, after autologous transplantation, to fight aggressive metastatic cells. In order to specifically isolate NK cells (which express the surface NKp30 receptor) from peripheral blood mononuclear cells, a ZnO immunoaffinity-based platform was developed by electrodeposition of the metal oxide on a flexible indium tin oxide (ITO)-coated polyethylene terephthalate (PET) substrate. The resulting crystalline and well-aligned ZnO nanorods (NRs) proved their efficiency in immobilizing monoclonal anti-human NKp30 antibodies (mAb), obviating the need for additional procedures for mAb immobilization. The presence of NK cells on the peripheral blood mononuclear cell (PBMCs) fraction was evaluated by the response to their natural ligand (B7-H6) using an acridine orange (AO)-based assay. The successful selection of NK cells from PBMCs by our nanoplatform was assessed by the photoluminescent properties of AO. This easy and straightforward ZnO-mAb nanoplatform paves the way for the design of biosensors for clinic diagnosis, and, due to its inherent biocompatibility, for the initial selection of NK cells for autotransplantation immunotherapies.
Horizontal ‘gene drives’ harness indigenous bacteria for bioremediation
Authors: French Katherine E. , Zhou Zhongrui , Terry Norman 
Published: September 2020

AbstractEngineering bacteria to clean-up oil spills is rapidly advancing but faces regulatory hurdles and environmental concerns. Here, we develop a new technology to harness indigenous soil microbial communities for bioremediation by flooding local populations with catabolic genes for petroleum hydrocarbon degradation. Overexpressing three enzymes (almA, xylE, p450cam) in Escherichia coli led to degradation of 60–99% of target hydrocarbon substrates. Mating experiments, fluorescence microscopy and TEM revealed indigenous bacteria could obtain these vectors from E. coli through several mechanisms of horizontal gene transfer (HGT), including conjugation and cytoplasmic exchange through nanotubes. Inoculating petroleum-polluted sediments with E. coli carrying the vector pSF-OXB15-p450camfusion showed that the E. coli cells died after five days but a variety of bacteria received and carried the vector for over 60 days after inoculation. Within 60 days, the total petroleum hydrocarbon content of the polluted soil was reduced by 46%. Pilot experiments show that vectors only persist in indigenous populations when under selection pressure, disappearing when this carbon source is removed. This approach to remediation could prime indigenous bacteria for degrading pollutants while providing minimal ecosystem disturbance.