bluuebunny/crossref_metadata_2025_split huggingface dataset:
Separating Physics and Dynamics Grids for Improved Computational Efficiency in Spectral Element Earth System Models
Authors: Hannah Walter M. , Bradley Andrew M. , Guba Oksana , Tang Qi , Golaz Jean‐Christophe , Wolfe Jon 
Published: June 2021

AbstractPrevious studies have shown that atmospheric models with a spectral element grid can benefit from putting physics calculations on a relatively coarse finite volume grid. Here we demonstrate an alternative high‐order, element‐based mapping approach used to implement a quasi‐equal‐area, finite volume physics grid in E3SM. Unlike similar methods, the new method in E3SM requires topology data purely local to each spectral element, which trivially allows for regional mesh refinement. Simulations with physics grids defined by 2 × 2, 3 × 3, and 4 × 4 divisions of each element are shown to verify that the alternative physics grid does not qualitatively alter the model solution. The model performance is substantially affected by the reduction of physics columns when using the 2 × 2 grid, which can increase the throughput of physics calculations by roughly 60%–120% depending on whether the computational resources are configured to maximize throughput or efficiency. A pair of regionally refined cases are also shown to highlight the refinement capability.
Full Waveform Inversion Beneath the Central Andes: Insight Into the Dehydration of the Nazca Slab and Delamination of the Back‐Arc Lithosphere
Authors: Gao Yajian , Tilmann Frederik , van Herwaarden Dirk‐Philip , Thrastarson Solvi , Fichtner Andreas , Heit Benjamin , Yuan Xiaohui , Schurr Bernd 
Published: June 2021

AbstractWe present a new seismic tomography model for the crust and upper mantle beneath the Central Andes based on multi‐scale full seismic waveform inversion, proceeding from long periods (40–80 s) over several steps down to 12–60 s. The spatial resolution and trade‐offs among parameters are estimated through the multi‐parameter point‐spread functions. P‐ and S‐wave velocity structures with spatial resolution of 30–40 km for the upper mantle and 20–25 km for the crust could be resolved in the central study region. In our study, the subducting Nazca slab is clearly imaged in the upper mantle, with dip‐angle variations from the north to the south. Bands of low velocities in the crust and mantle wedge indicate intense crustal partial melting and hydration of the mantle wedge beneath the frontal volcanic arc, respectively, and they are linked to the vigorous dehydration from the subducting Nazca plate and intermediate depth seismicity within the slab. These low‐velocity bands are interrupted at 19.8°–21°S, both in the crust and uppermost mantle, hinting at the lower extent of crustal partial melting and hydration of the mantle wedge. The variation of lithospheric high‐velocity anomalies below the back‐arc from north to south allows insight into the evolutionary foundering stages of the Central Andean margin. A high‐velocity layer beneath the southern Altiplano suggests underthrusting of the leading edge of the Brazilian Shield. In contrast, a steeply westward dipping high‐velocity block and low‐velocity lithospheric uppermost mantle beneath the southern Puna plateau hint at the ongoing lithospheric delamination.
Elastic Geobarometry for Anisotropic Inclusions in Anisotropic Host Minerals: Quartz‐in‐Zircon
Authors: Gonzalez Joseph P. , Mazzucchelli Mattia L. , Angel Ross J. , Alvaro Matteo 
Published: June 2021

AbstractCurrent models for elastic geobarometry have been developed with the assumption that the host and/or inclusion minerals are elastically isotropic. This assumption has limited applications of elastic thermobarometry to mineral inclusions contained in cubic quasi‐isotropic host minerals (e.g., garnet). Here, we report a new elastic model that takes into account the anisotropic elastic properties and relative crystallographic orientation (RCO) of a host‐inclusion system where both minerals are noncubic. This anisotropic elastic model can be used for host‐inclusion elastic thermobarometric calculations provided that the RCO and elastic properties of both the host and inclusion are known. We then used this anisotropic elastic model to numerically evaluate the effects of elastic anisotropy and RCO on the strains and stresses developed in a quartz inclusion entrapped in a zircon host after exhumation from known entrapment P‐T conditions to room P‐T conditions. We conclude that the anisotropic quartz‐in‐zircon elastic model is suitable for elastic thermobarometry and may be widely applicable to crustal rocks. Our results demonstrate that isotropic elastic models cannot be used to determine the entire strain state of an elastically anisotropic inclusion contained in an elastically anisotropic host mineral, and therefore may lead to errors on estimated remnant inclusion pressures.
Pre-emptive pharmacological inhibition of fatty acid–binding protein 4 attenuates kidney fibrosis by reprogramming tubular lipid metabolism
Authors: Chen Yuting , Dai Yue , Song Kaixin , Huang Yi , Zhang Le , Zhang Cuntai , Yan Qi , Gao Hongyu 
Published: June 2021

AbstractKidney fibrosis is a hallmark of chronic kidney disease (CKD) progression that is caused by tubular injury and dysregulated lipid metabolism. Genetic abolition fatty acid-binding protein 4 (FABP4), a key lipid transporter, has been reported to suppress kidney interstitial fibrosis. However, the role and underlying mechanism of chemical inhibition of FABP4 in fibrotic kidney have not been well-documented. Here, we examined preemptive the effect of a FABP4 inhibitor, BMS309403, on lipid metabolism of tubular epithelial cells (TECs) and progression of kidney fibrosis. The expression of FABP4 was significantly elevated, concomitated with the accumulation of lipid droplets in TECs during kidney fibrosis. Treatment with BMS309403 alleviated lipid deposition of TECs, as well as interstitial fibrotic responses both in unilateral ureteral obstruction (UUO)-engaged mice and TGF-β-induced TECs. Moreover, BMS309403 administration enhanced fatty acid oxidation (FAO) in TECs by regulating peroxisome proliferator-activated receptor γ (PPARγ) and restoring FAO-related enzyme activities; In addition, BMS309403 markedly reduced cell lipotoxicity, such as endoplasmic reticulum (ER) stress and apoptosis in fibrotic kidney. Taken together, our results suggest that preemptive pharmacological inhibition of FABP4 by BMS309403 rebalances abnormal lipid metabolism in TECs and attenuates the progression of kidney fibrosis, thus may hold therapeutic potential for the treatment of fibrotic kidney diseases.
FtsZ induces membrane deformations via torsional stress upon GTP hydrolysis
Authors: Ramirez-Diaz Diego A. , Merino-Salomón Adrián , Meyer Fabian , Heymann Michael , Rivas Germán , Bramkamp Marc , Schwille Petra 
Published: June 2021

AbstractFtsZ is a key component in bacterial cell division, being the primary protein of the presumably contractile Z ring. In vivo and in vitro, it shows two distinctive features that could so far, however, not be mechanistically linked: self-organization into directionally treadmilling vortices on solid supported membranes, and shape deformation of flexible liposomes. In cells, circumferential treadmilling of FtsZ was shown to recruit septum-building enzymes, but an active force production remains elusive. To gain mechanistic understanding of FtsZ dependent membrane deformations and constriction, we design an in vitro assay based on soft lipid tubes pulled from FtsZ decorated giant lipid vesicles (GUVs) by optical tweezers. FtsZ filaments actively transform these tubes into spring-like structures, where GTPase activity promotes spring compression. Operating the optical tweezers in lateral vibration mode and assigning spring constants to FtsZ coated tubes, the directional forces that FtsZ-YFP-mts rings exert upon GTP hydrolysis can be estimated to be in the pN range. They are sufficient to induce membrane budding with constricting necks on both, giant vesicles and E.coli cells devoid of their cell walls. We hypothesize that these forces result from torsional stress in a GTPase activity dependent manner.
Visible-light photoredox-catalyzed umpolung carboxylation of carbonyl compounds with CO2
Authors: Cao Guang-Mei , Hu Xin-Long , Liao Li-Li , Yan Si-Shun , Song Lei , Chruma Jason J. , Gong Li , Yu Da-Gang 
Published: June 2021

AbstractPhotoredox-mediated umpolung strategy provides an alternative pattern for functionalization of carbonyl compounds. However, general approaches towards carboxylation of carbonyl compounds with CO2remain scarce. Herein, we report a strategy for visible-light photoredox-catalyzed umpolung carboxylation of diverse carbonyl compounds with CO2by using Lewis acidic chlorosilanes as activating/protecting groups. This strategy is general and practical to generate valuable α-hydroxycarboxylic acids. It works well for challenging alkyl aryl ketones and aryl aldehydes, as well as for α-ketoamides and α-ketoesters, the latter two of which have never been successfully applied in umpolung carboxylations with CO2(to the best of our knowledge). This reaction features high selectivity, broad substrate scope, good functional group tolerance, mild reaction conditions and facile derivations of products to bioactive compounds, including oxypheonium, mepenzolate bromide, benactyzine, and tiotropium. Moreover, the formation of carbon radicals and carbanions as well as the key role of chlorosilanes are supported by control experiments.
Synergistic sequence contributions bias glycation outcomes
Authors: McEwen Joseph M. , Fraser Sasha , Guir Alexxandra L. Sosa , Dave Jaydev , Scheck Rebecca A. 
Published: June 2021

AbstractThe methylglyoxal-derived hydroimidazolone isomer, MGH-1, is an abundant advanced glycation end-product (AGE) associated with disease and age-related disorders. As AGE formation occurs spontaneously and without an enzyme, it remains unknown why certain sites on distinct proteins become modified with specific AGEs. Here, we use a combinatorial peptide library to determine the chemical features that favor MGH-1. When properly positioned, tyrosine is found to play an active mechanistic role that facilitates MGH-1 formation. This work offers mechanistic insight connecting multiple AGEs, including MGH-1 and carboxyethylarginine (CEA), and reconciles the role of negative charge in influencing glycation outcomes. Further, this study provides clear evidence that glycation outcomes can be influenced through long- or medium-range cooperative interactions. This work demonstrates that these chemical features also predictably template selective glycation on full-length protein targets expressed in mammalian cells. This information is vital for developing methods that control glycation in living cells and will enable the study of glycation as a functional post-translational modification.
An electrostatics method for converting a time-series into a weighted complex network
Authors: Tsiotas Dimitrios , Magafas Lykourgos , Argyrakis Panos 
Published: June 2021

AbstractThis paper proposes a new method for converting a time-series into a weighted graph (complex network), which builds on electrostatics in physics. The proposed method conceptualizes a time-series as a series of stationary, electrically charged particles, on which Coulomb-like forces can be computed. This allows generating electrostatic-like graphs associated with time-series that, additionally to the existing transformations, can be also weighted and sometimes disconnected. Within this context, this paper examines the structural similarity between five different types of time-series and their associated graphs that are generated by the proposed algorithm and the visibility graph, which is currently the most popular algorithm in the literature. The analysis compares the source (original) time-series with the node-series generated by network measures (that are arranged into the node-ordering of the source time-series), in terms of a linear trend, chaotic behaviour, stationarity, periodicity, and cyclical structure. It is shown that the proposed electrostatic graph algorithm generates graphs with node-measures that are more representative of the structure of the source time-series than the visibility graph. This makes the proposed algorithm more natural rather than algebraic, in comparison with existing physics-defined methods. The overall approach also suggests a methodological framework for evaluating the structural relevance between the source time-series and their associated graphs produced by any possible transformation.
The curcumin analog (PAC) suppressed cell survival and induced apoptosis and autophagy in oral cancer cells
Authors: Semlali Abdelhabib , Contant Camille , Al-Otaibi Basem , Al-Jammaz Ibrahim , Chandad Fatiha 
Published: June 2021

AbstractPAC (3,5-Bis (4-hydroxy-3-methoxybenzylidene)-N-methyl-4-piperidone), a novel bioactive curcumin analog, has been reported to have anticancer properties against various tumors. However, the anti-cancer effects of PAC on oral cavity squamous cell carcinoma were not studied yet. Our aim is to investigate the anti-oral cancer properties of PAC in vitro, and determine the molecular mechanisms underlying these effects. Viability assays including MTT and LDH were conducted to measure cell proliferation. Flow cytometry-based cytotoxicity assay was performed to detect autophagic cell death and oxidative stress markers. Western blotting was used for measuring protein expression/activation in apoptotic, autophagic and pro-carcinogenic cellular signaling pathways. We demonstrated that PAC preferentially and, in a dose, -dependent way kills oral cancer cells, but was not toxic to normal human gingival cells. PAC destabilizes cell-cycle distributions, inhibits the expression of oncogenes (cyclin D1) and that of cyclin-dependent kinase inhibitor (p21WAF1) is upregulated, increases the expression of p53 gene, and inhibits epithelial-mesenchymal transition markers in oral cancer cells. The PAC effect involve various signaling pathways including NF-κB, MAPK, Wnt, caspase-3/9 and PARP1. Finally, PAC demonstrated ability to induce autophagy, decrease production of reactive oxygen species, increase intracellular glutathione (GSH) activity, and reduce mitochondrial membrane potential in oral cancer cells. In conclusion, PAC inhibits the proliferation and increases the apoptosis and autophagy and oxidative stress of oral cancer cells. These effects involve ERK1/2, p38/JNK, NF-κB and Wnt cellular signaling pathways. Overall, our study suggests the potential use of PAC to treat oral cancer.
Nectar non-protein amino acids (NPAAs) do not change nectar palatability but enhance learning and memory in honey bees
Authors: Carlesso Daniele , Smargiassi Stefania , Pasquini Elisa , Bertelli Giacomo , Baracchi David 
Published: June 2021

AbstractFloral nectar is a pivotal element of the intimate relationship between plants and pollinators. Nectars are composed of a plethora of nutritionally valuable compounds but also hundreds of secondary metabolites (SMs) whose function remains elusive. Here we performed a set of behavioural experiments to study whether five ubiquitous nectar non-protein amino acids (NPAAs: β-alanine, GABA, citrulline, ornithine and taurine) interact with gustation, feeding preference, and learning and memory inApis mellifera. We showed that foragers were unable to discriminate NPAAs from water when only accessing antennal chemo-tactile information and that freely moving bees did not exhibit innate feeding preferences for NPAAs. Also, NPAAs did not alter food consumption or longevity in caged bees over 10 days. Taken together our data suggest that natural concentrations of NPAAs did not alter nectar palatability to bees. Olfactory conditioning assays showed that honey bees were more likely to learn a scent when it signalled a sucrose reward containing either β-alanine or GABA, and that GABA enhanced specific memory retention. Conversely, when ingested two hours prior to conditioning, GABA, β-alanine, and taurine weakened bees’ acquisition performances but not specific memory retention, which was enhanced in the case of β-alanine and taurine. Neither citrulline nor ornithine affected learning and memory. NPAAs in nectars may represent a cooperative strategy adopted by plants to attract beneficial pollinators.
Distributed groundwater recharge potentials assessment based on GIS model and its dynamics in the crystalline rocks of South India
Authors: Fauzia  , Surinaidu L. , Rahman Abdur , Ahmed Shakeel 
Published: June 2021

AbstractExtensive change in land use, climate, and over-exploitation of groundwater has increased pressure on aquifers, especially in the case of crystalline rocks throughout the world. To support sustainability in groundwater management require proper understating of groundwater dynamics and recharge potential. GIS based studies have gained immense popularity in groundwater exploration in recent years because they are fast and provide recent information on the resource for future growth. Thus, the present study utilized a GIS-based Weighted Overlay Index (WOI) model to identify the potential recharge zones and to gain deep knowledge of groundwater dynamics. The in situ infiltration tests have been carried out, which is the key process in groundwater recharge and is neglected in many cases for WOI. In the WOI, ten thematic layers from the parameters influencing and involved in the recharge process are considered to identify potential recharge zones. The results suggested a significant underestimation of recharge potential without considering site-specific infiltration rates that one needs to be considered. The present WOI model considered in situ infiltration information and classified the entire area into four recharge zones, good, moderate, poor, and very poor. The final integrated map compared with the real-time field data like water level fluctuation and infiltration to analyse occurrence and quantification of recharge. The estimated average groundwater draft is 21.9 mcm, while annual renewable recharge is only 5.7 mcm that causing a continuous fall of the groundwater table. The study is useful in selecting regions with more focussed recharge studies and suggested the need of reducing groundwater demand by changing cropping patterns through a predictive decision support tool.
Therapeutic hypercapnia for prevention of secondary ischemia after severe subarachnoid hemorrhage: physiological responses to continuous hypercapnia
Authors: Stetter Christian , Weidner Franziska , Lilla Nadine , Weiland Judith , Kunze Ekkehard , Ernestus Ralf-Ingo , Muellenbach Ralf Michael , Westermaier Thomas 
Published: June 2021

AbstractTemporary hypercapnia has been shown to increase cerebral blood flow (CBF) and might be used as a therapeutical tool in patients with severe subarachnoid hemorrhage (SAH). It was the aim of this study was to investigate the optimum duration of hypercapnia. This point is assumed to be the time at which buffer systems become active, cause an adaptation to changes of the arterial partial pressure of carbon dioxide (PaCO2) and annihilate a possible therapeutic effect. In this prospective interventional study in a neurosurgical ICU the arterial partial pressure of carbon dioxide (PaCO2) was increased to a target range of 55 mmHg for 120 min by modification of the respiratory minute volume (RMV) one time a day between day 4 and 14 in 12 mechanically ventilated poor-grade SAH-patients. Arterial blood gases were measured every 15 min. CBF and brain tissue oxygen saturation (StiO2) were the primary and secondary end points. Intracranial pressure (ICP) was controlled by an external ventricular drainage. Under continuous hypercapnia (PaCO2 of 53.17 ± 5.07), CBF was significantly elevated between 15 and 120 min after the start of hypercapnia. During the course of the trial intervention, cardiac output also increased significantly. To assess the direct effect of hypercapnia on brain perfusion, the increase of CBF was corrected by the parallel increase of cardiac output. The maximum direct CBF enhancing effect of hypercapnia of 32% was noted at 45 min after the start of hypercapnia. Thereafter, the CBF enhancing slowly declined. No relevant adverse effects were observed. CBF and StiO2 reproducibly increased by controlled hypercapnia in all patients. After 45 min, the curve of CBF enhancement showed an inflection point when corrected by cardiac output. It is concluded that 45 min might be the optimum duration for a therapeutic use and may provide an optimal balance between the benefits of hypercapnia and risks of a negative rebound effect after return to normal ventilation parameters.Trial registration: The study was approved by the institutional ethics committee (AZ 230/14) and registered at ClinicalTrials.gov (Trial-ID: NCT01799525). Registered 01/01/2015.
e-Nature Positive Emotions Photography Database (e-NatPOEM): affectively rated nature images promoting positive emotions
Authors: Dal Fabbro Daniela , Catissi Giulia , Borba Gustavo , Lima Luciano , Hingst-Zaher Erika , Rosa João , Victor Elivane , Bernardes Letícia , Souza Tinely , Leão Eliseth 
Published: June 2021

AbstractAffectively rated image databases have their main application in studies that require inducing distinct stimuli on subjects. Widespread databases are designed to cover a broad range of stimuli, from negative to positive (valence), and relaxed to excited (arousal). The availability of narrow domain databases, designed to cover and thoroughly analyze a few categories of images that induce a particular stimulus, is limited. We present a narrow domain affective database with positive images, named e-Nature Positive Emotions Photography Database (e-NatPOEM), consisting of 433 high-quality images produced by professional and amateur photographers. A total of 739 participants evaluated them using a web-based tool to input valence-arousal values and a single word describing the evoked feeling. Ratings per image ranged from 36 to 108, median: 57; first/third quartiles: 56/59. 84% of the images presented valence > middle of the scale and arousal < middle of the scale. Words describing the images were classified into semantical groups, being predominant: Peace/tranquility (39% of all words), Beauty (23%), and Positive states (15%). e-NatPOEM is free and publicly available, it is a valid resource for affective research, and presents the potential for clinical use to assist positive emotions promotion.
Identification and function of ETH receptor networks in the silkworm Bombyx mori
Authors: Daubnerová Ivana , Roller Ladislav , Satake Honoo , Zhang Chen , Kim Young-Joon , Žitňan Dušan 
Published: June 2021

AbstractInsect ecdysis triggering hormones (ETHs) released from endocrine Inka cells act on specific neurons in the central nervous system (CNS) to activate the ecdysis sequence. These primary target neurons express distinct splicing variants of ETH receptor (ETHR-A or ETHR-B). Here, we characterized both ETHR subtypes in the moth Bombyx mori in vitro and mapped spatial and temporal distribution of their expression within the CNS and peripheral organs. In the CNS, we detected non-overlapping expression patterns of each receptor isoform which showed dramatic changes during metamorphosis. Most ETHR-A and a few ETHR-B neurons produce multiple neuropeptides which are downstream signals for the initiation or termination of various phases during the ecdysis sequence. We also described novel roles of different neuropeptides during these processes. Careful examination of peripheral organs revealed ETHRs expression in specific cells of the frontal ganglion (FG), corpora allata (CA), H-organ and Malpighian tubules prior to each ecdysis. These data indicate that PETH and ETH are multifunctional hormones that act via ETHR-A and ETHR-B to control various functions during the entire development—the ecdysis sequence and associated behaviors by the CNS and FG, JH synthesis by the CA, and possible activity of the H-organ and Malpighian tubules.