bluuebunny/crossref_metadata_2025_split huggingface dataset:
An In‐Depth Seismological Analysis Revealing a Causal Link Between the 2017 MW 5.5 Pohang Earthquake and EGS Project
Authors: Woo J.‐U. , Kim M. , Sheen D.‐H. , Kang T.‐S. , Rhie J. , Grigoli F. , Ellsworth W. L. , Giardini D. 
Published: November 2019

AbstractHydraulic injection by the Pohang enhanced geothermal systems (EGSs) has been suspected to trigger the 2017 moment magnitude (MW) 5.5 Pohang earthquake in South Korea. The last stimulation experiment in the EGS was conducted only 2 months before the disaster, which has led to this suspicion. In this study, we conducted a seismic analysis on the earthquakes that have occurred around the EGS site in the past 10 years. The study included the construction of a velocity model, earthquake detection, the determination of hypocenters, magnitudes, focal mechanisms, and stress inversion, and a clustering analysis. No seismic activity was detected near the study area until November 2015 when there was a loss of a large quantity of heavy drilling mud. For three stimulations of a geothermal well, earthquakes sequentially migrated to the southwest along a fault plane, leading to the location of the mainshock. The delineated fault plane crossed the injection well at approximately 3,800 m, which corresponds to the borehole interval of not only the mud loss but also the breakage of the well's casing due to the mainshock rupture. These findings can be treated as empirical evidence for the hypothesis that the 2017 MW 5.5 Pohang earthquake was initiated on a critically stressed fault zone by the anthropogenic activity of fluid injection, consequentially releasing accumulated strain energy via tectonic loading.
Upscaling of Elastic Properties in Carbonates: A Modeling Approach Based on a Multiscale Geophysical Data Set
Authors: Bailly C. , Fortin J. , Adelinet M. , Hamon Y. 
Published: November 2019

AbstractLinking ultrasonic measurements made on samples, with sonic logs and seismic subsurface data, is a key challenge for the understanding of carbonate reservoirs. To deal with this problem, we investigate the elastic properties of dry lacustrine carbonates. At one study site, we perform a seismic refraction survey (100 Hz), as well as “sonic” (54 kHz) and ultrasonic (250 kHz) measurements directly on outcrop and ultrasonic measurements on samples (500 kHz). By comparing the median of each data set, we show that the P wave velocity decreases from laboratory to seismic scale. Nevertheless, the median of the sonic measurements acquired on outcrop surfaces seems to fit with the seismic data, meaning that sonic acquisition may be representative of seismic scale. To explain the variations due to upscaling, we relate the concept of representative elementary volume with the wavelength of each scale of study. Indeed, with upscaling, the wavelength varies from millimetric to pluri‐metric. This change of scale allows us to conclude that the behavior of P wave velocity is due to different geological features (matrix porosity, cracks, and fractures) related to the different wavelengths used. Based on effective medium theory, we quantify the pore aspect ratio at sample scale and the crack/fracture density at outcrop and seismic scales using a multiscale representative elementary volume concept. Results show that the matrix porosity that controls the ultrasonic P wave velocities is progressively lost with upscaling, implying that crack and fracture porosity impacts sonic and seismic P wave velocities, a result of paramount importance for seismic interpretation based on deterministic approaches.
Intergranular Clay Films Control Inelastic Deformation in the Groningen Gas Reservoir: Evidence From Split‐Cylinder Deformation Tests
Authors: Pijnenburg R. P. J. , Verberne B. A. , Hangx S. J. T. , Spiers C. J. 
Published: November 2019

AbstractProduction of oil and gas from sandstone reservoirs leads to small elastic and inelastic strains in the reservoir, which may induce surface subsidence and seismicity. While the elastic component is easily described, the inelastic component, and any rate‐sensitivity thereof remain poorly understood in the relevant small strain range (≤1.0%). To address this, we performed a sequence of five stress/strain‐cycling plus strain‐marker‐imaging experiments on a single split‐cylinder sample (porosity 20.4%) of Slochteren sandstone from the seismogenic Groningen gas field. The tests were performed under in situ conditions of effective confining pressure (40 MPa) and temperature (100 °C), exploring increasingly large differential stresses (up to 75 MPa) and/or axial strains (up to 4.8%) in consecutive runs. At the small strains relevant to producing reservoirs (≤1.0%), inelastic deformation was largely accommodated by deformation of clay‐filled grain contacts. High axial strains (>1.4%) led to pervasive intragranular cracking plus intergranular slip within localized, conjugate bands. Using a simplified sandstone model, we show that the magnitude of inelastic deformation produced in our experiments at small strains (≤1.0%) and stresses relevant to the Groningen reservoir can indeed be roughly accounted for by clay film deformation. Thus, inelastic compaction of the Groningen reservoir is expected to be largely governed by clay film deformation. Compaction by this mechanism is shown to be rate insensitive on production timescales and is anticipated to halt when gas production stops. However, creep by other processes cannot be eliminated. Similar, clay‐bearing sandstone reservoirs occur widespread globally, implying a wide relevance of our results.
Simulating a Mesoscale Convective System Using WRF With a New Spectral Bin Microphysics: 1: Hail vs Graupel
Authors: Shpund Jacob , Khain Alexander , Lynn Barry , Fan Jiwen , Han Bin , Ryzhkov Alexander , Snyder Jeffrey , Dudhia Jimy , Gill Dave 
Published: November 2019

AbstractA modified Fast Spectral Bin Microphysics scheme (FSBM‐2) embedded into the Weather Research and Forecasting (WRF) model is used to simulate a mesoscale deep convective system observed during the Midlatitude Continental Convective Clouds Experiment (MC3E). FSBM‐2 uses modified source codes as compared to the current FSBM (FSBM‐1). In contrast to FSBM‐1, FSBM‐2 can simulate hail of several centimeters in diameter and includes additional processes such as spontaneous breakup of raindrops and aerosol regeneration by drop evaporation. It is shown that allowing large hail particles of diameters exceeding about 1 cm substantially increases the agreement between the simulated and observed squall‐line structures in both the convective and stratiform regions. In contrast, if graupel particles are used to represent high‐density hydrometeors in convective areas, the ratio of convective‐to‐stratiform areas diverges from the ratio seen in observations and maximum radar reflectivities are substantially underestimated. Analysis of snow size distributions in the stratiform area shows an important link between the ice crystals formed by homogeneous freezing in the convective area to ice particle number concentration in the stratiform region. Simulated raindrop size distributions in the stratiform area below the melting level from FSBM‐2 show a good agreement with observations. The regeneration of cloud condensational nuclei (CCN) by droplet evaporation and detrainment of these CCN to the stratiform region increases the concentration of CCN there up to 8‐ to 9‐km altitude; the additional CCN penetrate clouds and produce new droplets, leading to some convection intensification.
Running exercise protects oligodendrocytes in the medial prefrontal cortex in chronic unpredictable stress rat model
Authors: Luo Yanmin , Xiao Qian , Wang Jin , Jiang Lin , Hu Menglan , Jiang Yanhong , Tang Jing , Liang Xin , Qi Yingqiang , Dou Xiaoyun , Zhang Yi , Huang Chunxia , Chen Linmu , Tang Yong 
Published: November 2019

AbstractPrevious postmortem and animal studies have shown decreases in the prefrontal cortex (PFC) volume and the number of glial cells in the PFC of depression. Running exercise has been shown to alleviate depressive symptoms. However, the effects of running exercise on the medial prefrontal cortex (mPFC) volume and oligodendrocytes in the mPFC of depressed patients and animals have not been investigated. To address these issues, adult male rats were subjected to chronic unpredictable stress (CUS) for 5 weeks, followed by treadmill running for 6 weeks. Then, the mPFC volume and the mPFC oligodendrocytes were investigated using stereology, immunohistochemistry, immunofluorescence and western blotting. Using a CUS paradigm that allowed for the analysis of anhedonia, we found that running exercise alleviated the deficits in sucrose preference, as well as the decrease in the mPFC volume. Meanwhile, we found that running exercise significantly increased the number of CNPase+oligodendrocytes and Olig2+oligodendrocytes, reduced the ratio between Olig2+/NG2+oligodendrocytes and Olig2+oligodendrocytes and increased myelin basic protein (MBP), CNPase and Olig2 protein expression in the mPFC of the CUS rat model. However, running exercise did not change NG2+oligodendrocyte number in the mPFC in these rats. These results indicated that running exercise promoted the differentiation of oligodendrocytes and myelin-forming ability in the mPFC in the context of depression. These findings suggest that the beneficial effects of running exercise on mPFC volume and oligodendrocytes in mPFC might be an important structural basis for the antidepressant effects of running exercise.
Dissection of gene expression datasets into clinically relevant interaction signatures via high-dimensional correlation maximization
Authors: Grau Michael , Lenz Georg , Lenz Peter 
Published: November 2019

AbstractGene expression is controlled by many simultaneous interactions, frequently measured collectively in biology and medicine by high-throughput technologies. It is a highly challenging task to infer from these data the generating effects and cooperating genes. Here, we present an unsupervised hypothesis-generating learning concept termed signal dissection by correlation maximization (SDCM) that dissects large high-dimensional datasets into signatures. Each signature captures a particular signal pattern that was consistently observed for multiple genes and samples, likely caused by the same underlying interaction. A key difference to other methods is our flexible nonlinear signal superposition model, combined with a precise regression technique. Analyzing gene expression of diffuse large B-cell lymphoma, our method discovers previously unidentified signatures that reveal significant differences in patient survival. These signatures are more predictive than those from various methods used for comparison and robustly validate across technological platforms. This implies highly specific extraction of clinically relevant gene interactions.
Integrating electric field modeling and neuroimaging to explain inter-individual variability of tACS effects
Authors: Kasten Florian H. , Duecker Katharina , Maack Marike C. , Meiser Arnd , Herrmann Christoph S. 
Published: November 2019

AbstractTranscranial electrical stimulation (tES) of the brain can have variable effects, plausibly driven by individual differences in neuroanatomy and resulting differences of the electric fields inside the brain. Here, we integrated individual simulations of electric fields during tES with source localization to predict variability of transcranial alternating current stimulation (tACS) aftereffects on α-oscillations. In two experiments, participants received 20-min of either α-tACS (1 mA) or sham stimulation. Magnetoencephalogram (MEG) was recorded for 10-min before and after stimulation. tACS caused a larger power increase in the α-band compared to sham. The variability of this effect was significantly predicted by measures derived from individual electric field modeling. Our results directly link electric field variability to variability of tACS outcomes, underline the importance of individualizing stimulation protocols, and provide a novel approach to analyze tACS effects in terms of dose-response relationships.
A database of high-resolution MS/MS spectra for lichen metabolites
Authors: Olivier-Jimenez Damien , Chollet-Krugler Marylène , Rondeau David , Beniddir Mehdi A. , Ferron Solenn , Delhaye Thomas , Allard Pierre-Marie , Wolfender Jean-Luc , Sipman Harrie J. M. , Lücking Robert , Boustie Joël , Le Pogam Pierre 
Published: November 2019

AbstractWhile analytical techniques in natural products research massively shifted to liquid chromatography-mass spectrometry, lichen chemistry remains reliant on limited analytical methods, Thin Layer Chromatography being the gold standard. To meet the modern standards of metabolomics within lichenochemistry, we announce the publication of an open access MS/MS library with 250 metabolites, coined LDB for Lichen DataBase, providing a comprehensive coverage of lichen chemodiversity. These were donated by the Berlin Garden and Botanical Museum from the collection of Siegfried Huneck to be analyzed by LC-MS/MS. Spectra at individual collision energies were submitted to MetaboLights (https://www.ebi.ac.uk/metabolights/MTBLS999) while merged spectra were uploaded to the GNPS platform (CCMSLIB00004751209 to CCMSLIB00004751517). Technical validation was achieved by dereplicating three lichen extracts using a Molecular Networking approach, revealing the detection of eleven unique molecules that would have been missed without LDB implementation to the GNPS. From a chemist’s viewpoint, this database should help streamlining the isolation of formerly unreported metabolites. From a taxonomist perspective, the LDB offers a versatile tool for the chemical profiling of newly reported species.
Wedge prism approach for simultaneous multichannel microscopy
Authors: Cai Hanna , Wang Yao L. , Wainner Richard T. , Iftimia Nicusor V. , Gabel Christopher V. , Chung Samuel H. 
Published: November 2019

AbstractMultichannel (multicolor) imaging has become a powerful technique in biology research for performing in vivo neuronal calcium imaging, colocalization of fluorescent labels, non-invasive pH measurement, and other procedures. We describe a novel add-on approach for simultaneous multichannel optical microscopy based on simple wedge prisms. Our device requires no alignment and is simple, robust, user-friendly, and less expensive than current commercial instruments based on switchable filters or dual-view strategies. Point spread function measurements and simulations in Zemax indicate a reduction in resolution in the direction orthogonal to the wedge interface and in the axial direction, without introducing aberration. These effects depend on the objective utilized and are most significant near the periphery of the field of view. We tested a two-channel device on C. elegans neurons in vivo and demonstrated comparable signals to a conventional dual-view instrument. We also tested a four-channel device on fixed chick embryo Brainbow samples and identified individual neurons by their spectra without extensive image postprocessing. Therefore, we believe that this technology has the potential for broad use in microscopy.
Statin-specific inhibition of Rab-GTPase regulates cPKC-mediated IKs internalization
Authors: Ronzier Elsa , Parks Xiaorong Xu , Qudsi Haani , Lopes Coeli M. 
Published: November 2019

AbstractStatins are prescribed for prevention and treatment of coronary artery disease. Statins have different cholesterol lowering abilities, with rosuvastatin and atorvastatin being the most effective, while statins like simvastatin and fluvastatin having lower effectiveness. Statins, in addition to their cholesterol lowering effects, can prevent isoprenylation of Rab-GTPase proteins, a protein family important for the regulation of membrane-bound protein trafficking. Here we show that endosomal localization of Rab-GTPases (Rab5, Rab7 and Rab11) was inhibited in a statin-specific manner, with stronger effects by fluvastatin, followed by simvastatin and atorvastatin, and with a limited effect by rosuvastatin. Fluvastatin inhibition of Rab5 has been shown to mediate cPKC-dependent trafficking regulation of the cardiac delayed rectifier KCNQ1/KCNE1 channels. We observed statin-specific inhibition of channel regulation consistent with statin-specific Rab-GTPase inhibition both in heterologous systems and cardiomyocytes. Our results uncover a non-cholesterol-reducing statin-specific effect of statins. Because Rab-GTPases are important regulators of membrane trafficking they may underlie statin specific pleiotropic effects. Therefore, statin-specificity may allow better treatment tailoring.
pH-depended protein shell dis- and reassembly of ferritin nanoparticles revealed by atomic force microscopy
Authors: Stühn Lukas , Auernhammer Julia , Dietz Christian 
Published: November 2019

AbstractFerritin, a protein that is present in the human body for a controlled iron storage and release, consists of a ferrihydrite core and a protein shell. Apoferritin, the empty shell of ferritin, can be modified to carry tailored properties exploitable for targeted and direct drug delivery. This protein shell has the ability to dis- and reassemble depending on the pH value of the liquid environment and can thus be filled with the desired substance. Here we observed the dis- and reassembly process of the protein shell of ferritin and apoferritin in situ and in real space using atomic force microscopy. Ferritin and apoferritin nanoparticles adsorbed on a mica substrate exhibited a change in their size by varying the pH value of the surrounding medium. Lowering the pH value of the solution led to a decrease in size of the nanoparticles whereas a successive increase of the pH value increased the particle size again. The pH dependent change in size could be related to the dis- and reassembling of the protein shell of ferritin and apoferritin. Supplementary imaging by bimodal magnetic force microscopy of ferritin molecules accomplished in air revealed a polygonal shape of the core and a three-fold symmetry of the protein shell providing valuable information about the substructure of the nanoparticles.
Unraveling Determinants of Affinity Enhancement in Dimeric Aptamers for a Dimeric Protein
Authors: Manochehry Sepehr , McConnell Erin M. , Li Yingfu 
Published: November 2019

AbstractHigh-affinity aptamers can be derived de novo by using stringent conditions in SELEX (Systematic Evolution of Ligands by EXponential enrichment) experiments or can be engineered post SELEX via dimerization of selected aptamers. Using electrophoretic mobility shift assays, we studied a series of heterodimeric and homodimeric aptamers, constructed from two DNA aptamers with distinct primary sequences and secondary structures, previously isolated for VEGF-165, a homodimeric protein. We investigated four factors envisaged to impact the affinity of a dimeric aptamer to a dimeric protein: (1) length of the linker between two aptamer domains, (2) linking orientation, (3) binding-site compatibility of two component aptamers in a heterodimeric aptamer, and (4) steric acceptability of the two identical aptamers in a homodimeric aptamer. All heterodimeric aptamers for VEGF-165 were found to exhibit monomeric aptamer-like affinity and the lack of affinity enhancement was attributed to binding-site overlap by the constituent aptamers. The best homodimeric aptamer showed 2.8-fold better affinity than its monomeric unit (Kd = 13.6 ± 2.7 nM compared to 37.9 ± 14 nM), however the barrier to further affinity enhancement was ascribed to steric interference of the constituent aptamers. Our findings point to the need to consider the issues of binding-site compatibility and spatial requirement of aptamers for the development of dimeric aptamers capable of bivalent recognition. Thus, determinants highlighted herein should be assessed in future multimerization efforts.
Carprofen-induced depletion of proton motive force reverses TetK-mediated doxycycline resistance in methicillin-resistant Staphylococcus pseudintermedius
Authors: Magnowska Zofia , Jana Bimal , Brochmann Rikke Prejh , Hesketh Andrew , Lametsch Rene , De Gobba Cristian , Guardabassi Luca 
Published: November 2019

AbstractWe previously showed that doxycycline (DOX) and carprofen (CPF), a veterinary non-steroidal anti-inflammatory drug, have synergistic antimicrobial activity against methicillin-resistant Staphylococcus pseudintermedius (MRSP) carrying the tetracycline resistance determinant TetK. To elucidate the molecular mechanism of this synergy, we investigated the effects of the two drugs, individually and in combination, using a comprehensive approach including RNA sequencing, two-dimensional differential in-gel electrophoresis, macromolecule biosynthesis assays and fluorescence spectroscopy. Exposure of TetK-positive MRSP to CPF alone resulted in upregulation of pathways that generate ATP and NADH, and promote the proton gradient. We showed that CPF is a proton carrier that dissipates the electrochemical potential of the membrane. In the presence of both CPF and DOX, the energy compensation strategy was attenuated by downregulation of all the processes involved, such as citric acid cycle, oxidative phosphorylation and ATP-providing arginine deiminase pathway. Furthermore, protein biosynthesis inhibition increased from 20% under DOX exposure alone to 75% upon simultaneous exposure to CPF. We conclude that synergistic interaction of the drugs restores DOX susceptibility in MRSP by compromising proton-motive-force-dependent TetK-mediated efflux of the antibiotic. MRSP is unable to counterbalance CPF-mediated PMF depletion by cellular metabolic adaptations, resulting in intracellular accumulation of DOX and inhibition of protein biosynthesis.
µ-opioid receptor-mediated downregulation of midline thalamic pathways to basal and central amygdala
Authors: Goedecke L. , Bengoetxea X. , Blaesse P. , Pape H.-C. , Jüngling K. 
Published: November 2019

AbstractBrain µ-opioid receptors (MOR) mediate reward and help coping with pain, social rejection, anxiety and depression. The dorsal midline thalamus (dMT) integrates visceral/emotional signals and biases behavior towards aversive or defensive states through projections to the amygdala. While a dense MOR expression in the dMT has been described, the exact cellular and synaptic mechanisms of µ-opioidergic modulation in the dMT-amygdala circuitry remain unresolved. Here, we hypothesized that MORs are important negative modulators of dMT-amygdala excitatory networks. Using retrograde tracers and targeted channelrhodopsin expression in combination with patch-clamp electrophysiology, we found that projections of dMT neurons onto both basal amygdala principal neurons (BA PN) and central amygdala (CeL) neurons are attenuated by stimulation of somatic or synaptic MORs. Importantly, dMT efferents to the amygdala drive feedforward excitation of centromedial amygdala neurons (CeM), which is dampened by MOR activation. This downregulation of excitatory activity in dMT-amygdala networks puts the µ-opioid system in a position to ameliorate aversive or defensive behavioral states associated with stress, withdrawal, physical pain or social rejection.