bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rippled Electron‐Scale Structure of a Dipolarization Front
Authors: Pan Dong‐Xiao , Khotyaintsev Yuri V. , Graham Daniel B. , Vaivads Andris , Zhou Xu‐Zhi , André Mats , Lindqvist Per‐Arne , Ergun Robert E. , Le Contel Olivier , Russell Christopher T. , Torbert Roy B. , Giles Barbara , Burch James L. 
Published: November 2018

AbstractWe use the Magnetospheric Multiscale mission to investigate electron‐scale structures at a dipolarization front. The four spacecraft are separated by electron scales and observe large differences in plasma and field parameters within the dipolarization front, indicating strong deviation from typically assumed plane or slightly curved front surface. We attribute this to ripples generated by the lower hybrid drift instability (LHDI) with wave number of kρe≃0.4 and maximum wave potential of ∼1 kV ∼kBTe. Power law‐like spectra of E⊥ with slope of −3 indicates the turbulent cascade of LHDI. LHDI is observed together with bursty high‐frequency parallel electric fields, suggesting coupling of LHDI to higher‐frequency electrostatic waves.
A New Method to Retrieve Thermospheric Parameters From Daytime Bottom‐Side Ne(h) Observations
Authors: Perrone L. , Mikhailov A. V. 
Published: November 2018

AbstractA new method to extract neutral composition (O, O2, N2), exospheric temperature Tex, vertical plasma drift, W, and the total solar Extreme Ultraviolet flux with λ ≤ 1050 Å from routine ionosonde bottom‐side electron density, Ne(h), observations has been proposed. The method can be used around noontime hours for all months of the year at middle latitudes where the ionospheric F‐layer is formed by solar Extreme Ultraviolet radiation. The uncertainty of the retrieved neutral gas density coincides with the announced Mean Relative Deviation ±(10‐15%) of CHAMP/STAR neutral gas density observations. The method also provides statistically significant better results in a comparison with modern Mass‐Spectrometer‐Incoherent‐Scatter, Jacchia‐Bowman 2008, and Drag Temperature Model 2013 empirical models. The thermospheric parameters retrieved for the St. Patrick Day magnetic storm and two so‐called Q‐disturbance periods are given as an example of the method application. The retrieved neutral gas densities for the St. Patrick Day storm are compared to Swarm‐B accelerometer observations. The proposed method may be considered as a useful tool for analyses of the state of the upper atmosphere under various geophysical conditions.
Oceanic Eddy Characteristics and Generation Mechanisms in the Kuroshio Extension Region
Authors: Ji Jinlin , Dong Changming , Zhang Biao , Liu Yu , Zou Bin , King Gregory P. , Xu Guangjun , Chen Dake 
Published: November 2018

AbstractThe Kuroshio Extension region is well known for its strong eddy activity. In this paper, using satellite altimetry‐measured sea surface height anomaly data from 1993 to 2012 in an extended Kuroshio Extension region (140–180°E, 25–45°N), we analyze eddy characteristics: eddy size, polarity, lifetime, intensity, trajectory, and spatial and temporal distributions. Using temperature and salinity vertical profiles measured by Argo floats, we examine the eddy impact on vertical stratification. During the 20‐year period, 7,574 eddies are identified (based on following complete eddy trajectories) with a lifetime equal to or longer than 4 weeks. The numbers of cyclonic and anticyclonic eddies are found to be approximately the same. The distribution of eddy sizes peaks at a radius of about 40 km. The radius at the peak is at the same order as the first baroclinic deformation radius or the horizontal shear scale of the Kuroshio flow. The normalized eddy statistical characteristics show that eddies have different characteristics at different stages of their lifetimes. Among eddies with lifetimes longer than 50 weeks, more anticyclonic (cyclonic) eddies are found north (south) of 35°N. In contrast, among eddies with lifetimes shorter than 20 weeks, more cyclonic (anticyclonic) eddies are found north (south) of 35°N. The asymmetric distribution of eddies suggests two different eddy generation mechanisms: (1) the development of meanders in the Kuroshio path leading to the pinch off of eddies with longer lifetime (larger size) and (2) horizontal shear instability (barotropic instability) leading to eddies of shorter life (smaller size). We further apply an eddy‐resolved numerical product to quantitatively investigate the eddy generation mechanisms.
Strong Contrast in Remote Black Carbon Aerosol Loadings Between the Atlantic and Pacific Basins
Authors: Katich Joseph M. , Samset B. H. , Bui T. Paul , Dollner M. , Froyd K. D. , Campuzano‐Jost P. , Nault B. A. , Schroder J. C. , Weinzierl B. , Schwarz J. P. 
Published: November 2018

AbstractMeasurements of black carbon (BC) aerosol mass concentration in remote air are sparse, leading to poorly constrained regions that models struggle to represent. Here we present a new data set of BC concentration over the remote Pacific and Atlantic basins from 80 N to 65°S latitude that was obtained as part of NASA's Atmospheric Tomography campaign in July/August 2016. More than 100 vertical profiles, extending from ~0.2 to 13 km altitude above mean sea level, reveal sharp contrasts in loadings between the two basins. Over the Pacific, we found average BC concentration vertical profiles to be largely consistent with seasonally matched data obtained in 2011. Substantially higher loads were observed over the Atlantic in the low to middle troposphere than in the Pacific, likely due to strong regional sources and reduced convective removal in the tropics in this basin. Atlantic and Pacific BC concentrations converge in the upper troposphere and lower stratosphere, reflecting similar high‐altitude background concentrations. Comparison of the Atlantic data to the Aerosol Comparisons between Observations and Models suite of models (Phase II) reinforces previous speculation about the ensemble in the remote by quantifying an upper‐troposphere model‐high‐bias of as much as two orders of magnitude over wide latitude bands. However, these direct BC measurements reveal Aerosol Comparisons between Observations and Models ensemble underestimation of biomass burning BC in the outflow of continental Africa by nearly a factor of 5. This high‐BC loading region likely dominates BC's direct radiative effect over remote areas of the Pacific and Atlantic basins during the month of August.
Radar Reflectivity and Altitude Distributions of Lightning Flashes as a Function of Three Main Storm Types
Authors: Mecikalski Retha M. , Carey Lawrence D. 
Published: November 2018

AbstractIn an effort to improve our knowledge on the horizontal and vertical distribution of lightning initiation and propagation, ~500 multicells (producing a total of 72,619 flashes), 27 mesoscale convective systems (producing 214,417 flashes) and 23 supercells (producing 169,861 flashes) that occurred over northern Alabama and southern Tennessee were analyzed using data from the North Alabama Lightning Mapping Array and the Multi‐Radar Multi‐Sensor suite. From this analysis, two‐dimensional (2‐D) histograms of where flashes initiated and propagated relative to radar reflectivity and altitude were created for each storm type. The peak of the distributions occurred between 8.0 and 10.0 km (−24.0 to −38.5 °C) and between 30 and 35 dBZ for flashes that initiated within multicellular storms. For flashes that initiated within mesoscale convective systems, these peaks were 8.0–9.0 km (−27.1 to −34.6 °C) and 30–35 dBZ, respectively, and for supercells, they were 10.0–12.0 km (−42.6 to −58.1 °C) and 35–40 dBZ, respectively. The 2‐D histograms for the flash propagations were slightly different than for the flash initiations and showed that flashes propagated in lower reflectivities as compared to where they initiated. The 2‐D histograms were also compared to test cases; the root‐mean‐square errors and the Pearson product moment correlation coefficient (R) were calculated with several of the comparisons having R values >0.7 while the root‐mean‐square errors were always ≤0.017 (≤10%), irrespective of storm type. Finally, the mean flash sizes for the multicell, mesoscale convective system, and supercell flashes were 8.3, 9.9, and 7.4 km, respectively.
A General Methodology for Climate‐Informed Approaches to Long‐Term Flood Projection—Illustrated With the Ohio River Basin
Authors: Schlef Katherine E. , François Baptiste , Robertson Andrew W. , Brown Casey 
Published: November 2018

AbstractEstimating future hydrologic floods under nonstationary climate is a key challenge for flood management. Climate‐informed approaches to long‐term flood projection are an appealing alternative to traditional modeling chains. This work formalizes climate‐informed approaches into a general methodology consisting of four steps: (1) selection of predictand representing extreme events, (2) identification of credible large‐scale predictors that mechanistically control the occurrence and magnitude of the predictand, (3) development of a statistical model relating the predictors to the predictand, and (4) projection of the predictand by forcing the model with predictor projections. These four steps, developed from a review of the current literature, are demonstrated for multiple gages in the northwest Ohio River Basin in the United States Midwest as a case study. Floods are defined as annual maximum series events in January through April and are linked to geopotential height and soil moisture predictors in a Bayesian linear regression model. The projections generally show a slight decrease in future flood magnitude and demonstrate the transparency of the climate‐informed approach. An initial step for more general application across the United States and remaining challenges associated with climate‐informed flood projection are discussed.
Elevated extracellular calcium ions promote proliferation and migration of mesenchymal stem cells via increasing osteopontin expression
Authors: Lee Mi Nam , Hwang Hee-Su , Oh Sin-Hye , Roshanzadeh Amir , Kim Jung-Woo , Song Ju Han , Kim Eung-Sam , Koh Jeong-Tae 
Published: November 2018

AbstractSupplementation of mesenchymal stem cells (MSCs) at sites of bone resorption is required for bone homeostasis because of the non-proliferation and short lifespan properties of the osteoblasts. Calcium ions (Ca2+) are released from the bone surfaces during osteoclast-mediated bone resorption. However, how elevated extracellular Ca2+ concentrations would alter MSCs behavior in the proximal sites of bone resorption is largely unknown. In this study, we investigated the effect of extracellular Ca2+ on MSCs phenotype depending on Ca2+ concentrations. We found that the elevated extracellular Ca2+ promoted cell proliferation and matrix mineralization of MSCs. In addition, MSCs induced the expression and secretion of osteopontin (OPN), which enhanced MSCs migration under the elevated extracellular Ca2+ conditions. We developed in vitro osteoclast-mediated bone resorption conditions using mouse calvaria bone slices and demonstrated Ca2+ is released from bone resorption surfaces. We also showed that the MSCs phenotype, including cell proliferation and migration, changed when the cells were treated with a bone resorption-conditioned medium. These findings suggest that the dynamic changes in Ca2+ concentrations in the microenvironments of bone remodeling surfaces modulate MSCs phenotype and thereby contribute to bone regeneration.
Transition path times of coupled folding and binding reveal the formation of an encounter complex
Authors: Sturzenegger Flurin , Zosel Franziska , Holmstrom Erik D. , Buholzer Karin J. , Makarov Dmitrii E. , Nettels Daniel , Schuler Benjamin 
Published: November 2018

AbstractThe association of biomolecules is the elementary event of communication in biology. Most mechanistic information of how the interactions between binding partners form or break is, however, hidden in the transition paths, the very short parts of the molecular trajectories from the encounter of the two molecules to the formation of a stable complex. Here we use single-molecule spectroscopy to measure the transition path times for the association of two intrinsically disordered proteins that form a folded dimer upon binding. The results reveal the formation of a metastable encounter complex that is electrostatically favored and transits to the final bound state within tens of microseconds. Such measurements thus open a new window into the microscopic events governing biomolecular interactions.
A gas breathing hydrogen/air biofuel cell comprising a redox polymer/hydrogenase-based bioanode
Authors: Szczesny Julian , Marković Nikola , Conzuelo Felipe , Zacarias Sónia , Pereira Inês A. C. , Lubitz Wolfgang , Plumeré Nicolas , Schuhmann Wolfgang , Ruff Adrian 
Published: November 2018

AbstractHydrogen is one of the most promising alternatives for fossil fuels. However, the power output of hydrogen/oxygen fuel cells is often restricted by mass transport limitations of the substrate. Here, we present a dual-gas breathing H2/air biofuel cell that overcomes these limitations. The cell is equipped with a hydrogen-oxidizing redox polymer/hydrogenase gas-breathing bioanode and an oxygen-reducing bilirubin oxidase gas-breathing biocathode (operated in a direct electron transfer regime). The bioanode consists of a two layer system with a redox polymer-based adhesion layer and an active, redox polymer/hydrogenase top layer. The redox polymers protect the biocatalyst from high potentials and oxygen damage. The bioanodes show remarkable current densities of up to 8 mA cm-2. A maximum power density of 3.6 mW cm-2 at 0.7 V and an open circuit voltage of up to 1.13 V were achieved in biofuel cell tests, representing outstanding values for a device that is based on a redox polymer-based hydrogenase bioanode.
Harnessing photoinduced electron transfer to optically determine protein sub-nanoscale atomic distances
Authors: Pantazis Antonios , Westerberg Karin , Althoff Thorsten , Abramson Jeff , Olcese Riccardo 
Published: November 2018

AbstractProteins possess a complex and dynamic structure, which is influenced by external signals and may change as they perform their biological functions. We present an optical approach, distance-encoding photoinduced electron transfer (DEPET), capable of the simultaneous study of protein structure and function. An alternative to FRET-based methods, DEPET is based on the quenching of small conjugated fluorophores by photoinduced electron transfer: a reaction that requires contact of the excited fluorophore with a suitable electron donor. This property allows DEPET to exhibit exceptional spatial and temporal resolution capabilities in the range pertinent to protein conformational change. We report the first implementation of DEPET on human large-conductance K+ (BK) channels under voltage clamp. We describe conformational rearrangements underpinning BK channel sensitivity to electrical excitation, in conducting channels expressed in living cells. Finally, we validate DEPET in synthetic peptide length standards, to evaluate its accuracy in measuring sub- and near-nanometer intramolecular distances.
Targeting 17q23 amplicon to overcome the resistance to anti-HER2 therapy in HER2+ breast cancer
Authors: Liu Yunhua , Xu Jiangsheng , Choi Hyun Ho , Han Cecil , Fang Yuanzhang , Li Yujing , Van der Jeught Kevin , Xu Hanchen , Zhang Lu , Frieden Michael , Wang Lifei , Eyvani Haniyeh , Sun Yifan , Zhao Gang , Zhang Yuntian , Liu Sheng , Wan Jun , Huang Cheng , Ji Guang , Lu Xiongbin , He Xiaoming , Zhang Xinna 
Published: November 2018

AbstractChromosome 17q23 amplification occurs in ~11% of human breast cancers. Enriched in HER2+ breast cancers, the 17q23 amplification is significantly correlated with poor clinical outcomes. In addition to the previously identified oncogene WIP1, we uncover an oncogenic microRNA gene, MIR21, in a majority of the WIP1-containing 17q23 amplicons. The 17q23 amplification results in aberrant expression of WIP1 and miR-21, which not only promotes breast tumorigenesis, but also leads to resistance to anti-HER2 therapies. Inhibiting WIP1 and miR-21 selectively inhibits the proliferation, survival and tumorigenic potential of the HER2+ breast cancer cells harboring 17q23 amplification. To overcome the resistance of trastuzumab-based therapies in vivo, we develop pH-sensitive nanoparticles for specific co-delivery of the WIP1 and miR-21 inhibitors into HER2+ breast tumors, leading to a profound reduction of tumor growth. These results demonstrate the great potential of the combined treatment of WIP1 and miR-21 inhibitors for the trastuzumab-resistant HER2+ breast cancers.
Lactobacillus elicits a 'Marmite effect' on the chicken cecal microbiome
Authors: Zou Angela , Sharif Shayan , Parkinson John 
Published: November 2018

AbstractThe poultry industry has traditionally relied on the use of antibiotic growth promoters (AGPs) to improve production efficiency and minimize infection. With the recent drive to eliminate the use of AGPs, novel alternatives are urgently required. Recently attention has turned to the use of synthetic communities that may be used to ‘seed’ the developing microbiome. The current challenge is identifying keystone taxa whose influences in the gut can be leveraged for probiotic development. To help define such taxa we present a meta-analysis of 16S rRNA surveys of 1572 cecal microbiomes generated from 19 studies. Accounting for experimental biases, consistent with previous studies, we find that AGP exposure can result in reduced microbiome diversity. Network community analysis defines groups of taxa that form stable clusters and further revealsLactobacillusto elicit a polarizing effect on the cecal microbiome, exhibiting relatively equal numbers of positive and negative interactions with other taxa. Our identification of stable taxonomic associations provides a valuable framework for developing effective microbial consortia as alternatives to AGPs.
Functional eubacteria species along with trans-domain gut inhabitants favour dysgenic diversity in oxalate stone disease
Authors: Suryavanshi Mangesh V. , Bhute Shrikant S. , Gune Rahul P. , Shouche Yogesh S. 
Published: November 2018

AbstractAnalyses across all three domains of life are necessary to advance our understanding of taxonomic dysbiosis in human diseases. In the present study, we assessed gut microbiota (eubacteria, archaea, and eukaryotes) of recurrent oxalate kidney stone suffers to explore the extent of trans-domain and functional species dysbiosis inside the gut. Trans-domain taxonomic composition, active oxalate metabolizer and butyrate-producing diversity were explored by utilizing frc-, but-, and buk- functional gene amplicon analysis. Operational taxonomic units (OTUs) level analyses confound with the observation that dysbiosis in gut microbiota is not just limited to eubacteria species, but also to other domains like archaea and eukaryotes. We found that some of healthy eubacterial population retained together with Oxalobacter formigenes and Lactobacillus plantarum colonization in disease condition (p < 0.001 & FDR = 0.05). Interestingly, trans-domain species diversity has been less shared and dysgenic taxa augmentation was found to be higher. Oxalate metabolizing bacterial species (OMBS) and butyrate-producing eubacteria species were found to be decreased in Oxalobacter non-colonizers; and Prevotella and Ruminococcus species which may contribute to oxalate metabolism and butyrate synthesis as well. Our study underscores fact that microbial dysbiosis is not limited to eubacteria only hence suggest the necessity of the trans-domain surveillance in metabolic diseases for intervention studies.
Lysosomal and network alterations in human mucopolysaccharidosis type VII iPSC-derived neurons
Authors: Bayó-Puxan Neus , Terrasso Ana Paula , Creyssels Sophie , Simão Daniel , Begon-Pescia Christina , Lavigne Marina , Salinas Sara , Bernex Florence , Bosch Assumpció , Kalatzis Vasiliki , Levade Thierry , Cuervo Ana Maria , Lory Philippe , Consiglio Antonella , Brito Catarina , Kremer Eric J. 
Published: November 2018

AbstractMucopolysaccharidosis type VII (MPS VII) is a lysosomal storage disease caused by deficient β-glucuronidase (β-gluc) activity. Significantly reduced β-gluc activity leads to accumulation of glycosaminoglycans (GAGs) in many tissues, including the brain. Numerous combinations of mutations in GUSB (the gene that codes for β-gluc) cause a range of neurological features that make disease prognosis and treatment challenging. Currently, there is little understanding of the molecular basis for MPS VII brain anomalies. To identify a neuronal phenotype that could be used to complement genetic analyses, we generated two iPSC clones derived from skin fibroblasts of an MPS VII patient. We found that MPS VII neurons exhibited reduced β-gluc activity and showed previously established disease-associated phenotypes, including GAGs accumulation, expanded endocytic compartments, accumulation of lipofuscin granules, more autophagosomes, and altered lysosome function. Addition of recombinant β-gluc to MPS VII neurons, which mimics enzyme replacement therapy, restored disease-associated phenotypes to levels similar to the healthy control. MPS VII neural cells cultured as 3D neurospheroids showed upregulated GFAP gene expression, which was associated with astrocyte reactivity, and downregulation of GABAergic neuron markers. Spontaneous calcium imaging analysis of MPS VII neurospheroids showed reduced neuronal activity and altered network connectivity in patient-derived neurospheroids compared to a healthy control. These results demonstrate the interplay between reduced β-gluc activity, GAG accumulation and alterations in neuronal activity, and provide a human experimental model for elucidating the bases of MPS VII-associated cognitive defects.
Pretreatment Inflammation-Based Markers Predict Survival Outcomes in Patients with Early Stage Hepatocellular Carcinoma After Radiofrequency Ablation
Authors: Chu Michelle Ong , Shen Chien-Heng , Chang Te-Sheng , Xu Huang-Wei , Yen Chih-Wei , Lu Sheng-Nan , Hung Chao-Hung 
Published: November 2018

AbstractThe prognostic significance of various systemic inflammation‐based markers has been explored in different cancers after surgery. This study aimed to investigate whether these markers could predict outcomes in patients with early-stage hepatocellular carcinoma (HCC) undergoing radiofrequency ablation (RFA). One hundred eighteen patients with newly diagnosed HCC within the Milan criteria receiving RFA as initial therapy were retrospectively enrolled. Pretreatment inflammation-based markers including the neutrophil to lymphocyte ratio (NLR), platelet to lymphocyte ratio (PLR) and prognostic nutritional index (PNI), together with other clinicopathologic parameters were collected. Cumulative overall survival (OS) and recurrence-free survival (RFS) were estimated by the Kaplan-Meier method and by multivariate analysis using Cox proportional hazard model. The 1-, 3-, and 5-year OS rates of patients were 90%, 67%, and 52%, respectively. Kaplan-Meier curves showed that baseline high NLR ≥ 2.5 (p = 0.006), low PNI < 40 (p = 0.005), history of end-stage renal disease (ESRD) (p = 0.005), non-Child-Pugh class A (p = 0.001) and elevated alpha-fetoprotein (AFP) ≥ 200 ng/mL (p = 0.005) significantly associated with the poor OS, whereas high PLR ≥ 100 did not. By multivariate analysis, high NLR ≥ 2.5 (hazard ratio (HR) 1.94; 95% confidence interval (CI), 1.05–3.59; p = 0.034), low PNI < 40 (HR 0.38; 95% CI, 0.20–0.72; p = 0.003), ESRD history (HR 3.60; 95% CI, 1.48–8.76; p = 0.005) and elevated AFP ≥ 200 ng/mL (HR 4.61; 95% CI, 1.75–12.13; p = 0.002) were independent factors. An elevated AFP level of ≥200 ng/mL was the significant factor associated with intrahepatic new RFS by univariate and multivariate analyses. In conclusion, pretreatment NLR and PNI are simple and useful predictors for OS in patients with early-stage HCC after RFA.