bluuebunny/crossref_metadata_2025 huggingface dataset:
Middle to Late Miocene Age for the End of Amphibolite‐Facies Mylonitization of the Alpine Schist, New Zealand: Implications for Onset of Transpression Across the Alpine Fault
Authors: Ring Uwe , Glodny Johannes , Angiboust Samuel , Little Tim , Lang Karl A.
Published: November 2019

We report five new Rb‐Sr muscovite‐based isochron ages, which are the first to constrain the timing of amphibolite‐facies mylonitization of the Alpine Schist in the Southern Alps of New Zealand. The ages range from 13.1 ± 4.3 to 8.9 ± 3.2 Ma (2σ uncertainties) for mylonite directly above the Alpine Fault. The weighted mean age of 10.74 ± 0.57 Ma is within uncertainty of a published 40Ar/39Ar illite/mica upper‐intercept age of 11.5 ± 0.5 Ma measured at the same locality. The end of amphibolite‐facies mylonitization occurred at metamorphic conditions of ~560–570 °C and ~0.9–1.1 GPa as derived from pseudosection analysis in the NCTiKFMASH system. We interpret Miocene metamorphism to reflect transpressional crustal thickening and formation of a thick crustal root supporting early Southern Alps topography at or prior to 10.74 ± 0.57 Ma. Additional ~2–1 Ma Rb‐Sr biotite, 40Ar/39Ar muscovite, and 40Ar/39Ar biotite ages reflect isotopic closure during rapid cooling along the Alpine Fault in the Pleistocene. The Miocene mylonitization ages and the Pleistocene cooling ages define a distinct two‐stage cooling and exhumation history for the Alpine Schist with initial cooling of ~10 °C/Myr and exhumation rates of 2–4 km/Myr. Final cooling since ~2 Ma was >100 °C/Myr at exhumation rates of ~5–6 km/Myr. We interpret the two‐phase cooling history by movement of the mylonite through a strongly nonlinear thermal structure. An older 60.5 ± 0.7 Ma metamorphic event is also preserved as a Rb‐Sr crystallization age of a predeformational muscovite‐plagioclase assemblage in a sheared pegmatite.
Using a Paleosurface to Constrain Low‐Temperature Thermochronological Data: Tectonic Evolution of the Cuevas Range, Central Andes
Authors: Zapata S. , Sobel E. R. , del Papa C. , Jelinek A. R. , Glodny J.
Published: November 2019

Dispersion of low‐temperature thermochronologic data from nine samples collected on a deformed paleosurface preserved on the Cuevas range (Central Andes) can be exploited to unravel complex thermal histories. The nine samples yielded data that have both intersample and intrasample dispersions; the data set includes apatite fission‐track ages (180–110 Ma), mean track lengths (11–13 μm), apatite helium (10–250 Ma), and zircon helium ages (180–348 Ma). We ran inverse thermal history models for each sample that reveal spatial variations of the Miocene reheating along the paleosurface. Next, we ran a multiple‐sample joint model to infer a common form for thermal history for all samples. Our results suggest that initial exhumation during the Famatinian orogeny was followed by a residence between ~2.5 and 7.0 km depth during the Paleozoic and the Triassic. The onset of Mesozoic rifting was responsible for an increase of the geothermal gradient and extensive horst exhumation, which brought the basement of the Cuevas range close to the surface (~1–2 km) in the Late Jurassic. Between the Late Cretaceous and the Paleocene, the combination of low relief, a humid climate, and low erosion rates (0.006–0.030 km/Ma) facilitated the development of the Cuevas paleosurface. During the Miocene, this paleosurface experienced differential reheating with a high geothermal gradient (>25 °C/km) due to the sedimentary cover and local magmatic heat sources. During the Andean orogeny, in the Pliocene, the Cuevas paleosurface was deformed, exhumed, and uplifted.
Generalization of Hop Distance‐Time Scaling and Particle Velocity Distributions via a Two‐Regime Formalism of Bedload Particle Motions
Authors: Wu Zi , Furbish David , Foufoula‐Georgiou Efi
Published: November 2019

To date, there is no consensus on the probability distribution of particle velocities during bedload transport, with some studies suggesting an exponential‐like distribution while others a Gaussian‐like distribution. Yet, the form of this distribution is key for the determination of sediment flux and the dispersion characteristics of tracers in rivers. Combining theoretical analysis of the Fokker‐Planck equation for particle motions, numerical simulations of the corresponding Langevin equation, and measurements of motion in high‐speed imagery from particle‐tracking experiments, we examine the statistics of bedload particle trajectories, revealing a two‐regime distance‐time (L‐Tp) scaling for the particle hops (measured from start to stop). We show that particles of short hop distances scale as L ~
giving rise to the Weibull‐like front of the hop distance distribution, while particles of long hop distances transition to a different scaling regime of L ~ Tp leading to the exponential‐like tail of the hop distance distribution. By demonstrating that the predominance of mostly long hop particles results in a Gaussian‐like velocity distribution, while a mixture of both short and long hop distance particles leads to an exponential‐like velocity distribution, we argue that the form of the probability distribution of particle velocities can depend on the physical environment within which particle transport occurs, explaining and unifying disparate views on particle velocity statistics reported in the literature.
Statistical Inference Over Persistent Homology Predicts Fluid Flow in Porous Media
Authors: Moon Chul , Mitchell Scott A. , Heath Jason E. , Andrew Matthew
Published: November 2019

We statistically infer fluid flow and transport properties of porous materials based on their geometry and connectivity, without the need for detailed We summarize structure by persistent homology and then determines the similarity of structures using image analysis and statistics. Longer term, this may enable quick and automated categorization of rocks into known archetypes. We first compute persistent homology of binarized 3D images of material subvolume samples. The persistence parameter is the signed Euclidean distance from inferred material interfaces, which captures the distribution of sizes of pores and grains. Each persistence diagram is converted into an image vector. We infer structural similarity by calculating image similarity. For each image vector, we compute principal components to extract features. We fit statistical models to features estimates material permeability, tortuosity, and anisotropy. We develop a Structural SIMilarity index to determine statistical representative elementary volumes.
Morphodynamic Modeling of Sediment Pulse Dynamics
Authors: Morgan Jacob A. , Nelson Peter A.
Published: November 2019

Sediment pulses, defined as discrete, temporary increases in sediment supply, enter channels through both natural and anthropogenic means. The movement of the resultant deposit (sediment wave) in coarse‐bedded channels is generally characterized by some combination of translation and dispersion; however, how sediment waves evolve over time is still poorly understood, potentially hampering restoration efforts that involve the introduction of sediment to channels. Here we use a one‐dimensional morphodynamic model to explore how different pulse characteristics affect sediment wave movement. Our one‐dimensional model uses the standard step backwater method to compute hydrodynamics and determines morphodynamics by computing bedload transport and retaining vertical grain size stratigraphy. We explore the effect of pulse mass, initial wave spread, and composition (grain size) on subsequent sediment wave dynamics. Our results suggest higher relative rates of sediment wave dispersion to advection for larger pulses, waves with a smaller initial spread, and pulses composed of coarser material. In all simulations sediment wave celerity and spreading rates decayed through time as a power function. Waves of smaller total mass decayed at faster rates than those of larger mass. Simulations also show that sediment pulses attain a terminal amplitude, suggesting that some sediment waves may not completely disperse. Larger terminal amplitudes were associated with larger pulses and pulses composed of coarser grains.
Genetic causes of primary aldosteronism
Authors: Seidel Eric , Schewe Julia , Scholl Ute I.
Published: November 2019

Primary aldosteronism is characterized by at least partially autonomous production of the adrenal steroid hormone aldosterone and is the most common cause of secondary hypertension. The most frequent subforms are idiopathic hyperaldosteronism and aldosterone-producing adenoma. Rare causes include unilateral hyperplasia, adrenocortical carcinoma and Mendelian forms (familial hyperaldosteronism). Studies conducted in the last eight years have identified somatic driver mutations in a substantial portion of aldosterone-producing adenomas, including the genesKCNJ5(encoding inwardly rectifying potassium channel GIRK4),CACNA1D(encoding a subunit of L-type voltage-gated calcium channel CaV1.3),ATP1A1(encoding a subunit of Na+/K+-ATPase),ATP2B3(encoding a Ca2+-ATPase), andCTNNB1(encoding ß-catenin). In addition, aldosterone-producing cells were recently reported to form small clusters (aldosterone-producing cell clusters) beneath the adrenal capsule. Such clusters accumulate with age and appear to be more frequent in individuals with idiopathic hyperaldosteronism. The fact that they are associated with somatic mutations implicated in aldosterone-producing adenomas also suggests a precursor function for adenomas. Rare germline variants ofCYP11B2(encoding aldosterone synthase),CLCN2(encoding voltage-gated chloride channel ClC-2),KCNJ5,CACNA1H(encoding a subunit of T-type voltage-gated calcium channel CaV3.2), andCACNA1Dhave been reported in different subtypes of familial hyperaldosteronism. Collectively, these studies suggest that primary aldosteronism is largely due to genetic mutations in single genes, with potential implications for diagnosis and therapy.
Microfluidics-assisted multiplexed biomarker detection for in situ mapping of immune cells in tumor sections
Authors: Migliozzi Daniel , Pelz Benjamin , Dupouy Diego G. , Leblond Anne-Laure , Soltermann Alex , Gijs Martin A. M.
Published: November 2019

Because of the close interaction between tumors and the immune system, immunotherapies are nowadays considered as the most promising treatment against cancer. In order to define the diagnosis and the subsequent therapy, crucial information about the immune cells at the tumor site is needed. Indeed, different types or activation status of cells may be indicative for specific and personalized treatments. Here, we present a quantitative method to identify ten different immuno-markers in the same tumor cut section, thereby saving precious samples and enabling correlative analysis on several cell families and their activation status in a tumor microenvironment context. We designed and fabricated a microfluidic chip with optimal thermomechanical and optical properties for fast delivery of reagents on tissue slides and for fully automatic imaging by integration with an optical microscope. The multiplexing capability of the system is enabled by an optimized cyclic immunofluorescence protocol, with which we demonstrated quantitative sequential immunostaining of up to ten biomarkers on the same tissue section. Furthermore, we developed high-quality image-processing algorithms to map each cell in the entire tissue. As proof-of-concept analyses, we identified coexpression and colocalization patterns of biomarkers to classify the immune cells and their activation status. Thanks to the quantitativeness and the automation of both the experimental and analytical methods, we believe that this multiplexing approach will meet the increasing clinical need of personalized diagnostics and therapy in cancer pathology.
Intrinsic connectomes are a predictive biomarker of remission in major depressive disorder
Authors: Korgaonkar Mayuresh S. , Goldstein-Piekarski Andrea N. , Fornito Alexander , Williams Leanne M.
Published: November 2019

Although major depressive disorder (MDD) is associated with altered functional coupling between disparate neural networks, the degree to which such measures are ameliorated by antidepressant treatment is unclear. It is also unclear whether functional connectivity can be used as a predictive biomarker of treatment response. Here, we used whole-brain functional connectivity analysis to identify neural signatures of remission following antidepressant treatment, and to identify connectomic predictors of treatment response. 163 MDD and 62 healthy individuals underwent functional MRI during pre-treatment baseline and 8-week follow-up sessions. Patients were randomized to escitalopram, sertraline or venlafaxine-XR antidepressants and assessed at follow-up for remission. Baseline measures of intrinsic functional connectivity between each pair of 333 regions were analyzed to identify pre-treatment connectomic features that distinguish remitters from non-remitters. We then interrogated these connectomic differences to determine if they changed post-treatment, distinguished patients from controls, and were modulated by medication type. Irrespective of medication type, remitters were distinguished from non-remitters by greater connectivity within the default mode network (DMN); specifically, between the DMN, fronto-parietal and somatomotor networks, the DMN and visual, limbic, auditory and ventral attention networks, and between the fronto-parietal and somatomotor networks with cingulo-opercular and dorsal attention networks. This baseline hypo-connectivity for non-remitters also distinguished them from controls and increased following treatment. In contrast, connectivity for remitters was higher than controls at baseline and also following remission, suggesting a trait-like connectomic characteristic. Increased functional connectivity within and between large-scale intrinsic brain networks may characterize acute recovery with antidepressants in depression.
Meta-analysis of cortical thickness abnormalities in medication-free patients with major depressive disorder
Authors: Li Qian , Zhao Youjin , Chen Ziqi , Long Jingyi , Dai Jing , Huang Xiaoqi , Lui Su , Radua Joaquim , Vieta Eduard , Kemp Graham J. , Sweeney John A. , Li Fei , Gong Qiyong
Published: November 2019

Alterations in cortical thickness have been identified in major depressive disorder (MDD), but findings have been variable and inconsistent. To date, no reliable tools have been available for the meta-analysis of surface-based morphometric (SBM) studies to effectively characterize what has been learned in previous studies, and drug treatments may have differentially impacted findings. We conducted a comprehensive meta-analysis of magnetic resonance imaging (MRI) studies that explored cortical thickness in medication-free patients with MDD, using a newly developed meta-analytic mask compatible with seed-based d mapping (SDM) meta-analytic software. We performed the meta-regression to explore the effects of demographics and clinical characteristics on variation in cortical thickness in MDD. Fifteen studies describing 529 patients and 586 healthy controls (HCs) were included. Medication-free patients with MDD, relative to HCs, showed a complex pattern of increased cortical thickness in some areas (posterior cingulate cortex, ventromedial prefrontal cortex, and anterior cingulate cortex) and decreased cortical thickness in others (gyrus rectus, orbital segment of the superior frontal gyrus, and middle temporal gyrus). Most findings in the whole sample analysis were confirmed in a meta-analysis of studies recruiting medication-naive patients. Using the new mask specifically developed for SBM studies, this SDM meta-analysis provides evidence for regional cortical thickness alterations in MDD, mainly involving increased cortical thickness in the default mode network and decreased cortical thickness in the orbitofrontal and temporal cortex.
Virtual-photon-mediated spin-qubit–transmon coupling
Authors: Landig A. J. , Koski J. V. , Scarlino P. , Müller C. , Abadillo-Uriel J. C. , Kratochwil B. , Reichl C. , Wegscheider W. , Coppersmith S. N. , Friesen Mark , Wallraff A. , Ihn T. , Ensslin K.
Published: November 2019

Spin qubits and superconducting qubits are among the promising candidates for realizing a solid state quantum computer. For the implementation of a hybrid architecture which can profit from the advantages of either approach, a coherent link is necessary that integrates and controllably couples both qubit types on the same chip over a distance that is several orders of magnitude longer than the physical size of the spin qubit. We realize such a link with a frequency-tunable high impedance SQUID array resonator. The spin qubit is a resonant exchange qubit hosted in a GaAs triple quantum dot. It can be operated at zero magnetic field, allowing it to coexist with superconducting qubits on the same chip. We spectroscopically observe coherent interaction between the resonant exchange qubit and a transmon qubit in both resonant and dispersive regimes, where the interaction is mediated either by real or virtual resonator photons.
Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis
Authors: Johnson Jethro S. , Spakowicz Daniel J. , Hong Bo-Young , Petersen Lauren M. , Demkowicz Patrick , Chen Lei , Leopold Shana R. , Hanson Blake M. , Agresta Hanako O. , Gerstein Mark , Sodergren Erica , Weinstock George M.
Published: November 2019

The 16S rRNA gene has been a mainstay of sequence-based bacterial analysis for decades. However, high-throughput sequencing of the full gene has only recently become a realistic prospect. Here, we use in silico and sequence-based experiments to critically re-evaluate the potential of the 16S gene to provide taxonomic resolution at species and strain level. We demonstrate that targeting of 16S variable regions with short-read sequencing platforms cannot achieve the taxonomic resolution afforded by sequencing the entire (~1500 bp) gene. We further demonstrate that full-length sequencing platforms are sufficiently accurate to resolve subtle nucleotide substitutions (but not insertions/deletions) that exist between intragenomic copies of the 16S gene. In consequence, we argue that modern analysis approaches must necessarily account for intragenomic variation between 16S gene copies. In particular, we demonstrate that appropriate treatment of full-length 16S intragenomic copy variants has the potential to provide taxonomic resolution of bacterial communities at species and strain level.
Geocoding of worldwide patent data
Authors: de Rassenfosse Gaétan , Kozak Jan , Seliger Florian
Published: November 2019

The dataset provides geographic coordinates for inventor and applicant locations in 18.8 million patent documents spanning over more than 30 years. The geocoded data are further allocated to the corresponding countries, regions and cities. When the address information was missing in the original patent document, we imputed it by using information from subsequent filings in the patent family. The resulting database can be used to study patenting activity at a fine-grained geographic level without creating bias towards the traditional, established patent offices.
New opportunities for designing effective small interfering RNAs
Authors: Valdés James J. , Miller Andrew D.
Published: November 2019

Small interfering RNAs (siRNAs) that silence genes of infectious diseases are potentially potent drugs. A continuing obstacle for siRNA-based drugs is how to improve their efficacy for adequate dosage. To overcome this obstacle, the interactions of antiviral siRNAs, tested in vivo, were computationally examined within the RNA-induced silencing complex (RISC). Thermodynamics data show that a persistent RISC cofactor is significantly more exothermic for effective antiviral siRNAs than their ineffective counterparts. Detailed inspection of viral RNA secondary structures reveals that effective antiviral siRNAs target hairpin or pseudoknot loops. These structures are critical for initial RISC interactions since they partially lack intramolecular complementary base pairing. Importing two temporary RISC cofactors from magnesium-rich hairpins and/or pseudoknots then kickstarts full RNA hybridization and hydrolysis. Current siRNA design guidelines are based on RNA primary sequence data. Herein, the thermodynamics of RISC cofactors and targeting magnesium-rich RNA secondary structures provide additional guidelines for improving siRNA design.
Combining super-resolution microscopy with neuronal network recording using magnesium fluoride thin films as cover layer for multi-electrode array technology
Authors: Schmidl L. , Schmidl G. , Gawlik A. , Dellith J. , Hübner U. , Tympel V. , Schmidl F. , Plentz J. , Geis C. , Haselmann H.
Published: November 2019

We present an approach for fabrication of reproducible, chemically and mechanically robust functionalized layers based on MgF2 thin films on thin glass substrates. These show great advantages for use in super-resolution microscopy as well as for multi-electrode-array fabrication and are especially suited for combination of these techniques. The transparency of the coated substrates with the low refractive index material is adjustable by the layer thickness and can be increased above 92%. Due to the hydrophobic and lipophilic properties of the thin crystalline MgF2 layers, the temporal stable adhesion needed for fixation of thin tissue, e.g. cryogenic brain slices is given. This has been tested using localization-based super-resolution microscopy with currently highest spatial resolution in light microscopy. We demonstrated that direct stochastic optical reconstruction microscopy revealed in reliable imaging of structures of central synapses by use of double immunostaining of post- (homer1 and GluA2) and presynaptic (bassoon) marker structure in a 10 µm brain slice without additional fixing of the slices. Due to the proven additional electrical insulating effect of MgF2 layers, surfaces of multi-electrode-arrays were coated with this material and tested by voltage-current-measurements. MgF2 coated multi-electrode-arrays can be used as a functionalized microscope cover slip for combination with live-cell super-resolution microscopy.
Performance of wild-Serbian Ganoderma lucidum mycelium in treating synthetic sewage loading using batch bioreactor
Authors: Mohd Hanafiah Zarimah , Wan Mohtar Wan Hanna Melini , Abu Hasan Hassimi , Jensen Henriette Stokbro , Klaus Anita , Wan-Mohtar Wan Abd Al Qadr Imad
Published: November 2019

The fluctuation of domestic wastewater characteristic inhibits the current conventional microbial-based treatment. The bioremediation fungi has received attention and reported to be an effective alternative to treat industrial wastewater. Similar efficient performance is envisaged for domestic wastewater whereby assessed performance of fungi for varying carbon-to-nitrogen ratios in domestic wastewater is crucial. Thus, the performance of pre-grown wild-Serbian Ganoderma lucidum mycelial pellets (GLMPs) was evaluated on four different synthetic domestic wastewaters under different conditions of initial pH (pH 4, 5, and 7) and chemical oxygen demand (COD) to nitrogen (COD/N) ratio of 3.6:1, 7.1:1, 14.2:1, and 17.8:1 (C3.6N1, C7.1N1, C14.2N1, and C17.8N1). The COD/N ratios with a constant concentration of ammonia–nitrogen (NH3–N) were chosen on the basis of the urban domestic wastewater characteristics sampled at the inlet basin of a sewage treatment plant (STP). The parameters of pH, COD, and NH3–N were measured periodically during the experiment. The wild-Serbian GLMPs efficiently removed the pollutants from the synthetic sewage. The COD/N ratio of C17.8N1 wastewater had the best COD and NH3–N removal, as compared to the lower COD/N ratio, and the shortest treatment time was obtained in an acidic environment at pH 4. The highest percentage for COD and NH3–N removal achieved was 96.0% and 93.2%, respectively. The results proved that the mycelium of GLMP has high potential in treating domestic wastewater, particularly at high organic content as a naturally sustainable bioremediation system.
Transcriptomic Analysis of mRNA-lncRNA-miRNA Interactions in Hepatocellular Carcinoma
Authors: Tang Xia , Feng Delong , Li Min , Zhou Jinxue , Li Xiaoyuan , Zhao Dachun , Hao Bingtao , Li Dewei , Ding Keyue
Published: November 2019

Fully elucidating the molecular mechanisms of non-coding RNAs (ncRNAs), including micro RNAs (miRNAs) and long non-coding RNAs (lncRNAs), underlying hepatocarcinogenesis is challenging. We characterized the expression profiles of ncRNAs and constructed a regulatory mRNA-lncRNA-miRNA (MLMI) network based on transcriptome sequencing (RNA-seq) of hepatocellular carcinoma (HCC, n = 9) patients. Of the identified miRNAs (n = 203) and lncRNAs (n = 1,090), we found 16 significantly differentially expressed (DE) miRNAs and three DE lncRNAs. The DE RNAs were highly enriched in 21 functional pathways implicated in HCC (p < 0.05), including p53, MAPK, and NAFLD signaling. Potential pairwise interactions between DE ncRNAs and mRNAs were fully characterized using in silico prediction and experimentally-validated evidence. We for the first time constructed a MLMI network of reciprocal interactions for 16 miRNAs, three lncRNAs, and 253 mRNAs in HCC. The predominant role of MEG3 in the MLMI network was validated by its overexpression in vitro that the expression levels of a proportion of MEG3-targeted miRNAs and mRNAs was changed significantly. Our results suggested that the comprehensive MLMI network synergistically modulated carcinogenesis, and the crosstalk of the network provides a new avenue to accurately describe the molecular mechanisms of hepatocarcinogenesis.
Improved Cas9 activity by specific modifications of the tracrRNA
Authors: Scott Tristan , Urak Ryan , Soemardy Citradewi , Morris Kevin V.
Published: November 2019

CRISPR/Cas is a transformative gene editing tool, that offers a simple and effective way to target a catalytic Cas9, the most widely used is derived fromStreptococcus pyogenes (SpCas9), with a complementary small guide RNA (sgRNA) to inactivate endogenous genes resulting from insertions and deletions (indels). CRISPR/Cas9 has been rapidly applied to basic research as well as expanded for potential clinical applications. Utilization ofspCas9 as an ribonuclearprotein complex (RNP) is considered the most safe and effective method to apply Cas9 technology, and the efficacy of this system is critically dependent on the ability of Cas9 to generate high levels of indels. We find here that novel sequence changes to the tracrRNA significantly improves Cas9 activity when delivered as an RNP. We demonstrate that a dual-guide RNA (dgRNA) with a modified tracrRNA can improve reporter knockdown and indel formation at several targets within the long terminal repeat (LTR) of HIV. Furthermore, the sequence-modified tracrRNAs improved Cas9-mediated reduction of CCR5 surface receptor expression in cell lines, which correlated with higher levels of indel formation. It was demonstrated that a Cas9 RNP with a sequence modified tracrRNA enhanced indel formation at the CCR5 target site in primary CD4+ T-cells. Finally, we show improved activity at two additional targets within the HBB locus and the BCL11A GATA site. Overall, the data presented here suggests that novel facile tracrRNA sequence changes could potentially be integrated with current dgRNA technology, and open up the possibility for the development of sequence modified tracrRNAs to improve Cas9 RNP activity.
Transcriptome analysis reveals autophagy as regulator of TGFβ/Smad-induced fibrogenesis in trabecular meshwork cells
Authors: Nettesheim April , Shim Myoung Sup , Hirt Josh , Liton Paloma B.
Published: November 2019

The trabecular meshwork (TM) is a specialized ocular tissue, which is responsible, together with the Schlemm’s canal (SC), for maintaining appropriate levels of intraocular pressure. Dysfunction of these tissues leads to ocular hypertension and increases the risk for developing glaucoma. Previous work by our laboratory revealed dysregulated autophagy in aging and in glaucomatous TM cells. In order to gain more insight in the role of autophagy in the TM pathophysiology, we have conducted transcriptome and functional network analyses of TM primary cells with silenced expression of the autophagy genes Atg5 and Atg7. Atg5/7-deficient TM cells showed changes in transcript levels of several fibrotic genes, including TGFβ2, BAMBI, and SMA. Furthermore, genetic and pharmacological inhibition of autophagy was associated with a parallel reduction in TGFβ-induced fibrosis, caused by a BAMBI-mediated reduced activation of Smad2/3 signaling in autophagy-deficient cells. At the same time, TGFβ treatment led to Smad2/3-dependent dysregulation of autophagy in TM cells, characterized by increased LC3-II levels and autophagic vacuoles content. Together, our results indicate a cross-talk between autophagy and TGFβ signaling in TM cells.
Electrochemical and DFT studies of brass corrosion inhibition in 3% NaCl in the presence of environmentally friendly compounds
Authors: Radovanović Milan B. , Tasić Žaklina Z. , Mihajlović Marija B. Petrović , Simonović Ana T. , Antonijević Milan M.
Published: November 2019

The effects of adenine, salicylaldoxime and 4(5)-methylimidazole on brass corrosion in NaCl were investigated. The investigation comprised electrochemical techniques, scanning electron microscopy and quantum chemical calculation. The results obtained by polarization measurements show that the examined compounds successfully inhibited the corrosion of brass. Additionally, the quantum mechanical calculations indicate that there is a correlation between energy gap and inhibition efficiency. Moreover, the inhibition mechanism includes the adsorption of the inhibitor on active sites on the electrode surface, which was confirmed by SEM-EDS analysis of the brass.
The intrinsic circadian clock in podocytes controls glomerular filtration rate
Authors: Ansermet Camille , Centeno Gabriel , Nikolaeva Svetlana , Maillard Marc P. , Pradervand Sylvain , Firsov Dmitri
Published: November 2019

Glomerular filtration rate (GFR), or the rate of primary urine formation, is the key indicator of renal function. Studies have demonstrated that GFR exhibits significant circadian rhythmicity and, that these rhythms are disrupted in a number of pathologies. Here, we tested a hypothesis that the circadian rhythm of GFR is driven by intrinsic glomerular circadian clocks. We used mice lacking the circadian clock protein BMAL1 specifically in podocytes, highly specialized glomerular cells critically involved in the process of glomerular filtration (Bmal1lox/lox/Nphs2-rtTA/LC1 or, cKO mice). Circadian transcriptome profiling performed on isolated glomeruli from control and cKO mice revealed that the circadian clock controls expression of multiple genes encoding proteins essential for normal podocyte function. Direct assessment of glomerular filtration by inulin clearance demonstrated that circadian rhythmicity in GFR was lost in cKO mice that displayed an ultradian rhythm of GFR with 12-h periodicity. The disruption of circadian rhythmicity in GFR was paralleled by significant changes in circadian patterns of urinary creatinine, sodium, potassium and water excretion and by alteration in the diurnal pattern of plasma aldosterone levels. Collectively, these results indicate that the intrinsic circadian clock in podocytes participate in circadian rhythmicity of GFR.
Author Correction: The influence of the Atlantic multidecadal oscillation on the eastern Andes low-level jet and precipitation in South America
Authors: Jones Charles , Carvalho Leila M. V.
Published: November 2019

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Measuring student engagement in the undergraduate general chemistry laboratory
Authors: Smith K. Christopher , Alonso Valeria
Published: November 2019

In this study a survey was developed to investigate students’ engagement during general chemistry laboratory sessions. Aspects of engagement surveyed included cognitive, behavioral, and emotional engagement, and the survey items were focused on activities during the pre-laboratory introduction, laboratory procedures, and data collection. Exploratory factor analysis of the results was conducted to determine the various underlying factors in the survey, and the scores of the general chemistry laboratory students along these underlying factors were compared. The findings supported the various dimensions of engagement reported in the literature.
Ultrafast labeling and high-fidelity imaging of mitochondria in cancer cells using an aggregation-enhanced emission fluorescent probe
Authors: Liu Li , Zou Qian , Leung Jong-Kai , Wang Jia-Li , Kam Chuen , Chen Sijie , Feng Shun , Wu Ming-Yu
Published: November 2019

An aggregation-enhanced emission probe was developed for ultrafast labeling and high-fidelity imaging of mitochondria in cancer cells with a high signal-to-noise ratio.
Facilitating charge transfer via a giant magnetoresistance effect for high-efficiency photocatalytic hydrogen production
Authors: Lei Qin , Long Xinxin , Chen Huanyu , Tan Jihua , Wang Xinming , Chen Rongzhi
Published: November 2019

CoCu alloy magnetic unit was implanted in photocatalytic system to improve photoinduced charge separation efficiency by regulating electron transfer pathway via giant magnetoresistance (GMR) effect, achieving significantly H2 production activity.
Reversible pyrrole-based proton storage/release in ruthenium(ii) complexes
Authors: Zhang Zheng-Hao , He Piao , Kang Shi-Rui , Liu Chao , Yi Xiao-Yi
Published: November 2019

Newly designed pyridylpyrrole Ru(ii) complexes are featured fast-responsive and reversible proton storage/release on Cα of pyrrole and act as an acid initiator in catalytic polymerization of 2,2-dimethyloxirane.
Band-bending induced passivation: high performance and stable perovskite solar cells using a perhydropoly(silazane) precursor
Authors: Kanda Hiroyuki , Shibayama Naoyuki , Huckaba Aron Joel , Lee Yonghui , Paek Sanghyun , Klipfel Nadja , Roldán-Carmona Cristina , Queloz Valentin Ianis Emmanuel , Grancini Giulia , Zhang Yi , Abuhelaiqa Mousa , Cho Kyung Taek , Li Mo , Mensi Mounir Driss , Kinge Sachin , Nazeeruddin Mohammad Khaja
Published: November 2019

It could successfully control the band-bending of the perovskite semiconductor, which led to improvement of the photovoltaic performance.
Staging Na/K-ion de-/intercalation of graphite retrieved from spent Li-ion batteries: in operando X-ray diffraction studies and an advanced anode material for Na/K-ion batteries
Authors: Liang Hao-Jie , Hou Bao-Hua , Li Wen-Hao , Ning Qiu-Li , Yang Xu , Gu Zhen-Yi , Nie Xue-Jiao , Wang Guang , Wu Xing-Long
Published: November 2019

The exhausted graphite from spent Li-ion batteries is recycled and reused as a favorable anode for Na/K-ion batteries, and the insights into structural de-/intercalation model are realized.
Enhanced electrochemical supercapacitor performance with a three-dimensional porous boron-doped diamond film
Authors: Wang Xue , He Yapeng , Guo Zhongcheng , Huang Hui , Zhang Panpan , Lin Haibo
Published: November 2019

A three-dimensional porous boron-doped diamond film is developed to enhance the electrochemical performance of supercapacitors in a wide potential window.
Intracellular GSH-responsive camptothecin delivery systems
Authors: Zhang Dan , Li Le , Ji Xiaohui , Gao Yanhong
Published: November 2019

Smart GSH-responsive camptothecin delivery systems for treatment of tumors and real-time monitoring in vivo and in vitro were described.
Core–shell (nano-SnX/nano-Li4Ti5O12)@C spheres (X = Se,Te) with high volumetric capacity and excellent cycle stability for lithium-ion batteries
Authors: Hu Xuebu , Shang Biao , Zeng Tianbiao , Peng Qimeng , Li Gang , Zou Yongjin , Zhang Yuxin
Published: November 2019

Core–shell structure (nano-SnSe/nano-Li4Ti5O12)@C and (nano-SnTe/nano-Li4Ti5O12)@C are designed with extraordinary lithium storage stability.
Ultrathin MXene/aramid nanofiber composite paper with excellent mechanical properties for efficient electromagnetic interference shielding
Authors: Xie Fan , Jia Fengfeng , Zhuo Longhai , Lu Zhaoqing , Si Lianmeng , Huang Jizhen , Zhang Meiyun , Ma Qin
Published: November 2019

ANFs were designed as an intermolecular cross-linker to reinforce MXene and the composite paper exhibited excellent EMI shielding performance with a multi-layered structure.
Cerium catalyst promoted C–S cross-coupling: synthesis of thioethers, dapsone and RN-18 precursors
Authors: Tavares Junior José M. da C. , da Silva Caren D. G. , dos Santos Beatriz F. , Souza Nicole S. , de Oliveira Aline R. , Kupfer Vicente L. , Rinaldi Andrelson W. , Domingues Nelson L. C.
Published: November 2019

In this work, we present a novel, efficient and green methodology for the synthesis of thioethers by the C–S cross-coupling reaction with the assistance of [Ce(l-Pro)2]2Ox as a heterogeneous catalyst in good to excellent yields.
Self-healing and shape-memory solid polymer electrolytes with high mechanical strength facilitated by a poly(vinyl alcohol) matrix
Authors: Jo Ye Hyang , Zhou Binghua , Jiang Ke , Li Shaoqiao , Zuo Cai , Gan Huihui , He Dan , Zhou Xingping , Xue Zhigang
Published: November 2019

This article reports PVA-based electrolytes with supramolecular networks formed via quadruple hydrogen bonding for lithium-ion batteries.
Plasma-engineered NiO nanosheets with enriched oxygen vacancies for enhanced electrocatalytic nitrogen fixation
Authors: Li Yu-biao , Liu Ya-ping , Wang Jing , Guo Ya-li , Chu Ke
Published: November 2019

Plasma technique can readily create the enriched oxygen vacancies which enable the NiO to be an active and durable catalyst for electrocatalytic fixation of N2 to NH3.
Effectiveness of the active learning in organic chemistry faculty development workshops
Authors: Houseknecht Justin B. , Bachinski Garrin J. , Miller Madelyn H. , White Sarah A. , Andrews Douglas M.
Published: November 2019

Active learning has been shown to improve student outcomes and learning, yet organic chemistry instructors have been slow to adopt these pedagogies. The Chemistry Collaborations, Workshops, and Communities of Scholars (cCWCS) Active Learning in Organic Chemistry (ALOC) workshops have sought to facilitate the adoption of active learning methods by helping participants define active learning and understand best practices, persuading them to incorporate these practices into their teaching, and supporting their implementation efforts through an online community, Organic Educational Resources (OrganicERs.org). The effectiveness of the workshops was measured over a two-year period using teaching self-efficacy and teaching practices instruments. Comparison to pre-workshop self-efficacy surveys found significant and sustained gains for knowledge about and belief in the efficacy of active learning methods (d = 1.18 compared to pre-workshop responses) and confidence in intention to implement (d = 0.60). Belief that they were implementing more active learning in their classrooms (d = 0.85) was corroborated by the teaching practices survey and survey of class time allocation which also showed statistically significant (p < 0.001) and sustained growth in student centered teaching (d = 1.00), formative assessment (d = 1.04), student–student interactions (d = 0.96), and the amount of class time spent with students working in groups (d = 0.68) for the workshop participants. Gains for participants in the 3 hour Active Learning in Organic Chemistry workshops at the 2016 Biennial Conference on Chemical Education (BCCE) were smaller than those in the 4 day ALOC workshops, but still meaningful. These results indicate that the 2015 and 2016 Active Learning in Organic Chemistry faculty development workshops effectively increased participants’ knowledge about, belief in the efficacy of, and implementation of active learning methods.
Linking a hierarchy of attitude effect to student engagement and chemistry achievement
Authors: Ross James , Guerra Evelyn , Gonzalez-Ramos Sheila
Published: November 2019

There are numerous influential factors contributing to students’ successful learning in introductory chemistry courses. One popularized factor is mathematical preparedness as gauged by a prerequisite mathematics grade or a standardized exam score. Less well known factors are students’ attitude toward the subject of chemistry or students’ involvement with chemistry. In this replication and extension study, students’ attitude in introductory chemistry courses, including a chemistry course designed for nursing and allied health students, was measured using the Attitude toward the Subject of Chemistry Inventory. Results show that a low-involvement hierarchy of attitude effect for students’ attitude toward chemistry, previously observed after 5 weeks, persists throughout a semester, and is likely widespread in classes across our department. Results also suggest a measurable difference between students’ emotional satisfaction with chemistry and their emotional attachment to chemistry, the latter of which is connected with their engagement with chemistry rather than their achievement in chemistry. Students’ low-involvement influence on chemistry achievement is being mediated predominantly by the affective subcomponent of their attitude. Attitudes are learned and a low-involvement hierarchy of attitude effect is susceptible to positive change. The results presented herein cement the reliability and generality of previous findings and extend those findings. The hierarchy of attitude effect can serve as a bifocal lens to capture evidence of students’ engagement with chemistry learning (learning process) as well as their chemistry achievement (learning product).
A HARPS RV search for planets around young nearby stars
Authors: Grandjean A. , Lagrange A.-M. , Keppler M. , Meunier N. , Mignon L. , Borgniet S. , Chauvin G. , Desidera S. , Galland F. , Messina S. , Sterzik M. , Pantoja B. , Rodet L. , Zicher N.
Published: November 2019

Context. Young nearby stars are good candidates in the search for planets with both radial velocity (RV) and direct imaging techniques. This, in turn, allows for the computation of the giant planet occurrence rates at all separations. The RV search around young stars is a challenge as they are generally faster rotators than older stars of similar spectral types and they exhibit signatures of magnetic activity (spots) or pulsation in their RV time series. Specific analyses are necessary to characterize, and possibly correct for, this activity.

Aims. Our aim is to search for planets around young nearby stars and to estimate the giant planet (GP) occurrence rates for periods up to 1000 days.

Methods. We used the HARPS spectrograph on the 3.6 m telescope at La Silla Observatory to observe 89 A−M young (<600 Myr) stars. We used our SAFIR (Spectroscopic data via Analysis of the Fourier Interspectrum Radial velocities) software to compute the RV and other spectroscopic observables. Then, we computed the companion occurrence rates on this sample.

Results. We confirm the binary nature of HD 177171, HD 181321 and HD 186704. We report the detection of a close low mass stellar companion for HIP 36985. No planetary companion was detected. We obtain upper limits on the GP (<13 MJup) and BD (∈ [13;80] MJup) occurrence rates based on 83 young stars for periods less than 1000 days, which are set, 2−2+3 and 1−1+3%.
Ellerman bombs and UV bursts: reconnection at different atmospheric layers
Authors: Ortiz Ada , Hansteen Viggo H. , Nóbrega-Siverio Daniel , van der Voort Luc Rouppe
Published: November 2019

The emergence of magnetic flux through the photosphere and into the outer solar atmosphere produces, amongst other dynamical phenomena, Ellerman bombs (EBs), which are observed in the wings of Hα and are due to magnetic reconnection in the photosphere below the chromospheric canopy. Signs of magnetic reconnection are also observed in other spectral lines, typical of the chromosphere or the transition region. An example are the ultraviolet (UV) bursts observed in the transition region lines of Si IV and the upper chromospheric lines of Mg II. In this work we analyze high-cadence, high-resolution coordinated observations between the Swedish 1m Solar Telescope (SST) and the Interface Region Imaging Spectrograph (IRIS) spacecraft. Hα images from the SST provide us with the positions, timings, and trajectories of EBs in an emerging flux region. Simultaneous, co-aligned IRIS slit-jaw images at 133 (C II, transition region), 140 (Si IV, transition region), and 279.6 (Mg II k, core, upper chromosphere) nm as well as spectroscopy in the far- and near-ultraviolet from the fast spectrograph raster allow us to study the possible chromospheric and transition region counterparts of those EBs. Our main goal is to study the possible temporal and spatial relationship between several reconnection events at different layers in the atmosphere (namely EBs and UV bursts), the timing history between them, and the connection of these dynamical phenomena to the ejection of surges in the chromosphere. We also investigate the properties of an extended UV burst and their variations across the burst domain. Our results suggest a scenario where simultaneous and co-spatial EBs and UV bursts are part of the same reconnection system occurring sequentially along a vertical or nearly vertical current sheet. Heating and bidirectional jets trace the location where reconnection takes place. These results support and expand those obtained from recent numerical simulations of magnetic flux emergence.
Comparison of Radiation Exposure of the Surgeon in Minimally Invasive Treatment of Osteoporotic Vertebral Fractures – Radiofrequency Kyphoplasty versus Balloon Kyphoplasty with Cement Delivery Systems (CDS)
Authors: Reißberg Steffen , Lüdeke Lina , Fritsch Michael
Published: November 2019

The aim of the present study was to compare the radiation exposure of the surgeon when using two different kyphoplasty systems for the minimally invasive treatment of osteoporotic vertebral body fractures. There was a preliminary investigation study by a Belgian working group from the ORAMED project (2010), which served as the basis and showed a dose reduction for the surgeon when using a balloon kyphoplasty system with cement delivery systems (CDS).

Materials and Methods A bipedicular balloon kyphoplasty system (Medtronic GmbH) with CDS and a unipedicular radiofrequency kyphoplasty system (StabiliT, DFine Europe GmbH) were used in solitary fractures in the thoracolumbar junction in 20 patients each. The patient groups were relatively homogeneous with a mean age of 76.9 years for balloon kyphoplasty and 75 years for radiofrequency kyphoplasty. As expected, the proportion of woman was higher in both groups. The mean BMI value was higher in the radiofrequency kyphoplasty group, and the patient with the highest BMI was also in this group. The workflows were defined in three steps. The working time and the fluoroscopic time were measured in the individual work steps and the dose was measured over all work steps by TLD chips (thermoluminescence detector) on the forehead, on the X-ray apron, on both wrists and on the left ankle. The dose area product was registered for the entire procedure.

Results In step 2, the main differences were found in working time and fluoroscopy time in transit. The difference was due to the bipedicular puncture for balloon kyphoplasty and the change of the working cannula, while only a unipedicular puncture was needed in radiofrequency kyphoplasty. The total fluoroscopy time over all procedures was three times longer than in balloon kyphoplasty and this was also reflected in the dose area product, which was more than twice that. The measured surface doses for the lenses were four times higher in balloon kyphoplasty. For the left wrist, the values for balloon kyphoplasty were about 8 times higher.

Conclusion Overall, from a radiophysical perspective, the use of a unipedicular kyphoplasty system must be recommended. Should balloon kyphoplasty be used for medical reasons, all radiation protection products (lead gloves, lead glass, radiation protection goggles and CDS) should be used, the surface doses for both hands must be detected by a ring dosimeter and the lens dose must be recorded and documented by a TLD on the radiation protection goggles.

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