bluuebunny/crossref_metadata_2025 huggingface dataset:
Along‐Margin Variations in Breakup Volcanism at the Eastern North American Margin
Authors: Greene John A. , Tominaga Masako , Miller Nathaniel C.
Published: November 2020

We model the magnetic signature of rift‐related volcanism to understand the distribution and volume of magmatic activity that occurred during the breakup of Pangaea and early Atlantic opening at the Eastern North American Margin (ENAM). Along‐strike variations in the amplitude and character of the prominent East Coast Magnetic Anomaly (ECMA) suggest that the emplacement of the volcanic layers producing this anomaly similarly varied along the margin. We use three‐dimensional magnetic forward modeling constrained by seismic interpretations to identify along‐margin variations in volcanic thickness and width that can explain the observed amplitude and character of the ECMA. Our model results suggest that the ECMA is produced by a combination of both first‐order (~600–1,000 km) and second‐order (~50–100 km) magmatic segmentation. The first‐order magmatic segmentation could have resulted from preexisting variations in crustal thickness and rheology developed during the tectonic amalgamation of Pangaea. The second‐order magmatic segmentation developed during continental breakup and likely influenced the segmentation and transform fault spacing of the initial, and modern, Mid‐Atlantic Ridge. These variations in magmatism show how extension and thermal weakening was distributed at the ENAM during continental breakup and how this breakup magmatism was related to both previous and subsequent Wilson cycle stages.
Reconstructing Western Boundary Current Stability in the North Atlantic Ocean for the Past 700 Kyr From Globorotalia truncatulinoides Coiling Ratios
Authors: Billups Katharina , Vizcaíno Maoli , Chiarello Josephine , Kaiser Emily A.
Published: November 2020

Down‐core changes in the coiling direction of Globorotalia truncatulinoides in the northwestern subtropical Atlantic (KNR140‐37PC and Ocean Drilling Program Sites 1063, 1059, 1056, 1058) provide a tracer for the hydrographic conditions in the western boundary current over the past 700 kyr (Marine Isotope Stage, MIS, 1–17). A consistent association between percent G. truncatulinoides (sinistral) abundances, total test counts, and bulk sediment CaCO3 content is established by MIS 11 suggesting a response to ocean‐atmosphere interactions during the mid Brunhes event. Commencing with MIS 11, interglacial maxima are associated with high total test counts and either distinct sinistral test minima (MIS 9e, 11c) or maxima (MIS 1, 5e, 7a). High sinistral test abundances with relatively high test counts is similar to the late Holocene relationship at the study sites. Low sinistral test abundances despite high test counts means that coiling ratios are dominated by dextral forms. We interpret this pattern to indicate more intense flow in the subtropical gyre either via the western boundary current drawing toward the gyre center, or a more northern influence of the North Equatorial and Antilles Currents. This suggests that the western boundary current may have been more intense during MIS 11c and MIS 9e then during MIS 7a, MIS 5e, and MIS 1 consistent with climate warm anomalies in northern Europe at these times. Regardless of the mechanism, the observation that minima and maxima in sinistral test abundances are prolonged at these times indicates that the western gyre boundary remained stable during relative warm intervals.
Partitioning of Historical Precipitation Into Evaporation and Runoff Based on Hydrologic Dynamics Identified With Recent SMAP Satellite Measurements
Authors: Akbar Ruzbeh , Short Gianotti Daniel J. , Salvucci Guido D. , Entekhabi Dara
Published: November 2020

Microwave brightness temperature observations from the NASA Soil Moisture Active Passive (SMAP) mission and gauge‐based precipitation data over the United States are used to reconstruct the soil water loss function and then historical (1979–2019) hydrological fluxes in the form of evapotranspiration (ET) and drainage (D) are quantified. Over the period of study, with the exception of snowy and hyper‐arid regions, we observe a correlation of R2 > 0.6 between SMAP‐precipitation derived drainage estimates and streamflow measurements from the U.S. Geological Survey (USGS). There is a bias between estimated drainage and USGS streamflow with an underestimation of about 1 mm day−1 in southwest United States to 3 mm day−1 in parts of the eastern United States. SMAP‐derived sensitivities of drainage and ET partitioning with respect to precipitation anomalies are also calculated. In parts of the Great Plains the drainage partitioning exhibits a near‐linear response, while in the southeast United States, the response is nonlinear. Partitioning also is examined for 6 four‐digit hydrologic unit basins wherein year‐to‐year variations in drainage partitioning are shown to be key mediators in translating precipitation anomalies into streamflow anomalies. Observation‐driven drainage and ET estimates are obtained without relying on full hydrologic and Land Surface Models (LSMs). This independence (isolation from model parameterization assumptions) provides a path toward using satellite‐derived landscape hydrological diagnostics to assess hydrologic models and LSMs as well as to guide their further development.
Water Temperature Controls for Regulated Canyon‐Bound Rivers
Authors: Mihalevich Bryce A. , Neilson Bethany T. , Buahin Caleb A. , Yackulic Charles B. , Schmidt John C.
Published: November 2020

Many canyon‐bound rivers have been dammed and downstream flow and water temperatures modified. In some regions, climate change is expected to cause lower storage in reservoirs and warmer release temperatures, which may further alter downstream flow and thermal regimes. To anticipate potential future changes, we first need to understand the dominant heat transfer mechanisms in canyon‐bound river systems. Toward this end, we adapt a dynamic process‐based river routing and temperature model to account for complex shading and radiation characteristics found in canyon‐bound rivers. We apply the model to a 362 km segment of the Colorado River in Grand Canyon National Park, USA to simulate temperature over an 18‐year period. Extensive temperature and flow data sets from within the canyon were used to assess model performance. At the most downstream gaging location, root mean square errors of hourly flow routing and temperature predictions were 11.5 m3/s and 0.93°C, respectively. We found that heat fluxes controlling temperatures were highly variable over space and time, primarily due to shortwave radiation dynamics and hydropeaking flow conditions. Additionally, the large differences between air and water temperature during summer periods resulted in high sensible and latent heat fluxes. Sensitivity analyses indicate that reservoir release temperatures are most influential above the RM88 gage (141 km below Glen Canyon Dam), while a combination of discharge, shortwave radiation, and air temperature become more important farther downstream. This study illustrates the importance of understanding the spatial and temporal variability of topographic shading when predicting water temperatures in canyon‐bound rivers.
Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters
Authors: Gazitúa M Consuelo , Vik Dean R , Roux Simon , Gregory Ann C , Bolduc Benjamin , Widner Brittany , Mulholland Margaret R , Hallam Steven J , Ulloa Osvaldo , Sullivan Matthew B
Published: November 2020

Viruses play an important role in the ecology and biogeochemistry of marine ecosystems. Beyond mortality and gene transfer, viruses can reprogram microbial metabolism during infection by expressing auxiliary metabolic genes (AMGs) involved in photosynthesis, central carbon metabolism, and nutrient cycling. While previous studies have focused on AMG diversity in the sunlit and dark ocean, less is known about the role of viruses in shaping metabolic networks along redox gradients associated with marine oxygen minimum zones (OMZs). Here, we analyzed relatively quantitative viral metagenomic datasets that profiled the oxygen gradient across Eastern Tropical South Pacific (ETSP) OMZ waters, assessing whether OMZ viruses might impact nitrogen (N) cycling via AMGs. Identified viral genomes encoded six N-cycle AMGs associated with denitrification, nitrification, assimilatory nitrate reduction, and nitrite transport. The majority of these AMGs (80%) were identified in T4-like Myoviridae phages, predicted to infect Cyanobacteria and Proteobacteria, or in unclassified archaeal viruses predicted to infect Thaumarchaeota. Four AMGs were exclusive to anoxic waters and had distributions that paralleled homologous microbial genes. Together, these findings suggest viruses modulate N-cycling processes within the ETSP OMZ and may contribute to nitrogen loss throughout the global oceans thus providing a baseline for their inclusion in the ecosystem and geochemical models.
Efficacy and safety of esaxerenone (CS-3150), a newly available nonsteroidal mineralocorticoid receptor blocker, in hypertensive patients with primary aldosteronism
Authors: Satoh Fumitoshi , Ito Sadayoshi , Itoh Hiroshi , Rakugi Hiromi , Shibata Hirotaka , Ichihara Atsuhiro , Omura Masao , Takahashi Katsutoshi , Okuda Yasuyuki , Iijima Setsuko
Published: November 2020

Mineralocorticoid receptor (MR) blockers are very beneficial for patients with hypertension and primary aldosteronism (PA). We investigated the efficacy and safety of a newly available nonsteroidal MR blocker, esaxerenone, in Japanese patients with hypertension and PA. A multicenter, open-label study was conducted in Japan between October 2016 and July 2017. Patients with hypertension and PA received 12 weeks of treatment with esaxerenone, initiated at 2.5 mg/day and escalated to 5 mg/day during week 2 or 4 of treatment, based on individual response. The only other permitted antihypertensive therapies were stable dosages of a Ca2+ channel blocker or α-blocker. The primary efficacy outcome was a change in sitting systolic and diastolic blood pressure (SBP/DBP) from baseline to the end of treatment. Forty-four patients were included; dose escalation to 5 mg/day was implemented for 41 of these patients. Significant decreases in SBP and DBP were observed (point estimates [95% confidence interval] −17.7 [−20.6, −14.7] and −9.5 [−11.7, −7.3] mmHg, respectively; both p < 0.0001 at the end of treatment). Significant BP reductions were evident from week 2 and continued through to week 8; BP remained stable until week 12. The antihypertensive effect of esaxerenone on SBP was significantly greater in females and in patients receiving monotherapy. The major drug-related adverse events were serum K+ increase and estimated glomerular filtration rate decrease (both 4.5%, n = 2); no gynecomastia or breast pain was observed. We conclude that esaxerenone is a potent MR blocker with favorable efficacy and safety profiles in patients with hypertension and PA.
Adding salt to expand voltage window of humid ionic liquids
Authors: Chen Ming , Wu Jiedu , Ye Ting , Ye Jinyu , Zhao Chang , Bi Sheng , Yan Jiawei , Mao Bingwei , Feng Guang
Published: November 2020

Humid hydrophobic ionic liquids—widely used as electrolytes—have narrowed electrochemical windows due to the involvement of water, absorbed on the electrode surface, in electrolysis. In this work, we performed molecular dynamics simulations to explore effects of adding Li salt in humid ionic liquids on the water adsorbed on the electrode surface. Results reveal that most of the water molecules are pushed away from both cathode and anode, by adding salt. The water remaining on the electrode is almost bound with Li+, having significantly lowered activity. The Li+-bonding and re-arrangement of the surface-adsorbed water both facilitate the inhibition of water electrolysis, and thus prevent the reduction of electrochemical windows of humid hydrophobic ionic liquids. This finding is testified by cyclic voltammetry measurements where salt-in-humid ionic liquids exhibit enlarged electrochemical windows. Our work provides the underlying mechanism and a simple but practical approach for protection of humid ionic liquids from electrochemical performance degradation.
Attosecond spectroscopy reveals alignment dependent core-hole dynamics in the ICl molecule
Authors: Marroux Hugo J. B. , Fidler Ashley P. , Ghosh Aryya , Kobayashi Yuki , Gokhberg Kirill , Kuleff Alexander I. , Leone Stephen R. , Neumark Daniel M.
Published: November 2020

The removal of electrons located in the core shells of molecules creates transient states that live between a few femtoseconds to attoseconds. Owing to these short lifetimes, time-resolved studies of these states are challenging and complex molecular dynamics driven solely by electronic correlation are difficult to observe. Here, we obtain few-femtosecond core-excited state lifetimes of iodine monochloride by using attosecond transient absorption on iodine 4d−16p transitions around 55 eV. Core-level ligand field splitting allows direct access of excited states aligned along and perpendicular to the ICl molecular axis. Lifetimes of 3.5 ± 0.4 fs and 4.3 ± 0.4 fs are obtained for core-hole states parallel to the bond and 6.5 ± 0.6 fs and 6.9 ± 0.6 fs for perpendicular states, while nuclear motion is essentially frozen on this timescale. Theory shows that the dramatic decrease of lifetime for core-vacancies parallel to the covalent bond is a manifestation of non-local interactions with the neighboring Cl atom of ICl.
Computer vision for pattern detection in chromosome contact maps
Authors: Matthey-Doret Cyril , Baudry Lyam , Breuer Axel , Montagne Rémi , Guiglielmoni Nadège , Scolari Vittore , Jean Etienne , Campeas Arnaud , Chanut Philippe Henri , Oriol Edgar , Méot Adrien , Politis Laurent , Vigouroux Antoine , Moreau Pierrick , Koszul Romain , Cournac Axel
Published: November 2020

Chromosomes of all species studied so far display a variety of higher-order organisational features, such as self-interacting domains or loops. These structures, which are often associated to biological functions, form distinct, visible patterns on genome-wide contact maps generated by chromosome conformation capture approaches such as Hi-C. Here we present Chromosight, an algorithm inspired from computer vision that can detect patterns in contact maps. Chromosight has greater sensitivity than existing methods on synthetic simulated data, while being faster and applicable to any type of genomes, including bacteria, viruses, yeasts and mammals. Our method does not require any prior training dataset and works well with default parameters on data generated with various protocols.
Alaskan carbon-climate feedbacks will be weaker than inferred from short-term experiments
Authors: Bouskill Nicholas J. , Riley William J. , Zhu Qing , Mekonnen Zelalem A. , Grant Robert F.
Published: November 2020

Climate warming is occurring fastest at high latitudes. Based on short-term field experiments, this warming is projected to stimulate soil organic matter decomposition, and promote a positive feedback to climate change. We show here that the tightly coupled, nonlinear nature of high-latitude ecosystems implies that short-term (<10 year) warming experiments produce emergent ecosystem carbon stock temperature sensitivities inconsistent with emergent multi-decadal responses. We first demonstrate that a well-tested mechanistic ecosystem model accurately represents observed carbon cycle and active layer depth responses to short-term summer warming in four diverse Alaskan sites. We then show that short-term warming manipulations do not capture the non-linear, long-term dynamics of vegetation, and thereby soil organic matter, that occur in response to thermal, hydrological, and nutrient transformations belowground. Our results demonstrate significant spatial heterogeneity in multi-decadal Arctic carbon cycle trajectories and argue for more mechanistic models to improve predictive capabilities.
Metal-organic framework and inorganic glass composites
Authors: Longley Louis , Calahoo Courtney , Limbach René , Xia Yang , Tuffnell Joshua M. , Sapnik Adam F. , Thorne Michael F. , Keeble Dean S. , Keen David A. , Wondraczek Lothar , Bennett Thomas D.
Published: November 2020

Metal-organic framework (MOF) glasses have become a subject of interest as a distinct category of melt quenched glass, and have potential applications in areas such as ion transport and sensing. In this paper we show how MOF glasses can be combined with inorganic glasses in order to fabricate a new family of materials composed of both MOF and inorganic glass domains. We use an array of experimental techniques to propose the bonding between inorganic and MOF domains, and show that the composites produced are more mechanically pliant than the inorganic glass itself.
AdipoR1/AdipoR2 dual agonist recovers nonalcoholic steatohepatitis and related fibrosis via endoplasmic reticulum-mitochondria axis
Authors: Xu Hongjiao , Zhao Qian , Song Nazi , Yan Zhibin , Lin Runfeng , Wu Shuohan , Jiang Lili , Hong Sihua , Xie Junqiu , Zhou Huihao , Wang Rui , Jiang Xianxing
Published: November 2020

Chronic nonalcoholic steatohepatitis (NASH) is a metabolic disorder that often leads to liver fibrosis, a condition with limited therapy options. Adiponectin is an adipocytokine that regulates glucose and lipid metabolism via binding to its receptors AdipoR1 and AdipoR2, and AdipoRs signaling is reported to enhance fatty acid oxidation and glucose uptake. Here, we synthesize and report an adiponectin-based agonist JT003, which potently improves insulin resistance in high fat diet induced NASH mice and suppresses hepatic stellate cells (HSCs) activation in CCl4 induced liver fibrosis. Mechanistic studies indicate that JT003 simultaneously stimulates AdipoR1- and AdipoR2- mediated signaling pathways as well as the PI3K-Akt pathway. Moreover, JT003 treatment significantly improves ER-mitochondrial axis function, which contributes to the reduced HSCs activation. Thus, the AdipoR1/AdipoR2 dual agonist improves both NASH and fibrosis in mice models, which provides the pharmacological and biological foundation for developing AdipoRs-based therapeutic agents on liver fibrosis.
Platycodin D enhances LDLR expression and LDL uptake via down-regulation of IDOL mRNA in hepatic cells
Authors: Choi Yu-Jeong , Lee Sol Ji , Kim Hyo In , Lee Hee Jung , Kang So Jung , Kim Tai Young , Cheon Chunhoo , Ko Seong-Gyu
Published: November 2020

The root of Platycodon grandiflorum (PG) has long been used as a traditional herbal medicine in Asian country. Platycondin D (PD), triterpenoid saponin that is a main constituent of PG, exhibits various biological activities such as anti-inflammatory, anti-oxidant, anti-diabetic, and anti-cancer effects. A previous study showed that PD had cholesterol-lowering effects in mice that develop hypercholesterolemia, but the underlying molecular mechanisms have not been elucidated during the last decade. Here, we demonstrated that both PG and PD markedly increased levels of cell surface low-density lipoprotein receptor (LDLR) by down-regulation of the E3 ubiquitin ligase named inducible degrader of the LDLR (IDOL) mRNA, leading to the enhanced uptake of LDL-derived cholesterol (LDL-C) in hepatic cells. Furthermore, cycloheximide chase analysis and in vivo ubiquitination assay revealed that PD increased the half-life of LDLR protein by reducing IDOL-mediated LDLR ubiquitination. Finally, we demonstrated that treatment of HepG2 cells with simvastatin in combination with PG and PD had synergistic effects on the improvement of LDLR expression and LDL-C uptake. Together, these results provide the first molecular evidence for anti-hypercholesterolemic activity of PD and suggest that PD alone or together with statin could be a potential therapeutic option in the treatment of atherosclerotic cardiovascular disease.
Design of optical meta-structures with applications to beam engineering using deep learning
Authors: Singh Robin , Agarwal Anu , Anthony Brian W.
Published: November 2020

Nanophotonics is a rapidly emerging field in which complex on-chip components are required to manipulate light waves. The design space of on-chip nanophotonic components, such as an optical meta surface which uses sub-wavelength meta-atoms, is often a high dimensional one. As such conventional optimization methods fail to capture the global optimum within the feasible search space. In this manuscript, we explore a Machine Learning (ML)-based method for the inverse design of the meta-optical structure. We present a data-driven approach for modeling a grating meta-structure which performs photonic beam engineering. On-chip planar photonic waveguide-based beam engineering offers the potential to efficiently manipulate photons to create excitation beams (Gaussian, focused and collimated) for lab-on-chip applications of Infrared, Raman and fluorescence spectroscopic analysis. Inverse modeling predicts meta surface design parameters based on a desired electromagnetic field outcome. Starting with the desired diffraction beam profile, we apply an inverse model to evaluate the optimal design parameters of the meta surface. Parameters such as the repetition period (in 2D axis), height and size of scatterers are calculated using a feedforward deep neural network (DNN) and convolutional neural network (CNN) architecture. A qualitative analysis of the trained neural network, working in tandem with the forward model, predicts the diffraction profile with a correlation coefficient as high as 0.996. The developed model allows us to rapidly estimate the desired design parameters, in contrast to conventional (gradient descent based or genetic optimization) time-intensive optimization approaches.
A modulation-doped heterostructure-based terahertz photoconductive antenna emitter with recessed metal contacts
Authors: Afalla Jessica , De Los Reyes Alexander , Cabello Neil Irvin , Vistro Victor DC Andres , Faustino Maria Angela , Ferrolino John Paul , Prieto Elizabeth Ann , Bardolaza Hannah , Catindig Gerald Angelo R. , Gonzales Karl Cedric , Mag-usara Valynn Katrine , Kitahara Hideaki , Somintac Armando S. , Salvador Arnel A. , Tani Masahiko , Estacio Elmer S.
Published: November 2020

We present the implementation of an efficient terahertz (THz) photoconductive antenna (PCA) emitter design that utilizes high mobility carriers in the two-dimensional electron gas (2DEG) of a modulation-doped heterostructure (MDH). The PCA design is fabricated with recessed metal electrodes in direct contact with the 2DEG region of the MDH. We compare the performance of the MDH PCA having recessed contacts with a PCA fabricated on bulk semi-insulating GaAs, on low temperature-grown GaAs, and a MDH PCA with the contacts fabricated on the surface. By recessing the contacts, the applied bias can effectively accelerate the high-mobility carriers within the 2DEG, which increases the THz power emission by at least an order of magnitude compared to those with conventional structures. The dynamic range (62 dB) and bandwidth characteristics (3.2 THz) in the power spectrum are shown to be comparable with the reference samples. Drude-Lorentz simulations corroborate the results that the higher-mobility carriers in the MDH, increase the THz emission. The saturation characteristics were also measured via optical fluence dependence, revealing a lower saturation value compared to the reference samples. The high THz conversion efficiency of the MDH-PCA with recessed contacts at low optical power makes it an attractive candidate for THz-time domain spectroscopy systems powered by low power fiber lasers.
Gene duplication, rather than epigenetic changes, drives FGF4 overexpression in KIT/PDGFRA/SDH/RAS-P WT GIST
Authors: Urbini Milena , Astolfi Annalisa , Indio Valentina , Nannini Margherita , Schipani Angela , Bacalini Maria Giulia , Angelini Sabrina , Ravegnini Gloria , Calice Giovanni , Del Gaudio Massimo , Secchiero Paola , Ulivi Paola , Gruppioni Elisa , Pantaleo Maria Abbondanza
Published: November 2020

Gastrointestinal stromal tumours that are wild type for KIT and PDGFRA are referred to as WT GISTs. Of these tumours, SDH-deficient (characterized by the loss of SDHB) and quadruple WT GIST (KIT/PDGFRA/SDH/RAS-P WT) subgroups were reported to display a marked overexpression of FGF4, identifying a putative common therapeutic target for the first time. In SDH-deficient GISTs, methylation of an FGF insulator region was found to be responsible for the induction of FGF4 expression. In quadruple WT, recurrent focal duplication of FGF3/FGF4 was reported; however, how it induced FGF4 expression was not investigated. To assess whether overexpression of FGF4 in quadruple WT could be driven by similar epigenetic mechanisms as in SDH-deficient GISTs, we performed global and locus-specific (on FGF4 and FGF insulator) methylation analyses. However, no epigenetic alterations were detected. Conversely, we demonstrated that in quadruple WT GISTs, FGF4 expression and the structure of the duplication were intimately connected, with the copy of FGF4 closer to the ANO1 super-enhancer being preferentially expressed. In conclusion, we demonstrated that in quadruple WT GISTs, FGF4 overexpression is not due to an epigenetic mechanism but rather to the specific genomic structure of the duplication. Even if FGF4 overexpression is driven by different molecular mechanisms, these findings support an increasing biologic relevance of the FGFR pathway in WT GISTs, both in SDH-deficient and quadruple WT GISTs, suggesting that it may be a common therapeutic target.
Bacteria coated cathodes as an in-situ hydrogen evolving platform for microbial electrosynthesis
Authors: Perona-Vico Elisabet , Feliu-Paradeda Laura , Puig Sebastià , Bañeras Lluis
Published: November 2020

Hydrogen is a key intermediate element in microbial electrosynthesis as a mediator of the reduction of carbon dioxide (CO2) into added value compounds. In the present work we aimed at studying the biological production of hydrogen in biocathodes operated at − 1.0 V vs. Ag/AgCl, using a highly comparable technology and CO2 as carbon feedstock. Ten bacterial strains were chosen from genera Rhodobacter, Rhodopseudomonas, Rhodocyclus, Desulfovibrio and Sporomusa, all described as hydrogen producing candidates. Monospecific biofilms were formed on carbon cloth cathodes and hydrogen evolution was constantly monitored using a microsensor. Eight over ten bacteria strains showed electroactivity and H2 production rates increased significantly (two to eightfold) compared to abiotic conditions for two of them (Desulfovibrio paquesii and Desulfovibrio desulfuricans). D. paquesii DSM 16681 exhibited the highest production rate (45.6 ± 18.8 µM min−1) compared to abiotic conditions (5.5 ± 0.6 µM min−1), although specific production rates (per 16S rRNA copy) were similar to those obtained for other strains. This study demonstrated that many microorganisms are suspected to participate in net hydrogen production but inherent differences among strains do occur, which are relevant for future developments of resilient biofilm coated cathodes as a stable hydrogen production platform in microbial electrosynthesis.
A revised definition for copal and its significance for palaeontological and Anthropocene biodiversity-loss studies
Authors: Solórzano-Kraemer Mónica M. , Delclòs Xavier , Engel Michael S. , Peñalver Enrique
Published: November 2020

The early fossilization steps of natural resins and associated terminology are a subject of constant debate. Copal and resin are archives of palaeontological and historical information, and their study is critical to the discovery of new and/or recently extinct species and to trace changes in forests during the Holocene. For such studies, a clear, suitable definition for copal is vital and is herein established. We propose an age range for copal (2.58 Ma—1760 AD), including Pleistocene and Holocene copals, and the novel term "Defaunation resin", defined as resin produced after the commencement of the Industrial Revolution. Defaunation resin is differentiated from Holocene copal as it was produced during a period of intense human transformative activities. Additionally, the “Latest Amber Bioinclusions Gap” (LABG) since the late Miocene to the end of the Pleistocene is hereby newly defined, and is characterized by its virtual absence of bioinclusions and the consequent lack of palaeontological information, which in part explains the historical differentiation between amber and copal. Crucial time intervals in the study of resin production, and of the biodiversity that could be contained, are now clarified, providing a framework for and focusing future research on bioinclusions preserved in copal and resin.
O-GlcNAc stabilizes SMAD4 by inhibiting GSK-3β-mediated proteasomal degradation
Authors: Kim Yeon Jung , Kang Min Jueng , Kim Eunah , Kweon Tae Hyun , Park Yun Soo , Ji Suena , Yang Won Ho , Yi Eugene C. , Cho Jin Won
Published: November 2020

O-linked β-N-acetylglucosamine (O-GlcNAc) is a post-translational modification which occurs on the hydroxyl group of serine or threonine residues of nucleocytoplasmic proteins. It has been reported that the presence of this single sugar motif regulates various biological events by altering the fate of target proteins, such as their function, localization, and degradation. This study identified SMAD4 as a novel O-GlcNAc-modified protein. SMAD4 is a component of the SMAD transcriptional complex, a major regulator of the signaling pathway for the transforming growth factor-β (TGF-β). TGF-β is a powerful promoter of cancer EMT and metastasis. This study showed that the amount of SMAD4 proteins changes according to cellular O-GlcNAc levels in human lung cancer cells. This observation was made based on the prolonged half-life of SMAD4 proteins. The mechanism behind this interaction was that O-GlcNAc impeded interactions between SMAD4 and GSK-3β which promote proteasomal degradation of SMAD4. In addition, O-GlcNAc modification on SMAD4 Thr63 was responsible for stabilization. As a result, defects in O-GlcNAcylation on SMAD4 Thr63 attenuated the reporter activity of luciferase, the TGF-β-responsive SMAD binding element (SBE). This study’s findings imply that cellular O-GlcNAc may regulate the TGF-β/SMAD signaling pathway by stabilizing SMAD4.
Histo-ELISA technique for quantification and localization of tissue components
Authors: Li Zhongmin , Goebel Silvia , Reimann Andreas , Ungerer Martin
Published: November 2020

A novel Histo-ELISA technique is intended to facilitate quantification of target tissue proteins in a tissue section and involves the selection of target regions in the tissue section, application of streptavidin-conjugated HRP (horseradish peroxidase), coupled with peroxidase substrate—TMB (3,3′,5,5′-tetramethylbenzidine), and staining dye evaluation with ELISA reader. The target protein content (weight per volume unit) was translated from optical densities by a reference standard curve, obtained via parallel staining of the targeted protein-coated slides. To validate the technique, we carried out quantifications of IgG extravasation in ischemic and nonischemic brain sections in a mouse stroke model. With those obtained data and the reference of immunohistochemistry scores assessed on the adjacent sections, accuracy, sensitivity, and precision for the technique were evaluated. For all evaluated parameters, Histo-ELISA performance was either comparable to or better than the standard immunohistochemistry. A comparison with the data from the repeated measurements yielded a rather low coefficient of variation. The results confirmed that the technique is a fairly reliable quantitative test with rather high sensitivity, accuracy, precision, and reproducibility for detecting target protein content in tissue sections and that its tissue distribution and related subsequent morphological changes can be observed at the same time.
A LC–MS method for 25-hydroxy-vitamin D3 measurements from dried blood spots for an epidemiological survey in India
Authors: Lote-Oke Rashmi , Pawar Jwala , Kulkarni Shriram , Sanas Prasanna , Kajale Neha , Gondhalekar Ketan , Khadilkar Vaman , Kamat Siddhesh , Khadilkar Anuradha
Published: November 2020

Vitamin D, a secosteroid, plays an important role in several physiological processes, and its deficiency can lead to numerous pathophysiological conditions in humans. The primary objective of this study was to develop and validate the robustness of a mass spectrometry-based method capable of quantifying 25(OH)D3 for an upcoming epidemiological survey in India and to pilot test it on healthy volunteers. We first describe the development and validation of various experimental parameters that ascertain the robustness and reliability of 25-hydroxy-vitamin D3 (25(OH)D3) extractions and quantitative measurements from Dried Blood Spot (DBS) samples, where we used eight disks of 3 mm each, punched from the circular spot covering the entire circumference of the spot. Next, we conducted a pilot study, comparing 25(OH)D3 levels from serum and DBS samples from 45 participants using a protocol developed for specifically this purpose. We found that the mean 25(OH)D3 concentrations in DBS samples were comparable to the serum levels (P > 0.05). In summary, our extraction and LC–MS protocol for quantitative 25(OH)D3 measurements are robust and reproducible, and will serve as an invaluable tool for upcoming epidemiological surveys in India and perhaps around the world.
Bio-fertilizer and rotten straw amendments alter the rhizosphere bacterial community and increase oat productivity in a saline–alkaline environment
Authors: Lu Peina , Bainard Luke D. , Ma Bin , Liu Jinghui
Published: November 2020

Saline–alkaline conditions can limit crop productivity and the role of soil microbes in nutrient cycling in arid and semi-arid regions throughout the world. A better understanding of how soil amendments and plant varieties affect rhizosphere microbial communities in saline–alkaline environments is important for the development of sustainable and productive agricultural systems under these challenging conditions. The objective of this study was to determine the effect of organic soil amendments on crop yield, soil physicochemical properties and rhizosphere bacterial communities of two oat cultivars in a saline–alkaline soil. The experiment was conducted in a semi-arid region of Northern China and involved growing two oat cultivars with varying levels of saline–alkaline tolerance under four different amendment treatments: (1) control (no amendments), (2) bio-fertilizer, (3) rotten straw, and (4) combination of bio-fertilizer and rotten straw. The combined bio-fertilizer and rotten straw amendment treatment resulted in the highest oat yields, reduced soil pH, and increased soil salt content for both cultivars. Baiyan2 (tolerant cultivar) had a higher bacterial α-diversity, relative abundance of Proteobacteria and Acidobacteria, and lower relative abundance of Firmicutes compared to Caoyou1 (sensitive cultivar). The rotten straw treatment and combined amendment treatment decreased bacterial α-diversity and the abundance of Proteobacteria, and increased the abundance of Firmicutes, which were positively correlated with soil salt, available nitrogen, phosphorous and potassium for both cultivars. Our study suggested using tolerant oat cultivars with the combined application of rotten straw and bio-fertilizer could be an effective strategy in remediating saline–alkaline soils.
Synergetic enhancement of electrochemical H2O2 detection in a nitrogen-doped carbon encapsulated FeCo alloy architecture
Authors: Chang Chunlin , Chen Qian , Fan Guangyin
Published: November 2020

A nitrogen-doped porous carbon encapsulated FeCo alloy architecture shows the synergetic enhancement of the electrochemical activity toward H2O2 detection.
Self-regenerative noble metal catalysts supported on high-entropy oxides
Authors: Chen Hao , Sun Yifan , Yang Shize , Wang Hui , Dmowski Wojciech , Egami Takeshi , Dai Sheng
Published: November 2020

A reversible temperature-dependent dissolution–exsolution process was discovered for noble metal species supported on high-entropy oxides, which indicates the potential to exploit the enhanced entropic effects to access self-regenerative catalysts.
Bioinspired metal complexes for energy-related photocatalytic small molecule transformation
Authors: Wu Hao-Lin , Li Xu-Bing , Tung Chen-Ho , Wu Li-Zhu
Published: November 2020

This article features the recent progress of bioinspired metal complexes as catalysts with high stability, specific selectivity and satisfactory efficiency to drive multiple-electron and multiple-proton related to small molecule transformation.
Proof-of-principle for two-stage photodynamic therapy: hypoxia triggered release of singlet oxygen
Authors: Ayan Seylan , Gunaydin Gurcan , Yesilgul-Mehmetcik Nisa , Gedik M. Emre , Seven Ozlem , Akkaya Engin U.
Published: November 2020

Singlet oxygen, which is stored in the form of an endoperoxide, released under hypoxic conditions typically prevalent in most tumors.
Halogen bonding between entirely negative fluorine atoms? Evidence from the crystal packing of some gold(i) and gold(iii) complexes with extensively fluorinated m-terphenyl ligands and triphenylphosphane
Authors: Sava Alexandru , Kegyes Krisztina T. , Popuş Bianca T. , Dan Bernadette C. , Silvestru Cristian , Raţ Ciprian I.
Published: November 2020

Intermolecular interactions between fluorine atoms, analogous to halogen bonding, are able to drive the solid-state arrangement of molecules.
Dynamic force spectroscopy for quantifying single-molecule organo–mineral interactions
Authors: Zhai Hang , Zhang Wenjun , Wang Lijun , Putnis Christine V.
Published: November 2020

Organo–mineral interactions have long been the focus in the fields of biomineralization and geomineralization, since such interactions not only modulate the dynamics of crystal nucleation and growth but may also change crystal phases, morphologies, and structures.
Analysis of an all-solid state nanobattery using molecular dynamics simulations under an external electric field
Authors: Ponce Victor , Galvez-Aranda Diego E. , Seminario Jorge M.
Published: November 2020

Speciation at the SEI and SSE of a solid-state nanobattery.
Aqueous solutions of binary ionic liquids: insight into structure, dynamics, and interface properties by molecular dynamics simulations and DFT methods
Authors: Heydari Dokoohaki Maryam , Zolghadr Amin Reza , Ghatee Mohammad Hadi , Klein Axel
Published: November 2020

Molecular dynamics simulations and density functional theory calculations were carried out on the effect of water on the intermolecular interactions in three IL binary mixtures.
Improvement of d–d interactions in density functional tight binding for transition metal ions with a ligand field model: assessment of a DFTB3+U model on nickel coordination compounds
Authors: Stepanovic Stepan , Lai Rui , Elstner Marcus , Gruden Maja , Garcia-Fernandez Pablo , Cui Qiang
Published: November 2020

DFTB3+U for transition metal systems.
Integrative structural modeling of a multidomain polo-like kinase
Authors: Ruan Hao , Kiselar Janna , Zhang Weilin , Li Siyang , Xiong Ruoyao , Liu Ying , Yang Sichun , Lai Luhua
Published: November 2020

Polo-like kinase 1 (PLK1) is a key regulator and coordinator for mitotic signaling that contains two major functional units of a kinase domain (KD) and a polo-box domain (PBD). The overall assembly of the KD and the PBD in PLK1 was reported.
Correction: The evolution of spiropyran: fundamentals and progress of an extraordinarily versatile photochrome
Authors: Kortekaas Luuk , Browne Wesley R.
Published: November 2020

Correction for ‘The evolution of spiropyran: fundamentals and progress of an extraordinarily versatile photochrome’ by Luuk Kortekaas et al., Chem. Soc. Rev., 2019, 48, 3406–3424, DOI: 10.1039/C9CS00203K.
Iron-catalyzed C–O bond functionalization of butyrolactam derivatives with various N-/C-nucleophiles
Authors: Ge Danhua , Wang Mao-Lin , Wang Xin , Chu Xue-Qiang
Published: November 2020

An iron-catalyzed C–O bond functionalization of butyrolactam derivatives with N-/C-nucleophiles to enable the synthesis of butyrolactam derivatives has been developed.
Synthesis of hydroxide-enriched cerium-doped oxy-sulfide catalyst for visible light-assisted reduction of Cr(vi)
Authors: Zeleke Misganaw Alemu , Kuo Dong-Hau
Published: November 2020

Semiconductor catalysts are significantly attractive materials for different cutting-edge applications, including the detoxification of toxic pollutants.
Electrophilic ring fluorination of 3,5-disubstituted pyrazoles: application to the formal synthesis of a neprilysin inhibitor key intermediate
Authors: Westermeyer Anne , Guillamot Gérard , Phansavath Phannarath , Ratovelomanana-Vidal Virginie
Published: November 2020

The access to a new family of unusual 4-fluorinated pyrazoles bearing acetal moities at the 3- or 5-position has been achieved by electrophilic fluorination using Selectfluor® with yields up to 67%.
Regio- and stereoselective intermolecular phenol coupling enzymes in secondary metabolite biosynthesis
Authors: Hüttel Wolfgang , Müller Michael
Published: November 2020

Phenol coupling enzymes, especially laccases and CYP-enzymes create an enormous diversity of biarylic secondary metabolites in fungi, plants, and bacteria. The enzymes and the elucidation of the corresponding metabolic pathways are presented.
Stabilizing the ferroelectric phase in HfO2-based films sputtered from ceramic targets under ambient oxygen
Authors: Mittmann Terence , Michailow Michail , Lomenzo Patrick D. , Gärtner Jan , Falkowski Max , Kersch Alfred , Mikolajick Thomas , Schroeder Uwe
Published: November 2020

The interplay of oxygen concentration and zirconium oxide concentration in thin HfxZr1−xO2 films significantly determines the phase and ferroelectric properties.
Interplay between spin crossover and proton migration along short strong hydrogen bonds
Authors: Jornet-Mollá Verónica , Giménez-Saiz Carlos , Cañadillas-Delgado Laura , Yufit Dmitry S. , Howard Judith A. K. , Romero Francisco M.
Published: November 2020

A proton migration across a short strong hydrogen bond can be triggered by spin crossover of a remote Fe2+ cation, with the onset of a photoinduced activation energy barrier for proton motion at low temperatures.
Decoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation sequencing technologies
Authors: Reddy Anireddy S.N. , Huang Jie , Syed Naeem H. , Ben-Hur Asa , Dong Suomeng , Gu Lianfeng
Published: November 2020

Next-generation sequencing (NGS) technologies - Illumina RNA-seq, Pacific Biosciences isoform sequencing (PacBio Iso-seq), and Oxford Nanopore direct RNA sequencing (DRS) - have revealed the complexity of plant transcriptomes and their regulation at the co-/post-transcriptional level. Global analysis of mature mRNAs, transcripts from nuclear run-on assays, and nascent chromatin-bound mRNAs using short as well as full-length and single-molecule DRS reads have uncovered potential roles of different forms of RNA polymerase II during the transcription process, and the extent of co-transcriptional pre-mRNA splicing and polyadenylation. These tools have also allowed mapping of transcriptome-wide start sites in cap-containing RNAs, poly(A) site choice, poly(A) tail length, and RNA base modifications. The emerging theme from recent studies is that reprogramming of gene expression in response to developmental cues and stresses at the co-/post-transcriptional level likely plays a crucial role in eliciting appropriate responses for optimal growth and plant survival under adverse conditions. Although the mechanisms by which developmental cues and different stresses regulate co-/post-transcriptional splicing are largely unknown, a few recent studies indicate that the external cues target spliceosomal and splicing regulatory proteins to modulate alternative splicing. In this review, we provide an overview of recent discoveries on the dynamics and complexities of plant transcriptomes, mechanistic insights into splicing regulation, and discuss critical gaps in co-/post-transcriptional research that need to be addressed using diverse genomic and biochemical approaches.
Fluorescent proteins for in vivo imaging, where's the biliverdin?
Authors: Montecinos-Franjola Felipe , Lin John Y. , Rodriguez Erik A.
Published: November 2020

Noninvasive fluorescent imaging requires far-red and near-infrared fluorescent proteins for deeper imaging. Near-infrared light penetrates biological tissue with blood vessels due to low absorbance, scattering, and reflection of light and has a greater signal-to-noise due to less autofluorescence. Far-red and near-infrared fluorescent proteins absorb light >600 nm to expand the color palette for imaging multiple biosensors and noninvasive in vivo imaging. The ideal fluorescent proteins are bright, photobleach minimally, express well in the desired cells, do not oligomerize, and generate or incorporate exogenous fluorophores efficiently. Coral-derived red fluorescent proteins require oxygen for fluorophore formation and release two hydrogen peroxide molecules. New fluorescent proteins based on phytochrome and phycobiliproteins use biliverdin IXα as fluorophores, do not require oxygen for maturation to image anaerobic organisms and tumor core, and do not generate hydrogen peroxide. The small Ultra-Red Fluorescent Protein (smURFP) was evolved from a cyanobacterial phycobiliprotein to covalently attach biliverdin as an exogenous fluorophore. The small Ultra-Red Fluorescent Protein is biophysically as bright as the enhanced green fluorescent protein, is exceptionally photostable, used for biosensor development, and visible in living mice. Novel applications of smURFP include in vitro protein diagnostics with attomolar (10−18 M) sensitivity, encapsulation in viral particles, and fluorescent protein nanoparticles. However, the availability of biliverdin limits the fluorescence of biliverdin-attaching fluorescent proteins; hence, extra biliverdin is needed to enhance brightness. New methods for improved biliverdin bioavailability are necessary to develop improved bright far-red and near-infrared fluorescent proteins for noninvasive imaging in vivo.
Comparing Speech Recognition for Listeners With Normal and Impaired Hearing: Simulations for Controlling Differences in Speech Levels and Spectral Shape
Authors: Fogerty Daniel , Madorskiy Rachel , Ahlstrom Jayne B. , Dubno Judy R.
Published: November 2020

Purpose

This study investigated methods used to simulate factors associated with reduced audibility, increased speech levels, and spectral shaping for aided older adults with hearing loss. Simulations provided to younger normal-hearing adults were used to investigate the effect of sensation level, speech presentation level, and spectral shape in comparison to older adults with hearing loss.

Method

Measures were assessed in quiet, steady-state noise, and speech-modulated noise. Older adults with hearing loss listened to speech that was spectrally shaped according to their hearing thresholds. Younger adults with normal hearing listened to speech that simulated the hearing-impaired group's (a) reduced audibility, (b) increased speech levels, and (c) spectral shaping. Group comparisons were made based on speech recognition performance and masking release. Additionally, younger adults completed measures of listening effort and perceived speech quality to assess if differences across simulations in these outcome measures were similar to those for speech recognition.

Results

Across the various simulations employed, testing in the presence of a threshold matching noise best matched differences in speech recognition and masking release between younger and older adults. This result remained consistent across the other two outcome measures.

Conclusions

A combination of audibility, speech level, and spectral shape factors is required to simulate differences between listeners with normal and impaired hearing in recognition, listening effort, and perceived speech quality. The use of spectrally shaped and amplified speech in the presence of threshold matching noise best provided this simulated control.

Supplemental Material

https://doi.org/10.23641/asha.13224632