bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vapor Isotope Probing of Typhoons Invading the Taiwan Region in 2016
Authors: Bhattacharya Sourendra K. , Sarkar Anindya , Liang Mao‐Chang 
Published: October 2022

AbstractEvery year, several typhoons originating from the West Pacific come close to Taiwan, modulating the regional weather through intense rainfall and enhanced humidity. The isotopic ratios (δ18O and δD) in the typhoon vapor evolve along its track due to rainout, recycling, and replenishment. In 2016, this signature was recorded in Taipei as typhoon vapors invaded the local atmosphere. After typhoon disintegration, the isotope ratios of the local atmosphere slowly return to the background value. The fall and rise in the ratios give rise to a V‐shaped variation. The processes controlling the fall (like moisture turnover, typhoon speed, wind speed, and direction) are fast (1–2 days). In contrast, the recovery is slow (several days) depending on the replacement rate of the local atmospheric moisture by incoming oceanic vapor. An isotope evolution model based on Rayleigh condensation and a box model of moisture mixing in the recovery phase are proposed and employed to explain the V‐shape. The combination of these two models for four major typhoons (Nepartak, Megi, Meranti, and Malakas) shows close agreement with observations. The evolution model suggests that the precipitation efficiency, PE (rainfall/overhead moisture), and typhoon size are two important parameters controlling the decrease in ratio. The characteristic turnover time of typhoon moisture (inverse of PE, obtained from European Centre for Medium‐Range Weather Forecasts fifth Re‐Analysis data) is estimated to be ∼2 days for a Pacific typhoon of 500 km radius. Our isotope study provides important constraints on the moisture budget of Pacific typhoons.
Cooling and Contraction of the Mesosphere and Lower Thermosphere From 2002 to 2021
Authors: Mlynczak Martin G. , Hunt Linda A. , Garcia Rolando R. , Harvey V. Lynn , Marshall Benjamin T. , Yue Jia , Mertens Christopher J. , Russell James M. 
Published: October 2022

AbstractWe examine the thermal structure of the mesosphere and lower thermosphere (MLT) using observations from 2002 through 2021 from the SABER instrument on the NASA TIMED satellite. These observations show that the MLT has significantly cooled and contracted between the years 2002 and 2019 (the year of the most recent solar minimum) due to a combination of a decline in the intensity of the 11‐year solar cycle and increasing carbon dioxide (CO2.) During this time the thickness of atmosphere between the 1 and 10−4 hPa pressure surfaces (approximately 48 and 105 km) has contracted by 1,333 m, of which 342 m is attributed to increasing CO2. All other pressure surfaces in the MLT have similarly contracted. We further postulate that the MLT in the two most recent solar minima (2008–2009 and 2019–2020) was very likely the coldest and thinnest since the beginning of the Industrial Age. The sensitivity of the MLT to a doubling of CO2 is shown to be −7.5 K based on observed trends in temperature and growth rates of CO2. Colder temperatures observed at 10−4 hPa in 2019 than in the prior solar minimum in 2009 may be due to a decrease of 5% in solar irradiance in the Schumann‐Runge band spectral region (175–200 nm).
A New Aerosol Dry Deposition Model for Air Quality and Climate Modeling
Authors: Pleim Jonathan E. , Ran Limei , Saylor Rick D. , Willison Jeff , Binkowski Francis S. 
Published: October 2022

AbstractDry deposition of aerosols from the atmosphere is an important but poorly understood and inadequately modeled process in atmospheric systems for climate and air quality. Comparisons of currently used aerosol dry deposition models to a compendia of published field measurement studies in various landscapes show very poor agreement over a wide range of particle sizes. In this study, we develop and test a new aerosol dry deposition model that is a modification of the current model in the Community Multiscale Air Quality (CMAQ) model. The new model agrees much better with measured dry deposition velocities across particle sizes. The key innovation is the addition of a second inertial impaction term for microscale obstacles such as leaf hairs, microscale ridges, and needleleaf edge effects. The most significant effect of the new model is to increase the mass dry deposition of the accumulation mode aerosols in CMAQ. Accumulation mode mass dry deposition velocities increase by almost an order of magnitude in forested areas with lesser increases for shorter vegetation. Peak PM2.5 concentrations are reduced in some forested areas by up to 40% in CMAQ simulations. Over the continuous United States, the new model reduced PM2.5 by an average of 16% for July 2018 at the Air Quality System monitoring sites. For summer 2018 simulations, bias and error of PM2.5 concentrations are significantly reduced, especially in forested areas.
Implementation of Dynamic Effective Rooting Depth in Evapotranspiration Model Deepens Understanding of Evapotranspiration Partitioning Under Soil Moisture Gradients in China
Authors: Shao Rui , Zhang Baoqing , He Xiaogang 
Published: October 2022

AbstractEvapotranspiration (ET) is a key component of water cycle and is strongly modulated by below‐ground (e.g., dynamic effective rooting depth, Zr) and above‐ground (e.g., LAI and canopy height, CH) vegetation dynamics. Existing studies mainly focus on the effect of above‐ground vegetation dynamics on ET, while it is still unclear how Zr affects ET. Moreover, it is challenging to parameterize Zr dynamically in large‐scale hydrological and biogeochemical models due to data scarcity. Here, we estimate Zr in China from 1982 to 2015 based on Guswa's carbon cost‐benefit model, and update ET partitioning algorithm by replacing CH with Zr in PT‐JPLsm model to form the PT‐JPLzr model. We find that root mean square error (RMSE) between modeled (based on PT‐JPLzr model) and observed ET is 8.25% lower than that of PT‐JPLsm model at 16 in‐situ ET observation sites. Comparing with T/ET from the satellite‐based products, our results highlight the improved performance of PT‐JPLzr (R2 = 0.66) due to incorporated Zr, which is superior to that of PT‐JPLsm model (R2 = 0.62). Transpiration (T) limited by changes in soil moisture (SM) is more sensitive to Zr than CH. Thus, Zr improves the PT‐JPL model performance by affecting the sensitivity of T to soil moisture deficit. Moreover, SM and LAI are main drivers of T/ET spatial variability in drier and wetter regions, respectively. These findings highlight the critical role of Zr in regulating the effects of soil moisture deficit on ET.
Chemolithoautotroph distributions across the subsurface of a convergent margin
Authors: Rogers Timothy J , Buongiorno Joy , Jessen Gerdhard L , Schrenk Matthew O , Fordyce James A , de Moor J Maarten , Ramírez Carlos J , Barry Peter H , Yücel Mustafa , Selci Matteo , Cordone Angela , Giovannelli Donato , Lloyd Karen G 
Published: October 2022

Abstract
Subducting oceanic crusts release fluids rich in biologically relevant compounds into the overriding plate, fueling subsurface chemolithoautotrophic ecosystems. To understand the impact of subsurface geochemistry on microbial communities, we collected fluid and sediments from 14 natural springs across a ~200 km transect across the Costa Rican convergent margin and performed shotgun metagenomics. The resulting 404 metagenome-assembled genomes (MAGs) cluster into geologically distinct regions based on MAG abundance patterns: outer forearc-only (25% of total relative abundance), forearc/arc-only (38% of total relative abundance), and delocalized (37% of total relative abundance) clusters. In the outer forearc, Thermodesulfovibrionia, Candidatus Bipolaricaulia, and Firmicutes have hydrogenotrophic sulfate reduction and Wood-Ljungdahl (WL) carbon fixation pathways. In the forearc/arc, Anaerolineae, Ca. Bipolaricaulia, and Thermodesulfovibrionia have sulfur oxidation, nitrogen cycling, microaerophilic respiration, and WL, while Aquificae have aerobic sulfur oxidation and reverse tricarboxylic acid carbon fixation pathway. Transformation-based canonical correspondence analysis shows that MAG distribution corresponds to concentrations of aluminum, iron, nickel, dissolved inorganic carbon, and phosphate. While delocalized MAGs appear surface-derived, the subsurface chemolithoautotrophic, metabolic, and taxonomic landscape varies by the availability of minerals/metals and volcanically derived inorganic carbon. However, the WL pathway persists across all samples, suggesting that this versatile, energy-efficient carbon fixation pathway helps shape convergent margin subsurface ecosystems.
Wide spectrum of neuronal and network phenotypes in human stem cell-derived excitatory neurons with Rett syndrome-associated MECP2 mutations
Authors: Mok Rebecca S. F. , Zhang Wenbo , Sheikh Taimoor I. , Pradeepan Kartik , Fernandes Isabella R. , DeJong Leah C. , Benigno Gabriel , Hildebrandt Matthew R. , Mufteev Marat , Rodrigues Deivid C. , Wei Wei , Piekna Alina , Liu Jiajie , Muotri Alysson R. , Vincent John B. , Muller Lyle , Martinez-Trujillo Julio , Salter Michael W. , Ellis James 
Published: October 2022

AbstractRett syndrome (RTT) is a severe neurodevelopmental disorder primarily caused by heterozygous loss-of-function mutations in the X-linked gene MECP2 that is a global transcriptional regulator. Mutations in the methyl-CpG binding domain (MBD) of MECP2 disrupt its interaction with methylated DNA. Here, we investigate the effect of a novel MECP2 L124W missense mutation in the MBD of an atypical RTT patient with preserved speech in comparison to severe MECP2 null mutations. L124W protein had a limited ability to disrupt heterochromatic chromocenters due to decreased binding dynamics. We isolated two pairs of isogenic WT and L124W induced pluripotent stem cells. L124W induced excitatory neurons expressed stable protein, exhibited increased input resistance and decreased voltage-gated Na+ and K+ currents, and their neuronal dysmorphology was limited to decreased dendritic complexity. Three isogenic pairs of MECP2 null neurons had the expected more extreme morphological and electrophysiological phenotypes. We examined development and maturation of L124W and MECP2 null excitatory neural network activity using micro-electrode arrays. Relative to isogenic controls, L124W neurons had an increase in synchronous network burst frequency, in contrast to MECP2 null neurons that suffered a significant decrease in synchronous network burst frequency and a transient extension of network burst duration. A biologically motivated computational neural network model shows the observed changes in network dynamics are explained by changes in intrinsic Na+ and K+ currents in individual neurons. Our multilevel results demonstrate that RTT excitatory neurons show a wide spectrum of morphological, electrophysiological and circuitry phenotypes that are dependent on the severity of the MECP2 mutation.
Protein synthesis inhibition and loss of homeostatic functions in astrocytes from an Alzheimer’s disease mouse model: a role for ER-mitochondria interaction
Authors: Tapella Laura , Dematteis Giulia , Moro Marianna , Pistolato Beatrice , Tonelli Elisa , Vanella Virginia Vita , Giustina Daniele , La Forgia Aleida , Restelli Elena , Barberis Elettra , Cali Tito , Brini Marisa , Villani Salvatore , Del Grosso Erika , Grilli Mariagrazia , Manfredi Marcello , Corazzari Marco , Grolla Ambra A. , Genazzani Armando A. , Lim Dmitry 
Published: October 2022

AbstractDeregulation of protein synthesis and ER stress/unfolded protein response (ER stress/UPR) have been reported in astrocytes. However, the relationships between protein synthesis deregulation and ER stress/UPR, as well as their role in the altered homeostatic support of Alzheimer’s disease (AD) astrocytes remain poorly understood. Previously, we reported that in astrocytic cell lines from 3xTg-AD mice (3Tg-iAstro) protein synthesis was impaired and ER-mitochondria distance was reduced. Here we show that impaired protein synthesis in 3Tg-iAstro is associated with an increase of p-eIF2α and downregulation of GADD34. Although mRNA levels of ER stress/UPR markers were increased two-three-fold, we found neither activation of PERK nor downstream induction of ATF4 protein. Strikingly, the overexpression of a synthetic ER-mitochondrial linker (EML) resulted in a reduced protein synthesis and augmented p-eIF2α without any effect on ER stress/UPR marker genes. In vivo, in hippocampi of 3xTg-AD mice, reduced protein synthesis, increased p-eIF2α and downregulated GADD34 protein were found, while no increase of p-PERK or ATF4 proteins was observed, suggesting that in AD astrocytes, both in vitro and in vivo, phosphorylation of eIF2α and impairment of protein synthesis are PERK-independent. Next, we investigated the ability of 3xTg-AD astrocytes to support metabolism and function of other cells of the central nervous system. Astrocyte-conditioned medium (ACM) from 3Tg-iAstro cells significantly reduced protein synthesis rate in primary hippocampal neurons. When added as a part of pericyte/endothelial cell (EC)/astrocyte 3D co-culture, 3Tg-iAstro, but not WT-iAstro, severely impaired formation and ramification of tubules, the effect, replicated by EML overexpression in WT-iAstro cells. Finally, a chemical chaperone 4-phenylbutyric acid (4-PBA) rescued protein synthesis, p-eIF2α levels in 3Tg-iAstro cells and tubulogenesis in pericyte/EC/3Tg-iAstro co-culture. Collectively, our results suggest that a PERK-independent, p-eIF2α-associated impairment of protein synthesis compromises astrocytic homeostatic functions, and this may be caused by the altered ER-mitochondria interaction.
Tmem65 is critical for the structure and function of the intercalated discs in mouse hearts
Authors: Teng Allen C. T. , Gu Liyang , Di Paola Michelle , Lakin Robert , Williams Zachary J. , Au Aaron , Chen Wenliang , Callaghan Neal I. , Zadeh Farigol Hakem , Zhou Yu-Qing , Fatah Meena , Chatterjee Diptendu , Jourdan L. Jane , Liu Jack , Simmons Craig A. , Kislinger Thomas , Yip Christopher M. , Backx Peter H. , Gourdie Robert G. , Hamilton Robert M. , Gramolini Anthony O. 
Published: October 2022

AbstractThe intercalated disc (ICD) is a unique membrane structure that is indispensable to normal heart function, yet its structural organization is not completely understood. Previously, we showed that the ICD-bound transmembrane protein 65 (Tmem65) was required for connexin43 (Cx43) localization and function in cultured mouse neonatal cardiomyocytes. Here, we investigate the functional and cellular effects of Tmem65 reductions on the myocardium in a mouse model by injecting CD1 mouse pups (3–7 days after birth) with recombinant adeno-associated virus 9 (rAAV9) harboring Tmem65 shRNA, which reduces Tmem65 expression by 90% in mouse ventricles compared to scrambled shRNA injection. Tmem65 knockdown (KD) results in increased mortality which is accompanied by eccentric hypertrophic cardiomyopathy within 3 weeks of injection and progression to dilated cardiomyopathy with severe cardiac fibrosis by 7 weeks post-injection. Tmem65 KD hearts display depressed hemodynamics as measured echocardiographically as well as slowed conduction in optical recording accompanied by prolonged PR intervals and QRS duration in electrocardiograms. Immunoprecipitation and super-resolution microscopy demonstrate a physical interaction between Tmem65 and sodium channel β subunit (β1) in mouse hearts and this interaction appears to be required for both the establishment of perinexal nanodomain structure and the localization of both voltage-gated sodium channel 1.5 (NaV1.5) and Cx43 to ICDs. Despite the loss of NaV1.5 at ICDs, whole-cell patch clamp electrophysiology did not reveal reductions in Na+ currents but did show reduced Ca2+ and K+ currents in Tmem65 KD cardiomyocytes in comparison to control cells. We conclude that disrupting Tmem65 function results in impaired ICD structure, abnormal cardiac electrophysiology, and ultimately cardiomyopathy.
A simple thermodynamic description of phase separation of Nup98 FG domains
Authors: Ng Sheung Chun , Görlich Dirk 
Published: October 2022

AbstractThe permeability barrier of nuclear pore complexes (NPCs) controls nucleocytoplasmic transport. It retains inert macromolecules but allows facilitated passage of nuclear transport receptors that shuttle cargoes into or out of nuclei. The barrier can be described as a condensed phase assembled from cohesive FG repeat domains, including foremost the charge-depleted FG domain of Nup98. We found that Nup98 FG domains show an LCST-type phase separation, and we provide comprehensive and orthogonal experimental datasets for a quantitative description of this behaviour. A derived thermodynamic model correlates saturation concentration with repeat number, temperature, and ionic strength. It allows estimating the enthalpy, entropy, and ΔG (0.2 kJ/mol, 0.1 kB·T) contributions per repeat to phase separation and inter-repeat cohesion. While changing the cohesion strength strongly impacts the strictness of barrier, these numbers provide boundary conditions for in-depth modelling not only of barrier assembly but also of NPC passage.
Genome-wide functional screening of drug-resistance genes in Plasmodium falciparum
Authors: Iwanaga Shiroh , Kubota Rie , Nishi Tsubasa , Kamchonwongpaisan Sumalee , Srichairatanakool Somdet , Shinzawa Naoaki , Syafruddin Din , Yuda Masao , Uthaipibull Chairat 
Published: October 2022

AbstractThe global spread of drug resistance is a major obstacle to the treatment of Plasmodium falciparum malaria. The identification of drug-resistance genes is an essential step toward solving the problem of drug resistance. Here, we report functional screening as a new approach with which to identify drug-resistance genes in P. falciparum. Specifically, a high-coverage genomic library of a drug-resistant strain is directly generated in a drug-sensitive strain, and the resistance gene is then identified from this library using drug screening. In a pilot experiment using the strain Dd2, the known chloroquine-resistant gene pfcrt is identified using the developed approach, which proves our experimental concept. Furthermore, we identify multidrug-resistant transporter 7 (pfmdr7) as a novel candidate for a mefloquine-resistance gene from a field-isolated parasite; we suggest that its upregulation possibly confers the mefloquine resistance. These results show the usefulness of functional screening as means by which to identify drug-resistance genes.
Exceptional catalytic activity of oxygen evolution reaction via two-dimensional graphene multilayer confined metal-organic frameworks
Authors: Lyu Siliu , Guo Chenxi , Wang Jianing , Li Zhongjian , Yang Bin , Lei Lecheng , Wang Liping , Xiao Jianping , Zhang Tao , Hou Yang 
Published: October 2022

AbstractOxygen evolution reaction (OER) plays a key role in many renewable energy technologies such as water splitting and metal-air batteries. Metal-organic frameworks (MOFs) are appealing to design efficient OER electrocatalysts, however, their intrinsic poor conductivity strongly hinders the activity. Here, we show a strategy to boost the OER activity of poor-conductive MOFs by confining them between graphene multilayers. The resultant NiFe-MOF//G gives a record-low overpotential of 106 mV to reach 10 mA cm−2 and retains the activity over 150 h, which is in significant contrast to 399 mV of the pristine NiFe-MOF. We use X-ray absorption spectroscopy (XAS) and computations to demonstrate that the nanoconfinement from graphene multilayers not only forms highly reactive NiO6-FeO5 distorted octahedral species in MOF structure but also lowers limiting potential for water oxidation reaction. We also demonstrate that the strategy is applicable to other MOFs of different structures to largely enhance their electrocatalytic activities.
Rapid protein assignments and structures from raw NMR spectra with the deep learning technique ARTINA
Authors: Klukowski Piotr , Riek Roland , Güntert Peter 
Published: October 2022

AbstractNuclear Magnetic Resonance (NMR) spectroscopy is a major technique in structural biology with over 11,800 protein structures deposited in the Protein Data Bank. NMR can elucidate structures and dynamics of small and medium size proteins in solution, living cells, and solids, but has been limited by the tedious data analysis process. It typically requires weeks or months of manual work of a trained expert to turn NMR measurements into a protein structure. Automation of this process is an open problem, formulated in the field over 30 years ago. We present a solution to this challenge that enables the completely automated analysis of protein NMR data within hours after completing the measurements. Using only NMR spectra and the protein sequence as input, our machine learning-based method, ARTINA, delivers signal positions, resonance assignments, and structures strictly without human intervention. Tested on a 100-protein benchmark comprising 1329 multidimensional NMR spectra, ARTINA demonstrated its ability to solve structures with 1.44 Å median RMSD to the PDB reference and to identify 91.36% correct NMR resonance assignments. ARTINA can be used by non-experts, reducing the effort for a protein assignment or structure determination by NMR essentially to the preparation of the sample and the spectra measurements.
Biferroelectricity of a homochiral organic molecule in both solid crystal and liquid crystal phases
Authors: Song Xian-Jiang , Chen Xiao-Gang , Liu Jun-Chao , Liu Qin , Zeng Yi-Piao , Tang Yuan-Yuan , Li Peng-Fei , Xiong Ren-Gen , Liao Wei-Qiang 
Published: October 2022

AbstractFerroelectricity, existing in either solid crystals or liquid crystals, gained widespread attention from science and industry for over a century. However, ferroelectricity has never been observed in both solid and liquid crystal phases of a material simultaneously. Inorganic ferroelectrics that dominate the market do not have liquid crystal phases because of their completely rigid structure caused by intrinsic chemical bonds. We report a ferroelectric homochiral cholesterol derivative, β-sitosteryl 4-iodocinnamate, where both solid and liquid crystal phases can exhibit the behavior of polarization switching as determined by polarization–voltage hysteresis loops and piezoresponse force microscopy measurements. The unique long molecular chain, sterol structure, and homochirality of β-sitosteryl 4-iodocinnamate molecules enable the formation of polar crystal structures with point group 2 in solid crystal phases, and promote the layered and helical structure in the liquid crystal phase with vertical polarization. Our findings demonstrate a compound that can show the biferroelectricity in both solid and liquid crystal phases, which would inspire further exploration of the interplay between solid and liquid crystal ferroelectric phases.