bluuebunny/crossref_metadata_2025_split huggingface dataset:
Processing and Validation of FORMOSAT‐7/COSMIC‐2 GLONASS Total Electron Content Observations
Authors: Pedatella N. M. , Zakharenkova I. , Braun J. J. , Cherniak I. , Hunt D. , Schreiner W. S. , Straus P. R. , Valant‐Weiss B. L. , Vanhove T. , Weiss J. , Wu Q. 
Published: May 2023

AbstractThe Formosa Satellite‐7/Constellation Observing System for Meteorology, Ionosphere, and Climate‐2 (FORMOSAT‐7/COSMIC‐2, F7/C2) Tri‐GNSS Radio Occultation System observes both Global Positioning System (GPS) and GLObalnaya NAvigazionnaya Sputnikovaya Sistema (GLONASS) slant total electron content (TEC). Space‐based TEC observations have historically relied on GPS signals, and the processing methodologies and data quality of GLONASS absolute TEC observations are thus less well established. We present a description of the differences in the processing for the F7/C2 GLONASS absolute TEC observations. This primarily entails estimation of a paired receiver‐transmitter differential code bias, which is needed due to the GLONASS usage of frequency‐division multiple access. We additionally perform a validation of the F7/C2 GLONASS absolute TEC observations through comparison with colocated F7/C2 GPS absolute TEC observations. Based on this comparison, we estimate the GLONASS absolute TEC error to be ∼2.6 TEC units (TECU), which is similar to previous estimates of the F7/C2 GPS absolute TEC error (∼2.5 TECU). This demonstrates that the F7/C2 GLONASS absolute TEC observations are generally similar in quality to the F7/C2 GPS absolute TEC observations, and are suitable for use by the operational and scientific communities.
Can We Detect Urban‐Scale CO2 Emission Changes Within Medium‐Sized Cities?
Authors: Mallia Derek V. , Mitchell Logan E. , Gonzalez Vidal Andres Eduardo , Wu Dien , Kunik Lewis , Lin John C. 
Published: May 2023

AbstractThe COVID‐19 pandemic resulted in a widespread lockdown during the spring of 2020. Measurements collected on a light rail system in the Salt Lake Valley (SLV), combined with observations from the Utah Urban Carbon Dioxide Network observed a notable decrease in urban CO2 concentrations during the spring of 2020 relative to previous years. These decreases coincided with a ∼30% reduction in average traffic volume. CO2 measurements across the SLV were used within a Bayesian inverse model to spatially allocate anthropogenic emission reductions for the first COVID‐19 lockdown. The inverse model was first used to constrain anthropogenic emissions for the previous year (2019) to provide the best possible estimate of emissions for 2020, before accounting for emission reductions observed during the COVID‐19 lockdown. The posterior emissions for 2019 were then used as the prior emission estimate for the 2020 COVID‐19 lockdown analysis. Results from the inverse analysis suggest that the SLV observed a 20% decrease in afternoon CO2 emissions from March to April 2020 (−90.5 tC hr−1). The largest reductions in CO2 emissions were centered over the northern part of the valley (downtown Salt Lake City), near major roadways, and potentially at industrial point sources. These results demonstrate that CO2 monitoring networks can track reductions in CO2 emissions even in medium‐sized cities like Salt Lake City.
Representing Eddy Diffusion in the Surface Boundary Layer of Ocean Models With General Vertical Coordinates
Authors: Marques Gustavo M. , Shao Andrew E. , Bachman Scott D. , Danabasoglu Gokhan , Bryan Frank O. 
Published: May 2023

AbstractThe mixing of tracers by mesoscale eddies, parameterized in many ocean general circulation models (OGCMs) as a diffusive‐advective process, contributes significantly to the distribution of tracers in the ocean. In the ocean interior, diffusive contribution occurs mostly along the direction parallel to local neutral density surfaces. However, near the surface of the ocean, small‐scale turbulence and the presence of the boundary itself break this constraint and the mesoscale transport occurs mostly along a plane parallel to the ocean surface (horizontal). Although this process is easily represented in OGCMs with geopotential vertical coordinates, the representation is more challenging in OGCMs that use a general vertical coordinate, where surfaces can be tilted with respect to the horizontal. We propose a method for representing the diffusive horizontal mesoscale fluxes within the surface boundary layer of general vertical coordinate OGCMs. The method relies on regridding/remapping techniques to represent tracers in a geopotential grid. Horizontal fluxes are calculated on this grid and then remapped back to the native grid, where fluxes are applied. The algorithm is implemented in an ocean model and tested in idealized and realistic settings. Horizontal diffusion can account for up to 10% of the total northward heat transport in the Southern Ocean and Western boundary current regions of the Northern Hemisphere. It also reduces the vertical stratification of the upper ocean, which results in an overall deepening of the surface boundary layer depth. Finally, enabling horizontal diffusion leads to meaningful reductions in the near‐surface global bias of potential temperature and salinity.
Targeting protein modifications in metabolic diseases: molecular mechanisms and targeted therapies
Authors: Wu Xiumei , Xu Mengyun , Geng Mengya , Chen Shuo , Little Peter J. , Xu Suowen , Weng Jianping 
Published: May 2023

AbstractThe ever-increasing prevalence of noncommunicable diseases (NCDs) represents a major public health burden worldwide. The most common form of NCD is metabolic diseases, which affect people of all ages and usually manifest their pathobiology through life-threatening cardiovascular complications. A comprehensive understanding of the pathobiology of metabolic diseases will generate novel targets for improved therapies across the common metabolic spectrum. Protein posttranslational modification (PTM) is an important term that refers to biochemical modification of specific amino acid residues in target proteins, which immensely increases the functional diversity of the proteome. The range of PTMs includes phosphorylation, acetylation, methylation, ubiquitination, SUMOylation, neddylation, glycosylation, palmitoylation, myristoylation, prenylation, cholesterylation, glutathionylation, S-nitrosylation, sulfhydration, citrullination, ADP ribosylation, and several novel PTMs. Here, we offer a comprehensive review of PTMs and their roles in common metabolic diseases and pathological consequences, including diabetes, obesity, fatty liver diseases, hyperlipidemia, and atherosclerosis. Building upon this framework, we afford a through description of proteins and pathways involved in metabolic diseases by focusing on PTM-based protein modifications, showcase the pharmaceutical intervention of PTMs in preclinical studies and clinical trials, and offer future perspectives. Fundamental research defining the mechanisms whereby PTMs of proteins regulate metabolic diseases will open new avenues for therapeutic intervention.
Hematopoietic reconstitution dynamics of mobilized- and bone marrow-derived human hematopoietic stem cells after gene therapy
Authors: Scala Serena , Ferrua Francesca , Basso-Ricci Luca , Dionisio Francesca , Omrani Maryam , Quaranta Pamela , Jofra Hernandez Raisa , Del Core Luca , Benedicenti Fabrizio , Monti Ilaria , Giannelli Stefania , Fraschetta Federico , Darin Silvia , Albertazzi Elena , Galimberti Stefania , Montini Eugenio , Calabria Andrea , Cicalese Maria Pia , Aiuti Alessandro 
Published: May 2023

AbstractMobilized peripheral blood is increasingly used instead of bone marrow as a source of autologous hematopoietic stem/progenitor cells for ex vivo gene therapy. Here, we present an unplanned exploratory analysis evaluating the hematopoietic reconstitution kinetics, engraftment and clonality in 13 pediatric Wiskott-Aldrich syndrome patients treated with autologous lentiviral-vector transduced hematopoietic stem/progenitor cells derived from mobilized peripheral blood (n = 7), bone marrow (n = 5) or the combination of the two sources (n = 1). 8 out of 13 gene therapy patients were enrolled in an open-label, non-randomized, phase 1/2 clinical study (NCT01515462) and the remaining 5 patients were treated under expanded access programs. Although mobilized peripheral blood- and bone marrow- hematopoietic stem/progenitor cells display similar capability of being gene-corrected, maintaining the engineered grafts up to 3 years after gene therapy, mobilized peripheral blood-gene therapy group shows faster neutrophil and platelet recovery, higher number of engrafted clones and increased gene correction in the myeloid lineage which correlate with higher amount of primitive and myeloid progenitors contained in hematopoietic stem/progenitor cells derived from mobilized peripheral blood. In vitro differentiation and transplantation studies in mice confirm that primitive hematopoietic stem/progenitor cells from both sources have comparable engraftment and multilineage differentiation potential. Altogether, our analyses reveal that the differential behavior after gene therapy of hematopoietic stem/progenitor cells derived from either bone marrow or mobilized peripheral blood is mainly due to the distinct cell composition rather than functional differences of the infused cell products, providing new frames of references for clinical interpretation of hematopoietic stem/progenitor cell transplantation outcome.
Enabling selective zinc-ion intercalation by a eutectic electrolyte for practical anodeless zinc batteries
Authors: Li Chang , Kingsbury Ryan , Thind Arashdeep Singh , Shyamsunder Abhinandan , Fister Timothy T. , Klie Robert F. , Persson Kristin A. , Nazar Linda F. 
Published: May 2023

AbstractTwo major challenges hinder the advance of aqueous zinc metal batteries for sustainable stationary storage: (1) achieving predominant Zn-ion (de)intercalation at the oxide cathode by suppressing adventitious proton co-intercalation and dissolution, and (2) simultaneously overcoming Zn dendrite growth at the anode that triggers parasitic electrolyte reactions. Here, we reveal the competition between Zn2+vsproton intercalation chemistry of a typical oxide cathode using ex-situ/operandotechniques, and alleviate side reactions by developing a cost-effective and non-flammable hybrid eutectic electrolyte. A fully hydrated Zn2+solvation structure facilitates fast charge transfer at the solid/electrolyte interface, enabling dendrite-free Zn plating/stripping with a remarkably high average coulombic efficiency of 99.8% at commercially relevant areal capacities of 4 mAh cm−2and function up to 1600 h at 8 mAh cm−2. By concurrently stabilizing Zn redox at both electrodes, we achieve a new benchmark in Zn-ion battery performance of 4 mAh cm−2anode-free cells that retain 85% capacity over 100 cycles at 25 °C. Using this eutectic-design electrolyte, Zn | |Iodine full cells are further realized with 86% capacity retention over 2500 cycles. The approach represents a new avenue for long-duration energy storage.
Incoherent nonadiabatic to coherent adiabatic transition of electron transfer in colloidal quantum dot molecules
Authors: Hou Bokang , Thoss Michael , Banin Uri , Rabani Eran 
Published: May 2023

AbstractElectron transfer is a fundamental process in chemistry, biology, and physics. One of the most intriguing questions concerns the realization of the transitions between nonadiabatic and adiabatic regimes of electron transfer. Using colloidal quantum dot molecules, we computationally demonstrate how the hybridization energy (electronic coupling) can be tuned by changing the neck dimensions and/or the quantum dot sizes. This provides a handle to tune the electron transfer from the incoherent nonadiabatic regime to the coherent adiabatic regime in a single system. We develop an atomistic model to account for several states and couplings to the lattice vibrations and utilize the mean-field mixed quantum-classical method to describe the charge transfer dynamics. Here, we show that charge transfer rates increase by several orders of magnitude as the system is driven to the coherent, adiabatic limit, even at elevated temperatures, and delineate the inter-dot and torsional acoustic modes that couple most strongly to the charge transfer dynamics.
Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets
Authors: Zhang Shilu , Pyne Saptarshi , Pietrzak Stefan , Halberg Spencer , McCalla Sunnie Grace , Siahpirani Alireza Fotuhi , Sridharan Rupa , Roy Sushmita 
Published: May 2023

AbstractCell type-specific gene expression patterns are outputs of transcriptional gene regulatory networks (GRNs) that connect transcription factors and signaling proteins to target genes. Single-cell technologies such as single cell RNA-sequencing (scRNA-seq) and single cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq), can examine cell-type specific gene regulation at unprecedented detail. However, current approaches to infer cell type-specific GRNs are limited in their ability to integrate scRNA-seq and scATAC-seq measurements and to model network dynamics on a cell lineage. To address this challenge, we have developed single-cell Multi-Task Network Inference (scMTNI), a multi-task learning framework to infer the GRN for each cell type on a lineage from scRNA-seq and scATAC-seq data. Using simulated and real datasets, we show that scMTNI is a broadly applicable framework for linear and branching lineages that accurately infers GRN dynamics and identifies key regulators of fate transitions for diverse processes such as cellular reprogramming and differentiation.
Directionality of developing skeletal muscles is set by mechanical forces
Authors: Sunadome Kazunori , Erickson Alek G. , Kah Delf , Fabry Ben , Adori Csaba , Kameneva Polina , Faure Louis , Kanatani Shigeaki , Kaucka Marketa , Dehnisch Ellström Ivar , Tesarova Marketa , Zikmund Tomas , Kaiser Jozef , Edwards Steven , Maki Koichiro , Adachi Taiji , Yamamoto Takuya , Fried Kaj , Adameyko Igor 
Published: May 2023

AbstractFormation of oriented myofibrils is a key event in musculoskeletal development. However, the mechanisms that drive myocyte orientation and fusion to control muscle directionality in adults remain enigmatic. Here, we demonstrate that the developing skeleton instructs the directional outgrowth of skeletal muscle and other soft tissues during limb and facial morphogenesis in zebrafish and mouse. Time-lapse live imaging reveals that during early craniofacial development, myoblasts condense into round clusters corresponding to future muscle groups. These clusters undergo oriented stretch and alignment during embryonic growth. Genetic perturbation of cartilage patterning or size disrupts the directionality and number of myofibrils in vivo. Laser ablation of musculoskeletal attachment points reveals tension imposed by cartilage expansion on the forming myofibers. Application of continuous tension using artificial attachment points, or stretchable membrane substrates, is sufficient to drive polarization of myocyte populations in vitro. Overall, this work outlines a biomechanical guidance mechanism that is potentially useful for engineering functional skeletal muscle.
Multi-neuron connection using multi-terminal floating–gate memristor for unsupervised learning
Authors: Won Ui Yeon , An Vu Quoc , Park Sung Bum , Park Mi Hyang , Dam Do Van , Park Hyun Jun , Yang Heejun , Lee Young Hee , Yu Woo Jong 
Published: May 2023

AbstractMulti-terminal memristor and memtransistor (MT-MEMs) has successfully performed complex functions of heterosynaptic plasticity in synapse. However, theses MT-MEMs lack the ability to emulate membrane potential of neuron in multiple neuronal connections. Here, we demonstrate multi-neuron connection using a multi-terminal floating-gate memristor (MT-FGMEM). The variable Fermi level (EF) in graphene allows charging and discharging of MT-FGMEM using horizontally distant multiple electrodes. Our MT-FGMEM demonstrates high on/off ratio over 105 at 1000 s retention about ~10,000 times higher than other MT-MEMs. The linear behavior between current (ID) and floating gate potential (VFG) in triode region of MT-FGMEM allows for accurate spike integration at the neuron membrane. The MT-FGMEM fully mimics the temporal and spatial summation of multi-neuron connections based on leaky-integrate-and-fire (LIF) functionality. Our artificial neuron (150 pJ) significantly reduces the energy consumption by 100,000 times compared to conventional neurons based on silicon integrated circuits (11.7 μJ). By integrating neurons and synapses using MT-FGMEMs, a spiking neurosynaptic training and classification of directional lines functioned in visual area one (V1) is successfully emulated based on neuron’s LIF and synapse’s spike-timing-dependent plasticity (STDP) functions. Simulation of unsupervised learning based on our artificial neuron and synapse achieves a learning accuracy of 83.08% on the unlabeled MNIST handwritten dataset.
Cryo-EM structure of the Saccharomyces cerevisiae Rpd3L histone deacetylase complex
Authors: Patel Avinash B. , Qing Jinkang , Tam Kelly H. , Zaman Sara , Luiso Maria , Radhakrishnan Ishwar , He Yuan 
Published: May 2023

AbstractThe Rpd3L histone deacetylase (HDAC) complex is an ancient 12-subunit complex conserved in a broad range of eukaryotes that performs localized deacetylation at or near sites of recruitment by DNA-bound factors. Here we describe the cryo-EM structure of this prototypical HDAC complex that is characterized by as many as seven subunits performing scaffolding roles for the tight integration of the only catalytic subunit, Rpd3. The principal scaffolding protein, Sin3, along with Rpd3 and the histone chaperone, Ume1, are present in two copies, with each copy organized into separate lobes of an asymmetric dimeric molecular assembly. The active site of one Rpd3 is completely occluded by a leucine side chain of Rxt2, while the tips of the two lobes and the more peripherally associated subunits exhibit varying levels of flexibility and positional disorder. The structure reveals unexpected structural homology/analogy between unrelated subunits in the fungal and mammalian complexes and provides a foundation for deeper interrogations of structure, biology, and mechanism of these complexes, as well as for the discovery of HDAC complex-specific inhibitors.
Generation of a mutator parasite to drive resistome discovery in Plasmodium falciparum
Authors: Kümpornsin Krittikorn , Kochakarn Theerarat , Yeo Tomas , Okombo John , Luth Madeline R. , Hoshizaki Johanna , Rawat Mukul , Pearson Richard D. , Schindler Kyra A. , Mok Sachel , Park Heekuk , Uhlemann Anne-Catrin , Jana Gouranga P. , Maity Bikash C. , Laleu Benoît , Chenu Elodie , Duffy James , Moliner Cubel Sonia , Franco Virginia , Gomez-Lorenzo Maria G. , Gamo Francisco Javier , Winzeler Elizabeth A. , Fidock David A. , Chookajorn Thanat , Lee Marcus C. S. 
Published: May 2023

AbstractIn vitro evolution of drug resistance is a powerful approach for identifying antimalarial targets, however, key obstacles to eliciting resistance are the parasite inoculum size and mutation rate. Here we sought to increase parasite genetic diversity to potentiate resistance selections by editing catalytic residues of Plasmodium falciparum DNA polymerase δ. Mutation accumulation assays reveal a ~5–8 fold elevation in the mutation rate, with an increase of 13–28 fold in drug-pressured lines. Upon challenge with the spiroindolone PfATP4-inhibitor KAE609, high-level resistance is obtained more rapidly and at lower inocula than wild-type parasites. Selections also yield mutants with resistance to an “irresistible” compound, MMV665794 that failed to yield resistance with other strains. We validate mutations in a previously uncharacterised gene, PF3D7_1359900, which we term quinoxaline resistance protein (QRP1), as causal for resistance to MMV665794 and a panel of quinoxaline analogues. The increased genetic repertoire available to this “mutator” parasite can be leveraged to drive P. falciparum resistome discovery.
Overestimated nitrogen loss from denitrification for natural terrestrial ecosystems in CMIP6 Earth System Models
Authors: Feng Maoyuan , Peng Shushi , Wang Yilong , Ciais Philippe , Goll Daniel S. , Chang Jinfeng , Fang Yunting , Houlton Benjamin Z. , Liu Gang , Sun Yan , Xi Yi 
Published: May 2023

AbstractDenitrification and leaching nitrogen (N) losses are poorly constrained in Earth System Models (ESMs). Here, we produce a global map of natural soil15N abundance and quantify soil denitrification N loss for global natural ecosystems using an isotope-benchmarking method. We show an overestimation of denitrification by almost two times in the 13 ESMs of the Sixth Phase Coupled Model Intercomparison Project (CMIP6, 73 ± 31 Tg N yr−1), compared with our estimate of 38 ± 11 Tg N yr−1, which is rooted in isotope mass balance. Moreover, we find a negative correlation between the sensitivity of plant production to rising carbon dioxide (CO2) concentration and denitrification in boreal regions, revealing that overestimated denitrification in ESMs would translate to an exaggeration of N limitation on the responses of plant growth to elevated CO2. Our study highlights the need of improving the representation of the denitrification in ESMs and better assessing the effects of terrestrial ecosystems on CO2mitigation.
Photoinhibiting via simultaneous photoabsorption and free-radical reaction for high-fidelity light-based bioprinting
Authors: He Ning , Wang Xiaonan , Shi Liyang , Li Jing , Mo Lan , Chen Feng , Huang Yuting , Liu Hairong , Zhu Xiaolong , Zhu Wei , Mao Yiqi , Han Xiaoxiao 
Published: May 2023

AbstractLight-based 3D bioprinting is now employed widely to fabricate geometrically complex constructs for various biomedical applications. However, the inherent light scattering defect creates significant challenges in patterning dilute hydrogels to form high-fidelity structures with fine-scale features. Herein, we introduce a photoinhibiting approach that can effectively suppress the light scattering effect via a mechanism of simultaneous photoabsorption and free-radical reaction. This biocompatible approach significantly improves the printing resolution (~1.2 - ~2.1 pixels depending on swelling) and shape fidelity (geometric error less than 5%), while minimising the costly trial-and-error procedures. The capability in patterning 3D complex constructs using different hydrogels is demonstrated by manufacturing various scaffolds featuring intricate multi-sized channels and thin-walled networks. Importantly, cellularised gyroid scaffolds (HepG2) are fabricated successfully, exhibiting high cell proliferation and functionality. The strategy established in this study promotes the printability and operability of light-based 3D bioprinting systems, allowing numerous new applications for tissue engineering.