bluuebunny/crossref_metadata_2025_split huggingface dataset:
Remote‐Sensing Derived Trends in Gross Primary Production Explain Increases in the CO2 Seasonal Cycle Amplitude
Authors: He Liyin , Byrne Brendan , Yin Yi , Liu Junjie , Frankenberg Christian 
Published: September 2022

AbstractAn increase in the seasonal cycle amplitude (SCA) of atmospheric CO2 since the 1960s has been observed in the Northern Hemisphere (NH). However, the underlying dominant drivers are still debated. The peak season CO2 uptake by vegetation is critical in shaping the CO2 seasonality. Using satellite‐upscaled gross primary production (GPP) from FLUXCOM and near‐infrared reflectance of vegetation (NIRV), we demonstrate that peak GPP has increased across the NH over the last two decades. We relate this productivity increase to changes in the CO2 SCA using an atmospheric transport model. The increased photosynthesis has strongly contributed to CO2 SCA trends, but with substantial latitudinal and longitudinal variations. Despite a general increase in the CO2 SCA, there are distinct regional differences. These differences are mainly controlled by regional biosphere carbon fluxes, with the remainder explained by non‐biome factors, including large‐scale atmospheric transport, changes in fossil fuel combustion, biomass burning and oceanic fluxes. Using the global flask and in situ CO2 measurement sites, we find that SCA trends at high latitude are mainly driven by increasingly productive natural ecosystems, whereas mid latitude sites around the Midwest United States are mainly impacted by intensified agriculture and atmospheric transport. Averaging across the 15 long‐term surface sites, forests contribute 26% (7%) to the SCA trends, while crops contribute 17% (24%) and the combined shrubland, grassland and wetland regions contribute 23% (37%) for simulations driven by FLUXCOM (NIRv) ecosystem fluxes. Our findings demonstrate that satellite inferred trends of ecosystem fluxes can capture the observed CO2 SCA trend.
The Influence of Magnetic Minerals on Induced Polarization Measurements in Sedimentary Rocks
Authors: Peshtani Klaudio , Weller Andreas , Saneiyan Sina , Slater Lee 
Published: September 2022

AbstractInduced polarization (IP) measurements in porous sedimentary rocks are modeled in terms of pore geometrical descriptors (PGD). Using an extensive data set composed of 241 sandstone, carbonate, and arenite samples, we identified a stronger relationship between IP parameters and volumetric magnetic susceptibility versus IP parameters and PGD. This finding suggests that even small concentrations of iron minerals in rocks typically thought to lack electron‐conducting minerals can significantly influence IP measurements. The combination of magnetic susceptibility with a pore geometrical descriptor term improves the empirical prediction of IP measurements relative to the use of pore geometrical descriptor terms alone. This suggests that small concentrations of iron minerals exert a strong control on the specific capacitance, a property that remains poorly understood. The lack of any relationship between magnetic susceptibility and the PGD confirms that the magnetic susceptibility provides additional information unrelated to PGD.
Investigating the Effect of Mantle Flow and Viscosity Structure on Surface Velocities in Alaska Using 3‐D Geodynamic Models
Authors: McConeghy Joseph , Flesch Lucy , Elliott Julie 
Published: September 2022

AbstractWe utilize 3‐D finite element geodynamic models, incorporating long‐term kinematic estimates of upper plate motion, to better understand the roles that viscosity structure and mantle tractions play in generating plate motions and continental interior deformation in Alaska. Surface deformation in the Pacific‐North American plate boundary zone in Alaska and northwest Canada is strongly influenced by the complex interactions between flat‐slab subduction, gravitational collapse and mantle tractions. Predictions of long‐term tectonic block motion derived from recent Global Positioning System datasets (GPS) reveal surface motions atypical of other continental convergent plate boundary zones. Specifically, in northern and northwestern Alaska, southeastward motion is observed directed back toward the plate boundary. Geodynamic models that incorporate a southeastward directed long‐wavelength mantle traction of ∼2.5–3.8 MPa best replicate surface velocities in Alaska. These mantle tractions, in conjunction with the collision of the Yakutat microplate, appear to drive the uplift and deformation in the Mackenzie Mountains. Furthermore, the extent of the northward motion in southern and central Alaska is controlled by the location of the leading edge of the Yakutat flat slab.
The Sources of Sea‐Level Changes in the Mediterranean Sea Since 1960
Authors: Calafat F. M. , Frederikse T. , Horsburgh K. 
Published: September 2022

AbstractPast sea‐level changes in the Mediterranean Sea are highly non‐uniform and can deviate significantly from both the global average sea‐level rise and changes in the nearby Atlantic. Understanding the causes of this spatial non‐uniformity is crucial to the success of coastal adaptation strategies. This, however, remains a challenge owing to the lack of long sea‐level records in the Mediterranean. Previous studies have addressed this challenge by reconstructing past sea levels through objective analysis of sea‐level observations. Such reconstructions have enabled significant progress toward quantifying sea‐level changes, however, they have difficulty capturing long‐term changes and provide little insight into the causes of the changes. Here, we combine data from tide gauges and altimetry with sea‐level fingerprints of contemporary land‐mass changes using spatial Bayesian methods to estimate the sources of sea‐level changes in the Mediterranean Sea since 1960. We find that, between 1960 and 1989, sea level in the Mediterranean fell at an average rate of −0.3 ± 0.5 mm yr−1, due to an increase in atmospheric pressure over the basin and opposing sterodynamic and land‐mass contributions. After 1989, Mediterranean sea level started accelerating rapidly, driven by both sterodynamic changes and land‐ice loss, reaching an average rate of 3.6 ± 0.3 mm yr−1 in the period 2000–2018. The rate of sea‐level rise shows considerable spatial variation in the Mediterranean Sea, primarily reflecting changes in the large‐scale circulation of the basin. Since 2000, sea level has been rising faster in the Adriatic, Aegean, and Levantine Seas than anywhere else in the Mediterranean Sea.
Global Vertical Distribution of Water Vapor on Mars: Results From 3.5 Years of ExoMars‐TGO/NOMAD Science Operations
Authors: Aoki S. , Vandaele A. C. , Daerden F. , Villanueva G. L. , Liuzzi G. , Clancy R. T. , Lopez‐Valverde M. A. , Brines A. , Thomas I. R. , Trompet L. , Erwin J. T. , Neary L. , Robert S. , Piccialli A. , Holmes J. A. , Patel M. R. , Yoshida N. , Whiteway J. , Smith M. D. , Ristic B. , Bellucci G. , Lopez‐Moreno J. J. , Fedorova A. A. 
Published: September 2022

AbstractWe present water vapor vertical distributions on Mars retrieved from 3.5 years of solar occultation measurements by Nadir and Occultation for Mars Discovery onboard the ExoMars Trace Gas Orbiter, which reveal a strong contrast between aphelion and perihelion water climates. In equinox periods, most of water vapor is confined into the low‐middle latitudes. In aphelion periods, water vapor sublimated from the northern polar cap is confined into very low altitudes—water vapor mixing ratios observed at the 0–5 km lower boundary of measurement decrease by an order of magnitude at the approximate altitudes of 15 and 30 km for the latitudes higher than 50°N and 30–50°N, respectively. The vertical confinement of water vapor at northern middle latitudes around aphelion is more pronounced in the morning terminators than evening, perhaps controlled by the diurnal cycle of cloud formation. Water vapor is also observed over the low latitude regions in the aphelion southern hemisphere (0–30°S) mostly below 10–20 km, which suggests north‐south transport of water still occurs. In perihelion periods, water vapor sublimated from the southern polar cap directly reaches high altitudes (>80 km) over high southern latitudes, suggesting more effective transport by the meridional circulation without condensation. We show that heating during perihelion, sporadic global dust storms, and regional dust storms occurring annually around 330° of solar longitude (LS) are the main events to supply water vapor to the upper atmosphere above 70 km.
Thermospheric Conditions Associated With the Loss of 40 Starlink Satellites
Authors: Zhang Yongliang , Paxton Larry J. , Schaefer Robert , Swartz William H. 
Published: September 2022

AbstractWe analyzed far ultraviolet data from Defense Meteorological Satellite Program (DMSP)/Special Sensor Ultraviolet Spectrographic Imager (SSUSI) and Thermosphere Ionosphere Mesosphere Energetics and Dynamics (TIMED)/Global Ultraviolet Imager (GUVI) and found significant changes in the thermospheric density and composition during the 3–5 February 2022 storm when 40 Starlink satellites started to re‐enter the atmosphere associated with increased neutral drag at an altitude around 210 km. The standard NRLMSISE‐00 model predicts only ∼5% increase in neutral density at 210 km. TIMED/GUVI observations showed a clear increase in the thermospheric N2/O column density ratio and an increase in the nitric oxide (NO) column density, indicating high thermospheric density, and temperature. DMSP SSUSI 130.4 nm limb data showed a clear increase in neutral density in the low latitude region (−30°–30°). On the duskside (17:32 LT), the density increase (compared to the pre‐storm density) is around 11%–18% at 210 km and around 18%–26% at 520 km. On the dawn‐side (05:19 LT), the density increase is more significant, 40%–59% at 210 km and ∼300% at 520 km. There are a few reasons for the dawn‐dusk asymmetry in the relative density increase: (a) the pre‐storm background density or heat capacity is lower on the dawn‐side than that on the duskside, (b) stronger auroral heating was observed on the dawnside based on analysis of auroral images, (c) the thermosphere density enhancement partially recovered when the disturbance co‐rotated with the Earth from dawn to dusk side due to enhanced infrared cooling by NO. Note that the neutral density increase is expected to be much higher at high latitudes where the neutral disturbances are initiated.
Integration of Deep Learning and Information Theory for Designing Monitoring Networks in Heterogeneous Aquifer Systems
Authors: Chen Junjun , Dai Zhenxue , Dong Shuning , Zhang Xiaoying , Sun Guifang , Wu Jichun , Ershadnia Reza , Yin Shangxian , Soltanian Mohamad Reza 
Published: September 2022

AbstractGroundwater monitoring networks are direct sources of information for revealing subsurface system dynamic processes. However, designing such networks is difficult due to uncertainties in the spatial heterogeneity of aquifer parameters such as permeability (k). This study combines deep learning and information theory with an optimization framework to address network design problems in heterogeneous aquifer systems. The framework first employs a generative adversarial network to parameterize heterogeneous k distribution using a low‐dimensional latent representation. Then, surrogate models are developed based on the deep neural networks to perform uncertainty quantification of pressure heads and solute concentrations at locations of pre‐designed candidate monitoring stations. The monitoring stations are then ranked using the greedy search algorithm based on the maximum information minimum redundancy (MIMR) criterion. In order to depict the importance of each candidate monitoring location, the hotspot maps of the selection probability (Ps) are derived from MIMR repetition results. Comprehensive monitoring networks derived from the hotspot maps are then conducted as the final monitoring stations to improve monitoring information compared to MIMR results. Additionally, nine entropy quantization strategies are compared to evaluate their effects on monitoring network optimization results. Results indicate that caution should be taken when selecting entropy quantization strategies to achieve the accuracy required for model calibration and to improve the efficiency of monitoring optimization. Considering high‐dimensional uncertainties associated with aquifer parameters, the developed framework can provide important insights for monitoring network designs in various earth observational projects.
Grid cell remapping under three-dimensional object and social landmarks detected by implantable microelectrode arrays for the medial entorhinal cortex
Authors: Xu Zhaojie , Mo Fan , Yang Gucheng , Fan Penghui , Wang Yiding , Lu Botao , Xie Jingyu , Dai Yuchuan , Song Yilin , He Enhui , Xu Shihong , Liu Juntao , Wang Mixia , Cai Xinxia 
Published: September 2022

AbstractGrid cells with stable hexagonal firing patterns in the medial entorhinal cortex (MEC) carry the vital function of serving as a metric for the surrounding environment. Whether this mechanism processes only spatial information or involves nonspatial information remains elusive. Here, we fabricated an MEC-shaped microelectrode array (MEA) to detect the variation in neural spikes and local field potentials of the MEC when rats forage in a square enclosure with a planar, three-dimensional object and social landmarks in sequence. The results showed that grid cells exhibited rate remapping under social conditions in which spike firing fields closer to the social landmark had a higher firing rate. Furthermore, global remapping showed that hexagonal firing patterns were rotated and scaled when the planar landmark was replaced with object and social landmarks. In addition, when grid cells were activated, the local field potentials were dominated by the theta band (5–8 Hz), and spike phase locking was observed at troughs of theta oscillations. Our results suggest the pattern separation mechanism of grid cells in which the spatial firing structure and firing rate respond to spatial and social information, respectively, which may provide new insights into how the brain creates a cognitive map.
Nucleus of the solitary tract A2 neurons control feeding behaviors via projections to the paraventricular hypothalamus
Authors: Murphy Stephanie , Collis Glynn Metika , Dixon Tiarani N. , Grill Harvey J. , McNally Gavan P. , Ong Zhi Yi 
Published: September 2022

AbstractHindbrain NTS neurons are highly attuned to internal physiological and external environmental factors that contribute to the control of food intake but the relevant neural phenotypes and pathways remain elusive. Here, we investigated the role of NTS A2 neurons and their projections in the control of feeding behaviors. In male TH Cre rats, we first confirmed selective targeting of NTS A2 neurons and showed that chemogenetic stimulation of these neurons significantly suppressed dark cycle food intake, deprivation re-feed and high fat diet intake. Despite reducing intake, activation of NTS A2 neurons had no effect on food approach, anxiety-like behaviors, locomotor activity, blood glucose levels nor did it induce nausea/malaise, thus revealing a selective role for these neurons in the consummatory aspect of food intake control. Pathway-specific mapping and manipulation of NTS A2 neurons showed that these effects were mediated by NTS A2 neurons projecting to the paraventricular nucleus of the hypothalamus (PVH) because chemogenetic activation of these projections, but not projections to bed nucleus of the stria terminalis (BNST), reduced food intake. Cell-type specific analyses demonstrated that activation of NTS A2 neurons recruited both PVH oxytocin (OT)- and corticotropin-releasing factor (CRF)-expressing neurons, and plasma analyses showed increased plasma corticosterone following NTS A2 stimulation. While we also showed that chemogenetic inhibition of NTS A2 neurons attenuated the intake inhibitory effects of CCK, the specificity of transgene expression was low. Together, these findings showed that NTS A2 neurons are sufficient to control the consummatory aspects of feeding, regardless of energy status or food palatability and identified their projections to PVH, but not BNST, in food intake control.
WRN promotes bone development and growth by unwinding SHOX-G-quadruplexes via its helicase activity in Werner Syndrome
Authors: Tian Yuyao , Wang Wuming , Lautrup Sofie , Zhao Hui , Li Xiang , Law Patrick Wai Nok , Dinh Ngoc-Duy , Fang Evandro Fei , Cheung Hoi Hung , Chan Wai-Yee 
Published: September 2022

AbstractWerner Syndrome (WS) is an autosomal recessive disorder characterized by premature aging due to mutations of the WRN gene. A classical sign in WS patients is short stature, but the underlying mechanisms are not well understood. Here we report that WRN is indispensable for chondrogenesis, which is the engine driving the elongation of bones and determines height. Zebrafish lacking wrn exhibit impairment of bone growth and have shorter body stature. We pinpoint the function of WRN to its helicase domain. We identify short-stature homeobox (SHOX) as a crucial and direct target of WRN and find that the WRN helicase core regulates the transcriptional expression of SHOX via unwinding G-quadruplexes. Consistent with this, shox−/− zebrafish exhibit impaired bone growth, while genetic overexpression of SHOX or shox expression rescues the bone developmental deficiency induced in WRN/wrn-null mutants both in vitro and in vivo. Collectively, we have identified a previously unknown function of WRN in regulating bone development and growth through the transcriptional regulation of SHOX via the WRN helicase domain, thus illuminating a possible approach for new therapeutic strategies.
Serum neutralization activity declines but memory B cells persist after cure of chronic hepatitis C
Authors: Nishio Akira , Hasan Sharika , Park Heiyoung , Park Nana , Salas Jordan H. , Salinas Eduardo , Kardava Lela , Juneau Paul , Frumento Nicole , Massaccesi Guido , Moir Susan , Bailey Justin R. , Grakoui Arash , Ghany Marc G. , Rehermann Barbara 
Published: September 2022

AbstractThe increasing incidence of hepatitis C virus (HCV) infections underscores the need for an effective vaccine. Successful vaccines to other viruses generally depend on a long-lasting humoral response. However, data on the half-life of HCV-specific responses are lacking. Here we study archived sera and mononuclear cells that were prospectively collected up to 18 years after cure of chronic HCV infection to determine the role of HCV antigen in maintaining neutralizing antibody and B cell responses. We show that HCV-neutralizing activity decreases rapidly in potency and breadth after curative treatment. In contrast, HCV-specific memory B cells persist, and display a restored resting phenotype, normalized chemokine receptor expression and preserved ability to differentiate into antibody-secreting cells. The short half-life of HCV-neutralizing activity is consistent with a lack of long-lived plasma cells. The persistence of HCV-specific memory B cells and the reduced inflammation after cure provide an opportunity for vaccination to induce protective immunity against re-infection.
Unleashing the potential of noncanonical amino acid biosynthesis to create cells with precision tyrosine sulfation
Authors: Chen Yuda , Jin Shikai , Zhang Mengxi , Hu Yu , Wu Kuan-Lin , Chung Anna , Wang Shichao , Tian Zeru , Wang Yixian , Wolynes Peter G. , Xiao Han 
Published: September 2022

AbstractDespite the great promise of genetic code expansion technology to modulate structures and functions of proteins, external addition of ncAAs is required in most cases and it often limits the utility of genetic code expansion technology, especially to noncanonical amino acids (ncAAs) with poor membrane internalization. Here, we report the creation of autonomous cells, both prokaryotic and eukaryotic, with the ability to biosynthesize and genetically encode sulfotyrosine (sTyr), an important protein post-translational modification with low membrane permeability. These engineered cells can produce site-specifically sulfated proteins at a higher yield than cells fed exogenously with the highest level of sTyr reported in the literature. We use these autonomous cells to prepare highly potent thrombin inhibitors with site-specific sulfation. By enhancing ncAA incorporation efficiency, this added ability of cells to biosynthesize ncAAs and genetically incorporate them into proteins greatly extends the utility of genetic code expansion methods.
Enzymatic synthesis of benzylisoquinoline alkaloids using a parallel cascade strategy and tyrosinase variants
Authors: Wang Yu , Subrizi Fabiana , Carter Eve M. , Sheppard Tom D. , Ward John M. , Hailes Helen C. 
Published: September 2022

AbstractBenzylisoquinoline alkaloid derived pharmaceuticals are widely applied in modern medicines. Recent studies on the microbial production of benzylisoquinolines have highlighted key biological syntheses towards these natural products. Routes to non-natural benzylisoquinolines have been less explored, particularly halogenated compounds which are more challenging. Here, we show the use of a tyrosinase, tyrosine decarboxylase, transaminase, and norcoclaurine synthase which are combined in a parallel cascade design, in order to generate halogenated benzylisoquinoline alkaloids in high enantiomeric excess. Notably, mutagenesis studies are applied to generate tyrosinase mutants, which enhance the acceptance of halogenated tyrosines for use in the biocatalytic cascades developed.
Clustering by measuring local direction centrality for data with heterogeneous density and weak connectivity
Authors: Peng Dehua , Gui Zhipeng , Wang Dehe , Ma Yuncheng , Huang Zichen , Zhou Yu , Wu Huayi 
Published: September 2022

AbstractClustering is a powerful machine learning method for discovering similar patterns according to the proximity of elements in feature space. It is widely used in computer science, bioscience, geoscience, and economics. Although the state-of-the-art partition-based and connectivity-based clustering methods have been developed, weak connectivity and heterogeneous density in data impede their effectiveness. In this work, we propose a boundary-seeking Clustering algorithm using the local Direction Centrality (CDC). It adopts a density-independent metric based on the distribution of K-nearest neighbors (KNNs) to distinguish between internal and boundary points. The boundary points generate enclosed cages to bind the connections of internal points, thereby preventing cross-cluster connections and separating weakly-connected clusters. We demonstrate the validity of CDC by detecting complex structured clusters in challenging synthetic datasets, identifying cell types from single-cell RNA sequencing (scRNA-seq) and mass cytometry (CyTOF) data, recognizing speakers on voice corpuses, and testifying on various types of real-world benchmarks.