bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaporation From Six Water Bodies of Various Sizes in East Asia: An Analysis on Size Dependency
Authors: Han Songjun , Guo Fangju 
Published: May 2023

AbstractOne pond and five lakes in East Asia with area from 0.05 to 3,000 km2 were comparatively investigated to reveal the size‐dependency of the evaporation and its radiation and aerodynamic contributions. The available energy controls on the annual evaporation are independent on the sizes of the six water bodies, but the ratio of evaporation to Penman's open water evaporation decreases with areas from almost unity at the small pond to around 0.8 at the two large lakes. The aerodynamic related parameters of three combination equations can be well represented by the water body areas with a power law, which is attributed to the decreasing mass transfer coefficient with the fetch of the water body. The increasing size‐dependent wind speed offsets the effect of mass transfer coefficient, making the energy partitioning and evaporation rate size independent. Results imply that the energy‐based equations can be used for evaporation without considering the water body size in the study area. The size‐dependent parameters of the combination equations are required to be further investigated with more lakes.
National‐Scale Detection of Reservoir Impacts Through Hydrological Signatures
Authors: Salwey S. , Coxon G. , Pianosi F. , Singer M. B. , Hutton C. 
Published: May 2023

AbstractReservoirs play a vital role in the supply and management of water resources and their operation can significantly alter downstream flow. Despite this, reservoirs are frequently excluded or poorly represented in large‐scale hydrological models, which can be partly attributed to a lack of open‐access data describing reservoir operations, inflow and storage. To help inform the development of reservoir operation schemes, we collate a suite of hydrological signatures designed to detect the impacts of reservoirs on the flow regime at large‐scales from downstream flow records only. By removing the need for pre‐and‐post‐reservoir flow timeseries (a requirement of many pre‐existing techniques), these signatures facilitate the assessment of flow alteration across a much wider range of catchments. To demonstrate their application, we calculate the signatures across Great Britain in 111 benchmark (i.e., near‐natural) catchments and 186 reservoir catchments (where at least one upstream reservoir is present). We find that abstractions from water resource reservoirs induce deficits in the water balance, and that pre‐defined flow releases (e.g., the compensation flow) reduce variability in the downstream flow duration curve and in intra‐annual low flows. By comparing signatures in benchmark and reservoir catchments, we define thresholds above which the influence of reservoirs can be distinguished from natural variability and identify 40 catchments significantly impacted by the presence of reservoirs. The signatures also provide insights into local reservoir operations, which can inform the development of tailored reservoir operation schemes, and identify locations where current modeling practices (which lack reservoir representation) will be insufficient.
Trade‐Offs Between Spatial and Temporal Accuracy of Complementary Relationship Models for Evaporation in an Ungauged Basin
Authors: Zhang Xiaolong , Han Songjun , Wang Yan , Kong Xiaole , Guo Ying , Shen Yanjun , Zhang Yinsheng , Shen Yan‐Jun 
Published: May 2023

AbstractThe complementary relationship (CR) between actual and potential evaporation has undergone rapid development over the past decades. Commonly, the evaluation of CR models does not comprehensively cover spatial and temporal aspects of model performance; thus, the spatial and temporal accuracy and parameter sensitivity of different CR models remain relatively unknown, especially in ungauged basins. We examine the spatial and temporal performance and parameter sensitivity of four CR models with fixed parameters at the monthly scale over the source region of the Yellow River in China. Additionally, two CR models with distributed parameters were selected as comparisons. Because of the lack of evaporation spatiotemporal “true” values, the corrected water‐balance‐derived evaporation was used as the temporal reference, and the ensemble mean of multiple evaporation products was used as the spatial reference. We find that trade‐offs between the spatial and temporal accuracy of CR models with fixed parameters for basin evaporation should be considered in the application. Although four CR models with fixed parameters exhibited different spatial and temporal performances, their overall performance was generally similar. The parameters of CR models had consistent spatial and temporal sensitivities, and the sensitivity of parameter αe was stronger than that of other parameters. This study demonstrates that CR models with distributed parameters have a promising future in estimating basin or regional evaporation. An integrated spatial and temporal evaluation framework can better distinguish the performance of CR models. The methodologies can be used as a guideline for evaluating and calibrating CR models that match an application's needs.
Modeling the Day‐To‐Day Variability of Midnight Equatorial Plasma Bubbles With SAMI3/SD‐WACCM‐X
Authors: Chou Min‐Yang , Yue Jia , Sassi Fabrizio , McDonald Sarah , Tate Jennifer , Pedatella Nicholas , Randall Cora E. , Harvey V. Lynn 
Published: May 2023

AbstractIt is well‐known that equatorial plasma bubbles (EPBs) are highly correlated to the post‐sunset rise of the ionosphere on a climatological basis. However, when proceeding to the daily EPB development, what controls the day‐to‐day/longitudinal variability of EPBs remains a puzzle. In this study, we investigate the underlying physics responsible for the day‐to‐day/longitudinal variability of EPBs using the Sami3 is A Model of the Ionosphere (SAMI3) and the Specified Dynamics Whole Atmosphere Community Climate Model with thermosphere‐ionosphere eXtension (SD‐WACCM‐X). Simulation results on October 20, 22, and 24, 2020 were presented. SAMI3/SD‐WACCM‐X self‐consistently generated midnight EPBs on October 20 and 24, displaying irregular and regular spatial distributions, respectively. However, EPBs are absent on October 22. We investigate the role of gravity waves on upwelling growth and EPB development and discuss how gravity waves contribute to the distributions of EPBs. We found the westward wind associated with solar terminator waves and gravity waves induces polarization electric fields that map to the equatorial ionosphere from higher latitudes, resulting in midnight vertical drift enhancement and retrograde plasma flow. The upward vertical drift and retrograde flow further lead to shear flow instability and midnight plasma vortex, creating background conditions identical to the post‐sunset ionosphere. This provides conditions favorable for the upwelling growth and EPB development. The converging and diverging winds associated with solar terminator waves and midnight temperature maximum also affect the longitudinal distribution of EPBs. The absence of EPBs on October 22 is related to the weak westward wind associated with solar terminator waves.
Efficient ultrafast laser writing with appropriate polarization
Authors: Li Xiujian , Xie Wenke 
Published: May 2023

AbstractAppropriate polarization utilization makes the electric field vector direction and the statistically oriented localized states suitable for enhancing light-matter interactions so as to improve the efficiency of ultrafast laser writing, which will remarkably reduce the pulse energy and increase the processing speed for high density optical data storage, as well as manufacturing three-dimensional integrated optics and geometric phase optical elements.
Mania-related effects on structural brain changes in bipolar disorder – a narrative review of the evidence
Authors: Abé Christoph , Liberg Benny , Klahn Anna Luisa , Petrovic Predrag , Landén Mikael 
Published: May 2023

AbstractCross-sectional neuroimaging studies show that bipolar disorder is associated with structural brain abnormalities, predominantly observed in prefrontal and temporal cortex, cingulate gyrus, and subcortical regions. However, longitudinal studies are needed to elucidate whether these abnormalities presage disease onset or are consequences of disease processes, and to identify potential contributing factors. Here, we narratively review and summarize longitudinal structural magnetic resonance imaging studies that relate imaging outcomes to manic episodes. First, we conclude that longitudinal brain imaging studies suggest an association of bipolar disorder with aberrant brain changes, including both deviant decreases and increases in morphometric measures. Second, we conclude that manic episodes have been related to accelerated cortical volume and thickness decreases, with the most consistent findings occurring in prefrontal brain areas. Importantly, evidence also suggests that in contrast to healthy controls, who in general show age-related cortical decline, brain metrics remain stable or increase during euthymic periods in bipolar disorder patients, potentially reflecting structural recovering mechanisms. The findings stress the importance of preventing manic episodes. We further propose a model of prefrontal cortical trajectories in relation to the occurrence of manic episodes. Finally, we discuss potential mechanisms at play, remaining limitations, and future directions.
Glycosylation and behavioral symptoms in neurological disorders
Authors: Pradeep Prajitha , Kang Hyeyeon , Lee Boyoung 
Published: May 2023

AbstractGlycosylation, the addition of glycans or carbohydrates to proteins, lipids, or other glycans, is a complex post-translational modification that plays a crucial role in cellular function. It is estimated that at least half of all mammalian proteins undergo glycosylation, underscoring its importance in the functioning of cells. This is reflected in the fact that a significant portion of the human genome, around 2%, is devoted to encoding enzymes involved in glycosylation. Changes in glycosylation have been linked to various neurological disorders, including Alzheimer’s disease, Parkinson’s disease, autism spectrum disorder, and schizophrenia. Despite its widespread occurrence, the role of glycosylation in the central nervous system remains largely unknown, particularly with regard to its impact on behavioral abnormalities in brain diseases. This review focuses on examining the role of three types of glycosylation: N-glycosylation, O-glycosylation, and O-GlcNAcylation, in the manifestation of behavioral and neurological symptoms in neurodevelopmental, neurodegenerative, and neuropsychiatric disorders.
The mitochondrial protein TIMM44 is required for angiogenesis in vitro and in vivo
Authors: Ma Zhou-rui , Li Hong-Peng , Cai Shi-zhong , Du Sheng-Yang , Chen Xia , Yao Jin , Cao Xu , Zhen Yun-Fang , Wang Qian 
Published: May 2023

AbstractThe mitochondrial integrity and function in endothelial cells are essential for angiogenesis. TIMM44 (translocase of inner mitochondrial membrane 44) is essential for integrity and function of mitochondria. Here we explored the potential function and the possible mechanisms of TIMM44 in angiogenesis. In HUVECs, human retinal microvascular endothelial cells and hCMEC/D3 brain endothelial cells, silence of TIMM44 by targeted shRNA largely inhibited cell proliferation, migration and in vitro capillary tube formation. TIMM44 silencing disrupted mitochondrial functions in endothelial cells, causing mitochondrial protein input arrest, ATP reduction, ROS production, and mitochondrial depolarization, and leading to apoptosis activation. TIMM44 knockout, by Cas9-sgRNA strategy, also disrupted mitochondrial functions and inhibited endothelial cell proliferation, migration and in vitro capillary tube formation. Moreover, treatment with MB-10 (“MitoBloCK-10”), a TIMM44 blocker, similarly induced mitochondrial dysfunction and suppressed angiogenic activity in endothelial cells. Contrarily, ectopic overexpression of TIMM44 increased ATP contents and augmented endothelial cell proliferation, migration and in vitro capillary tube formation. In adult mouse retinas, endothelial knockdown of TIMM44, by intravitreous injection of endothelial specific TIMM44 shRNA adenovirus, inhibited retinal angiogenesis, causing vascular leakage, acellular capillary growth, and retinal ganglion cells degeneration. Significant oxidative stress was detected in TIMM44-silenced retinal tissues. Moreover, intravitreous injection of MB-10 similarly induced oxidative injury and inhibited retinal angiogenesis in vivo. Together, the mitochondrial protein TIMM44 is important for angiogenesis in vitro and in vivo, representing as a novel and promising therapeutic target of diseases with abnormal angiogenesis.
Double DAP-seq uncovered synergistic DNA binding of interacting bZIP transcription factors
Authors: Li Miaomiao , Yao Tao , Lin Wanru , Hinckley Will E. , Galli Mary , Muchero Wellington , Gallavotti Andrea , Chen Jin-Gui , Huang Shao-shan Carol 
Published: May 2023

AbstractMany eukaryotic transcription factors (TF) form homodimer or heterodimer complexes to regulate gene expression. Dimerization of BASIC LEUCINE ZIPPER (bZIP) TFs are critical for their functions, but the molecular mechanism underlying the DNA binding and functional specificity of homo- versus heterodimers remains elusive. To address this gap, we present the double DNA Affinity Purification-sequencing (dDAP-seq) technique that maps heterodimer binding sites on endogenous genomic DNA. Using dDAP-seq we profile twenty pairs of C/S1 bZIP heterodimers and S1 homodimers in Arabidopsis and show that heterodimerization significantly expands the DNA binding preferences of these TFs. Analysis of dDAP-seq binding sites reveals the function of bZIP9 in abscisic acid response and the role of bZIP53 heterodimer-specific binding in seed maturation. The C/S1 heterodimers show distinct preferences for the ACGT elements recognized by plant bZIPs and motifs resembling the yeast GCN4 cis-elements. This study demonstrates the potential of dDAP-seq in deciphering the DNA binding specificities of interacting TFs that are key for combinatorial gene regulation.
Molecular determinants of inhibition of UCP1-mediated respiratory uncoupling
Authors: Gagelin Antoine , Largeau Corentin , Masscheleyn Sandrine , Piel Mathilde S. , Calderón-Mora Daniel , Bouillaud Frédéric , Hénin Jérôme , Miroux Bruno 
Published: May 2023

AbstractBrown adipose tissue expresses uncoupling protein 1 (UCP1), which dissipates energy as heat, making it a target for treating metabolic disorders. Here, we investigate how purine nucleotides inhibit respiration uncoupling by UCP1. Our molecular simulations predict that GDP and GTP bind UCP1 in the common substrate binding site in an upright orientation, where the base moiety interacts with conserved residues R92 and E191. We identify a triplet of uncharged residues, F88/I187/W281, forming hydrophobic contacts with nucleotides. In yeast spheroplast respiration assays, both I187A and W281A mutants increase the fatty acid-induced uncoupling activity of UCP1 and partially suppress the inhibition of UCP1 activity by nucleotides. The F88A/I187A/W281A triple mutant is overactivated by fatty acids even at high concentrations of purine nucleotides. In simulations, E191 and W281 interact with purine but not pyrimidine bases. These results provide a molecular understanding of the selective inhibition of UCP1 by purine nucleotides.
Catch bond models may explain how force amplifies TCR signaling and antigen discrimination
Authors: Choi Hyun-Kyu , Cong Peiwen , Ge Chenghao , Natarajan Aswin , Liu Baoyu , Zhang Yong , Li Kaitao , Rushdi Muaz Nik , Chen Wei , Lou Jizhong , Krogsgaard Michelle , Zhu Cheng 
Published: May 2023

AbstractThe TCR integrates forces in its triggering process upon interaction with pMHC. Force elicits TCR catch-slip bonds with strong pMHCs but slip-only bonds with weak pMHCs. We develop two models and apply them to analyze 55 datasets, demonstrating the models’ ability to quantitatively integrate and classify a broad range of bond behaviors and biological activities. Comparing to a generic two-state model, our models can distinguish class I from class II MHCs and correlate their structural parameters with the TCR/pMHC’s potency to trigger T cell activation. The models are tested by mutagenesis using an MHC and a TCR mutated to alter conformation changes. The extensive comparisons between theory and experiment provide model validation and testable hypothesis regarding specific conformational changes that control bond profiles, thereby suggesting structural mechanisms for the inner workings of the TCR mechanosensing machinery and plausible explanations of why and how force may amplify TCR signaling and antigen discrimination.
Methionine consumption by cancer cells drives a progressive upregulation of PD-1 expression in CD4 T cells
Authors: Pandit Mahesh , Kil Yun-Seo , Ahn Jae-Hee , Pokhrel Ram Hari , Gu Ye , Mishra Sunil , Han Youngjoo , Ouh Yung-Taek , Kang Ben , Jeong Myeong Seon , Kim Jong-Oh , Nam Joo-Won , Ko Hyun-Jeong , Chang Jae-Hoon 
Published: May 2023

AbstractProgrammed cell death protein 1 (PD-1), expressed on tumor-infiltrating T cells, is a T cell exhaustion marker. The mechanisms underlying PD-1 upregulation in CD4 T cells remain unknown. Here we develop nutrient-deprived media and a conditional knockout female mouse model to study the mechanism underlying PD-1 upregulation. Reduced methionine increases PD-1 expression on CD4 T cells. The genetic ablation of SLC43A2 in cancer cells restores methionine metabolism in CD4 T cells, increasing the intracellular levels of S-adenosylmethionine and yielding H3K79me2. Reduced H3K79me2 due to methionine deprivation downregulates AMPK, upregulates PD-1 expression and impairs antitumor immunity in CD4 T cells. Methionine supplementation restores H3K79 methylation and AMPK expression, lowering PD-1 levels. AMPK-deficient CD4 T cells exhibit increased endoplasmic reticulum stress and Xbp1s transcript levels. Our results demonstrate that AMPK is a methionine-dependent regulator of the epigenetic control of PD-1 expression in CD4 T cells, a metabolic checkpoint for CD4 T cell exhaustion.
Probing spin dynamics of ultra-thin van der Waals magnets via photon-magnon coupling
Authors: Zollitsch Christoph W. , Khan Safe , Nam Vu Thanh Trung , Verzhbitskiy Ivan A. , Sagkovits Dimitrios , O’Sullivan James , Kennedy Oscar W. , Strungaru Mara , Santos Elton J. G. , Morton John J. L. , Eda Goki , Kurebayashi Hidekazu 
Published: May 2023

AbstractLayered van der Waals (vdW) magnets can maintain a magnetic order even down to the single-layer regime and hold promise for integrated spintronic devices. While the magnetic ground state of vdW magnets was extensively studied, key parameters of spin dynamics, like the Gilbert damping, crucial for designing ultra-fast spintronic devices, remains largely unexplored. Despite recent studies by optical excitation and detection, achieving spin wave control with microwaves is highly desirable, as modern integrated information technologies predominantly are operated with these. The intrinsically small numbers of spins, however, poses a major challenge to this. Here, we present a hybrid approach to detect spin dynamics mediated by photon-magnon coupling between high-Q superconducting resonators and ultra-thin flakes of Cr2Ge2Te6 (CGT) as thin as 11 nm. We test and benchmark our technique with 23 individual CGT flakes and extract an upper limit for the Gilbert damping parameter. These results are crucial in designing on-chip integrated circuits using vdW magnets and offer prospects for probing spin dynamics of monolayer vdW magnets.
Single-pulse terahertz spectroscopy monitoring sub-millisecond time dynamics at a rate of 50 kHz
Authors: Couture Nicolas , Cui Wei , Lippl Markus , Ostic Rachel , Fandio Défi Junior Jubgang , Yalavarthi Eeswar Kumar , Vishnuradhan Aswin , Gamouras Angela , Joly Nicolas Y. , Ménard Jean-Michel 
Published: May 2023

AbstractSlow motion movies allow us to see intricate details of the mechanical dynamics of complex phenomena. If the images in each frame are replaced by terahertz (THz) waves, such movies can monitor low-energy resonances and reveal fast structural or chemical transitions. Here, we combine THz spectroscopy as a non-invasive optical probe with a real-time monitoring technique to demonstrate the ability to resolve non-reproducible phenomena at 50k frames per second, extracting each of the generated THz waveforms every 20 μs. The concept, based on a photonic time-stretch technique to achieve unprecedented data acquisition speeds, is demonstrated by monitoring sub-millisecond dynamics of hot carriers injected in silicon by successive resonant pulses as a saturation density is established. Our experimental configuration will play a crucial role in revealing fast irreversible physical and chemical processes at THz frequencies with microsecond resolution to enable new applications in fundamental research as well as in industry.
EmbryoNet: using deep learning to link embryonic phenotypes to signaling pathways
Authors: Čapek Daniel , Safroshkin Matvey , Morales-Navarrete Hernán , Toulany Nikan , Arutyunov Grigory , Kurzbach Anica , Bihler Johanna , Hagauer Julia , Kick Sebastian , Jones Felicity , Jordan Ben , Müller Patrick 
Published: May 2023

AbstractEvolutionarily conserved signaling pathways are essential for early embryogenesis, and reducing or abolishing their activity leads to characteristic developmental defects. Classification of phenotypic defects can identify the underlying signaling mechanisms, but this requires expert knowledge and the classification schemes have not been standardized. Here we use a machine learning approach for automated phenotyping to train a deep convolutional neural network, EmbryoNet, to accurately identify zebrafish signaling mutants in an unbiased manner. Combined with a model of time-dependent developmental trajectories, this approach identifies and classifies with high precision phenotypic defects caused by loss of function of the seven major signaling pathways relevant for vertebrate development. Our classification algorithms have wide applications in developmental biology and robustly identify signaling defects in evolutionarily distant species. Furthermore, using automated phenotyping in high-throughput drug screens, we show that EmbryoNet can resolve the mechanism of action of pharmaceutical substances. As part of this work, we freely provide more than 2 million images that were used to train and test EmbryoNet.