bluuebunny/crossref_metadata_2025_split huggingface dataset:
Atomic and Molecular Databases Open Science for a sustainable world
Authors: Dubernet M. L. , Berriman G.B. , Barklem P. , Choi K. , Foster A. , Gordon I. , Hill C. , Kim J. , Kwon D.H. , Linnartz H. , Ralchenko Yu. , Salama F. , Shmagun H. , Schilke P. , Seo D. , Shim J. , Shin S. , Song M.-Y. , Tennyson J. , Vastel C. 
Published: March 2024

AbstractThe building of online atomic and molecular databases for astrophysics and for other research fields started with the beginning of the internet. These databases have encompassed different forms: databases of individual research groups exposing their own data, databases providing collected data from the refereed literature, databases providing evaluated compilations, databases providing repositories for individuals to deposit their data, and so on. They were, and are, the replacement for literature compilations with the goal of providing more complete and in particular easily accessible data services to the users communities. Such initiatives involve not only scientific work on the data, but also the characterization of data, which comes with the “standardization” of metadata and of the relations between metadata, as recently developed in different communities. This contribution aims at providing a representative overview of the atomic and molecular databases ecosystem, which is available to the astrophysical community and addresses different issues linked to the use and management of data and databases. The information provided in this paper is related to the keynote lecture “Atomic and Molecular Databases: Open Science for better science and a sustainable world” whose slides can be found at DOI : doi.org/10.5281/zenodo.6979352 on the Zenodo repository connected to the “cb5-labastro” Zenodo Community (https://zenodo.org/communities/cb5-labastro).
The Importance of Producing and Characterizing Laboratory Analogs of (Exo)Planetary Atmospheric Aerosols
Authors: Sciamma-O’Brien Ella , Hörst Sarah M. , Roush Ted L. , Salama Farid 
Published: March 2024

AbstractExperimental studies are key to investigating the physical and chemical processes that drive cloud and haze formation from gas and solid phase molecular precursors in (exo)planetary environments, and validating the theoretical calculations used in models of (exo)planetary atmospheres. They allow characterizing the physical, optical, and chemical properties of laboratory-generated analogs, hence providing critical input parameters to models for observational data analysis. In this paper, we present examples of (1) experiments performed with different facilities to produce analogs of Titan and exoplanet atmospheric aerosols from gas phase molecular precursors, and (2) the characterization of these analogs to provide information on their composition, morphology, and optical constants to the scientific community. We also introduce the recently launched NASA Center for Optical Constants (NCOC), which will provide this critical data to the scientific community for (exo)planetary-relevant ices and organic refractory materials produced in the laboratory from the irradiation of gas and ice precursors.
Land Data Assimilation: Harmonizing Theory and Data in Land Surface Process Studies
Authors: Li Xin , Liu Feng , Ma Chunfeng , Hou Jinliang , Zheng Donghai , Ma Hanqing , Bai Yulong , Han Xujun , Vereecken Harry , Yang Kun , Duan Qingyun , Huang Chunlin 
Published: March 2024

AbstractData assimilation plays a dual role in advancing the “scientific” understanding and serving as an “engineering tool” for the Earth system sciences. Land data assimilation (LDA) has evolved into a distinct discipline within geophysics, facilitating the harmonization of theory and data and allowing land models and observations to complement and constrain each other. Over recent decades, substantial progress has been made in the theory, methodology, and application of LDA, necessitating a holistic and in‐depth exploration of its full spectrum. Here, we present a thorough review elucidating the theoretical and methodological developments in LDA and its distinctive features. This encompasses breakthroughs in addressing strong nonlinearities in land surface processes, exploring the potential of machine learning approaches in data assimilation, quantifying uncertainties arising from multiscale spatial correlation, and simultaneously estimating model states and parameters. LDA has proven successful in enhancing the understanding and prediction of various land surface processes (including soil moisture, snow, evapotranspiration, streamflow, groundwater, irrigation and land surface temperature), particularly within the realms of water and energy cycles. This review outlines the development of global, regional, and catchment‐scale LDA systems and software platforms, proposing grand challenges of generating land reanalysis and advancing coupled land‒atmosphere DA. We lastly highlight the opportunities to expand the applications of LDA from pure geophysical systems to coupled natural and human systems by ingesting a deluge of Earth observation and social sensing data. The paper synthesizes current LDA knowledge and provides a steppingstone for its future development, particularly in promoting dual driven theory‐data land processes studies.
The Role of the Peak Radius of Maximum Wind Contraction Rate Preceding the Peak Intensification Rate on Tropical Cyclone Lifetime Maximum Intensity
Authors: Wang Yilei , Wu Qiaoyan 
Published: March 2024

AbstractThe prevalence of the maximum radius of maximum wind (RMW) contraction rate for the tropical cyclone (TC) before the maximum TC intensification rate has been observed in several previous studies. However, it remains unclear whether and how the maximum RMW contraction rate preceding the maximum TC intensification rate affects the TC lifetime maximum intensity (LMI). In this study, tropical cyclones are grouped into three types depending on whether the peak RMW contraction rate precedes, occurs simultaneously with, or lags the time of the peak intensification rate in the North Atlantic and western North Pacific. Results indicate that when the maximum RMW contraction rate occurs before the maximum intensification rate, TCs are more likely to gain a greater LMI. TCs with the time of maximum RMW contraction rate preceding the time of the maximum intensification rate are more likely to achieve a small RMW and intermediate intensity after the maximum RMW contraction rate period, which is conducive to higher intensification rates. An intermediate initial intensity and higher maximum intensification rate both lead to a greater LMI. Environmental factors are also examined but are found to have little impact on the LMI for the three types of TCs. This work suggests that TCs with a higher LMI are often characterized by a notable maximum rate of RMW contraction before the peak intensification rate and helps to a better understanding of TC structure and intensity changes.
Sensitivity of Simulated Fire‐Generated Circulations to Fuel Characteristics During Large Wildfires
Authors: Roberts Matthew , Lareau Neil P. , Juliano Timothy W. , Shamsaei Kasra , Ebrahimian Hamed , Kosovic Branko 
Published: March 2024

AbstractCoupled fire‐atmosphere models often struggle to simulate important fire processes like fire generated flows, deep flaming fronts, extreme updrafts, and stratospheric smoke injection during large wildfires. This study uses the coupled fire‐atmosphere model, WRF‐Fire, to examine the sensitivities of some of these phenomena to the modeled total fuel load and its consumption. Specifically, the 2020 Bear Fire and 2021 Caldor Fire in California's Sierra Nevada are simulated using three fuel loading scenarios (1X, 4X, and 8X LANDFIRE derived surface fuel), while controlling the fire rate of spread using observations. This approach helps isolate the fuel loading and consumption needed to produce fire‐generated winds and plume rise comparable to radar observations of these events. Increasing fuel loads and corresponding fire residence time in WRF‐Fire leads to deep plumes in excess of 10 km, strong vertical velocities of 40–45 m s−1, and combustion fronts several kilometers in width (in the along wind direction). These results indicate that LANDFIRE‐based surface fuel loads in WRF‐Fire likely under‐represent fuel loading, having significant implications for simulating landscape‐scale wildfire processes, associated impacts on spread, and fire‐atmosphere feedbacks.
Estimating π Using the Topography of the Terrestrial Planets
Authors: Vasseur Jérémie , Wadsworth Fabian B. 
Published: March 2024

AbstractIt is π‐day 2024 (March 14th) and to celebrate, we ask the question: can π be estimated accurately using the shape of the terrestrial planets and the Moon? We proceed by using models for the planet topographies in slices of constant latitude and computing π as the ratio of the circumference to the diameter in each slice. We define the circumference as the topographically undulating perimeter of the slice (which deviates from the circular section of the reference ellipsoid). We define the diameter as the distance connecting two opposite points on the topography model through the center of the slice. This gives us a distribution of π estimates for each latitude slice and overall for each planetary body. The distribution and accuracy of the π estimates we compute are a representation of how smooth and circular latitude slices of the terrestrial planets are. We find that Mercury and Venus are particularly good at predicting π because they are relatively smooth and the topographic deviations from the reference ellipsoid are small compared with Mars, Earth, and the Moon. In the spirit of π‐day, this mathematical exercise motivates an interest in planetary geophysics and shape.
Gephyrin phosphorylation facilitates sexually dimorphic development and function of parvalbumin interneurons in the mouse hippocampus
Authors: Campbell Benjamin F. N. , Cruz-Ochoa Natalia , Otomo Kanako , Lukacsovich David , Espinosa Pedro , Abegg Andrin , Luo Wenshu , Bellone Camilla , Földy Csaba , Tyagarajan Shiva K. 
Published: March 2024

AbstractThe precise function of specialized GABAergic interneuron subtypes is required to provide appropriate synaptic inhibition for regulating principal neuron excitability and synchronization within brain circuits. Of these, parvalbumin-type (PV neuron) dysfunction is a feature of several sex-biased psychiatric and brain disorders, although, the underlying developmental mechanisms are unclear. While the transcriptional action of sex hormones generates sexual dimorphism during brain development, whether kinase signaling contributes to sex differences in PV neuron function remains unexplored. In the hippocampus, we report that gephyrin, the main inhibitory post-synaptic scaffolding protein, is phosphorylated at serine S268 and S270 in a developmentally-dependent manner in both males and females. When examining GphnS268A/S270A mice in which site-specific phosphorylation is constitutively blocked, we found that sex differences in PV neuron density in the hippocampal CA1 present in WT mice were abolished, coincident with a female-specific increase in PV neuron-derived terminals and increased inhibitory input onto principal cells. Electrophysiological analysis of CA1 PV neurons indicated that gephyrin phosphorylation is required for sexually dimorphic function. Moreover, while male and female WT mice showed no difference in hippocampus-dependent memory tasks, GphnS268A/S270A mice exhibited sex- and task-specific deficits, indicating that gephyrin phosphorylation is differentially required by males and females for convergent cognitive function. In fate mapping experiments, we uncovered that gephyrin phosphorylation at S268 and S270 establishes sex differences in putative PV neuron density during early postnatal development. Furthermore, patch-sequencing of putative PV neurons at postnatal day 4 revealed that gephyrin phosphorylation contributes to sex differences in the transcriptomic profile of developing interneurons. Therefore, these early shifts in male-female interneuron development may drive adult sex differences in PV neuron function and connectivity. Our results identify gephyrin phosphorylation as a new substrate organizing PV neuron development at the anatomical, functional, and transcriptional levels in a sex-dependent manner, thus implicating kinase signaling disruption as a new mechanism contributing to the sex-dependent etiology of brain disorders.
The role of RNA-modifying proteins in renal cell carcinoma
Authors: Alhammadi Muna A. , Bajbouj Khuloud , Talaat Iman M. , Hamoudi Rifat 
Published: March 2024

AbstractGene expression is one of the most critical cellular processes. It is controlled by complex mechanisms at the genomic, epigenomic, transcriptomic, and proteomic levels. Any aberration in these mechanisms can lead to dysregulated gene expression. One recently discovered process that controls gene expression includes chemical modifications of RNA molecules by RNA-modifying proteins, a field known as epitranscriptomics. Epitranscriptomics can regulate mRNA splicing, nuclear export, stabilization, translation, or induce degradation of target RNA molecules. Dysregulation in RNA-modifying proteins has been found to contribute to many pathological conditions, such as cancer, diabetes, obesity, cardiovascular diseases, and neurological diseases, among others. This article reviews the role of epitranscriptomics in the pathogenesis and progression of renal cell carcinoma. It summarizes the molecular function of RNA-modifying proteins in the pathogenesis of renal cell carcinoma.
COVID-19 related neurological manifestations in Parkinson’s disease: has ferroptosis been a suspect?
Authors: Jia Fengju , Han Jing 
Published: March 2024

AbstractA rising number of patient cases point to a probable link between SARS-CoV-2 infection and Parkinson’s disease (PD), yet the mechanisms by which SARS-CoV-2 affects the brain and generates neuropsychiatric symptoms in COVID-19 patients remain unknown. Ferroptosis, a distinct iron-dependent non-apoptotic type of cell death characterized by lipid peroxidation and glutathione depletion, a key factor in neurological disorders. Ferroptosis may have a pathogenic role in COVID-19, according to recent findings, however its potential contributions to COVID-19-related PD have not yet been investigated. This review covers potential paths for SARS-CoV-2 infection of the brain. Among these putative processes, ferroptosis may contribute to the etiology of COVID-19-associated PD, potentially providing therapeutic methods.
RBBP6 maintains glioblastoma stem cells through CPSF3-dependent alternative polyadenylation
Authors: Lin Peng , Chen Wenyan , Long Zhilin , Yu Jichuan , Yang Jiayao , Xia Zhen , Wu Qiulian , Min Xinyu , Tang Jing , Cui Ya , Liu Fuyi , Wang Chun , Zheng Jian , Li Wei , Rich Jeremy N. , Li Lei , Xie Qi 
Published: March 2024

AbstractGlioblastoma is one of the most lethal malignant cancers, displaying striking intratumor heterogeneity, with glioblastoma stem cells (GSCs) contributing to tumorigenesis and therapeutic resistance. Pharmacologic modulators of ubiquitin ligases and deubiquitinases are under development for cancer and other diseases. Here, we performed parallel in vitro and in vivo CRISPR/Cas9 knockout screens targeting human ubiquitin E3 ligases and deubiquitinases, revealing the E3 ligase RBBP6 as an essential factor for GSC maintenance. Targeting RBBP6 inhibited GSC proliferation and tumor initiation. Mechanistically, RBBP6 mediated K63-linked ubiquitination of Cleavage and Polyadenylation Specific Factor 3 (CPSF3), which stabilized CPSF3 to regulate alternative polyadenylation events. RBBP6 depletion induced shortening of the 3’UTRs of MYC competing-endogenous RNAs to release miR-590-3p from shortened UTRs, thereby decreasing MYC expression. Targeting CPSF3 with a small molecular inhibitor (JTE-607) reduces GSC viability and inhibits in vivo tumor growth. Collectively, RBBP6 maintains high MYC expression in GSCs through regulation of CPSF3-dependent alternative polyadenylation, providing a potential therapeutic paradigm for glioblastoma.
In-section Click-iT detection and super-resolution CLEM analysis of nucleolar ultrastructure and replication in plants
Authors: Franek Michal , Koptašíková Lenka , Mikšátko Jíří , Liebl David , Macíčková Eliška , Pospíšil Jakub , Esner Milan , Dvořáčková Martina , Fajkus Jíří 
Published: March 2024

AbstractCorrelative light and electron microscopy (CLEM) is an important tool for the localisation of target molecule(s) and their spatial correlation with the ultrastructural map of subcellular features at the nanometre scale. Adoption of these advanced imaging methods has been limited in plant biology, due to challenges with plant tissue permeability, fluorescence labelling efficiency, indexing of features of interest throughout the complex 3D volume and their re-localization on micrographs of ultrathin cross-sections. Here, we demonstrate an imaging approach based on tissue processing and embedding into methacrylate resin followed by imaging of sections by both, single-molecule localization microscopy and transmission electron microscopy using consecutive CLEM and same-section CLEM correlative workflow. Importantly, we demonstrate that the use of a particular type of embedding resin is not only compatible with single-molecule localization microscopy but shows improvements in the fluorophore blinking behavior relative to the whole-mount approaches. Here, we use a commercially available Click-iT ethynyl-deoxyuridine cell proliferation kit to visualize the DNA replication sites of wild-typeArabidopsis thalianaseedlings, as well asfasciata1andnucleolin1plants and apply our in-section CLEM imaging workflow for the analysis of S-phase progression and nucleolar organization in mutant plants with aberrant nucleolar phenotypes.
The influence of cortical activity on perception depends on behavioral state and sensory context
Authors: Russell Lloyd E. , Fişek Mehmet , Yang Zidan , Tan Lynn Pei , Packer Adam M. , Dalgleish Henry W. P. , Chettih Selmaan N. , Harvey Christopher D. , Häusser Michael 
Published: March 2024

AbstractThe mechanistic link between neural circuit activity and behavior remains unclear. While manipulating cortical activity can bias certain behaviors and elicit artificial percepts, some tasks can still be solved when cortex is silenced or removed. Here, mice were trained to perform a visual detection task during which we selectively targeted groups of visually responsive and co-tuned neurons in L2/3 of primary visual cortex (V1) for two-photon photostimulation. The influence of photostimulation was conditional on two key factors: the behavioral state of the animal and the contrast of the visual stimulus. The detection of low-contrast stimuli was enhanced by photostimulation, while the detection of high-contrast stimuli was suppressed, but crucially, only when mice were highly engaged in the task. When mice were less engaged, our manipulations of cortical activity had no effect on behavior. The behavioral changes were linked to specific changes in neuronal activity. The responses of non-photostimulated neurons in the local network were also conditional on two factors: their functional similarity to the photostimulated neurons and the contrast of the visual stimulus. Functionally similar neurons were increasingly suppressed by photostimulation with increasing visual stimulus contrast, correlating with the change in behavior. Our results show that the influence of cortical activity on perception is not fixed, but dynamically and contextually modulated by behavioral state, ongoing activity and the routing of information through specific circuits.
The bone ecosystem facilitates multiple myeloma relapse and the evolution of heterogeneous drug resistant disease
Authors: Bishop Ryan T. , Miller Anna K. , Froid Matthew , Nerlakanti Niveditha , Li Tao , Frieling Jeremy S. , Nasr Mostafa M. , Nyman Karl J. , Sudalagunta Praneeth R. , Canevarolo Rafael R. , Silva Ariosto Siqueira , Shain Kenneth H. , Lynch Conor C. , Basanta David 
Published: March 2024

AbstractMultiple myeloma (MM) is an osteolytic malignancy that is incurable due to the emergence of treatment resistant disease. Defining how, when and where myeloma cell intrinsic and extrinsic bone microenvironmental mechanisms cause relapse is challenging with current biological approaches. Here, we report a biology-driven spatiotemporal hybrid agent-based model of the MM-bone microenvironment. Results indicate MM intrinsic mechanisms drive the evolution of treatment resistant disease but that the protective effects of bone microenvironment mediated drug resistance (EMDR) significantly enhances the probability and heterogeneity of resistant clones arising under treatment. Further, the model predicts that targeting of EMDR deepens therapy response by eliminating sensitive clones proximal to stroma and bone, a finding supported by in vivo studies. Altogether, our model allows for the study of MM clonal evolution over time in the bone microenvironment and will be beneficial for optimizing treatment efficacy so as to significantly delay disease relapse.
Structure of orthoreovirus RNA chaperone σNS, a component of viral replication factories
Authors: Zhao Boyang , Hu Liya , Kaundal Soni , Neetu Neetu , Lee Christopher H. , Somoulay Xayathed , Sankaran Banumathi , Taylor Gwen M. , Dermody Terence S. , Venkataram Prasad B. V. 
Published: March 2024

AbstractThe mammalian orthoreovirus (reovirus) σNS protein is required for formation of replication compartments that support viral genome replication and capsid assembly. Despite its functional importance, a mechanistic understanding of σNS is lacking. We conducted structural and biochemical analyses of a σNS mutant that forms dimers instead of the higher-order oligomers formed by wildtype (WT) σNS. The crystal structure shows that dimers interact with each other using N-terminal arms to form a helical assembly resembling WT σNS filaments in complex with RNA observed using cryo-EM. The interior of the helical assembly is of appropriate diameter to bind RNA. The helical assembly is disrupted by bile acids, which bind to the same site as the N-terminal arm. This finding suggests that the N-terminal arm functions in conferring context-dependent oligomeric states of σNS, which is supported by the structure of σNS lacking an N-terminal arm. We further observed that σNS has RNA chaperone activity likely essential for presenting mRNA to the viral polymerase for genome replication. This activity is reduced by bile acids and abolished by N-terminal arm deletion, suggesting that the activity requires formation of σNS oligomers. Our studies provide structural and mechanistic insights into the function of σNS in reovirus replication.