bluuebunny/crossref_metadata_2025_split huggingface dataset:
Health misinformation and freedom of expression: considerations for policymakers
Authors: Marecos João , Shattock Ethan , Bartlett Oliver , Goiana-da-Silva Francisco , Maheswaran Hendramoorthy , Ashrafian Hutan , Darzi Ara 
Published: January 2023

AbstractHealth misinformation, most visibly following the COVID-19 infodemic, is an urgent threat that hinders the success of public health policies. It likely contributed, and will continue to contribute, to avoidable deaths. Policymakers around the world are being pushed to tackle this problem. Legislative acts have been rolled out or announced in many countries and at the European Union level. The goal of this paper is not to review particular legislative initiatives, or to assess the impact and efficacy of measures implemented by digital intermediaries, but to reflect on the high constitutional and ethical stakes involved in tackling health misinformation through speech regulation. Our findings suggest that solutions focused on regulating speech are likely to encounter significant constraints, as policymakers grasp with the limitations imposed by freedom of expression and ethical considerations. Solutions focused on empowering individuals – such as media literacy initiatives, fact-checking or credibility labels – are one way to avoid such hurdles.
In‐Flight Calibration of Near‐Infrared Reflectance Spectra Measured by the Zhurong Mars Rover
Authors: Lin Honglei , Xu Rui , Lin Yangting , Xu Xuesen , Wu Bing , Gou Sheng , Wei Yong 
Published: January 2023

AbstractThe Zhurong rover of the China's first Mars Exploration Mission successfully landed on the northern plain of Mars and measured near‐infrared (NIR) reflectance spectra with the Mars Surface Composition Detector (MarSCoDe). There was only orbital NIR hyperspectral data before the success of the Zhurong and Perseverance rovers in 2021. The in situ spectral measurements by the rover face different problems when compared with orbital measurements in data analysis, and thus need a new process pipeline. We analyzed the factors affecting the quality of the NIR spectra acquired by the Zhurong rover, including temperature variation of the detector, non‐homogeneous properties of the calibration panels, the atmosphere transmission and Martian dust buildup on the calibration panels. We then identified that the Martian dust buildup on the calibration panels is the main factor affecting the spectra, causing significant discrepancies between the reflectance calibrated with the white and gray panels, respectively, and the systematically higher reflectance values of the Martian soils measured by the Zhurong rover than those by other missions. We proposed a spectral unmixing strategy to restore the radiance of clean calibration panels on the rover and then derived the reflectance spectra with an uncertainty of ∼14%. The method has been tested by simulation experiments in laboratory. The data quality of the in situ NIR spectra of the Zhurong rover is significantly improved after the calibrations based on our pipeline, which is critical for mineral identification on small scales and calibrations of the orbital remote sensing data.
Fluvial and Marine Depositional Environments Determined From Groundwater Chemistry and Calculated Clay‐Cation Compositions
Authors: Jones Cole R. , Capuano Regina M. 
Published: January 2023

AbstractCation mole precents (XCa, XMg, and XNa) on clay minerals in a siliciclastic coastal aquifer calculated from groundwater compositions, can aid in distinguishing fluvial from marine sediments and locate the fluvial/marine transition zone. The clay‐cation compositions of two clay‐rich siliciclastic coastal aquifers calculated from the composition of the groundwater were compared to the location of fluvial, fluvial‐marine transition and marine environments identified by traditional core, well log and paleontological analyses. The traditionally defined fluvial depositional environment is distinguished by clays with low XNa < 8% (for 92% of the samples) and high XCa from 55% to 98% with the remainder XMg. In comparison, the traditionally defined marine depositional environment is distinguished by clays with higher XNa > 8.0% (for 86% of the samples) and lower XCa ranging from 5% to 39% with the remainder XMg. The traditionally defined fluvial/marine transition zone has values overlapping the fluvial and marine end members, with 59% with XNa < 8% (fluvial) and 41% with XNa > 8% (marine), and XCa ranging from 45% to 98% with the remainder XMg. Calculations support that the excess Na (XNa > 8%) on marine clays can be retained for 10s of millions of years despite flushing with meteoric water, because of the high clay content in marine sediments. The calculated cation composition of clays deposited from river water are XNa < 8%. In contrast XNa 8%–54% is possible for seawater equilibrated clays supporting that the values found in the different depositional zones are possible. Calculated cation compositions might supplement traditional stratigraphic interpretations in distinguishing fluvial/marine depositional environments.
Single-molecule visualization of mRNA circularization during translation
Authors: Kim Byungju , Seol Jincheol , Kim Yoon Ki , Lee Jong-Bong 
Published: January 2023

AbstractTranslation is mediated by precisely orchestrated sequential interactions among translation initiation components, mRNA, and ribosomes. Biochemical, structural, and genetic techniques have revealed the fundamental mechanism that determines what occurs and when, where and in what order. Most mRNAs are circularized via the eIF4E–eIF4G–PABP interaction, which stabilizes mRNAs and enhances translation by recycling ribosomes. However, studies using single-molecule fluorescence imaging have allowed for the visualization of complex data that opposes the traditional “functional circularization” theory. Here, we briefly introduce single-molecule techniques applied to studies on mRNA circularization and describe the results of in vitro and live-cell imaging. Finally, we discuss relevant insights and questions gained from single-molecule research related to translation.
White matter lesion load determines exercise-induced dopaminergic plasticity and working memory gains in aging
Authors: von Cederwald Bryn Farnsworth , Johansson Jarkko , Riklund Katrine , Karalija Nina , Boraxbekk Carl-Johan 
Published: January 2023

AbstractAge-related dopamine reductions have been suggested to contribute to maladaptive working memory (WM) function in older ages. One promising intervention approach is to increase physical activity, as this has been associated with plasticity of the striatal dopamine system and WM improvements, however with individual differences in efficacy. The present work focused on the impact of individual differences in white-matter lesion burden upon dopamine D2-like receptor (DRD2) availability and WM changes in response to a 6 months physical activity intervention. While the intervention altered striatal DRD2 availability and WM performance in individuals with no or only mild lesions (p < 0.05), no such effects were found in individuals with moderate-to-severe lesion severity (p > 0.05). Follow-up analyses revealed a similar pattern for processing speed, but not for episodic memory performance. Linear analyses further revealed that lesion volume (ml) at baseline was associated with reduced DRD2 availability (r = −0.41, p < 0.05), and level of DRD2 change (r = 0.40, p < 0.05). Taken together, this study underlines the necessity to consider cerebrovascular health in interventions with neurocognitive targets. Future work should assess whether these findings extend beyond measures of DRD2 availability and WM.
Human zygotic genome activation is initiated from paternal genome
Authors: Yuan Shenli , Zhan Jianhong , Zhang Jingye , Liu Zhenbo , Hou Zhenzhen , Zhang Chuanxin , Yi Lizhi , Gao Lei , Zhao Han , Chen Zi-Jiang , Liu Jiang , Wu Keliang 
Published: January 2023

AbstractAlthough parental genomes undergo extensive epigenetic reprogramming to be equalized after fertilization, whether they play different roles in human zygotic genome activation (ZGA) remains unknown. Here, we mapped parental transcriptomes by using human parthenogenetic (PG) and androgenetic (AG) embryos during ZGA. Our data show that human ZGA is launched at the 8-cell stage in AG and bi-parental embryos, but at the morula stage in PG embryos. In contrast, mouse ZGA occurs at the same stage in PG and AG embryos. Mechanistically, primate-specific ZNF675 with AG-specific expression plays a role in human ZGA initiated from paternal genome at the 8-cell stage. AG-specifically expressed LSM1 is also critical for human maternal RNA degradation (MRD) and ZGA. The allelic expressions of ZNF675 and LSM1 are associated with their allelically epigenetic states. Notably, the paternally specific expressions of ZNF675 and LSM1 are also observed in diploid embryos. Collectively, human ZGA is initiated from paternal genome.
Correlated evolution of social organization and lifespan in mammals
Authors: Zhu Pingfen , Liu Weiqiang , Zhang Xiaoxiao , Li Meng , Liu Gaoming , Yu Yang , Li Zihao , Li Xuanjing , Du Juan , Wang Xiao , Grueter Cyril C. , Li Ming , Zhou Xuming 
Published: January 2023

AbstractDiscerning the relationship between sociality and longevity would permit a deeper understanding of how animal life history evolved. Here, we perform a phylogenetic comparative analysis of ~1000 mammalian species on three states of social organization (solitary, pair-living, and group-living) and longevity. We show that group-living species generally live longer than solitary species, and that the transition rate from a short-lived state to a long-lived state is higher in group-living than non-group-living species, altogether supporting the correlated evolution of social organization and longevity. The comparative brain transcriptomes of 94 mammalian species identify 31 genes, hormones and immunity-related pathways broadly involved in the association between social organization and longevity. Further selection features reveal twenty overlapping pathways under selection for both social organization and longevity. These results underscore a molecular basis for the influence of the social organization on longevity.
Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples
Authors: Mirzazadeh Reza , Andrusivova Zaneta , Larsson Ludvig , Newton Phillip T. , Galicia Leire Alonso , Abalo Xesús M. , Avijgan Mahtab , Kvastad Linda , Denadai-Souza Alexandre , Stakenborg Nathalie , Firsova Alexandra B. , Shamikh Alia , Jurek Aleksandra , Schultz Niklas , Nistér Monica , Samakovlis Christos , Boeckxstaens Guy , Lundeberg Joakim 
Published: January 2023

AbstractSpatially resolved transcriptomics has enabled precise genome-wide mRNA expression profiling within tissue sections. The performance of methods targeting the polyA tails of mRNA relies on the availability of specimens with high RNA quality. Moreover, the high cost of currently available spatial resolved transcriptomics assays requires a careful sample screening process to increase the chance of obtaining high-quality data. Indeed, the upfront analysis of RNA quality can show considerable variability due to sample handling, storage, and/or intrinsic factors. We present RNA-Rescue Spatial Transcriptomics (RRST), a workflow designed to improve mRNA recovery from fresh frozen specimens with moderate to low RNA quality. First, we provide a benchmark of RRST against the standard Visium spatial gene expression protocol on high RNA quality samples represented by mouse brain and prostate cancer samples. Then, we test the RRST protocol on tissue sections collected from five challenging tissue types, including human lung, colon, small intestine, pediatric brain tumor, and mouse bone/cartilage. In total, we analyze 52 tissue sections and demonstrate that RRST is a versatile, powerful, and reproducible protocol for fresh frozen specimens of different qualities and origins.
Host-microbe co-metabolism via MCAD generates circulating metabolites including hippuric acid
Authors: Pruss Kali M. , Chen Haoqing , Liu Yuanyuan , Van Treuren William , Higginbottom Steven K. , Jarman John B. , Fischer Curt R. , Mak Justin , Wong Beverly , Cowan Tina M. , Fischbach Michael A. , Sonnenburg Justin L. , Dodd Dylan 
Published: January 2023

AbstractThe human gut microbiota produces dozens of small molecules that circulate in blood, accumulate to comparable levels as pharmaceutical drugs, and influence host physiology. Despite the importance of these metabolites to human health and disease, the origin of most microbially-produced molecules and their fate in the host remains largely unknown. Here, we uncover a host-microbe co-metabolic pathway for generation of hippuric acid, one of the most abundant organic acids in mammalian urine. Combining stable isotope tracing with bacterial and host genetics, we demonstrate reduction of phenylalanine to phenylpropionic acid by gut bacteria; the host re-oxidizes phenylpropionic acid involving medium-chain acyl-CoA dehydrogenase (MCAD). Generation of germ-free male and female MCAD−/− mice enabled gnotobiotic colonization combined with untargeted metabolomics to identify additional microbial metabolites processed by MCAD in host circulation. Our findings uncover a host-microbe pathway for the abundant, non-toxic phenylalanine metabolite hippurate and identify β-oxidation via MCAD as a novel mechanism by which mammals metabolize microbiota-derived metabolites.
Mechanism of hormone and allosteric agonist mediated activation of follicle stimulating hormone receptor
Authors: Duan Jia , Xu Peiyu , Zhang Huibing , Luan Xiaodong , Yang Jiaqi , He Xinheng , Mao Chunyou , Shen Dan-Dan , Ji Yujie , Cheng Xi , Jiang Hualiang , Jiang Yi , Zhang Shuyang , Zhang Yan , Xu H. Eric 
Published: January 2023

AbstractFollicle stimulating hormone (FSH) is an essential glycoprotein hormone for human reproduction, which functions are mediated by a G protein-coupled receptor, FSHR. Aberrant FSH-FSHR signaling causes infertility and ovarian hyperstimulation syndrome. Here we report cryo-EM structures of FSHR in both inactive and active states, with the active structure bound to FSH and an allosteric agonist compound 21 f. The structures of FSHR are similar to other glycoprotein hormone receptors, highlighting a conserved activation mechanism of hormone-induced receptor activation. Compound 21 f formed extensive interactions with the TMD to directly activate FSHR. Importantly, the unique residue H6157.42 in FSHR plays an essential role in determining FSHR selectivity for various allosteric agonists. Together, our structures provide a molecular basis of FSH and small allosteric agonist-mediated FSHR activation, which could inspire the design of FSHR-targeted drugs for the treatment of infertility and controlled ovarian stimulation for in vitro fertilization.
Global vegetation resilience linked to water availability and variability
Authors: Smith Taylor , Boers Niklas 
Published: January 2023

AbstractQuantifying the resilience of vegetated ecosystems is key to constraining both present-day and future global impacts of anthropogenic climate change. Here we apply both empirical and theoretical resilience metrics to remotely-sensed vegetation data in order to examine the role of water availability and variability in controlling vegetation resilience at the global scale. We find a concise global relationship where vegetation resilience is greater in regions with higher water availability. We also reveal that resilience is lower in regions with more pronounced inter-annual precipitation variability, but find less concise relationships between vegetation resilience and intra-annual precipitation variability. Our results thus imply that the resilience of vegetation responds differently to water deficits at varying time scales. In view of projected increases in precipitation variability, our findings highlight the risk of ecosystem degradation under ongoing climate change.
Epigenetic control of cellular crosstalk defines gastrointestinal organ fate and function
Authors: Smith Ryan J. , Liang Minggao , Loe Adrian Kwan Ho , Yung Theodora , Kim Ji-Eun , Hudson Matthew , Wilson Michael D. , Kim Tae-Hee 
Published: January 2023

AbstractEpithelial-mesenchymal signaling in the gastrointestinal system is vital in establishing regional identity during organogenesis and maintaining adult stem cell homeostasis. Although recent work has demonstrated that Wnt ligands expressed by mesenchymal cells are required during gastrointestinal development and stem cell homeostasis, epigenetic mechanisms driving spatiotemporal control of crosstalk remain unknown. Here, we demonstrate that gastrointestinal mesenchymal cells control epithelial fate and function through Polycomb Repressive Complex 2-mediated chromatin bivalency. We find that while key lineage-determining genes possess tissue-specific chromatin accessibility, Polycomb Repressive Complex 2 controls Wnt expression in mesenchymal cells without altering accessibility. We show that reduction of mesenchymal Wnt secretion rescues gastrointestinal fate and proliferation defects caused by Polycomb Repressive Complex 2 loss. We demonstrate that mesenchymal Polycomb Repressive Complex 2 also regulates niche signals to maintain stem cell function in the adult intestine. Our results highlight a broadly permissive chromatin architecture underlying regionalization in mesenchymal cells, then demonstrate further how chromatin architecture in niches can influence the fate and function of neighboring cells.
Molecular insights into the gating mechanisms of voltage-gated calcium channel CaV2.3
Authors: Gao Yiwei , Xu Shuai , Cui Xiaoli , Xu Hao , Qiu Yunlong , Wei Yiqing , Dong Yanli , Zhu Boling , Peng Chao , Liu Shiqi , Zhang Xuejun Cai , Sun Jianyuan , Huang Zhuo , Zhao Yan 
Published: January 2023

AbstractHigh-voltage-activated R-type CaV2.3 channel plays pivotal roles in many physiological activities and is implicated in epilepsy, convulsions, and other neurodevelopmental impairments. Here, we determine the high-resolution cryo-electron microscopy (cryo-EM) structure of human CaV2.3 in complex with the α2δ1 and β1 subunits. The VSDII is stabilized in the resting state. Electrophysiological experiments elucidate that the VSDII is not required for channel activation, whereas the other VSDs are essential for channel opening. The intracellular gate is blocked by the W-helix. A pre-W-helix adjacent to the W-helix can significantly regulate closed-state inactivation (CSI) by modulating the association and dissociation of the W-helix with the gate. Electrostatic interactions formed between the negatively charged domain on S6II, which is exclusively conserved in the CaV2 family, and nearby regions at the alpha-interacting domain (AID) and S4-S5II helix are identified. Further functional analyses indicate that these interactions are critical for the open-state inactivation (OSI) of CaV2 channels.
Tailored cluster states with high threshold under biased noise
Authors: Claes Jahan , Bourassa J. Eli , Puri Shruti 
Published: January 2023

AbstractFault-tolerant cluster states form the basis for scalable measurement-based quantum computation. Recently, new stabilizer codes for scalable circuit-based quantum computation have been introduced that have very high thresholds under biased noise where the qubit predominantly suffers from one type of error, e.g. dephasing. However, extending these advances in stabilizer codes to generate high-threshold cluster states for biased noise has been a challenge, as the standard method for foliating stabilizer codes to generate fault-tolerant cluster states does not preserve the noise bias. In this work, we overcome this barrier by introducing a generalization of the cluster state that allows us to foliate stabilizer codes in a bias-preserving way. As an example of our approach, we construct a foliated version of the XZZX code which we call the XZZX cluster state. We demonstrate that under a circuit-level-noise model, our XZZX cluster state has a threshold more than double the usual cluster state when dephasing errors are more likely than errors that cause bit flips by a factor of order ~100 or more.
Caravan - A global community dataset for large-sample hydrology
Authors: Kratzert Frederik , Nearing Grey , Addor Nans , Erickson Tyler , Gauch Martin , Gilon Oren , Gudmundsson Lukas , Hassidim Avinatan , Klotz Daniel , Nevo Sella , Shalev Guy , Matias Yossi 
Published: January 2023

AbstractHigh-quality datasets are essential to support hydrological science and modeling. Several CAMELS (Catchment Attributes and Meteorology for Large-sample Studies) datasets exist for specific countries or regions, however these datasets lack standardization, which makes global studies difficult. This paper introduces a dataset calledCaravan(a series of CAMELS) that standardizes and aggregates seven existing large-sample hydrology datasets. Caravan includes meteorological forcing data, streamflow data, and static catchment attributes (e.g., geophysical, sociological, climatological) for 6830 catchments. Most importantly, Caravan is both a dataset and open-source software that allows members of the hydrology community to extend the dataset to new locations by extracting forcing data and catchment attributes in the cloud. Our vision is for Caravan to democratize the creation and use of globally-standardized large-sample hydrology datasets. Caravan is a truly global open-source community resource.
AerialWaste dataset for landfill discovery in aerial and satellite images
Authors: Torres Rocio Nahime , Fraternali Piero 
Published: January 2023

AbstractIllegal landfills are sites where garbage is dumped violating waste management laws. Aerial images enable the use of photo interpretation for territory scanning and landfill detection but this practice is hindered by the manual nature of this task which also requires expert knowledge. Deep Learning methods can help capture the analysts’ expertise and build automated landfill discovery tools. However, this goal requires public high-quality datasets for model training and testing. At present no such datasets exist and this gap penalizes the research toward scalable and accurate landfill discovery methods. We present a dataset for landfill detection featuring airborne, WorldView-3, and GoogleEarth images annotated by professional photo interpreters. It comprises 3,478 positive and 6,956 negative examples. Most positive instances are characterized by metadata: the type of waste, its storage mode, the type of the site, and the evidence and severity of the illicit. The dataset has been technically validated by building an accurate landfill detector and is accompanied by a visualization and annotation tool.