bluuebunny/crossref_metadata_2025_split huggingface dataset:
Local Network Interaction as a Mechanism for Wealth Inequality
Authors: Yu Shao-Tzu , Wang Peng , Kabudula Chodziwadziwa W. , Gareta Dickman , Harling Guy , Houle Brian 
Published: June 2024

AbstractGiven limited institutional resources, low-income populations often rely on social networks to improve their socioeconomic outcomes. However, it remains in question whether small-scale social interactions could affect large-scale economic inequalities in under-resourced contexts. Here, we leverage population-level data from one of the poorest South African settings to construct a large-scale, geographically defined, inter-household social network. Using a multilevel network model, we show that having social ties in close geographic proximity is associated with stable household asset conditions, while geographically distant ties correlate to changes in asset allocation. Notably, we find that localised network interactions are associated with an increase in wealth inequality at the regional level, demonstrating how macro-level inequality may arise from micro-level social processes. Our findings highlight the importance of understanding complex social connections underpinning inter-household resource dynamics, and raise the potential of large-scale social assistance programs to reduce disparities in resource-ownership by accounting for local social constraints.
Mapping fast DNA polymerase exchange during replication
Authors: Xu Longfu , Halma Matthew T. J. , Wuite Gijs J. L. 
Published: June 2024

AbstractDespite extensive studies on DNA replication, the exchange mechanisms of DNA polymerase during replication remain unclear. Existing models propose that this exchange is facilitated by protein partners like helicase. Here we present data, employing a combination of mechanical DNA manipulation and single fluorescent protein observation, that reveal DNA polymerase undergoing rapid and autonomous exchange during replication not coordinated by other proteins. The DNA polymerase shows fast unbinding and rebinding dynamics, displaying a preference for either exonuclease or polymerase activity, or pausing events, during each brief binding event. We also observed a ‘memory effect’ in DNA polymerase rebinding, i.e., the enzyme tends to preserve its prior activity upon reassociation. This effect, potentially linked to the ssDNA/dsDNA junction’s conformation, might play a role in regulating binding preference enabling high processivity amidst rapid protein exchange. Taken together, our findings support an autonomous replication model that includes rapid protein exchange, burst of activity, and a ‘memory effect’ while moving processively forward.
Viral modulation of type II interferon increases T cell adhesion and virus spread
Authors: Jacobsen Carina , Plückebaum Nina , Ssebyatika George , Beyer Sarah , Mendes-Monteiro Lucas , Wang Jiayi , Kropp Kai A. , González-Motos Víctor , Steinbrück Lars , Ritter Birgit , Rodríguez-González Claudio , Böning Heike , Nikolouli Eirini , Kinchington Paul R. , Lachmann Nico , Depledge Daniel P. , Krey Thomas , Viejo-Borbolla Abel 
Published: June 2024

AbstractDuring primary varicella zoster virus (VZV) infection, infected lymphocytes drive primary viremia, causing systemic dissemination throughout the host, including the skin. This results in cytokine expression, including interferons (IFNs), which partly limit infection. VZV also spreads from skin keratinocytes to lymphocytes prior to secondary viremia. It is not clear how VZV achieves this while evading the cytokine response. Here, we show that VZV glycoprotein C (gC) binds IFN-γ and modifies its activity, increasing the expression of a subset of IFN-stimulated genes (ISGs), including intercellular adhesion molecule 1 (ICAM1), chemokines and immunomodulatory genes. The higher ICAM1 protein level at the plasma membrane of keratinocytes facilitates lymphocyte function-associated antigen 1-dependent T cell adhesion and expression of gC during infection increases VZV spread to peripheral blood mononuclear cells. This constitutes the discovery of a strategy to modulate IFN-γ activity, upregulating a subset of ISGs, promoting enhanced lymphocyte adhesion and virus spread.
An electron-blocking interface for garnet-based quasi-solid-state lithium-metal batteries to improve lifespan
Authors: Zhang Chang , Yu Jiameng , Cui Yuanyuan , Lv Yinjie , Zhang Yue , Gao Tianyi , He Yuxi , Chen Xin , Li Tao , Lin Tianquan , Mi Qixi , Yu Yi , Liu Wei 
Published: June 2024

AbstractGarnet oxide is one of the most promising solid electrolytes for solid-state lithium metal batteries. However, the traditional interface modification layers cannot completely block electron migrating from the current collector to the interior of the solid-state electrolyte, which promotes the penetration of lithium dendrites. In this work, a highly electron-blocking interlayer composed of potassium fluoride (KF) is deposited on garnet oxide Li6.4La3Zr1.4Ta0.6O12 (LLZTO). After reacting with melted lithium metal, KF in-situ transforms to KF/LiF interlayer, which can block the electron leakage and inhibit lithium dendrite growth. The Li symmetric cells using the interlayer show a long cycle life of ~3000 hours at 0.2 mA cm−2 and over 350 hours at 0.5 mA cm−2 respectively. Moreover, an ionic liquid of LiTFSI in C4mim-TFSI is screened to wet the LLZTO|LiNi0.8Co0.1Mn0.1O2 (NCM) positive electrode interfaces. The Li|KF-LLZTO | NCM cells present a specific capacity of 109.3 mAh g−1, long lifespan of 3500 cycles and capacity retention of 72.5% at 25 °C and 2 C (380 mA g−1) with an average coulombic efficiency of 99.99%. This work provides a simple and integrated strategy on high-performance quasi-solid-state lithium metal batteries.
Increased reactivity of the paraventricular nucleus of the hypothalamus and decreased threat responding in male rats following psilocin administration
Authors: Effinger Devin P. , Hoffman Jessica L. , Mott Sarah E. , Magee Sarah N. , Quadir Sema G. , Rollison Christian S. , Toedt Daniel , Echeveste Sanchez Maria , High Margaret W. , Hodge Clyde W. , Herman Melissa A. 
Published: June 2024

AbstractPsychedelics have experienced renewed interest following positive clinical effects, however the neurobiological mechanisms underlying effects remain unclear. The paraventricular nucleus of the hypothalamus (PVN) plays an integral role in stress response, autonomic function, social behavior, and other affective processes. We investigated the effect of psilocin, the psychoactive metabolite of psilocybin, on PVN reactivity in Sprague Dawley rats. Psilocin increased stimulus-independent PVN activity as measured by c-Fos expression in male and female rats. Psilocin increased PVN reactivity to an aversive air-puff stimulus in males but not females. Reactivity was restored at 2- and 7-days post-injection with no group differences. Additionally, prior psilocin injection did not affect PVN reactivity following acute restraint stress. Experimental groups sub-classified by baseline threat responding indicate that increased male PVN reactivity is driven by active threat responders. These findings identify the PVN as a significant site of psychedelic drug action with implications for threat responding behavior.
Global turnover of soil mineral-associated and particulate organic carbon
Authors: Zhou Zhenghu , Ren Chengjie , Wang Chuankuan , Delgado-Baquerizo Manuel , Luo Yiqi , Luo Zhongkui , Du Zhenggang , Zhu Biao , Yang Yuanhe , Jiao Shuo , Zhao Fazhu , Cai Andong , Yang Gaihe , Wei Gehong 
Published: June 2024

AbstractSoil organic carbon (SOC) persistence is predominantly governed by mineral protection, consequently, soil mineral-associated (MAOC) and particulate organic carbon (POC) turnovers have different impacts on the vulnerability of SOC to climate change. Here, we generate the global MAOC and POC maps using 8341 observations and then infer the turnover times of MAOC and POC by a data-model integration approach. Global MAOC and POC storages are $${975}_{964}^{987}$$

975

964

987

Pg C (mean with 5% and 95% quantiles) and $${330}_{323}^{337}$$

330

323

337

Pg C, while global mean MAOC and POC turnover times are $${129}_{45}^{383}$$

129

45

383

yr and $${23}_{5}^{82}$$

23

5

82

yr in the top meter, respectively. Climate warming-induced acceleration of MAOC and POC decomposition is greater in subsoil than that in topsoil. Overall, the global atlas of MAOC and POC turnover, together with the global distributions of MAOC and POC stocks, provide a benchmark for Earth system models to diagnose SOC-climate change feedback.
Machine learning workflow for edge computed arrhythmia detection in exploration class missions
Authors: Mani Cyril , Paul Tanya S. , Archambault Patrick M. , Marois Alexandre 
Published: June 2024

AbstractDeep-space missions require preventative care methods based on predictive models for identifying in-space pathologies. Deploying such models requires flexible edge computing, which Open Neural Network Exchange (ONNX) formats enable by optimizing inference directly on wearable edge devices. This work demonstrates an innovative approach to point-of-care machine learning model pipelines by combining this capacity with an advanced self-optimizing training scheme to classify periods of Normal Sinus Rhythm (NSR), Atrial Fibrillation (AFIB), and Atrial Flutter (AFL). 742 h of electrocardiogram (ECG) recordings were pre-processed into 30-second normalized samples where variable mode decomposition purged muscle artifacts and instrumentation noise. Seventeen heart rate variability and morphological ECG features were extracted by convoluting peak detection with Gaussian distributions and delineating QRS complexes using discrete wavelet transforms. The decision tree classifier’s features, parameters, and hyperparameters were self-optimized through stratified triple nested cross-validation ranked on F1-scoring against cardiologist labeling. The selected model achieved a macro F1-score of 0.899 with 0.993 for NSR, 0.938 for AFIB, and 0.767 for AFL. The most important features included median P-wave amplitudes, PRR20, and mean heart rates. The ONNX-translated pipeline took 9.2 s/sample. This combination of our self-optimizing scheme and deployment use case of ONNX demonstrated overall accurate operational tachycardia detection.
Weightlessness leads to an increase granulosa cells in the growing follicle
Authors: Kikina Anna Yu. , Matrosova Mariia S. , Gorbacheva Elena Yu. , Gogichaeva Ksenia K. , Toniyan Konstantin A. , Boyarintsev Valery V. , Kotov Oleg V. , Ogneva Irina V. 
Published: June 2024

AbstractThe participation of women in space programs of increasing flight duration requires research of their reproductive system from the perspective of subsequent childbearing and healthy aging. For the first time, we present hormonal and structural data on the dynamics of recovery after a 157-day space flight in a woman of reproductive age. There were no clinically significant changes in the reproductive system, but detailed analysis shows that weightlessness leads to an increase in the proportion of early antral follicles and granulosa cells in large antral follicles. Returning to Earth’s gravity reduces the number and diameter of early antral follicles.
T cell independent antibody responses with class switch and memory using peptides anchored on liposomes
Authors: Hjálmsdóttir Ásdís , Hasler Fabio , Waeckerle-Men Ying , Duda Agathe , López-Deber María Pilar , Pihlgren Maria , Vukicevic Marija , Kündig Thomas M. , Johansen Pål 
Published: June 2024

AbstractVaccines generally require T lymphocytes for B-cell activation and immunoglobulin class switching in response to peptide or protein antigens. In the absence of T cells, limited IgG class switch takes place, germinal centers are short-lived, and the B cells lack memory. Here, immunization of mice with liposomes containing 15mer peptides and monophosphoryl lipid A (MPLA) as adjuvant, induced T-cell independent (TI) IgG class switch within three days, as well as germinal center formation. The antibody responses were long-lived, strictly dependent on Toll-like receptor 4 (TLR4) signaling, partly dependent on Bruton’s tyrosine kinase (BTK) signal transmission, and independent of signaling through T-cell receptors, MHC class II and inflammasome. The antibody response showed characteristics of both TI type 1 and TI type 2. All IgG subclasses could be boosted months after primary immunization, and the biological function of the secreted antibodies was demonstrated in murine models of allergic anaphylaxis and of bacterial infection. Moreover, antibody responses after immunization with peptide- and MPLA-loaded liposomes could be triggered in neonatal mice and in mice receiving immune-suppressants. This study demonstrates T-cell independent endogenous B-cell memory and recall responses in vivo using a peptide antigen. The stimulation of these antibody responses required a correct and dense assembly and administration of peptide and adjuvant on the surface of liposomes. In the future, TI vaccines may prove beneficial in pathological conditions in which T-cell immunity is compromised through disease or medicines or when rapid, antibody-mediated immune protection is needed.
Spatially distributed atmospheric boundary layer properties in Houston – A value-added observational dataset
Authors: Lamer Katia , Mages Zackary , Treserras Bernat Puigdomènech , Walter Paul , Zhu Zeen , Rapp Anita D. , Nowotarski Christopher J. , Brooks Sarah D. , Flynn James , Sharma Milind , Klein Petra , Spencer Michelle , Smith Elizabeth , Gebauer Joshua , Bell Tyler , Bunting Lydia , Griggs Travis , Wagner Timothy J. , McKeown Katherine 
Published: June 2024

AbstractIn 2022, Houston, TX became a nexus for field campaigns aiming to further our understanding of the feedbacks between convective clouds, aerosols and atmospheric boundary layer (ABL) properties. Houston’s proximity to the Gulf of Mexico and Galveston Bay motivated the collection of spatially distributed observations to disentangle coastal and urban processes. This paper presents a value-added ABL dataset derived from observations collected by eight research teams over 46 days between 2 June - 18 September 2022. The dataset spans 14 sites distributed within a ~80-km radius around Houston. Measurements from three types of instruments are analyzed to objectively provide estimates of nine ABL parameters, both thermodynamic (potential temperature, and relative humidity profiles and thermodynamic ABL depth) and dynamic (horizontal wind speed and direction, mean vertical velocity, updraft and downdraft speed profiles, and dynamical ABL depth). Contextual information about cloud occurrence is also provided. The dataset is prepared on a uniform time-height grid of 1 h and 30 m resolution to facilitate its use as a benchmark for forthcoming numerical simulations and the fundamental study of atmospheric processes.
Making Mathematical Research Data FAIR: Pathways to Improved Data Sharing
Authors: Conrad Tim O. F. , Ferrer Eloi , Mietchen Daniel , Pusch Larissa , Stegmüller Johannes , Schubotz Moritz 
Published: June 2024

AbstractThe sharing and citation of research data is becoming increasingly recognized as an essential building block in scientific research across various fields and disciplines. Sharing research data allows other researchers to reproduce results, replicate findings, and build on them. Ultimately, this will foster faster cycles in knowledge generation. Some disciplines, such as astronomy or bioinformatics, already have a long history of sharing data; many others do not. The current landscape of available systems for sharing research data is diverse. In this article, we conduct a detailed analysis of existing web-based systems, specifically focusing on mathematical research data.
Integrating Iso-seq and RNA-seq data for the reannotation of the greater amberjack genome
Authors: Zhao Yuanli , Chen Zonggui , Hu Meidi , Liu Hairong , Zhao Haiping , Huang Yang , Jiang Mouyan , Li Shengkang , Li Guangli , Zhu Chunhua , Hu Wei , Luo Daji 
Published: June 2024

AbstractThe greater amberjack is a very important fishery species with high commercial value, and it is distributed worldwide. Transcriptome-based studies on S. dumerili have been limited by an inadequate reference genome and a lack of well-annotated full-length transcripts. In this study, a total of 12 tissues from juvenile and adult fish both sexes were collected for next-generation RNA sequencing (RNA-seq) and full-length isoform sequencing (Iso-seq). For Iso-seq, a total of 163,218, 149,716, and 189,169 high-quality unique transcript sequences were obtained, with an N50 of 5,441, 5,255, and 5,939, from juvenile, adult male and adult female S. dumerili, respectively. We integrated the Iso-seq and RNA-seq data to construct a comprehensive gene annotation and systematically profiled the dynamics of gene expression across the 12 tissues. Our gene models had greater detail and accuracy than those from NCBI and Ensembl, with more precise polyA locations. These resources serve as a foundation for functional genomic studies and provide valuable insights into the molecular mechanisms underlying the development, reproduction and commercial traits of amberjack.
Validation and refinement of cropland map in southwestern China by harnessing ten contemporary datasets
Authors: Cui Yifeng , Dong Jinwei , Zhang Chao , Yang Jilin , Chen Na , Guo Peng , Di Yuanyuan , Chen Mengxi , Li Aiwen , Liu Ronggao 
Published: June 2024

AbstractAccurate cropland map serves as the cornerstone of effective agricultural monitoring. Despite the continuous enrichment of remotely sensed cropland maps, pervasive inconsistencies have impeded their further application. This issue is particularly evident in areas with limited valid observations, such as southwestern China, which is characterized by its complex topography and fragmented parcels. In this study, we constructed multi-sourced samples independent of the data producers, taking advantage of open-source validation datasets and sampling to rectify the accuracy of ten contemporary cropland maps in southwestern China, decoded their inconsistencies, and generated a refined cropland map (CroplandSyn) by leveraging ten state-of-the-art remotely sensed cropland maps released from 2021 onwards using the self-adaptive threshold method. Validations, conducted at both prefecture and county scales, underscored the superiority of the refined cropland map, aligning more closely with national land survey data. The refined cropland map and samples are publicly available to users. Our study offers valuable insights for improving agricultural practices and land management in under-monitored areas by providing high-quality cropland maps and validation datasets.
A thermosurvey dataset: Older adults’ experiences and adaptation to urban heat and climate change
Authors: Jancewicz Barbara , Wrotek Małgorzata 
Published: June 2024

AbstractWe introduce the thermosurvey dataset, a comprehensive collection focusing on the thermal comfort, heat-related experiences, health, socioeconomic status, and perceptions of older adults (aged 65 and over) in Warsaw and Madrid. The two cities differ greatly in their heat experiences, but due to climate change, both face increasing temperatures. The study aimed to understand how heat affects cities’ older adult population and how we can better adapt to rising temperatures. We call the study a thermosurvey because it connects traditional survey data with temperature and humidity measurements done before, after and during the interview, offering a holistic view of the participants’ thermal environments. The dataset can be used to better understand thermal comfort, the interplay of health and heat experiences, and the relationship between experiences and climate change views. We hope our data will enable scholars to analyse the impact of climate change on older adults and to develop strategies to help them adapt to a warming climate.
Chromosome-level genome assembly of Cnidium monnieri, a highly demanded traditional Chinese medicine
Authors: Wang Zixuan , He Jiaxin , Qi Qi , Wang Kaixuan , Tang Huanying , Feng Yimeng , Zhao Xinyue , Yi Shanyong , Zhao Yucheng , Xu Dingqiao 
Published: June 2024

AbstractCnidium monnieri, a medicinal herb of the Cnidium genus and the Apiaceae family, is among the most important traditional Chinese medicines and is widely distributed in China. However, to date, no C. monnieri-related genomic information has been described. In this study, we assembled the C. monnieri genome of approximately 1210.23 Mb with a contig N50 of 83.14 Mb. Using PacBio HiFi and Hi-C sequencing data, we successfully anchored 93.86% of the assembled sequences to 10 pseudochromosomes (2n = 20). We predicted a total of 37,460 protein-coding genes, with 97.02% of them being functionally annotated in Non-Redundant, Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and other databases. In addition, we identified 2,778 tRNAs, 4,180 rRNAs, 258 miRNAs, and 1,700 snRNAs in the genome. This is the first reported C. monnieri genome. Hopefully, the availability of this chromosome-level reference genome provides a significant basis for upcoming natural product-related biosynthetic pathway assessment in C. monnieri.
Synthetic data generation for a longitudinal cohort study – evaluation, method extension and reproduction of published data analysis results
Authors: Kühnel Lisa , Schneider Julian , Perrar Ines , Adams Tim , Moazemi Sobhan , Prasser Fabian , Nöthlings Ute , Fröhlich Holger , Fluck Juliane 
Published: June 2024

AbstractAccess to individual-level health data is essential for gaining new insights and advancing science. In particular, modern methods based on artificial intelligence rely on the availability of and access to large datasets. In the health sector, access to individual-level data is often challenging due to privacy concerns. A promising alternative is the generation of fully synthetic data, i.e., data generated through a randomised process that have similar statistical properties as the original data, but do not have a one-to-one correspondence with the original individual-level records. In this study, we use a state-of-the-art synthetic data generation method and perform in-depth quality analyses of the generated data for a specific use case in the field of nutrition. We demonstrate the need for careful analyses of synthetic data that go beyond descriptive statistics and provide valuable insights into how to realise the full potential of synthetic datasets. By extending the methods, but also by thoroughly analysing the effects of sampling from a trained model, we are able to largely reproduce significant real-world analysis results in the chosen use case.