bluuebunny/crossref_metadata_2025_split huggingface dataset:
TCAF1 promotes TRPV2-mediated Ca2+ release in response to cytosolic DNA to protect stressed replication forks
Authors: Kong Lingzhen , Cheng Chen , Cheruiyot Abigael , Yuan Jiayi , Yang Yichan , Hwang Sydney , Foust Daniel , Tsao Ning , Wilkerson Emily , Mosammaparast Nima , Major Michael B. , Piston David W. , Li Shan , You Zhongsheng 
Published: May 2024

AbstractThe protection of the replication fork structure under stress conditions is essential for genome maintenance and cancer prevention. A key signaling pathway for fork protection involves TRPV2-mediated Ca2+ release from the ER, which is triggered after the generation of cytosolic DNA and the activation of cGAS/STING. This results in CaMKK2/AMPK activation and subsequent Exo1 phosphorylation, which prevent aberrant fork processing, thereby ensuring genome stability. However, it remains poorly understood how the TRPV2 channel is activated by the presence of cytosolic DNA. Here, through a genome-wide CRISPR-based screen, we identify TRPM8 channel-associated factor 1 (TCAF1) as a key factor promoting TRPV2-mediated Ca2+ release under replication stress or other conditions that activate cGAS/STING. Mechanistically, TCAF1 assists Ca2+ release by facilitating the dissociation of STING from TRPV2, thereby relieving TRPV2 repression. Consistent with this function, TCAF1 is required for fork protection, chromosomal stability, and cell survival after replication stress.
Functional and structural dissection of glycosyltransferases underlying the glycodiversity of wolfberry-derived bioactive ingredients lycibarbarspermidines
Authors: Li Shao-Yang , Wang Gao-Qian , Long Liang , Gao Jia-Ling , Zhou Zheng-Qun , Wang Yong-Heng , Lv Jian-Ming , Chen Guo-Dong , Hu Dan , Abe Ikuro , Gao Hao 
Published: May 2024

AbstractLycibarbarspermidines are unusual phenolamide glycosides characterized by a dicaffeoylspermidine core with multiple glycosyl substitutions, and serve as a major class of bioactive ingredients in the wolfberry. So far, little is known about the enzymatic basis of the glycosylation of phenolamides including dicaffeoylspermidine. Here, we identify five lycibarbarspermidine glycosyltransferases, LbUGT1-5, which are the first phenolamide-type glycosyltransferases and catalyze regioselective glycosylation of dicaffeoylspermidines to form structurally diverse lycibarbarspermidines in wolfberry. Notably, LbUGT3 acts as a distinctive enzyme that catalyzes a tandem sugar transfer to the ortho-dihydroxy group on the caffeoyl moiety to form the unusual ortho-diglucosylated product, while LbUGT1 accurately discriminates caffeoyl and dihydrocaffeoyl groups to catalyze a site-selective sugar transfer. Crystal structure analysis of the complexes of LbUGT1 and LbUGT3 with UDP, combined with molecular dynamics simulations, revealed the structural basis of the difference in glycosylation selectivity between LbUGT1 and LbUGT3. Site-directed mutagenesis illuminates a conserved tyrosine residue (Y389 in LbUGT1 and Y390 in LbUGT3) in PSPG box that plays a crucial role in regulating the regioselectivity of LbUGT1 and LbUGT3. Our study thus sheds light on the enzymatic underpinnings of the chemical diversity of lycibarbarspermidines in wolfberry, and expands the repertoire of glycosyltransferases in nature.
The link between ancient microbial fluoride resistance mechanisms and bioengineering organofluorine degradation or synthesis
Authors: Stockbridge Randy B. , Wackett Lawrence P. 
Published: May 2024

AbstractFluorinated organic chemicals, such as per- and polyfluorinated alkyl substances (PFAS) and fluorinated pesticides, are both broadly useful and unusually long-lived. To combat problems related to the accumulation of these compounds, microbial PFAS and organofluorine degradation and biosynthesis of less-fluorinated replacement chemicals are under intense study. Both efforts are undermined by the substantial toxicity of fluoride, an anion that powerfully inhibits metabolism. Microorganisms have contended with environmental mineral fluoride over evolutionary time, evolving a suite of detoxification mechanisms. In this perspective, we synthesize emerging ideas on microbial defluorination/fluorination and fluoride resistance mechanisms and identify best approaches for bioengineering new approaches for degrading and making organofluorine compounds.
Environment-induced heritable variations are common in Arabidopsis thaliana
Authors: Lin Xiaohe , Yin Junjie , Wang Yifan , Yao Jing , Li Qingshun Q. , Latzel Vit , Bossdorf Oliver , Zhang Yuan-Ye 
Published: May 2024

AbstractParental or ancestral environments can induce heritable phenotypic changes, but whether such environment-induced heritable changes are a common phenomenon remains unexplored. Here, we subject 14 genotypes of Arabidopsis thaliana to 10 different environmental treatments and observe phenotypic and genome-wide gene expression changes over four successive generations. We find that all treatments caused heritable phenotypic and gene expression changes, with a substantial proportion stably transmitted over all observed generations. Intriguingly, the susceptibility of a genotype to environmental inductions could be predicted based on the transposon abundance in the genome. Our study thus challenges the classic view that the environment only participates in the selection of heritable variation and suggests that the environment can play a significant role in generating of heritable variations.
Loop-extruders alter bacterial chromosome topology to direct entropic forces for segregation
Authors: Harju Janni , van Teeseling Muriel C. F. , Broedersz Chase P. 
Published: May 2024

AbstractEntropic forces have been argued to drive bacterial chromosome segregation during replication. In many bacterial species, however, specifically evolved mechanisms, such as loop-extruding SMC complexes and the ParABS origin segregation system, contribute to or are even required for chromosome segregation, suggesting that entropic forces alone may be insufficient. The interplay between and the relative contributions of these segregation mechanisms remain unclear. Here, we develop a biophysical model showing that purely entropic forces actually inhibit bacterial chromosome segregation until late replication stages. By contrast, our model reveals that loop-extruders loaded at the origins of replication, as observed in many bacterial species, alter the effective topology of the chromosome, thereby redirecting and enhancing entropic forces to enable accurate chromosome segregation during replication. We confirm our model predictions with polymer simulations: purely entropic forces do not allow for concurrent replication and segregation, whereas entropic forces steered by specifically loaded loop-extruders lead to robust, global chromosome segregation during replication. Finally, we show how loop-extruders can complement locally acting origin separation mechanisms, such as the ParABS system. Together, our results illustrate how changes in the geometry and topology of the polymer, induced by DNA-replication and loop-extrusion, impact the organization and segregation of bacterial chromosomes.
Complete telomere-to-telomere genomes uncover virulence evolution conferred by chromosome fusion in oomycete plant pathogens
Authors: Zhang Zhichao , Zhang Xiaoyi , Tian Yuan , Wang Liyuan , Cao Jingting , Feng Hui , Li Kainan , Wang Yan , Dong Suomeng , Ye Wenwu , Wang Yuanchao 
Published: May 2024

AbstractVariations in chromosome number are occasionally observed among oomycetes, a group that includes many plant pathogens, but the emergence of such variations and their effects on genome and virulence evolution remain ambiguous. We generated complete telomere-to-telomere genome assemblies for Phytophthora sojae, Globisporangium ultimum, Pythium oligandrum, and G. spinosum. Reconstructing the karyotype of the most recent common ancestor in Peronosporales revealed that frequent chromosome fusion and fission drove changes in chromosome number. Centromeres enriched with Copia-like transposons may contribute to chromosome fusion and fission events. Chromosome fusion facilitated the emergence of pathogenicity genes and their adaptive evolution. Effectors tended to duplicate in the sub-telomere regions of fused chromosomes, which exhibited evolutionary features distinct to the non-fused chromosomes. By integrating ancestral genomic dynamics and structural predictions, we have identified secreted Ankyrin repeat-containing proteins (ANKs) as a novel class of effectors in P. sojae. Phylogenetic analysis and experiments further revealed that ANK is a specifically expanded effector family in oomycetes. These results revealed chromosome dynamics in oomycete plant pathogens, and provided novel insights into karyotype and effector evolution.
Plasmodium falciparum infection in humans and mosquitoes influence natural Anopheline biting behavior and transmission
Authors: Markwalter Christine F. , Lapp Zena , Abel Lucy , Kimachas Emmah , Omollo Evans , Freedman Elizabeth , Chepkwony Tabitha , Amunga Mark , McCormick Tyler , Bérubé Sophie , Mangeni Judith N. , Wesolowski Amy , Obala Andrew A. , Taylor Steve M. , Prudhomme O’Meara Wendy 
Published: May 2024

AbstractThe human infectious reservoir ofPlasmodium falciparumis governed by transmission efficiency during vector-human contact and mosquito biting preferences. Understanding biting bias in a natural setting can help target interventions to interrupt transmission. In a 15-month cohort in western Kenya, we detectedP. falciparumin indoor-restingAnophelesand human blood samples by qPCR and matched mosquito bloodmeals to cohort participants using short-tandem repeat genotyping. Using risk factor analyses and discrete choice models, we assessed mosquito biting behavior with respect to parasite transmission. Biting was highly unequal; 20% of people received 86% of bites. Biting rates were higher on males (biting rate ratio (BRR): 1.68; CI: 1.28–2.19), children 5–15 years (BRR: 1.49; CI: 1.13–1.98), andP. falciparum-infected individuals (BRR: 1.25; CI: 1.01–1.55). In aggregate,P. falciparum-infected school-age (5–15 years) boys accounted for 50% of bites potentially leading to onward transmission and had an entomological inoculation rate 6.4x higher than any other group. Additionally, infectious mosquitoes were nearly 3x more likely than non-infectious mosquitoes to biteP. falciparum-infected individuals (relative risk ratio 2.76, 95% CI 1.65–4.61). Thus, persistentP. falciparumtransmission was characterized by disproportionate onward transmission from school-age boys and by the preference of infected mosquitoes to feed upon infected people.
CO electrolysis to multicarbon products over grain boundary-rich Cu nanoparticles in membrane electrode assembly electrolyzers
Authors: Li Hefei , Wei Pengfei , Liu Tianfu , Li Mingrun , Wang Chao , Li Rongtan , Ye Jinyu , Zhou Zhi-You , Sun Shi-Gang , Fu Qiang , Gao Dunfeng , Wang Guoxiong , Bao Xinhe 
Published: May 2024

AbstractProducing valuable chemicals like ethylene via catalytic carbon monoxide conversion is an important nonpetroleum route. Here we demonstrate an electrochemical route for highly efficient synthesis of multicarbon (C2+) chemicals from CO. We achieve a C2+ partial current density as high as 4.35 ± 0.07 A cm−2 at a low cell voltage of 2.78 ± 0.01 V over a grain boundary-rich Cu nanoparticle catalyst in an alkaline membrane electrode assembly (MEA) electrolyzer, with a C2+ Faradaic efficiency of 87 ± 1% and a CO conversion of 85 ± 3%. Operando Raman spectroscopy and density functional theory calculations reveal that the grain boundaries of Cu nanoparticles facilitate CO adsorption and C − C coupling, thus rationalizing a qualitative trend between C2+ production and grain boundary density. A scale-up demonstration using an electrolyzer stack with five 100 cm2 MEAs achieves high C2+ and ethylene formation rates of 118.9 mmol min−1 and 1.2 L min−1, respectively, at a total current of 400 A (4 A cm−2) with a C2+ Faradaic efficiency of 64%.
The cage effect of electron beam irradiation damage in cryo-electron microscopy
Authors: Li Yi , Kang Dong-Dong , Dai Jia-Yu , Wang Lin-Wang 
Published: May 2024

AbstractElectron beam irradiation can cause damage to biological and organic samples, as determined via transmission electron microscopy (TEM). Cryo-electron microscopy (cryo-EM) significantly reduces such damage by quickly freezing the environmental water around organic molecules. However, there are multiple hypotheses about the mechanism of cryo-protection in cryo-EM. A lower temperature can cause less molecular dissociation in the first stage, or frozen water can have a “cage” effect by preventing the dissociated fragments from flying away. In this work, we use real-time time-dependent density functional theory molecular dynamics(rt-TDDFT-MD) simulations to study the related dynamics. We use our recently developed natural orbital branching (NOB) algorithm to describe the molecular dissociation process after the molecule is ionized. We find that despite the difference in surrounding water molecules at different temperatures, the initial dissociation process is similar. On the other hand, the dissociated fragments fly away at room temperature, while they remain in the same cage when frozen water is used. Our results provide direct support for the cage effect mechanism.
A brief tablet-based intervention benefits linguistic and communicative abilities in toddlers and preschoolers
Authors: Peña Marcela , Vásquez-Venegas Constanza , Cortés Patricia , Pittaluga Enrica , Herrera Mitzy , Pino Esteban J. , Escobar Raul G. , Dehaene-Lambertz Ghislaine , Guevara Pamela 
Published: May 2024

AbstractYoung children’s linguistic and communicative abilities are foundational for their academic achievement and overall well-being. We present the positive outcomes of a brief tablet-based intervention aimed at teaching toddlers and preschoolers new word-object and letter-sound associations. We conducted two experiments, one involving toddlers ( ~ 24 months old, n = 101) and the other with preschoolers ( ~ 42 months old, n = 152). Using a pre-post equivalent group design, we measured the children’s improvements in language and communication skills resulting from the intervention. Our results showed that the intervention benefited toddlers’ verbal communication and preschoolers’ speech comprehension. Additionally, it encouraged vocalizations in preschoolers and enhanced long-term memory for the associations taught in the study for all participants. In summary, our study demonstrates that the use of a ludic tablet-based intervention for teaching new vocabulary and pre-reading skills can improve young children’s linguistic and communicative abilities, which are essential for future development.
Global high-resolution growth projections dataset for rooftop area consistent with the shared socioeconomic pathways, 2020–2050
Authors: Joshi Siddharth , Zakeri Behnam , Mittal Shivika , Mastrucci Alessio , Holloway Paul , Krey Volker , Shukla Priyadarshi Ramprasad , O’Gallachoir Brian , Glynn James 
Published: May 2024

AbstractAssessment of current and future growth in the global rooftop area is important for understanding and planning for a robust and sustainable decentralised energy system. These estimates are also important for urban planning studies and designing sustainable cities thereby forwarding the ethos of the Sustainable Development Goals 7 (clean energy), 11 (sustainable cities), 13 (climate action) and 15 (life on land). Here, we develop a machine learning framework that trains on big data containing ~700 million open-source building footprints, global land cover, road, and population datasets to generate globally harmonised estimates of growth in rooftop area for five different future growth narratives covered by Shared Socioeconomic Pathways. The dataset provides estimates for ~3.5 million fishnet tiles of 1/8 degree spatial resolution with data on gross rooftop area for five growth narratives covering years 2020–2050 in decadal time steps. This single harmonised global dataset can be used for climate change, energy transition, biodiversity, urban planning, and disaster risk management studies covering continental to conurbation geospatial levels.
A large-scale multivariate soccer athlete health, performance, and position monitoring dataset
Authors: Midoglu Cise , Kjæreng Winther Andreas , Boeker Matthias , Dahl Pettersen Susann , Pedersen Sigurd , Ragab Nourhan , Kupka Tomas , Hicks Steven A. , Bredsgaard Randers Morten , Jain Ramesh , Dagenborg Håvard J. , Pettersen Svein Arne , Johansen Dag , Riegler Michael A. , Halvorsen Pål 
Published: May 2024

AbstractData analysis for athletic performance optimization and injury prevention is of tremendous interest to sports teams and the scientific community. However, sports data are often sparse and hard to obtain due to legal restrictions, unwillingness to share, and lack of personnel resources to be assigned to the tedious process of data curation. These constraints make it difficult to develop automated systems for analysis, which require large datasets for learning. We therefore present SoccerMon, the largest soccer athlete dataset available today containing both subjective and objective metrics, collected from two different elite women’s soccer teams over two years. Our dataset contains 33,849 subjective reports and 10,075 objective reports, the latter including over six billion GPS position measurements. SoccerMon can not only play a valuable role in developing better analysis and prediction systems for soccer, but also inspire similar data collection activities in other domains which can benefit from subjective athlete reports, GPS position information, and/or time-series data in general.
Time-of-Flight MRA of Intracranial Aneurysms with Interval Surveillance, Clinical Segmentation and Annotations
Authors: de Nys Chloe M. , Liang Ee Shern , Prior Marita , Woodruff Maria A. , Novak James I. , Murphy Ashley R. , Li Zhiyong , Winter Craig D. , Allenby Mark C. 
Published: May 2024

AbstractIntracranial aneurysms (IAs) are present in 2–6% of the global population and can be catastrophic upon rupture with a mortality rate of 30–50%. IAs are commonly detected through time-of-flight magnetic resonance angiography (TOF-MRA), however, this data is rarely available for research and training purposes. The provision of imaging resources such as TOF-MRA images is imperative to develop new strategies for IA detection, rupture prediction, and surgical training. To support efforts in addressing data availability bottlenecks, we provide an open-access TOF-MRA dataset comprising 63 patients, of which 24 underwent interval surveillance imaging by TOF-MRA. Patient scans were evaluated by a neuroradiologist, providing aneurysm and vessel segmentations, clinical annotations, 3D models, in addition to 3D Slicer software environments containing all this data for each patient. This dataset is the first to provide interval surveillance imaging for supporting the understanding of IA growth and stability. This dataset will support computational and experimental research into IA dynamics and assist surgical and radiology training in IA treatment.
Direct comparison of mass cytometry and single-cell RNA sequencing of human peripheral blood mononuclear cells
Authors: Su Emily Y. , Fread Kristen , Goggin Sarah , Zunder Eli R. , Cahan Patrick 
Published: May 2024

AbstractSingle-cell methods offer a high-resolution approach for characterizing cell populations. Many studies rely on single-cell transcriptomics to draw conclusions regarding cell state and behavior, with the underlying assumption that transcriptomic readouts largely parallel their protein counterparts and subsequent activity. However, the relationship between transcriptomic and proteomic measurements is imprecise, and thus datasets that probe the extent of their concordance will be useful to refine such conclusions. Additionally, novel single-cell analysis tools often lack appropriate gold standard datasets for the purposes of assessment. Integrative (combining the two data modalities) and predictive (using one modality to improve results from the other) approaches in particular, would benefit from transcriptomic and proteomic data from the same sample of cells. For these reasons, we performed single-cell RNA sequencing, mass cytometry, and flow cytometry on a split-sample of human peripheral blood mononuclear cells. We directly compare the proportions of specific cell types resolved by each technique, and further describe the extent to which protein and mRNA measurements correlate within distinct cell types.
Chromosome-level genome assembly and annotation of the cold-water species Ophiura sarsii
Authors: Han Chen , Zhang Qian , Li Yixuan , Sun Yuyao , Dong Yue , Ge Meiling , Li Zhong , Hu Xuying , Liu Bing , Zhang Xuelei , Wang Zongling , Xu Qinzeng 
Published: May 2024

AbstractThe cold-water species Ophiura sarsii, a brittle star, is a key echinoderm in the Arctic continental shelf region, highly sensitive to climate change. However, the absence of a high-quality genome has hindered a thorough understanding of its adaptive evolution. In this study, we reported the first chromosome-level genome assembly of O. sarsii. The genome assembly totalled 1.57 Gb, encompassing 19 chromosomes with a GC content of 37.11% and a scaffold N50 length of 78.03 Mb. The Benchmarking Universal Single-Copy Orthologs (BUSCO) assessment yielded a completeness estimate of 93.5% for this assembly. We predicted a total of 27,099 protein-coding genes, with 25,079 functionally annotated. The genome was comprised of 58.09% transposable elements. This chromosome-level genome of O. sarsii contributes to our understanding of the origin and evolution of marine organisms.
Structural, radiation shielding, thermal and dynamic mechanical analysis for waste rubber/EPDM rubber composite loaded with Fe2O3 for green environment
Authors: AbdelKader M. M. , Abou-Laila M. T. , El-Deeb M. S. S. , Taha Eman O. , El-Deeb A. S. 
Published: May 2024

AbstractIncreasing waste rubber recycling produces a specious range of products for many valuable applications. Waste Rubber/EPDM composite with different concentrations was prepared. Infrared spectroscopy (FTIR) is used to identify the chemical composition. A water absorption test, Dynamic mechanical analysis (DMA), and Thermal Gravimetric Analysis (TGA) were performed. The (75/25) WR/EPDM rubber composite exhibited the best behavior with the highest mechanical performance. Fe2O3 was added to (75/25) WR/EPDM rubber composite. Water absorption, FTIR, TGA, and DMA were investigated. The composite performance was improved with increasing Fe2O3 content. The linear attenuation coefficients (μ) were also measured as a function of the concentrations of Fe2O3 for γ-ray energy 662 keV by using 137Cs point source; the radiation shielding can be denoted by numbers of parameters like mass attenuation coefficient (μm), half value layer (HVL), Tenth value layer TVL and radiation protection efficiency (RPE%), radiation protection efficiency increased as Fe2O3 increased.