bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multifaceted membrane interactions of human Atg3 promote LC3-phosphatidylethanolamine conjugation during autophagy
Authors: Ye Yansheng , Tyndall Erin R. , Bui Van , Bewley Maria C. , Wang Guifang , Hong Xupeng , Shen Yang , Flanagan John M. , Wang Hong-Gang , Tian Fang 
Published: September 2023

AbstractAutophagosome formation, a crucial step in macroautophagy (autophagy), requires the covalent conjugation of LC3 proteins to the amino headgroup of phosphatidylethanolamine (PE) lipids. Atg3, an E2-like enzyme, catalyzes the transfer of LC3 from LC3-Atg3 to PEs in targeted membranes. Here we show that the catalytically important C-terminal regions of human Atg3 (hAtg3) are conformationally dynamic and directly interact with the membrane, in collaboration with its N-terminal membrane curvature-sensitive helix. The functional relevance of these interactions was confirmed by in vitro conjugation and in vivo cellular assays. Therefore, highly curved phagophoric rims not only serve as a geometric cue for hAtg3 recruitment, but also their interaction with hAtg3 promotes LC3-PE conjugation by targeting its catalytic center to the membrane surface and bringing substrates into proximity. Our studies advance the notion that autophagosome biogenesis is directly guided by the spatial interactions of Atg3 with highly curved phagophoric rims.
Antibiotic hyper-resistance in a class I aminoacyl-tRNA synthetase with altered active site signature motif
Authors: Brkic A. , Leibundgut M. , Jablonska J. , Zanki V. , Car Z. , Petrovic Perokovic V. , Marsavelski A. , Ban N. , Gruic-Sovulj I. 
Published: September 2023

AbstractAntibiotics target key biological processes that include protein synthesis. Bacteria respond by developing resistance, which increases rapidly due to antibiotics overuse. Mupirocin, a clinically used natural antibiotic, inhibits isoleucyl-tRNA synthetase (IleRS), an enzyme that links isoleucine to its tRNAIle for protein synthesis. Two IleRSs, mupirocin-sensitive IleRS1 and resistant IleRS2, coexist in bacteria. The latter may also be found in resistant Staphylococcus aureus clinical isolates. Here, we describe the structural basis of mupirocin resistance and unravel a mechanism of hyper-resistance evolved by some IleRS2 proteins. We surprisingly find that an up to 103-fold increase in resistance originates from alteration of the HIGH motif, a signature motif of the class I aminoacyl-tRNA synthetases to which IleRSs belong. The structural analysis demonstrates how an altered HIGH motif could be adopted in IleRS2 but not IleRS1, providing insight into an elegant mechanism for coevolution of the key catalytic motif and associated antibiotic resistance.
Discovery of a three-proton insertion mechanism in α-molybdenum trioxide leading to enhanced charge storage capacity
Authors: Lei Yongjiu , Zhao Wenli , Yin Jun , Ma Yinchang , Zhao Zhiming , Yin Jian , Khan Yusuf , Hedhili Mohamed Nejib , Chen Long , Wang Qingxiao , Yuan Youyou , Zhang Xixiang , Bakr Osman M. , Mohammed Omar F. , Alshareef Husam N. 
Published: September 2023

AbstractThe α-molybdenum trioxide has attracted much attention for proton storage owing to its easily modified bilayer structure, fast proton insertion kinetics, and high theoretical specific capacity. However, the fundamental science of the proton insertion mechanism in α-molybdenum trioxide has not been fully understood. Herein, we uncover a three-proton intercalation mechanism in α-molybdenum trioxide using a specially designed phosphoric acid based liquid crystalline electrolyte. The semiconductor-to-metal transition behavior and the expansion of the lattice interlayers of α-molybdenum trioxide after trapping one mole of protons are verified experimentally and theoretically. Further investigation of the morphology of α-molybdenum trioxide indicates its fracture behavior upon the proton intercalation process, which creates diffusion channels for hydronium ions. Notably, the observation of an additional redox behavior at low potential endows α-molybdenum trioxide with an improved specific discharge capacity of 362 mAh g−1.
Epigenome-wide association analysis of infant bronchiolitis severity: a multicenter prospective cohort study
Authors: Zhu Zhaozhong , Li Yijun , Freishtat Robert J. , Celedón Juan C. , Espinola Janice A. , Harmon Brennan , Hahn Andrea , Camargo Carlos A. , Liang Liming , Hasegawa Kohei 
Published: September 2023

AbstractBronchiolitis is the most common lower respiratory infection in infants, yet its pathobiology remains unclear. Here we present blood DNA methylation data from 625 infants hospitalized with bronchiolitis in a 17-center prospective study, and associate them with disease severity. We investigate differentially methylated CpGs (DMCs) for disease severity. We characterize the DMCs based on their association with cell and tissues types, biological pathways, and gene expression. Lastly, we also examine the relationships of severity-related DMCs with respiratory and immune traits in independent cohorts. We identify 33 DMCs associated with severity. These DMCs are differentially methylated in blood immune cells. These DMCs are also significantly enriched in multiple tissues (e.g., lung) and cells (e.g., small airway epithelial cells), and biological pathways (e.g., interleukin-1-mediated signaling). Additionally, these DMCs are associated with respiratory and immune traits (e.g., asthma, lung function, IgE levels). Our study suggests the role of DNA methylation in bronchiolitis severity.
Microgravity and evasion of plant innate immunity by human bacterial pathogens
Authors: Totsline Noah , Kniel Kalmia E. , Bais Harsh P. 
Published: September 2023

AbstractSpaceflight microgravity and modeled-microgravity analogs (MMA) broadly alter gene expression and physiology in both pathogens and plants. Research elucidating plant and bacterial responses to normal gravity or microgravity has shown the involvement of both physiological and molecular mechanisms. Under true and simulated microgravity, plants display differential expression of pathogen-defense genes while human bacterial pathogens exhibit increased virulence, antibiotic resistance, stress tolerance, and reduced LD50 in animal hosts. Human bacterial pathogens including Salmonella enterica and E. coli act as cross-kingdom foodborne pathogens by evading and suppressing the innate immunity of plants for colonization of intracellular spaces. It is unknown if evasion and colonization of plants by human pathogens occurs under microgravity and if there is increased infection capability as demonstrated using animal hosts. Understanding the relationship between microgravity, plant immunity, and human pathogens could prevent potentially deadly outbreaks of foodborne disease during spaceflight. This review will summarize (1) alterations to the virulency of human pathogens under microgravity and MMA, (2) alterations to plant physiology and gene expression under microgravity and MMA, (3) suppression and evasion of plant immunity by human pathogens under normal gravity, (4) studies of plant-microbe interactions under microgravity and MMA. A conclusion suggests future study of interactions between plants and human pathogens under microgravity is beneficial to human safety, and an investment in humanity’s long and short-term space travel goals.
Melting of glacier ice enhanced by bursting air bubbles
Authors: Wengrove Meagan E. , Pettit Erin C. , Nash Jonathan D. , Jackson Rebecca H. , Skyllingstad Eric D. 
Published: September 2023

AbstractFeedbacks between ice melt, glacier flow and ocean circulation can rapidly accelerate ice loss at tidewater glaciers and alter projections of sea-level rise. At the core of these projections is a model for ice melt that neglects the fact that glacier ice contains pressurized bubbles of air due to its formation from compressed snow. Current model estimates can underpredict glacier melt at termini outside the region influenced by the subglacial discharge plume by a factor of 10–100 compared with observations. Here we use laboratory-scale experiments and theoretical arguments to show that the bursting of pressurized bubbles from glacier ice could be a source of this discrepancy. These bubbles eject air into the seawater, delivering additional buoyancy and impulses of turbulent kinetic energy to the boundary layer, accelerating ice melt. We show that real glacier ice melts 2.25 times faster than clear bubble-free ice when driven by natural convection in a laboratory setting. We extend these results to the geophysical scale to show how bubble dynamics contribute to ice melt from tidewater glaciers. Consequently, these results could increase the accuracy of modelled predictions of ice loss to better constrain sea-level rise projections globally.
World’s human migration patterns in 2000–2019 unveiled by high-resolution data
Authors: Niva Venla , Horton Alexander , Virkki Vili , Heino Matias , Kosonen Maria , Kallio Marko , Kinnunen Pekka , Abel Guy J. , Muttarak Raya , Taka Maija , Varis Olli , Kummu Matti 
Published: September 2023

AbstractDespite being a topical issue in public debate and on the political agenda for many countries, a global-scale, high-resolution quantification of migration and its major drivers for the recent decades remained missing. We created a global dataset of annual net migration between 2000 and 2019 (~10 km grid, covering the areas of 216 countries or sovereign states), based on reported and downscaled subnational birth (2,555 administrative units) and death (2,067 administrative units) rates. We show that, globally, around 50% of the world’s urban population lived in areas where migration accelerated urban population growth, while a third of the global population lived in provinces where rural areas experienced positive net migration. Finally, we show that, globally, socioeconomic factors are more strongly associated with migration patterns than climatic factors. While our method is dependent on census data, incurring notable uncertainties in regions where census data coverage or quality is low, we were able to capture migration patterns not only between but also within countries, as well as by socioeconomic and geophysical zonings. Our results highlight the importance of subnational analysis of migration—a necessity for policy design, international cooperation and shared responsibility for managing internal and international migration.
Quartet RNA reference materials improve the quality of transcriptomic data through ratio-based profiling
Authors: Yu Ying , Hou Wanwan , Liu Yaqing , Wang Haiyan , Dong Lianhua , Mai Yuanbang , Chen Qingwang , Li Zhihui , Sun Shanyue , Yang Jingcheng , Cao Zehui , Zhang Peipei , Zi Yi , Liu Ruimei , Gao Jian , Zhang Naixin , Li Jingjing , Ren Luyao , Jiang He , Shang Jun , Zhu Sibo , Wang Xiaolin , Qing Tao , Bao Ding , Li Bingying , Li Bin , Suo Chen , Pi Yan , Wang Xia , Dai Fangping , Scherer Andreas , Mattila Pirkko , Han Jinxiong , Zhang Lijun , Jiang Hui , Thierry-Mieg Danielle , Thierry-Mieg Jean , Xiao Wenming , Hong Huixiao , Tong Weida , Wang Jing , Li Jinming , Fang Xiang , Jin Li , Xu Joshua , Qian Feng , Zhang Rui , Shi Leming , Zheng Yuanting 
Published: September 2023

Abstract
Certified RNA reference materials are indispensable for assessing the reliability of RNA sequencing to detect intrinsically small biological differences in clinical settings, such as molecular subtyping of diseases. As part of the Quartet Project for quality control and data integration of multi-omics profiling, we established four RNA reference materials derived from immortalized B-lymphoblastoid cell lines from four members of a monozygotic twin family. Additionally, we constructed ratio-based transcriptome-wide reference datasets between two samples, providing cross-platform and cross-laboratory ‘ground truth’. Investigation of the intrinsically subtle biological differences among the Quartet samples enables sensitive assessment of cross-batch integration of transcriptomic measurements at the ratio level. The Quartet RNA reference materials, combined with the ratio-based reference datasets, can serve as unique resources for assessing and improving the quality of transcriptomic data in clinical and biological settings.
Diagnostic performance of circulating biomarkers for non-alcoholic steatohepatitis
Authors: Sanyal Arun J. , Shankar Sudha S. , Yates Katherine P. , Bolognese James , Daly Erika , Dehn Clayton A. , Neuschwander-Tetri Brent , Kowdley Kris , Vuppalanchi Raj , Behling Cynthia , Tonascia James , Samir Anthony , Sirlin Claude , Sherlock Sarah P. , Fowler Kathryn , Heymann Helen , Kamphaus Tania N. , Loomba Rohit , Calle Roberto A. 
Published: September 2023

AbstractThere are no approved diagnostic biomarkers for at-risk non-alcoholic steatohepatitis (NASH), defined by the presence of NASH, high histological activity and fibrosis stage ≥2, which is associated with higher incidence of liver-related events and mortality. FNIH-NIMBLE is a multi-stakeholder project to support regulatory approval of NASH-related biomarkers. The diagnostic performance of five blood-based panels was evaluated in an observational (NASH CRN DB2) cohort (n = 1,073) with full spectrum of non-alcoholic fatty liver disease (NAFLD). The panels were intended to diagnose at-risk NASH (NIS4), presence of NASH (OWLiver) or fibrosis stages >2, >3 or 4 (enhanced liver fibrosis (ELF) test, PROC3 and FibroMeter VCTE). The prespecified performance metric was an area under the receiver operating characteristic curve (AUROC) ≥0.7 and superiority over alanine aminotransferase for disease activity and the FIB-4 test for fibrosis severity. Multiple biomarkers met these metrics. NIS4 had an AUROC of 0.81 (95% confidence interval: 0.78–0.84) for at-risk NASH. The AUROCs of the ELF test, PROC3 and FibroMeterVCTE for clinically significant fibrosis (≥stage 2), advanced fibrosis (≥stage 3) or cirrhosis (stage 4), respectively, were all ≥0.8. ELF and FibroMeter VCTE outperformed FIB-4 for all fibrosis endpoints. These data represent a milestone toward qualification of several biomarker panels for at-risk NASH and also fibrosis severity in individuals with NAFLD.
SECURES-Met: A European meteorological data set suitable for electricity modelling applications
Authors: Formayer Herbert , Nadeem Imran , Leidinger David , Maier Philipp , Schöniger Franziska , Suna Demet , Resch Gustav , Totschnig Gerhard , Lehner Fabian 
Published: September 2023

AbstractThe modelling of electricity production and demand requires highly specific and comprehensive meteorological data. One challenge is the high temporal frequency as electricity production and demand modelling typically is done with hourly data. On the other side the European electricity market is highly connected, so that a pure country-based modelling is not expedient and at least the whole European Union (EU) area has to be considered. Additionally, the spatial resolution of the data set must be able to represent the thermal conditions, which requires high spatial resolution at least in mountainous regions. All these requirements lead to huge data amounts for historic observations and even more for climate change projections for the whole 21st century. Thus, we have developed the aggregated European wide climate data set SECURES-Met that has a temporal resolution of one hour, covers the whole EU area and other selected European countries, has a reasonable size but considers the high spatial variability.
A pan-European dataset revealing variability in lithic technology, toolkits, and artefact shapes ~15-11 kya
Authors: Hussain Shumon T. , Riede Felix , Matzig David N. , Biard Miguel , Crombé Philippe , Fernández-Lopéz de Pablo Javier , Fontana Federica , Groß Daniel , Hess Thomas , Langlais Mathieu , Mevel Ludovic , Mills William , Moník Martin , Naudinot Nicolas , Posch Caroline , Rimkus Tomas , Stefański Damian , Vandendriessche Hans 
Published: September 2023

AbstractComparative macro-archaeological investigations of the human deep past rely on the availability of unified, quality-checked datasets integrating different layers of observation. Information on the durable and ubiquitous record of Paleolithic stone artefacts and technological choices are especially pertinent to this endeavour. We here present a large expert-sourced collaborative dataset for the study of stone tool technology and artefact shape evolution across Europe between ~15.000 and 11.000 years before present. The dataset contains a compendium of key sites from the study period, and data on lithic technology and toolkit composition at the level of the cultural taxa represented by those sites. The dataset further encompasses 2D shapes of selected lithic artefact groups (armatures, endscrapers, and borers/perforators) shared between cultural taxa. These data offer novel possibilities to explore between-regional patterns of material culture change to reveal scale-dependent processes of long-term technological evolution in mobile hunter-gatherer societies at the end of the Pleistocene. Our dataset facilitates state-of-the-art quantitative analyses and showcases the benefits of collaborative data collation and synthesis.
RNA sequencing transcriptomics and metabolomics in three poultry breeds
Authors: Zhu Qidong , Cai Yuanli , Xiao Chuanpi , Kong Linglian , Pan Xue , Song Bochen , Song Zhigang 
Published: September 2023

AbstractChickens are remarkably versatile animals that are used as model organisms for biomedical research. Here, we performed metabolomic and RNA sequencing (RNA-Seq) transcriptomic analyses of the hypothalamus, liver tissue and serum of poultry with different genetic backgrounds, providing detailed information for hypothalamus and liver tissue at the transcriptional level and for liver tissue and serum at the metabolite level. We present two datasets generated from 36 samples from three poultry breeds using high-throughput RNA-Seq and liquid chromatography coupled with mass spectrometry acquisition (LC/MS). The transcriptomic and metabolomic data obtained for poultry of different genetic backgrounds will be a valuable resource for further studies on this model organism.
Inhibition of selenoprotein synthesis is not the mechanism by which auranofin inhibits growth of Clostridioides difficile
Authors: Johnstone Michael A. , Holman Matthew A. , Self William T. 
Published: September 2023

AbstractClostridioides difficile infections (CDIs) are responsible for a significant number of antibiotic-associated diarrheal cases. The standard-of-care antibiotics for C. difficile are limited to fidaxomicin and vancomycin, with the recently obsolete metronidazole recommended if both are unavailable. No new antimicrobials have been approved for CDI since fidaxomicin in 2011, despite varying rates of treatment failure among all standard-of-care drugs. Drug repurposing is a rational strategy to generate new antimicrobials out of existing therapeutics approved for other indications. Auranofin is a gold-containing anti-rheumatic drug with antimicrobial activity against C. difficile and other microbes. In a previous report, our group hypothesized that inhibition of selenoprotein biosynthesis was auranofin’s primary mechanism of action against C. difficile. However, in this study, we discovered that C. difficile mutants lacking selenoproteins are still just as sensitive to auranofin as their respective wild-type strains. Moreover, we found that selenite supplementation dampens the activity of auranofin against C. difficile regardless of the presence of selenoproteins, suggesting that selenite’s neutralization of auranofin is not because of compensation for a chemically induced selenium deficiency. Our results clarify the findings of our original study and may aid drug repurposing efforts in discovering the compound’s true mechanism of action against C. difficile.
Contactless deformation of fluid interfaces by acoustic radiation pressure
Authors: Sisombat Félix , Devaux Thibaut , Haumesser Lionel , Callé Samuel 
Published: September 2023

AbstractReversible and programmable shaping of surfaces promises wide-ranging applications in tunable optics and acoustic metasurfaces. Based on acoustic radiation pressure, contactless and real-time deformation of fluid interface can be achieved. This paper presents an experimental and numerical study to characterize the spatiotemporal properties of the deformation induced by acoustic radiation pressure. Using localized ultrasonic excitation, we report the possibility of on-demand tailoring of the induced protrusion at water–air interface in space and time, depending on the shape of the input pressure field. The experimental method used to measure the deformation of the water surface in space and time shows close agreement with simulations. We demonstrate that acoustic radiation pressure allows shaping protrusion at fluid interfaces, which could be changed into a various set of spatiotemporal distributions, considering simple parameters of the ultrasonic excitation. This paves the way for novel approach to design programmable space and time-dependent gratings at fluid interfaces.
Sustained xanthophyll pigments-related photoprotective NPQ is involved in photoinhibition in the haptophyte Tisochrysis lutea
Authors: Lacour T. , Robert E. , Lavaud J. 
Published: September 2023

AbstractDynamic xanthophyll cycle (XC) related non-photochemical quenching (NPQd, also called qE) is present in most phototrophs. It allows dissipating excess light energy under adverse growing conditions. Generally, NPQd rapidly reverses for photosynthesis to resume when light intensity decreases back toward optimal intensity. Under certain environmental conditions and/or in some species, NPQ can be strongly sustained (NPQs showing hours-to-days relaxation kinetics). Tisochrysis lutea is a South Pacific haptophyte phytoplankton with a strong potential for aquaculture and biotechnology applications. It was previously reported to show a surprisingly low NPQd capacity while synthesizing large amounts of diatoxanthin (Dt), a pigment involved in the XC. In order to better understand this paradox, we investigated the characteristics of NPQ in T. lutea under various growth conditions of light and nutrient availability (different photoperiods, low and high light, nutrient starvations). We found a strong NPQs, unmeasurable with usual fluorometry protocols. Along with confirming the involvement of Dt in both NPQd and NPQs (by using the dithiothreitol inhibitor), we highlighted a strong relationship between Dt and the maximum quantum yield of photochemistry (Fv/Fm) across growing conditions and during relaxation experiments in darkness. It suggests that changes in Fv/Fm, usually attributed to the ‘photoinhibitory’ quenching (qI), are simultaneously largely impacted by photoprotective NPQ. The overlap of xanthophyll pigments-related photoprotective NPQ with several other mechanisms involved in the cell response (Photosystem II photoinactivation, changes in pigments composition, and detoxification by antioxidants) to energy unbalance is further discussed. Our findings question both how widespread NPQs is in the global ocean, particularly in nutrient starved environments (oligotrophic waters) and situations (post-bloom), and the use of adapted active fluorescence protocols (i.e. with extended NPQ relaxation period prior to measurement).