bluuebunny/crossref_metadata_2025_split huggingface dataset:
A telomere-to-telomere genome assembly of Zhonghuang 13, a widely-grown soybean variety from the original center of Glycine max
Authors: Zhang Anqi , Kong Tangchao , Sun Baiquan , Qiu Shizheng , Guo Jiahe , Ruan Shuyong , Guo Yu , Guo Jirui , Zhang Zhishuai , Liu Yue , Hu Zheng , Jiang Tao , Liu Yadong , Cao Shuqi , Sun Shi , Wu Tingting , Hong Huilong , Jiang Bingjun , Yang Maoxiang , Yao Xiangyu , Hu Yang , Liu Bo , Han Tianfu , Wang Yadong 
Published: September 2023

AbstractSoybean (Glycine max) stands as a globally significant agricultural crop, and the comprehensive assembly of its genome is of paramount importance for unraveling its biological characteristics and evolutionary history. Nevertheless, previous soybean genome assemblies have harbored gaps and incompleteness, which have constrained in-depth investigations into soybean. Here, we present the first Telomere-to-Telomere (T2T) assembly of the Chinese soybean cultivar “Zhonghuang 13” (ZH13) genome, termed ZH13-T2T, utilizing PacBio Hifi and ONT ultralong reads. We employed a multi-assembler approach, integrating Hifiasm, NextDenovo, and Canu, to minimize biases and enhance assembly accuracy. The assembly spans 1,015,024,879 bp, effectively resolving all 393 gaps that previously plagued the reference genome. Our annotation efforts identified 50,564 high-confidence protein-coding genes, 707 of which are novel. ZH13-T2T revealed longer chromosomes, 421 not-aligned regions (NARs), 112 structure variations (SVs), and a substantial expansion of repetitive element compared to earlier assemblies. Specifically, we identified 25.67 Mb of tandem repeats, an enrichment of 5S and 48S rDNAs, and characterized their genotypic diversity. In summary, we deliver the first complete Chinese soybean cultivar T2T genome. The comprehensive annotation, along with precise centromere and telomere characterization, as well as insights into structural variations, further enhance our understanding of soybean genetics and evolution.
Micro-PINGUIN: Microtiter plate-based ice nucleation detection in gallium with an infrared camera
Authors: Wieber Corina , Jeppesen Mads Rosenhøj , Finster Kai , Melvad Claus , Šantl-Temkiv Tina 
Published: September 2023

AbstractIce nucleation particles play a crucial role in atmospheric processes e.g., they can trigger ice formation in clouds and thus influence their lifetime and optical properties. The quantification and characterization of these particles require reliable and precise measurement techniques. In this publication, we present a novel droplet freezing instrument to measure immersion freezing of biotic and abiotic ice-nucleating particles within the temperature range of 0 °C to −25 °C. Immersion freezing of the samples is investigated using 384-well PCR plates with a sample volume of 30 µl. Nucleation events are detected with high precision using a thermal camera that records the increase in infrared emission due to the latent heat release. To maximize the thermal contact between the PCR plate and the surrounding cooling unit, we use a gallium bath as a mount for the PCR plate. The combination of good thermal connectivity and precise temperature recording enables accurate (± 0.81 °C at −10 °C) and reproducible (± 0.20 °C) detection of the nucleation temperatures.For comparison with already existing instruments, the new ice nucleation instrument, “micro-PINGUIN”, was characterized using Snomax®(hereafter Snomax) and Illite NX suspensions. The results are in agreement with what has been reported in the literature for the already existing instruments. Consequently, the results that will be produced using the micro-PINGUIN are of good quality and can be compared to the results produced by other validated instruments for the study of immersion freezing of various ice nucleating particles. Further, we investigated the reproducibility of experiments using Snomax suspensions and found poor reproducibility when suspensions were prepared freshly even if the same batch of Snomax is used. This could be attributed to substrate heterogeneity, aging effects, and dilution errors. The reproducibility of the measurements is greatly improved for Snomax suspensions that are prepared in advance and stored frozen in aliquots. Thus, we suggest the use of suspensions frozen in aliquots for further reproducibility measurements and intercomparison studies.
Dissolving microneedle array patches containing mesoporous silica nanoparticles of different pore sizes as a tunable sustained release platform
Authors: Paris Juan L. , Vora Lalitkumar K. , Pérez-Moreno Ana M. , Naser Yara A. , Anjani Qonita Kurnia , Cañas José Antonio , Torres María José , Mayorga Cristobalina , Donnelly Ryan F. 
Published: September 2023

AbstractDissolving microneedle array patches (DMAPs) enable efficient and painless delivery of therapeutic molecules across thestratum corneumand into the upper layers of the skin. Furthermore, this delivery strategy can be combined with the sustained release of nanoparticles to enhance the therapeutic potential in a wide variety of pathological scenarios. Among the different types of nanoparticles that can be included in microneedle formulations, mesoporous silica nanoparticles (MSNs) of tuneable pore sizes constitute a promising tool as drug delivery systems for cargos of a wide range of molecular weights. However, the development of efficient methods to produce DMAP containing large amounts of MSNs of different pore sizes has not been reported. In this work, DMAP containing MSNs with varying pore sizes was prepared and characterized. After synthesizing and characterizing MSNs, the pore size of the nanoparticles (in the range of 3 to 13 nm for S-MSN and XL-MSN, respectively) was observed to influence the loading and release of both small and large molecules, using fluorescein and ovalbumin (OVA) as model cargos. Moreover, a new preparation method was developed to produce DMAP containing large amounts of these MSNs located mainly in the microneedle tips. The successful insertion of these DMAPs was confirmedin vitro(using Parafilm),ex vivo(using excised neonatal porcine skin) andin vivo(in the back of mice) models. The dissolution of the microneedles and deposition of the nanoparticles inside the skin were also confirmed bothex vivoandin vivousing fluorescent nanoparticles, with complete microneedle dissolution after 2 h of insertionin vivo. Through histological studies, the microneedle-delivered MSNs were found to end up inside antigen presenting cells in the skin tissue (either F4/80+macrophages or CD11c+dendritic cells). For this reason, the uptake and biological effect of the MSNs was evaluatedin vitroin dendritic cells, showing that while smaller pore MSNs were taken up by cells more efficiently (with over 80 % of S-MSN uptake compared toca. 55 % for XL-MSNs), the dendritic cells treated with OVA- loaded XL-MSNs underwent the largest degree of activation (inducing over 25 % of CD40 expression compared to less than 2 % for OVA-loaded S- MSNs). Finally, the immune response to OVA-loaded XL-MSNs in mice was evaluated after repeated administration either subcutaneously or through DMAP. The results of this experiment showed comparable levels of anti-ovalbumin immunoglobulin generation through both routes of administration (with significant production of OVA-specific IgG1 and IgG2b antibodies), highlighting the good potential of this delivery platform for vaccination or immunotherapy applications.
Spatial association between distributed β-amyloid and tau varies with cognition
Authors: Carbonell Felix , McNicoll Carolann , Zijdenbos Alex P. , Bedell Barry J. ,   Alzheimer’s Disease Neuroimaging Initiative
Published: September 2023

AbstractSeveral PET studies have explored the relationship between β-amyloid load and tau uptake at the early stages of Alzheimer’s disease (AD) progression. Most of these studies have focused on the linear relationship between β-amyloid and tau at the local level and their synergistic effect on different AD biomarkers. We hypothesize that patterns of spatial association between β-amyloid and tau might be uncovered using alternative association metrics that account for linear as well as more complex, possible nonlinear dependencies. In the present study, we propose a new Canonical Distance Correlation Analysis (CDCA) to generate distinctive spatial patterns of the cross-correlation structure between tau, as measured by [18F]flortaucipir PET, and β-amyloid, as measured by [18F]florbetapir PET, from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) study. We found that the CDCA-based β-amyloid scores were not only maximally distance-correlated to tau in cognitively normal (CN) controls and mild cognitive impairment (MCI), but also differentiated between low and high levels of β-amyloid uptake. The most distinctive spatial association pattern was characterized by a spread of β-amyloid covering large areas of the cortex and localized tau in the entorhinal cortex. More importantly, this spatial dependency varies according to cognition, which cannot be explained by the uptake differences in β-amyloid or tau between CN and MCI subjects. Hence, the CDCA-based scores might be more accurate than the amyloid or tau SUVR for the enrollment in clinical trials of those individuals on the path of cognitive deterioration.
Polysaccharides fromBalanophora harlandiiHook: Isolation, Characterization, and Anti-Inflammation Activities
Authors: Li Yuanyang , Li Xueqing , Yuan Qi , Zhu Leiqi , Xia Fangqi , Wang Yaqi , Xue Mengzhen , He Yumin , Yuan Chengfu 
Published: September 2023

ABSTRACTBalanophora harlandiiHook (B. harlandii), a folk medicine, has been traditionally employed to treat traumatic bleeding, gastroenteritis, icteric hepatitis, hemorrhoids, and other conditions. In this work, polysaccharides with anti-inflammatory effects were extracted and purified fromB. harlandii.The extraction conditions were optimized, and the properties of one purified neutral fraction, denoted as BHPs-W-S3, were analyzed. Gel permeation chromatography (GPC) was carried out to measure the molecular weight. The structure of BHPs-W-S3 was assessed based on monosaccharide composition analysis, Fourier transform infrared (FT-IR) spectroscopy, methylation analysis, and nuclear magnetic resonance (NMR) spectroscopy. BHPs-W-S3 has a molecular weight of 14.1 kDa, and its three main monosaccharides are glucose, galactose, and mannose with a molar ratio of 6.4:1.7:1.1. Its main chain consists of →6)-α-D-Glcp-(1→, →4,6)-α-D-Glcp-(1→, →6)-β-D-Galp-(1→, →3,6)-β-D-Galp-(1→, and it has branch chains at the O-4 and/or O-3 positions. In addition,in vitroexperiments show that the polysaccharides fromB. harlandican decrease the phosphorylation level of p65 and IKB-α in LPS-induced RAW264.7 cells to reduce the expression of the pro-inflammatory genes such as TNF-α, IL-6, and IL-1β.Abstract Figure
Stakeholder perspectives on contributors to delayed and inaccurate diagnosis of cardiovascular disease: a UK-based qualitative study
Authors: Abdullayev K , Gorvett O , Sochiera A , Laidlaw L , Chico TJA , Manktelow M , Buckley O , Condell J , Van Arkel RJ , Diaz-Zuccarini V , Matcham Faith 
Published: September 2023

AbstractObjectiveThe aim of this study is to understand stakeholder experiences of cardiovascular disease (CVD) diagnosis to support the development of technological solutions that meet current needs. Specifically, we aimed to identify challenges faced by stakeholders in the process of diagnosis of CVD; to identify discrepancies between patient and clinician experiences of CVD diagnosis, and to make recommendations for the requirements of future health technology solutions intended to improve CVD diagnosis.DesignThe qualitative data was obtained using semi-structured focus groups and 1-1 interviews.ParticipantsUK-based individuals (N = 32) with lived experience of diagnosis of CVD (n = 23) and clinicians with experience in diagnosing CVD (n = 9).ResultsThematic analysis of focus groups and interview transcripts produced four key themes related to challenges contributing to delayed or inaccurate diagnosis of CVD: Symptom Interpretation, Patient Characteristics, Patient-Clinician Interactions, and Systemic Challenges. Sub-themes from each theme are discussed in depth.ConclusionsChallenges related to time and communication were greatest for both stakeholder groups, however there were differences in other areas, for example patient experiences highlighted difficulties with the psychological aspects of diagnosis and interpreting ambiguous symptoms, while clinicians emphasised the role of individual patient differences and the lack of rapport in contributing to delays or inaccurate diagnosis. Key takeaways from this qualitative study were summarised into a table of considerations to highlight key areas that require prioritisation for future research aiming to improve the efficiency and accuracy of CVD diagnosis using digital technologies.
Transcatheter or Surgical Aortic Valve Replacement in Patients with Severe Aortic Stenosis and Small Aortic Annulus: A Randomized Clinical Trial
Authors: Rodés-Cabau Josep , Ribeiro Henrique , Mohammadi Siamak , Serra Vicenç , Al-Atassi Talal , Iniguez Andres , Vilalta Victoria , Nombela-Franco Luis , de Ibarra Jose Ignacio Saez , Auffret Vincent , Forcillo Jessica , Conradi Lenard , Urena Marina , Moris Cesar , Muñoz-Garcia Antonio , Paradis Jean-Michel , Dumont Eric , Kalavrouziotis Dimitri , Pomerantzeff Pablo Maria , Rosa Vitor Emer Egypto , Lopes Mariana Pezzute , Sureda Carles , Jimenez Diaz Victor Alfonso , Giuliani Carlos , Avvedimento Marisa , Pelletier-Beaumont Emilie , Pibarot Philippe 
Published: September 2023

ABSTRACTBACKGROUNDThe optimal treatment in patients with severe aortic stenosis (AS) and small aortic annulus (SAA) remains to be determined. The objectives of this study were to compare the hemodynamic and clinical outcomes between transcatheter aortic valve replacement (TAVR) and surgical aortic valve replacement (SAVR) in patients with a SAA.METHODSProspective multicenter international randomized trial performed in 15 university hospitals. Participants were 151 patients with severe AS and SAA (mean diameter <23 mm) were randomized (1:1) to TAVR (n=77) vs SAVR (n=74), The primary outcome was impaired valve hemodynamics (i.e. severe prosthesis patient mismatch [PPM] or moderate-severe aortic regurgitation [AR]) at 60 days as evaluated by Doppler-echocardiography and analyzed in a central echocardiography core laboratory. Clinical events were secondary outcomes.RESULTSThe mean age of the participants was 75±5 years, with 93 of women, a median STS of 2.5 (1.7-3.3)%, and a mean annulus diameter of 21.1±1.2 mm.CONCLUSIONSThis trial will provide clinicians with scientific evidence to determine if population with smaller aortic anatomy in the setting of severe AS maybe better suited to TAVR compared with SAVR.TRIAL REGISTRATIONClinicaltrials.gov:NCT03383445
Comparative reservoir competence ofPeromyscus leucopus, C57BL/6J, and C3H/HeN forBorrelia burgdorferiB31
Authors: Bourgeois Jeffrey S. , You Stephanie S. , Clendenen Luke H. , Shrestha Muskan , Petnicki-Ocwieja Tanja , Telford Sam R , Hu Linden T. 
Published: September 2023

AbstractBorrelia burgdorferi, a Lyme disease spirochete, causes a range of acute and chronic maladies in humans. However, a primary vertebrate reservoir in the United States, the white-footed deermousePeromyscus leucopus, is reported not to have reduced fitness following infection. While laboratory strains ofMus musculusmice have successfully been leveraged to model acute human Lyme disease, the ability for these rodents to modelB. burgdorferi-P. leucopusinteractions remains understudied. Here we compared infection ofP. leucopuswithB. burgdorferiB31 with infection of the traditionalB. burgdorferimurine models—C57BL/6J and C3H/HeNMus musculus, which develop signs of inflammation akin to human disease. We find thatB. burgdorferiwere able to reach much higher burdens (10- to 30-times higher) in multipleM. musculusskin sites, and that the overall dynamics of infection differed between the two rodent species. We also found thatP. leucopusremained transmissive to larvalIxodes scapularisfor a far shorter period than eitherM. musculusstrain. In line with these observations, we found thatP. leucopusdoes launch a modest but sustained inflammatory response againstB. burgdorferiin the skin, which we hypothesize leads to reduced bacterial viability and rodent-to-tick transmission in these hosts. Similarly, we also observe evidence of inflammation in infectedP. leucopushearts. These observations provide new insight into reservoir species and theB. burgdorferienzootic cycle.ImportanceA Lyme disease-causing bacteria,Borrelia burgdorferi, must alternate between infecting a vertebrate host—usually rodents or birds—and ticks. In order to be successful in that endeavor the bacteria must avoid being killed by the vertebrate host before it can infect a new larval tick. In this work we examine howB. burgdorferiand one of its primary vertebrate reservoirs,Peromyscus leucopus, interact during an experimental infection. We find thatB. burgdorferiappear to colonize its natural host less successfully than conventional laboratory mouse models which aligns with a sustained seemingly anti-bacterial response byP. leucopusagainst the microbe. These data enhance our understanding ofP. leucopushost-pathogen interactions and could potentially serve as a foundation to uncover ways to disrupt the spread ofB. burgdorferiin nature.
Structural pathway for class III PI 3-kinase activation by the myristoylated GTP-binding pseudokinase VPS15
Authors: Cook Annan S. I. , Chen Minghao , Ren Xuefeng , Rao Shanlin , Garcia Samantha N. , Claveras Cabezudo Ainara , Iavarone Anthony T. , Hummer Gerhard , Hurley James H. 
Published: September 2023

AbstractThe class III phosphatidylinositol (PI) 3-kinase complexes I and II (PI3KC3-C1 and -C2) are central to the initiation of macroautophagy and endosomal maturation, respectively. Through three-dimensional classification of a large cryo-EM dataset of human PI3KC3-C1 bound to the small GTPase RAB1A, we were able to map the structural pathway of enzyme activation. The inactive conformation is stabilized by anN-myristoyl modification of the pseudokinase (PK) subunit VPS15. TheN-myristate is sequestered in the N-lobe of the VPS15 PK domain, which stabilizes a series of interactions whereby VPS15 sequesters and blocks the catalytic and membrane binding units of the VPS34 lipid kinase. In the activated conformation, theN-myristate and the VPS34 lipid kinase domain are liberated to interact with membranes and catalyze PI3P formation. The VPS15 PK domain contains a unique Arg at the gatekeeper position and binds tightly to GTP. GTP binding structurally stabilizes theN-myristate “in” conformation, which promotes the inactive conformation. This pathway provides a general mechanism for PI3KC3 activation in autophagy and endosome biogenesis and a roadmap for their pharmacological upregulation.
Phylogenomics and ancestral reconstruction of Korarchaeota reveals genomic adaptation to habitat switching
Authors: Tahon Guillaume , Köstlbacher Stephan , Pelve Erik A. , Baker Brett J. , Saw Jimmy H. , Eme Laura , Tamarit Daniel , Schön Max Emil , Ettema Thijs J. G. 
Published: September 2023

AbstractOur knowledge of archaeal diversity and evolution has expanded rapidly in the past decade. However, hardly any genomes of the phylum Korarchaeota have been obtained due to the difficulty in accessing their natural habitats and – possibly – their limited abundance. As a result, many aspects of Korarchaeota biology, physiology and evolution remain enigmatic. Here, we expand this phylum with five high-quality metagenome-assembled genomes. This improved taxon sampling combined with sophisticated phylogenomic analyses robustly places Korarchaeota at the base of TACK and Asgard clades, revisiting the phylum’s long-assumed position. Furthermore, we observe a clear split between terrestrial and marine thermal clades. Gene tree-aware ancestral reconstructions suggest that the last Korarchaeota common ancestor was a thermophilic autotroph. In contrast, Korarchaeaceae, the lineage where environmental transitions occurred, shifted towards a heterotrophic lifestyle. Terrestrial Korarchaeota gained manycasand CARF genes indicating they may need to manage viral infections. Together, our study provides new insights into these early diverging Archaea and suggests that gradual gene gain and loss shaped their adaptation to different thermal environments.ImportanceKorarchaeota are an ancient group of archaea, but their biology, physiology and evolution have remained obscure. Analysis of five novel Korarchaeota MAGs, and publicly available reference data provides robust phylogenomic evidence that Korarchaeota are placed at the base of Asgard archaea and TACK, revisiting the phylum’s long-assumed position. Gene content reconstruction suggests a versatile thermophilic and autotrophic last Korarchaeota common ancestor. Environmental distribution surveying of public databases places all Korarchaeota in thermophilic environments and indicates that their habitat is limited to hydrothermal vents and hot springs. Our modeling indicates at least two transitions linked to habitat switching between these environments in the evolutionary history of Korarchaeota. Both are linked to a significant alteration of the inferred ancestral gene content, including a shift towards a heterotrophic and potential scavenging lifestyle. Furthermore, hot spring Korarchaeota acquired various genes participating in resistance to viruses, suggesting they may need to manage frequent viral threats.
A complex and dynamic redox network regulating oxygen reduction at photosystem I
Authors: Hani Umama , Naranjo Belen , Shimakawa Ginga , Espinasse Christophe , Vanacker Hélène , Sétif Pierre , Rintamäki Eevi , Issakidis-Bourguet Emmanuelle , Krieger-Liszkay Anja 
Published: September 2023

AbstractThiol-dependent redox regulations of enzyme activities play a central role in regulating photosynthesis. Beside the regulation of metabolic pathways, alternative electron transport has been shown to be subjected to thiol-dependent regulation. We investigated the regulation of O2reduction at photosystem I. The level of O2reduction in leaves and isolated thylakoid membranes depends on the photoperiod in which plants are grown. We used a set of Arabidopsis mutant plants affected in the stromal, membrane and lumenal thiol network to study the redox protein partners involved in regulating O2reduction. Light-dependent O2reduction was determined in leaves and in thylakoids of plants grown in short day and long day conditions using a spin-trapping EPR assay. In wild type samples from short day, ROS generation was twice the amount of that in samples from long day, while this difference was abolished in several redoxin mutants. An in vitro reconstitution assays showed that thioredoxin m, NADPH-dependent reductase C (NTRC) and NADPH are required for high O2reduction levels in long day thylakoids. Using isolated photosystem I, we also show that reduction of a PSI protein is responsible for the increase in O2reduction. Furthermore, differences in the membrane localization of thioredoxins m and 2-Cys peroxiredoxin were demonstrated between thylakoids of short day and long day plants. Finally, we propose a model of redox regulation of O2reduction according to the reduction power of the stroma and the capabilities of the different thiol-containing proteins to form a network of redox interactions.