bluuebunny/crossref_metadata_2025_split huggingface dataset:
GWAS, MWAS and mGWAS provide insights into precision agriculture based on genotype-dependent microbial effects in foxtail millet
Authors: Wang Yayu , Wang Xiaolin , Sun Shuai , Jin Canzhi , Su Jianmu , Wei Jinpu , Luo Xinyue , Wen Jiawen , Wei Tong , Sahu Sunil Kumar , Zou Hongfeng , Chen Hongyun , Mu Zhixin , Zhang Gengyun , Liu Xin , Xu Xun , Gram Lone , Yang Huanming , Wang Ertao , Liu Huan 
Published: October 2022

AbstractGenetic and environmental factors collectively determine plant growth and yield. In the past 20 years, genome-wide association studies (GWAS) have been conducted on crops to decipher genetic loci that contribute to growth and yield, however, plant genotype appears to be insufficient to explain the trait variations. Here, we unravel the associations between genotypic, phenotypic, and rhizoplane microbiota variables of 827 foxtail millet cultivars by an integrated GWAS, microbiome-wide association studies (MWAS) and microbiome genome-wide association studies (mGWAS) method. We identify 257 rhizoplane microbial biomarkers associated with six key agronomic traits and validated the microbial-mediated growth effects on foxtail millet using marker strains isolated from the field. The rhizoplane microbiota composition is mainly driven by variations in plant genes related to immunity, metabolites, hormone signaling and nutrient uptake. Among these, the host immune gene FLS2 and transcription factor bHLH35 are widely associated with the microbial taxa of the rhizoplane. We further uncover a plant genotype-microbiota interaction network that contributes to phenotype plasticity. The microbial-mediated growth effects on foxtail millet are dependent on the host genotype, suggesting that precision microbiome management could be used to engineer high-yielding cultivars in agriculture systems.
High-resolution genome topology of human retina uncovers super enhancer-promoter interactions at tissue-specific and multifactorial disease loci
Authors: Marchal Claire , Singh Nivedita , Batz Zachary , Advani Jayshree , Jaeger Catherine , Corso-Díaz Ximena , Swaroop Anand 
Published: October 2022

AbstractChromatin organization and enhancer-promoter contacts establish unique spatiotemporal gene expression patterns in distinct cell types. Non-coding genetic variants can influence cellular phenotypes by modifying higher-order transcriptional hubs and consequently gene expression. To elucidate genomic regulation in human retina, we mapped chromatin contacts at high resolution and integrated with super-enhancers (SEs), histone marks, binding of CTCF and select transcription factors. We show that topologically associated domains (TADs) with central SEs exhibit stronger insulation and augmented contact with retinal genes relative to TADs with edge SEs. Merging genome-wide expression quantitative trait loci (eQTLs) with topology map reveals physical links between 100 eQTLs and corresponding eGenes associated with retinal neurodegeneration. Additionally, we uncover candidate genes for susceptibility variants linked to age-related macular degeneration and glaucoma. Our study of high-resolution genomic architecture of human retina provides insights into genetic control of tissue-specific functions, suggests paradigms for missing heritability, and enables the dissection of common blinding disease phenotypes.
Observation of boundary induced chiral anomaly bulk states and their transport properties
Authors: Wang Mudi , Ma Qiyun , Liu Shan , Zhang Ruo-Yang , Zhang Lei , Ke Manzhu , Liu Zhengyou , Chan C. T. 
Published: October 2022

AbstractThe most useful property of topological materials is perhaps the robust transport of topological edge modes, whose existence depends on bulk topological invariants. This means that we need to make volumetric changes to many atoms in the bulk to control the transport properties of the edges in a sample. We suggest here that we can do the reverse in some cases: the properties of the edge can be used to induce chiral transport phenomena in some bulk modes. Specifically, we show that a topologically trivial 2D hexagonal phononic crystal slab (waveguide) bounded by hard-wall boundaries guarantees the existence of bulk modes with chiral anomaly inside a pseudogap due to finite size effect. We experimentally observed robust valley-selected transport, complete valley state conversion, and valley focusing of the chiral anomaly bulk states (CABSs) in such phononic crystal waveguides. The same concept also applies to electromagnetics.
Covalent bond shortening and distortion induced by pressurization of thorium, uranium, and neptunium tetrakis aryloxides
Authors: Shephard Jacob J. , Berryman Victoria E. J. , Ochiai Tatsumi , Walter Olaf , Price Amy N. , Warren Mark R. , Arnold Polly L. , Kaltsoyannis Nikolas , Parsons Simon 
Published: October 2022

AbstractCovalency involving the 5f orbitals is regularly invoked to explain the reactivity, structure and spectroscopic properties of the actinides, but the ionic versus covalent nature of metal-ligand bonding in actinide complexes remains controversial. The tetrakis 2,6-di-tert-butylphenoxide complexes of Th, U and Np form an isostructural series of crystal structures containing approximately tetrahedral MO4 cores. We show that up to 3 GPa the Th and U crystal structures show negative linear compressibility as the OMO angles distort. At 3 GPa the angles snap back to their original values, reverting to a tetrahedral geometry with an abrupt shortening of the M-O distances by up to 0.1 Å. The Np complex shows similar but smaller effects, transforming above 2.4 GPa. Electronic structure calculations associate the M-O bond shortening with a change in covalency resulting from increased contributions to the M-O bonding by the metal 6d and 5f orbitals, the combination promoting MO4 flexibility at little cost in energy.
Migration of solidification grain boundaries and prediction
Authors: Liu Hongmei , Lu Shenglu , Zhang Yingbo , Chen Hui , Chen Yungui , Qian Ma 
Published: October 2022

AbstractSolidification processing is essential to the manufacture of various metal products, including additive manufacturing. Solidification grain boundaries (SGBs) result from the solidification of the last liquid film between two abutting grains of different orientations. They can migrate, but unlike normal GB migration, SGB migration (SGBM) decouples SGBs from solidification microsegregation, further affecting material properties. Here, we first show the salient features of SGBM in magnesium-tin alloys solidified with cooling rates of 8−1690 °C/s. A theoretical model is then developed for SGBM in dilute binary alloys, focusing on the effect of solute type and content, and applied to 10 alloy systems with remarkable agreement. SGMB does not depend on cooling rate or time but relates to grain size. It tends to occur athermally. The findings of this study extend perspectives on solidification grain structure formation and control for improved performance (e.g. hot or liquation cracking during reheating, intergranular corrosion or fracture).
Nanoparticulate cell-free DNA scavenger for treating inflammatory bone loss in periodontitis
Authors: Huang Hanyao , Pan Weiyi , Wang Yifan , Kim Hye Sung , Shao Dan , Huang Baoding , Ho Tzu-Chieh , Lao Yeh-Hsing , Quek Chai Hoon , Shi Jiayu , Chen Qianming , Shi Bing , Zhang Shengmin , Zhao Lei , Leong Kam W. 
Published: October 2022

AbstractPeriodontitis is a common type of inflammatory bone loss and a risk factor for systemic diseases. The pathogenesis of periodontitis involves inflammatory dysregulation, which represents a target for new therapeutic strategies to treat periodontitis. After establishing the correlation of cell-free DNA (cfDNA) level with periodontitis in patient samples, we test the hypothesis that the cfDNA-scavenging approach will benefit periodontitis treatment. We create a nanoparticulate cfDNA scavenger specific for periodontitis by coating selenium-doped hydroxyapatite nanoparticles (SeHANs) with cationic polyamidoamine dendrimers (PAMAM-G3), namely G3@SeHANs, and compare the activities of G3@SeHANs with those of soluble PAMAM-G3 polymer. Both G3@SeHANs and PAMAM-G3 inhibit periodontitis-related proinflammation in vitro by scavenging cfDNA and alleviate inflammatory bone loss in a mouse model of ligature-induced periodontitis. G3@SeHANs also regulate the mononuclear phagocyte system in a periodontitis environment, promoting the M2 over the M1 macrophage phenotype. G3@SeHANs show greater therapeutic effects than PAMAM-G3 in reducing proinflammation and alveolar bone loss in vivo. Our findings demonstrate the importance of cfDNA in periodontitis and the potential for using hydroxyapatite-based nanoparticulate cfDNA scavengers to ameliorate periodontitis.
Deficiency of the frontotemporal dementia gene GRN results in gangliosidosis
Authors: Boland Sebastian , Swarup Sharan , Ambaw Yohannes A. , Malia Pedro C. , Richards Ruth C. , Fischer Alexander W. , Singh Shubham , Aggarwal Geetika , Spina Salvatore , Nana Alissa L. , Grinberg Lea T. , Seeley William W. , Surma Michal A. , Klose Christian , Paulo Joao A. , Nguyen Andrew D. , Harper J. Wade , Walther Tobias C. , Farese Robert V. 
Published: October 2022

AbstractHaploinsufficiency of GRN causes frontotemporal dementia (FTD). The GRN locus produces progranulin (PGRN), which is cleaved to lysosomal granulin polypeptides. The function of lysosomal granulins and why their absence causes neurodegeneration are unclear. Here we discover that PGRN-deficient human cells and murine brains, as well as human frontal lobes from GRN-mutation FTD patients have increased levels of gangliosides, glycosphingolipids that contain sialic acid. In these cells and tissues, levels of lysosomal enzymes that catabolize gangliosides were normal, but levels of bis(monoacylglycero)phosphates (BMP), lipids required for ganglioside catabolism, were reduced with PGRN deficiency. Our findings indicate that granulins are required to maintain BMP levels to support ganglioside catabolism, and that PGRN deficiency in lysosomes leads to gangliosidosis. Lysosomal ganglioside accumulation may contribute to neuroinflammation and neurodegeneration susceptibility observed in FTD due to PGRN deficiency and other neurodegenerative diseases.
Search and processing of Holliday junctions within long DNA by junction-resolving enzymes
Authors: Kaczmarczyk Artur P. , Déclais Anne-Cécile , Newton Matthew D. , Boulton Simon J. , Lilley David M. J. , Rueda David S. 
Published: October 2022

AbstractResolution of Holliday junctions is a critical intermediate step of homologous recombination in which junctions are processed by junction-resolving endonucleases. Although binding and cleavage are well understood, the question remains how the enzymes locate their substrate within long duplex DNA. Here we track fluorescent dimers of endonuclease I on DNA, presenting the complete single-molecule reaction trajectory for a junction-resolving enzyme finding and cleaving a Holliday junction. We show that the enzyme binds remotely to dsDNA and then undergoes 1D diffusion. Upon encountering a four-way junction, a catalytically-impaired mutant remains bound at that point. An active enzyme, however, cleaves the junction after a few seconds. Quantitative analysis provides a comprehensive description of the facilitated diffusion mechanism. We show that the eukaryotic junction-resolving enzyme GEN1 also undergoes facilitated diffusion on dsDNA until it becomes located at a junction, so that the general resolution trajectory is probably applicable to many junction resolving enzymes.
Integrated analysis of cervical squamous cell carcinoma cohorts from three continents reveals conserved subtypes of prognostic significance
Authors: Chakravarthy Ankur , Reddin Ian , Henderson Stephen , Dong Cindy , Kirkwood Nerissa , Jeyakumar Maxmilan , Rodriguez Daniela Rothschild , Martinez Natalia Gonzalez , McDermott Jacqueline , Su Xiaoping , Egawa Nagayasau , Fjeldbo Christina S. , Skingen Vilde Eide , Lyng Heidi , Halle Mari Kyllesø , Krakstad Camilla , Soleiman Afschin , Sprung Susanne , Lechner Matt , Ellis Peter J. I. , Wass Mark , Michaelis Martin , Fiegl Heidi , Salvesen Helga , Thomas Gareth J. , Doorbar John , Chester Kerry , Feber Andrew , Fenton Tim R. 
Published: October 2022

AbstractHuman papillomavirus (HPV)-associated cervical cancer is a leading cause of cancer deaths in women. Here we present an integrated multi-omic analysis of 643 cervical squamous cell carcinomas (CSCC, the most common histological variant of cervical cancer), representing patient populations from the USA, Europe and Sub-Saharan Africa and identify two CSCC subtypes (C1 and C2) with differing prognosis. C1 and C2 tumours can be driven by either of the two most common HPV types in cervical cancer (16 and 18) and while HPV16 and HPV18 are overrepresented among C1 and C2 tumours respectively, the prognostic difference between groups is not due to HPV type. C2 tumours, which comprise approximately 20% of CSCCs across these cohorts, display distinct genomic alterations, including loss or mutation of theSTK11tumour suppressor gene, increased expression of several immune checkpoint genes and differences in the tumour immune microenvironment that may explain the shorter survival associated with this group. In conclusion, we identify two therapy-relevant CSCC subtypes that share the same defining characteristics across three geographically diverse cohorts.
Uncertainty modulates visual maps during noninstrumental information demand
Authors: Li Yvonne , Daddaoua Nabil , Horan Mattias , Foley Nicholas C. , Gottlieb Jacqueline 
Published: October 2022

AbstractAnimals are intrinsically motivated to obtain information independently of instrumental incentives. This motivation depends on two factors: a desire to resolve uncertainty by gathering accurate information and a desire to obtain positively-valenced observations, which predict favorable rather than unfavorable outcomes. To understand the neural mechanisms, we recorded parietal cortical activity implicated in prioritizing stimuli for spatial attention and gaze, in a task in which monkeys were free (but not trained) to obtain information about probabilistic non-contingent rewards. We show that valence and uncertainty independently modulated parietal neuronal activity, and uncertainty but not reward-related enhancement consistently correlated with behavioral sensitivity. The findings suggest uncertainty-driven and valence-driven information demand depend on partially distinct pathways, with the former being consistently related to parietal responses and the latter depending on additional mechanisms implemented in downstream structures.
Prevalence and mechanisms of somatic deletions in single human neurons during normal aging and in DNA repair disorders
Authors: Kim Junho , Huang August Yue , Johnson Shelby L. , Lai Jenny , Isacco Laura , Jeffries Ailsa M. , Miller Michael B. , Lodato Michael A. , Walsh Christopher A. , Lee Eunjung Alice 
Published: October 2022

AbstractReplication errors and various genotoxins cause DNA double-strand breaks (DSBs) where error-prone repair creates genomic mutations, most frequently focal deletions, and defective repair may lead to neurodegeneration. Despite its pathophysiological importance, the extent to which faulty DSB repair alters the genome, and the mechanisms by which mutations arise, have not been systematically examined reflecting ineffective methods. Here, we develop PhaseDel, a computational method to detect focal deletions and characterize underlying mechanisms in single-cell whole genome sequences (scWGS). We analyzed high-coverage scWGS of 107 single neurons from 18 neurotypical individuals of various ages, and found that somatic deletions increased with age and in highly expressed genes in human brain. Our analysis of 50 single neurons from DNA repair-deficient diseases with progressive neurodegeneration (Cockayne syndrome, Xeroderma pigmentosum, and Ataxia telangiectasia) reveals elevated somatic deletions compared to age-matched controls. Distinctive mechanistic signatures and transcriptional associations suggest roles for somatic deletions in neurodegeneration.
Common anti-cancer therapies induce somatic mutations in stem cells of healthy tissue
Authors: Kuijk Ewart , Kranenburg Onno , Cuppen Edwin , Van Hoeck Arne 
Published: October 2022

AbstractGenome-wide mutation analyses have revealed that specific anti-cancer drugs are highly mutagenic to cancer cells, but the mutational impact of anti-cancer therapies on normal cells is not known. Here, we examine genome-wide somatic mutation patterns in 42 healthy adult stem cells (ASCs) of the colon or the liver from 14 cancer patients (mean of 3.2 ASC per donor) that received systemic chemotherapy and/or local radiotherapy. The platinum-based chemo-drug Oxaliplatin induces on average 535 ± 260 mutations in colon ASC, while 5-FU shows a complete mutagenic absence in most, but not all colon ASCs. In contrast with the colon, normal liver ASCs escape mutagenesis from systemic treatment with Oxaliplatin and 5-FU. Thus, while chemotherapies are highly effective at killing cancer cells, their systemic use also increases the mutational burden of long-lived normal stem cells responsible for tissue renewal thereby increasing the risk for developing second cancers.
Marker-free co-selection for successive rounds of prime editing in human cells
Authors: Levesque Sébastien , Mayorga Diana , Fiset Jean-Philippe , Goupil Claudia , Duringer Alexis , Loiselle Andréanne , Bouchard Eva , Agudelo Daniel , Doyon Yannick 
Published: October 2022

AbstractPrime editing enables the introduction of precise point mutations, small insertions, or short deletions without requiring donor DNA templates. However, efficiency remains a key challenge in a broad range of human cell types. In this work, we design a robust co-selection strategy through coediting of the ubiquitous and essential sodium/potassium pump (Na+/K+ ATPase). We readily engineer highly modified pools of cells and clones with homozygous modifications for functional studies with minimal pegRNA optimization. This process reveals that nicking the non-edited strand stimulates multiallelic editing but often generates tandem duplications and large deletions at the target site, an outcome dictated by the relative orientation of the protospacer adjacent motifs. Our approach streamlines the production of cell lines with multiple genetic modifications to create cellular models for biological research and lays the foundation for the development of cell-type specific co-selection strategies.
Using modelled relationships and satellite observations to attribute modelled aerosol biases over biomass burning regions
Authors: Zhong Qirui , Schutgens Nick , van der Werf Guido R. , van Noije Twan , Bauer Susanne E. , Tsigaridis Kostas , Mielonen Tero , Checa-Garcia Ramiro , Neubauer David , Kipling Zak , Kirkevåg Alf , Olivié Dirk J. L. , Kokkola Harri , Matsui Hitoshi , Ginoux Paul , Takemura Toshihiko , Le Sager Philippe , Rémy Samuel , Bian Huisheng , Chin Mian 
Published: October 2022

AbstractBiomass burning (BB) is a major source of aerosols that remain the most uncertain components of the global radiative forcing. Current global models have great difficulty matching observed aerosol optical depth (AOD) over BB regions. A common solution to address modelled AOD biases is scaling BB emissions. Using the relationship from an ensemble of aerosol models and satellite observations, we show that the bias in aerosol modelling results primarily from incorrect lifetimes and underestimated mass extinction coefficients. In turn, these biases seem to be related to incorrect precipitation and underestimated particle sizes. We further show that boosting BB emissions to correct AOD biases over the source region causes an overestimation of AOD in the outflow from Africa by 48%, leading to a double warming effect compared with when biases are simultaneously addressed for both aforementioned factors. Such deviations are particularly concerning in a warming future with increasing emissions from fires.
Random forest incorporating ab-initio calculations for corrosion rate prediction with small sample Al alloys data
Authors: Ji Yucheng , Li Ni , Cheng Zhanming , Fu Xiaoqian , Ao Min , Li Menglin , Sun Xiaoguang , Chowwanonthapunya Thee , Zhang Dawei , Xiao Kui , Ren Jingli , Dey Poulumi , Li Xiaogang , Dong Chaofang 
Published: October 2022

AbstractCorrosion jeopardizes the materials longevity and engineering safety, hence the corrosion rate needs to be forecasted so as to better guide materials selection. Although field exposure experiments are dependable, the prohibitive cost and their time-consuming nature make it difficult to obtain large dataset for machine learning. Here, we propose a strategy Integrating Ab-initio Calculations with Random Forest (IACRF) to optimize the model, thereby estimating the corrosion rate of Al alloys in diverse environments. Based on the thermodynamic assessment of the secondary phases, the ab-initio calculation quantities, especially the work function, significantly improved the prediction accuracy with respect to small-sample Al alloys corrosion dataset. To build a better generic prediction model, the most accessible and effective features are identified to train IACRF. Finally, the independent field exposure experiments in Southeast Asia have proven the generalization ability of IACRF in which the average prediction accuracy is improved up to 91%.
High-mobility two-dimensional carriers from surface Fermi arcs in magnetic Weyl semimetal films
Authors: Kaneta-Takada Shingo , Wakabayashi Yuki K. , Krockenberger Yoshiharu , Nomura Toshihiro , Kohama Yoshimitsu , Nikolaev Sergey A. , Das Hena , Irie Hiroshi , Takiguchi Kosuke , Ohya Shinobu , Tanaka Masaaki , Taniyasu Yoshitaka , Yamamoto Hideki 
Published: October 2022

AbstractHigh-mobility two-dimensional carriers originating from surface Fermi arcs in magnetic Weyl semimetals are highly desired for accessing exotic quantum transport phenomena and for topological electronics applications. Here, we demonstrate high-mobility two-dimensional carriers that show quantum oscillations in magnetic Weyl semimetal SrRuO3 epitaxial films by systematic angle-dependent, high-magnetic field magnetotransport experiments. The exceptionally high-quality SrRuO3 films were grown by state-of-the-art oxide thin film growth technologies driven by machine-learning algorithm. The quantum oscillations for the 10-nm SrRuO3 film show a high quantum mobility of 3.5 × 103 cm2/Vs, a light cyclotron mass, and two-dimensional angular dependence, which possibly come from the surface Fermi arcs. The linear thickness dependence of the phase shift of the quantum oscillations provides evidence for the non-trivial nature of the quantum oscillations mediated by the surface Fermi arcs. In addition, at low temperatures and under magnetic fields of up to 52 T, the quantum limit of SrRuO3 manifests the chiral anomaly of the Weyl nodes. Emergence of the hitherto hidden two-dimensional Weyl states in a ferromagnetic oxide paves the way to explore quantum transport phenomena for topological oxide electronics.