bluuebunny/crossref_metadata_2025_split huggingface dataset:
Binary dopant segregation enables hematite-based heterostructures for highly efficient solar H2O2 synthesis
Authors: Zhang Zhujun , Tsuchimochi Takashi , Ina Toshiaki , Kumabe Yoshitaka , Muto Shunsuke , Ohara Koji , Yamada Hiroki , Ten-no Seiichiro L. , Tachikawa Takashi 
Published: March 2022

AbstractDopant segregation, frequently observed in ionic oxides, is useful for engineering materials and devices. However, due to the poor driving force for ion migration and/or the presence of substantial grain boundaries, dopants are mostly confined within a nanoscale region. Herein, we demonstrate that core–shell heterostructures are formed by oriented self-segregation using one-step thermal annealing of metal-doped hematite mesocrystals at relatively low temperatures in air. The sintering of highly ordered interfaces between the nanocrystal subunits inside the mesocrystal eliminates grain boundaries, leaving numerous oxygen vacancies in the bulk. This results in the efficient segregation of dopants (~90%) on the external surface, which forms their oxide overlayers. The optimized photoanode based on hematite mesocrystals with oxide overlayers containing Sn and Ti dopants realises high activity (~0.8 μmol min−1 cm−2) and selectivity (~90%) for photoelectrochemical H2O2 production, which provides a wide range of application for the proposed concept.
The Chengjiang Biota inhabited a deltaic environment
Authors: Saleh Farid , Qi Changshi , Buatois Luis A. , Mángano M. Gabriela , Paz Maximiliano , Vaucher Romain , Zheng Quanfeng , Hou Xian-Guang , Gabbott Sarah E. , Ma Xiaoya 
Published: March 2022

AbstractThe Chengjiang Biota is the earliest Phanerozoic soft-bodied fossil assemblage offering the most complete snapshot of Earth’s initial diversification, the Cambrian Explosion. Although palaeobiologic aspects of this biota are well understood, the precise sedimentary environment inhabited by this biota remains debated. Herein, we examine a non-weathered core from the Yu’anshan Formation including the interval preserving the Chengjiang Biota. Our data indicate that the succession was deposited as part of a delta influenced by storm floods (i.e., produced by upstream river floods resulting from ocean storms). Most Chengjiang animals lived in an oxygen and nutrient-rich delta front environment in which unstable salinity and high sedimentation rates were the main stressors. This unexpected finding allows for sophisticated ecological comparisons with other Burgess Shale-type deposits and emphasizes that the long-held view of Burgess Shale-type faunas as snapshots of stable distal shelf and slope communities needs to be revised based on recent sedimentologic advances.
PCBP2 maintains antiviral signaling homeostasis by regulating cGAS enzymatic activity via antagonizing its condensation
Authors: Gu Haiyan , Yang Jing , Zhang Jiayu , Song Ying , Zhang Yao , Xu Pengfei , Zhu Yuanxiang , Wang Liangliang , Zhang Pengfei , Li Lin , Chen Dahua , Sun Qinmiao 
Published: March 2022

AbstractCyclic GMP-AMP synthase (cGAS) plays a major role in detecting pathogenic DNA. It produces cyclic dinucleotide cGAMP, which subsequently binds to the adaptor protein STING and further triggers antiviral innate immune responses. However, the molecular mechanisms regulating cGAS enzyme activity remain largely unknown. Here, we characterize the cGAS-interacting protein Poly(rC)-binding protein 2 (PCBP2), which plays an important role in controlling cGAS enzyme activity, thereby mediating appropriate cGAS-STING signaling transduction. We find that PCBP2 overexpression reduces cGAS-STING antiviral signaling, whereas loss of PCBP2 significantly increases cGAS activity. Mechanistically, we show that PCBP2 negatively regulates anti-DNA viral signaling by specifically interacting with cGAS but not other components. Moreover, PCBP2 decreases cGAS enzyme activity by antagonizing cGAS condensation, thus ensuring the appropriate production of cGAMP and balancing cGAS-STING signal transduction. Collectively, our findings provide insight into how the cGAS-mediated antiviral signaling is regulated.
Assessment of global health risk of antibiotic resistance genes
Authors: Zhang Zhenyan , Zhang Qi , Wang Tingzhang , Xu Nuohan , Lu Tao , Hong Wenjie , Penuelas Josep , Gillings Michael , Wang Meixia , Gao Wenwen , Qian Haifeng 
Published: March 2022

AbstractAntibiotic resistance genes (ARGs) have accelerated microbial threats to human health in the last decade. Many genes can confer resistance, but evaluating the relative health risks of ARGs is complex. Factors such as the abundance, propensity for lateral transmission and ability of ARGs to be expressed in pathogens are all important. Here, an analysis at the metagenomic level from various habitats (6 types of habitats, 4572 samples) detects 2561 ARGs that collectively conferred resistance to 24 classes of antibiotics. We quantitatively evaluate the health risk to humans, defined as the risk that ARGs will confound the clinical treatment for pathogens, of these 2561 ARGs by integrating human accessibility, mobility, pathogenicity and clinical availability. Our results demonstrate that 23.78% of the ARGs pose a health risk, especially those which confer multidrug resistance. We also calculate the antibiotic resistance risks of all samples in four main habitats, and with machine learning, successfully map the antibiotic resistance threats in global marine habitats with over 75% accuracy. Our novel method for quantitatively surveilling the health risk of ARGs will help to manage one of the most important threats to human and animal health.
Comparative effectiveness and safety of homologous two-dose ChAdOx1 versus heterologous vaccination with ChAdOx1 and BNT162b2
Authors: Hermosilla Eduardo , Coma Ermengol , Xie Junqing , Feng Shuo , Cabezas Carmen , Méndez-Boo Leonardo , Fina Francesc , Ballo Elisabet , Martínez Montserrat , Medina-Peralta Manuel , Argimon Josep Maria , Prieto-Alhambra Daniel 
Published: March 2022

AbstractSmall trials have suggested that heterologous vaccination with first-dose ChAdOx1 and second-dose BNT162b2 may generate a better immune response than homologous vaccination with two doses of ChAdOx1. In this cohort analysis, we use linked data from Catalonia (Spain), where those aged <60 who received a first dose of ChAdOx1 could choose between ChAdOx1 and BNT162b2 for their second dose. Comparable cohorts were obtained after exact-matching 14,325/17,849 (80.3%) people receiving heterologous vaccination to 14,325/149,386 (9.6%) receiving homologous vaccination by age, sex, region, and date of second dose. Of these, 464 (3.2%) in the heterologous and 694 (4.8%) in the homologous groups developed COVID-19 between 1st June 2021 and 5th December 2021. The resulting hazard ratio (95% confidence interval) is 0.66 [0.59–0.74], favouring heterologous vaccination. The two groups had similar testing rates and safety outcomes. Sensitivity and negative control outcome analyses confirm these findings. In conclusion, we demonstrate that a heterologous vaccination schedule with ChAdOx1 followed by BNT162b2 was more efficacious than and similarly safe to homologous vaccination with two doses of ChAdOx1. Most of the infections in our study occurred when Delta was the predominant SARS-CoV-2 variant in Spain. These data agree with previous phase 2 randomised trials.
UACA locus is associated with breast cancer chemoresistance and survival
Authors: Zhu Qianqian , Schultz Emily , Long Jirong , Roh Janise M. , Valice Emily , Laurent Cecile A. , Radimer Kelly H. , Yan Li , Ergas Isaac J. , Davis Warren , Ranatunga Dilrini , Gandhi Shipra , Kwan Marilyn L. , Bao Ping-Ping , Zheng Wei , Shu Xiao-Ou , Ambrosone Christine , Yao Song , Kushi Lawrence H. 
Published: March 2022

AbstractFew germline genetic variants have been robustly linked with breast cancer outcomes. We conducted trans-ethnic meta genome-wide association study (GWAS) of overall survival (OS) in 3973 breast cancer patients from the Pathways Study, one of the largest prospective breast cancer survivor cohorts. A locus spanning the UACA gene, a key regulator of tumor suppressor Par-4, was associated with OS in patients taking Par-4 dependent chemotherapies, including anthracyclines and anti-HER2 therapy, at a genome-wide significance level ($$P = 1.27 \times 10^{ - 9}$$

P
=
1.27
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1

0

−
9

). This association was confirmed in meta-analysis across four independent prospective breast cancer cohorts (combined hazard ratio = 1.84, $$P = 1.28 \times 10^{ - 11}$$

P
=
1.28
×
1

0

−
11

). Transcriptome-wide association study revealed higher UACA gene expression was significantly associated with worse OS ($$P = 4.68 \times 10^{ - 7}$$

P
=
4.68
×
1

0

−
7

). Our study identified the UACA locus as a genetic predictor of patient outcome following treatment with anthracyclines and/or anti-HER2 therapy, which may have clinical utility in formulating appropriate treatment strategies for breast cancer patients based on their genetic makeup.
Quantum coherence bounds the distributed discords
Authors: Jin Zhi-Xiang , Li-Jost Xianqing , Fei Shao-Ming , Qiao Cong-Feng 
Published: March 2022

AbstractEstablishing quantum correlations between two remote parties by sending an information carrier is an essential step of many protocols in quantum information processing. We obtain trade-off relations between discords and coherence within a bipartite system. Then we study the distribution of coherence in a bipartite quantum state by using the relations of relative entropy and mutual information. We show that the increase of the relative entropy of discord between two remote parties is bounded by the nonclassical correlations quantified by the relative entropy of coherence between the carrier and two remote parties, providing an optimal protocol for discord distribution and showing that quantum correlations are the essential resource for such tasks.
Inhibition of calcium-triggered secretion by hydrocarbon-stapled peptides
Authors: Lai Ying , Fois Giorgio , Flores Jose R. , Tuvim Michael J. , Zhou Qiangjun , Yang Kailu , Leitz Jeremy , Peters John , Zhang Yunxiang , Pfuetzner Richard A. , Esquivies Luis , Jones Philip , Frick Manfred , Dickey Burton F. , Brunger Axel T. 
Published: March 2022

AbstractMembrane fusion triggered by Ca2+ is orchestrated by a conserved set of proteins to mediate synaptic neurotransmitter release, mucin secretion and other regulated exocytic processes1–4. For neurotransmitter release, the Ca2+ sensitivity is introduced by interactions between the Ca2+ sensor synaptotagmin and the SNARE complex5, and sequence conservation and functional studies suggest that this mechanism is also conserved for mucin secretion6. Disruption of Ca2+-triggered membrane fusion by a pharmacological agent would have therapeutic value for mucus hypersecretion as it is the major cause of airway obstruction in the pathophysiology of respiratory viral infection, asthma, chronic obstructive pulmonary disease and cystic fibrosis7–11. Here we designed a hydrocarbon-stapled peptide that specifically disrupts Ca2+-triggered membrane fusion by interfering with the so-called primary interface between the neuronal SNARE complex and the Ca2+-binding C2B domain of synaptotagmin-1. In reconstituted systems with these neuronal synaptic proteins or with their airway homologues syntaxin-3, SNAP-23, VAMP8, synaptotagmin-2, along with Munc13-2 and Munc18-2, the stapled peptide strongly suppressed Ca2+-triggered fusion at physiological Ca2+ concentrations. Conjugation of cell-penetrating peptides to the stapled peptide resulted in efficient delivery into cultured human airway epithelial cells and mouse airway epithelium, where it markedly and specifically reduced stimulated mucin secretion in both systems, and substantially attenuated mucus occlusion of mouse airways. Taken together, peptides that disrupt Ca2+-triggered membrane fusion may enable the therapeutic modulation of mucin secretory pathways.
Autonomic aging – A dataset to quantify changes of cardiovascular autonomic function during healthy aging
Authors: Schumann Andy , Bär Karl-Jürgen 
Published: March 2022

AbstractAutonomic regulation of blood pressure and cardiac rhythm progressively declines with increasing age. Impaired cardiovascular control promotes a variety of age-related cardio-vascular conditions. This study aims to provide a database of high-resolution biological signals to describe the effect of healthy aging on cardiovascular regulation. Electrocardiogram and continuous non-invasive blood pressure signals were recorded simultaneously at rest in 1,121 healthy volunteers. With this database, we provide raw signals as well as basic demographic information such as gender and body mass index. To demonstrate validity of the acquired data, we present the well-known decline of heart rate variability with increasing age in this database.
Multi-scanner and multi-modal lumbar vertebral body and intervertebral disc segmentation database
Authors: Khalil Yasmina Al , Becherucci Edoardo A. , Kirschke Jan S. , Karampinos Dimitrios C. , Breeuwer Marcel , Baum Thomas , Sollmann Nico 
Published: March 2022

AbstractMagnetic resonance imaging (MRI) is widely utilized for diagnosing and monitoring of spinal disorders. For a number of applications, particularly those related to quantitative MRI, an essential step towards achieving reliable and objective measurements is the segmentation of the examined structures. Performed manually, such process is time-consuming and prone to errors, posing a bottleneck to its clinical applicability. A more efficient analysis would be achieved by automating a segmentation process. However, routine spine MRI acquisitions pose several challenges for achieving robust and accurate segmentations, due to varying MRI acquisition characteristics occurring in data acquired from different sites. Moreover, heterogeneous annotated datasets, collected from multiple scanners with different pulse sequence protocols, are limited. Thus, we present a manually segmented lumbar spine MRI database containing a wide range of data obtained from multiple scanners and pulse sequences, with segmentations of lumbar vertebral bodies and intervertebral discs. The database is intended for the use in developing and testing of automated lumbar spine segmentation algorithms in multi-domain scenarios.
R code and downstream analysis objects for the scRNA-seq atlas of normal and tumorigenic human breast tissue
Authors: Chen Yunshun , Pal Bhupinder , Lindeman Geoffrey J. , Visvader Jane E. , Smyth Gordon K. 
Published: March 2022

AbstractBreast cancer is a common and highly heterogeneous disease. Understanding cellular diversity in the mammary gland and its surrounding micro-environment across different states can provide insight into cancer development in the human breast. Recently, we published a large-scale single-cell RNA expression atlas of the human breast spanning normal, preneoplastic and tumorigenic states. Single-cell expression profiles of nearly 430,000 cells were obtained from 69 distinct surgical tissue specimens from 55 patients. This article extends the study by providing quality filtering thresholds, downstream processed R data objects, complete cell annotation and R code to reproduce all the analyses. Data quality assessment measures are presented and details are provided for all the bioinformatic analyses that produced results described in the study.
Genome-wide identification, phylogenetic and expression pattern analysis of MADS-box family genes in foxtail millet (Setaria italica)
Authors: Lai Dili , Yan Jun , He Ailing , Xue Guoxing , Yang Hao , Feng Liang , Wei Xiaobao , Li Long , Xiang Dabing , Ruan Jingjun , Fan Yu , Cheng Jianping 
Published: March 2022

AbstractFoxtail millet (Setaria italica) is rich in nutrients and extremely beneficial to human health. We identified and comprehensively analyzed 89 MADS-box genes in the foxtail millet genome. According to the classification of MADS-box genes in Arabidopsis thaliana and rice, the SiMADS-box genes were divided into M-type (37) and MIKC-type (52). During evolution, the differentiation of MIKC-type MADS-box genes occurred before that of monocotyledons and dicotyledons. The SiMADS-box gene structure has undergone much differentiation, and the number of introns in the MIKC-type subfamily is much greater than that in the M-type subfamily. Analysis of gene duplication events revealed that MIKC-type MADS-box gene segmental duplication accounted for the vast majority of gene duplication events, and MIKC-type MADS-box genes played a major role in the amplification of SiMADS-box genes. Collinearity analysis showed highest collinearity between foxtail millet and maize MADS-box genes. Analysis of tissue-specific expression showed that SiMADS-box genes are highly expressed throughout the grain-filling process. Expression analysis of SiMADS-box genes under eight different abiotic stresses revealed many stress-tolerant genes, with induced expression of SiMADS33 and SiMADS78 under various stresses warranting further attention. Further, some SiMADS-box proteins may interact under external stress. This study provides insights for MADS-box gene mining and molecular breeding of foxtail millet in the future.
New age constraints on the Lower Jurassic Pliensbachian–Toarcian Boundary at Chacay Melehue (Neuquén Basin, Argentina)
Authors: Al-Suwaidi Aisha H. , Ruhl Micha , Jenkyns Hugh C. , Damborenea Susana E. , Manceñido Miguel O. , Condon Daniel J. , Angelozzi Gladys N. , Kamo Sandra L. , Storm Marisa , Riccardi Alberto C. , Hesselbo Stephen P. 
Published: March 2022

AbstractThe Pliensbachian–Toarcian boundary interval is characterized by a ~ 3‰ negative carbon-isotope excursion (CIE) in organic and inorganic marine and terrestrial archives from sections in Europe, such as Peniche (Portugal) and Hawsker Bottoms, Yorkshire (UK). A new high-resolution organic-carbon isotope record, illustrating the same chemostratigraphic feature, is presented from the Southern Hemisphere Arroyo Chacay Melehue section, Chos Malal, Argentina, corroborating the global significance of this disturbance to the carbon cycle. The negative carbon-isotope excursion, mercury and organic-matter enrichment are accompanied by high-resolution ammonite and nannofossil biostratigraphy together with U–Pb CA-ID-TIMS geochronology derived from intercalated volcanic ash beds. A new age of ~ 183.73 + 0.35/− 0.50 Ma for the Pliensbachian–Toarcian boundary, and 182.77 + 0.11/− 0.15 for the tenuicostatum–serpentinum zonal boundary, is assigned based on high-precision U–Pb zircon geochronology and a Bayesian Markov chain Monte Carlo (MCMC) stratigraphic age model.
First evidence of ranunculids in Early Cretaceous tropics
Authors: Gobo William Vieira , Kunzmann Lutz , Iannuzzi Roberto , Bachelier Julien B. , Coiffard Clément 
Published: March 2022

AbstractEarly Cretaceous floras containing angiosperms were described from several geographic areas, nearly from the Arctic to the Antarctic, and are crucial to understand their evolution and radiation. However, most of these records come from northern mid-latitudes whereas those of lower paleolatitude areas, such as the Crato Fossil Lagerstätte in NE Brazil, are less studied. Here, we describe from this region of northern Gondwanan origin, two fossil-species of eudicots belonging to a new extinct genus Santaniella gen. nov. Together with several vegetative axes and leaves, anatomically well-preserved fruits with seeds and persistent perianth-like organs allowed us to reconstruct its potential affinities with ranunculids, and presumably Ranunculaceae. Previous records putatively assigned to Ranunculales are all from mid-latitudes, and their first unequivocal occurrence in a low-latitude area supports further the hypothesis of a widespread radiation of the earliest diverging eudicot lineage by this early age.
Automated quality assessment of large digitised histology cohorts by artificial intelligence
Authors: Haghighat Maryam , Browning Lisa , Sirinukunwattana Korsuk , Malacrino Stefano , Khalid Alham Nasullah , Colling Richard , Cui Ying , Rakha Emad , Hamdy Freddie C. , Verrill Clare , Rittscher Jens 
Published: March 2022

AbstractResearch using whole slide images (WSIs) of histopathology slides has increased exponentially over recent years. Glass slides from retrospective cohorts, some with patient follow-up data are digitised for the development and validation of artificial intelligence (AI) tools. Such resources, therefore, become very important, with the need to ensure that their quality is of the standard necessary for downstream AI development. However, manual quality control of large cohorts of WSIs by visual assessment is unfeasible, and whilst quality control AI algorithms exist, these focus on bespoke aspects of image quality, e.g. focus, or use traditional machine-learning methods, which are unable to classify the range of potential image artefacts that should be considered. In this study, we have trained and validated a multi-task deep neural network to automate the process of quality control of a large retrospective cohort of prostate cases from which glass slides have been scanned several years after production, to determine both the usability of the images at the diagnostic level (considered in this study to be the minimal standard for research) and the common image artefacts present. Using a two-layer approach, quality overlays of WSIs were generated from a quality assessment (QA) undertaken at patch-level at $$5\times$$

5
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magnification. From these quality overlays the slide-level quality scores were predicted and then compared to those generated by three specialist urological pathologists, with a Pearson correlation of 0.89 for overall ‘usability’ (at a diagnostic level), and 0.87 and 0.82 for focus and H&E staining quality scores respectively. To demonstrate its wider potential utility, we subsequently applied our QA pipeline to the TCGA prostate cancer cohort and to a colorectal cancer cohort, for comparison. Our model, designated as PathProfiler, indicates comparable predicted usability of images from the cohorts assessed (86–90% of WSIs predicted to be usable), and perhaps more significantly is able to predict WSIs that could benefit from an intervention such as re-scanning or re-staining for quality improvement. We have shown in this study that AI can be used to automate the process of quality control of large retrospective WSI cohorts to maximise their utility for research.