bluuebunny/crossref_metadata_2025 huggingface dataset:
The Zircon Story of the Niger River: Time‐Structure Maps of the West African Craton and Discontinuous Propagation of Provenance Signals Across a Disconnected Sediment‐Routing System
Authors: Pastore Guido , Garzanti Eduardo , Vermeesch Pieter , Bayon Germain , Resentini Alberto , Braquet Nadine , Overare Brume
Published: November 2023

The Niger River drains a large part of the West African Craton, where rocks ranging in age from Paleoarchean to recent offer an unexcelled opportunity to map the diverse time structures of sediment sources and provide essential information for provenance diagnoses. In this study, U‐Pb zircon dating is complemented with bulk‐sand geochemical (Zr, Hf, REE) and Nd‐Hf isotope data to pin‐point parent rocks of zircon grains and draw inferences on sediment generation across sub‐Saharan western Africa. In Upper Niger sand, zircon ages pass from exclusively Archean in Guinea headwaters to dominantly Paleoproterozoic in the Inner Delta in Mali, testifying to the progressive dilution by tributary sediment derived from the Birimian domain. Zircon ages abruptly change to dominantly Neoproterozoic downstream of the Inner Delta, becoming indistinguishable from those in Saharan eolian dunes across the Sahel. Most of the sediment generated in the headwaters is thus dumped in the marshlands and bedload is reconstituted downstream by recycling eolian sand. Zircon grains in the Lower Niger yielded virtually the same U‐Pb ages as in Benue sediment, indicating an overwhelming supply from the Benue tributary. In the Niger Delta, however, Archean zircons reappear, and both εNd and εHf values become notably more negative, indicating extensive reworking of sand deposited along the coastal plain at earlier times of wetter climate, when artificial barriers to the sediment flux did not exist in the upper to middle Niger River catchment.
Inhibition of PDGFRβ alleviates endothelial cell apoptotic injury caused by DRP-1 overexpression and mitochondria fusion failure after mitophagy
Authors: An Xiaohong , Ma Xiao , Liu Heng , Song Jing , Wei Tiange , Zhang Rongzhan , Zhan Xiao , Li Hongyang , Zhou Jia
Published: November 2023

Kawasaki disease (KD), described as “mucocutaneous lymph node syndrome”, affects infants and toddlers. Patients with KD suffer from an inflammatory cascade leading to vasculitis with a predilection for coronary arteries. While the symptoms and pathogenesis of KD have received more and more attention, the precise mechanisms are still debated. Researches show that endothelial dysfunction process in KD leads to arterial damage and affect clinical outcome. In this study, we constructed a Candida albicans water soluble fraction (CAWS)-induced KD murine model and penetrated investigating the mechanisms behind endothelial dysfunction. CAWS-induced mice presented remarkably elevated vascular endothelial cell growth factor (VEGF) levels. Abundant expression of VEGF was documented in all vessels that showed edema from acute KD. It has been reported that Platelet-derived growth factor (PDGF) co-expression normalizes VEGF-induced aberrant angiogenesis. Hyperexpression of PDGFRβ was induced in the thickened medial layer and vascular endothelium of KD mice. Masitinib (Mas) is an oral tyrosine kinase inhibitor of numerous targets, which can selectively target PDGFR signaling. We set out to explore whether Mas could regulate coronary pathology in KD. Mas administration significantly reduced the VEGF-induced endothelial cells migration. NOX4 was activated in vascular endothelial cells to produce more ROS. Mitochondrial dysregulated fission and mitophagy caused by DRP-1 overexpression precipitated the arterial endothelial cells injury. Here, mitophagy seemed to work as the driving force of DRP-1/Bak/BNIP3-dependent endothelial cells apoptosis. In summary, how mitophagy is regulated by DRP-1 under pathologic status is critical and complex, which may contribute to the development of specific therapeutic interventions in cardiovascular diseases patients, for example Masatinib, the inhibitor of PDGFRβ.

Facts and questions

Kawasaki disease causing systemic vasculitis, affects infants and toddlers.

Coronary artery injury remains the major causes of morbidity and mortality.

DRP-1 overexpression induces DRP-1/Bak/BNIP3-dependent endothelial cells apoptosis.

PDGFRβ was high-expressed in the thickened medial layer of CAWS-induced KD mice.

Inhibition of PDGFRβ signaling alleviates arterial endothelial cells injury.
The long non-coding RNA TAZ-AS202 promotes lung cancer progression via regulation of the E2F1 transcription factor and activation of Ephrin signaling
Authors: Gobbi Giulia , Grieco Alessandra , Torricelli Federica , Sauta Elisabetta , Santandrea Giacomo , Zanetti Eleonora , Fantini Valentina , Reggiani Francesca , Strocchi Silvia , Paci Massimiliano , Vohra Manik , Saladi Srinivas Vinod , Ambrosetti Davide Carlo , Ciarrocchi Alessia , Sancisi Valentina
Published: November 2023

Long non-coding RNAs (lncRNAs) are transcripts without coding potential that are pervasively expressed from the genome and have been increasingly reported to play crucial roles in all aspects of cell biology. They have been also heavily implicated in cancer development and progression, with both oncogenic and tumor suppressor functions. In this work, we identified and characterized a novel lncRNA, TAZ-AS202, expressed from the TAZ genomic locus and exerting pro-oncogenic functions in non-small cell lung cancer. TAZ-AS202 expression is under the control of YAP/TAZ-containing transcriptional complexes. We demonstrated that TAZ-AS202 is overexpressed in lung cancer tissue, compared with surrounding lung epithelium. In lung cancer cell lines TAZ-AS202 promotes cell migration and cell invasion. TAZ-AS202 regulates the expression of a set of genes belonging to cancer-associated pathways, including WNT and EPH-Ephrin signaling. The molecular mechanism underlying TAZ-AS202 function does not involve change of TAZ expression or activity, but increases the protein level of the transcription factor E2F1, which in turn regulates the expression of a large set of target genes, including the EPHB2 receptor. Notably, the silencing of both E2F1 and EPHB2 recapitulates TAZ-AS202 silencing cellular phenotype, indicating that they are essential mediators of its activity. Overall, this work unveiled a new regulatory mechanism that, by increasing E2F1 protein, modifies the non-small cell lung cancer cells transcriptional program, leading to enhanced aggressiveness features. The TAZ-AS202/E2F1/EPHB2 axis may be the target for new therapeutic strategies.
In-cell structural insight into the stability of sperm microtubule doublet
Authors: Tai Linhua , Yin Guoliang , Huang Xiaojun , Sun Fei , Zhu Yun
Published: November 2023

The propulsion for mammalian sperm swimming is generated by flagella beating. Microtubule doublets (DMTs) along with microtubule inner proteins (MIPs) are essential structural blocks of flagella. However, the intricate molecular architecture of intact sperm DMT remains elusive. Here, by in situ cryo-electron tomography, we solved the in-cell structure of mouse sperm DMT at 4.5–7.5 Å resolutions, and built its model with 36 kinds of MIPs in 48 nm periodicity. We identified multiple copies of Tektin5 that reinforce Tektin bundle, and multiple MIPs with different periodicities that anchor the Tektin bundle to tubulin wall. This architecture contributes to a superior stability of A-tubule than B-tubule of DMT, which was revealed by structural comparison of DMTs from the intact and deformed axonemes. Our work provides an overall molecular picture of intact sperm DMT in 48 nm periodicity that is essential to understand the molecular mechanism of sperm motility as well as the related ciliopathies.
Qa-SNARE syntaxin 18 mediates lipid droplet fusion with SNAP23 and SEC22B
Authors: Fu Yuhui , Ding Binbin , Liu Xiaoxia , Zhao Shangang , Chen Fang , Li Linsen , Zhu Yi , Zhao Jingxuan , Yuan Zhen , Shen Yafeng , Yang Chaofeng , Shao Mengle , Chen She , Bickel Perry E. , Zhong Qing
Published: November 2023

Lipid droplets (LDs) are dynamic lipid storage organelles that can sense and respond to changes in systemic energy balance. The size and number of LDs are controlled by complex and delicate mechanisms, among which, whether and which SNARE proteins mediate LD fusion, and the mechanisms governing this process remain poorly understood. Here we identified a SNARE complex, syntaxin 18 (STX18)–SNAP23–SEC22B, that is recruited to LDs to mediate LD fusion. STX18 targets LDs with its transmembrane domain spanning the phospholipid monolayer twice. STX18–SNAP23–SEC22B complex drives LD fusion in adiposome lipid mixing and content mixing in vitro assays. CIDEC/FSP27 directly binds STX18, SEC22B, and SNAP23, and promotes the lipid mixing of SNAREs-reconstituted adiposomes by promoting LD clustering. Knockdown of STX18 in mouse liver via AAV resulted in smaller liver and reduced LD size under high-fat diet conditions. All these results demonstrate a critical role of the SNARE complex STX18–SNAP23–SEC22B in LD fusion.
A smooth tubercle bacillus from Ethiopia phylogenetically close to the Mycobacterium tuberculosis complex
Authors: Yenew Bazezew , Ghodousi Arash , Diriba Getu , Tesfaye Ephrem , Cabibbe Andrea Maurizio , Amare Misikir , Moga Shewki , Alemu Ayinalem , Dagne Binyam , Sinshaw Waganeh , Mollalign Hilina , Meaza Abyot , Tadesse Mengistu , Gamtesa Dinka Fikadu , Abebaw Yeshiwork , Seid Getachew , Zerihun Betselot , Getu Melak , Chiacchiaretta Matteo , Gaudin Cyril , Marceau Michael , Didelot Xavier , Tolera Getachew , Abdella Saro , Kebede Abebaw , Getahun Muluwork , Mehammed Zemedu , Supply Philip , Cirillo Daniela Maria
Published: November 2023

The Mycobacterium tuberculosis complex (MTBC) includes several human- and animal-adapted pathogens. It is thought to have originated in East Africa from a recombinogenic Mycobacterium canettii-like ancestral pool. Here, we describe the discovery of a clinical tuberculosis strain isolated in Ethiopia that shares archetypal phenotypic and genomic features of M. canettii strains, but represents a phylogenetic branch much closer to the MTBC clade than to the M. canettii strains. Analysis of genomic traces of horizontal gene transfer in this isolate and previously identified M. canettii strains indicates a persistent albeit decreased recombinogenic lifestyle near the emergence of the MTBC. Our findings support that the MTBC emergence from its putative free-living M. canettii-like progenitor is evolutionarily very recent, and suggest the existence of a continuum of further extant derivatives from ancestral stages, close to the root of the MTBC, along the Great Rift Valley.
Assessing the value of integrating national longitudinal shopping data into respiratory disease forecasting models
Authors: Dolan Elizabeth , Goulding James , Marshall Harry , Smith Gavin , Long Gavin , Tata Laila J.
Published: November 2023

The COVID-19 pandemic led to unparalleled pressure on healthcare services. Improved healthcare planning in relation to diseases affecting the respiratory system has consequently become a key concern. We investigated the value of integrating sales of non-prescription medications commonly bought for managing respiratory symptoms, to improve forecasting of weekly registered deaths from respiratory disease at local levels across England, by using over 2 billion transactions logged by a UK high street retailer from March 2016 to March 2020. We report the results from the novel AI (Artificial Intelligence) explainability variable importance tool Model Class Reliance implemented on the PADRUS model (Prediction of Amount of Deaths by Respiratory disease Using Sales). PADRUS is a machine learning model optimised to predict registered deaths from respiratory disease in 314 local authority areas across England through the integration of shopping sales data and focused on purchases of non-prescription medications. We found strong evidence that models incorporating sales data significantly out-perform other models that solely use variables traditionally associated with respiratory disease (e.g. sociodemographics and weather data). Accuracy gains are highest (increases in R2 (coefficient of determination) between 0.09 to 0.11) in periods of maximum risk to the general public. Results demonstrate the potential to utilise sales data to monitor population health with information at a high level of geographic granularity.
Inferring mitochondrial and cytosolic metabolism by coupling isotope tracing and deconvolution
Authors: Stern Alon , Fokra Mariam , Sarvin Boris , Alrahem Ahmad Abed , Lee Won Dong , Aizenshtein Elina , Sarvin Nikita , Shlomi Tomer
Published: November 2023

The inability to inspect metabolic activities within distinct subcellular compartments has been a major barrier to our understanding of eukaryotic cell metabolism. Previous work addressed this challenge by analyzing metabolism in isolated organelles, which grossly bias metabolic activity. Here, we describe a method for inferring physiological metabolic fluxes and metabolite concentrations in mitochondria and cytosol based on isotope tracing experiments performed with intact cells. This is made possible by computational deconvolution of metabolite isotopic labeling patterns and concentrations into cytosolic and mitochondrial counterparts, coupled with metabolic and thermodynamic modelling. Our approach lowers the uncertainty regarding compartmentalized fluxes and concentrations by one and three orders of magnitude compared to existing modelling approaches, respectively. We derive a quantitative view of mitochondrial and cytosolic metabolic activities in central carbon metabolism across cultured cell lines without performing cell fractionation, finding major variability in compartmentalized malate-aspartate shuttle fluxes. We expect our approach for inferring metabolism at a subcellular resolution to be instrumental for a variety of studies of metabolic dysfunction in human disease and for bioengineering.
A knowledge-guided pre-training framework for improving molecular representation learning
Authors: Li Han , Zhang Ruotian , Min Yaosen , Ma Dacheng , Zhao Dan , Zeng Jianyang
Published: November 2023

Learning effective molecular feature representation to facilitate molecular property prediction is of great significance for drug discovery. Recently, there has been a surge of interest in pre-training graph neural networks (GNNs) via self-supervised learning techniques to overcome the challenge of data scarcity in molecular property prediction. However, current self-supervised learning-based methods suffer from two main obstacles: the lack of a well-defined self-supervised learning strategy and the limited capacity of GNNs. Here, we propose Knowledge-guided Pre-training of Graph Transformer (KPGT), a self-supervised learning framework to alleviate the aforementioned issues and provide generalizable and robust molecular representations. The KPGT framework integrates a graph transformer specifically designed for molecular graphs and a knowledge-guided pre-training strategy, to fully capture both structural and semantic knowledge of molecules. Through extensive computational tests on 63 datasets, KPGT exhibits superior performance in predicting molecular properties across various domains. Moreover, the practical applicability of KPGT in drug discovery has been validated by identifying potential inhibitors of two antitumor targets: hematopoietic progenitor kinase 1 (HPK1) and fibroblast growth factor receptor 1 (FGFR1). Overall, KPGT can provide a powerful and useful tool for advancing the artificial intelligence (AI)-aided drug discovery process.
CDC7 inhibition induces replication stress-mediated aneuploid cells with an inflammatory phenotype sensitizing tumors to immune checkpoint blockade
Authors: Morita Tomoko Yamamori , Yu Jie , Kashima Yukie , Kamata Ryo , Yamamoto Gaku , Minamide Tatsunori , Mashima Chiaki , Yoshiya Miyuki , Sakae Yuta , Yamauchi Toyohiro , Hakozaki Yumi , Kageyama Shun-ichiro , Nakamura Akito , Lightcap Eric , Tanaka Kosuke , Niu Huifeng , Kannan Karuppiah , Ohashi Akihiro
Published: November 2023

Serine/threonine kinase, cell division cycle 7 (CDC7) is critical for initiating DNA replication. TAK-931 is a specific CDC7 inhibitor, which is a next-generation replication stress (RS) inducer. This study preclinically investigates TAK-931 antitumor efficacy and immunity regulation. TAK-931 induce RS, generating senescence-like aneuploid cells, which highly expressed inflammatory cytokines and chemokines (senescence-associated secretory phenotype, SASP). In vivo multilayer-omics analyses in gene expression panel, immune panel, immunohistochemistry, RNA sequencing, and single-cell RNA sequencing reveal that the RS-mediated aneuploid cells generated by TAK-931 intensively activate inflammatory-related and senescence-associated pathways, resulting in accumulation of tumor-infiltrating immune cells and potent antitumor immunity and efficacy. Finally, the combination of TAK-931 and immune checkpoint inhibitors profoundly enhance antiproliferative activities. These findings suggest that TAK-931 has therapeutic antitumor properties and improved clinical benefits in combination with conventional immunotherapy.
Balancing elementary steps enables coke-free dry reforming of methane
Authors: Yu Jiaqi , Le Tien , Jing Dapeng , Stavitski Eli , Hunter Nicholas , Lalit Kanika , Leshchev Denis , Resasco Daniel E. , Sargent Edward H. , Wang Bin , Huang Wenyu
Published: November 2023

Balancing kinetics, a crucial priority in catalysis, is frequently achieved by sacrificing activity of elementary steps to suppress side reactions and enhance catalyst stability. Dry reforming of methane (DRM), a process operated at high temperature, usually involves fast C-H activation but sluggish carbon removal, resulting in coke deposition and catalyst deactivation. Studies focused solely on catalyst innovation are insufficient in addressing coke formation efficiently. Herein, we develop coke-free catalysts that balance kinetics of elementary steps for overall thermodynamics optimization. Beginning from a highly active cobalt aluminum oxide (CoAl2O4) catalyst that is susceptible to severe coke formation, we substitute aluminum (Al) with gallium (Ga), reporting a CoAl0.5Ga1.5O4-R catalyst that performs DRM stably over 1000 hours without observable coke deposition. We find that Ga enhances DRM stability by suppressing C-H activation to balance carbon removal. A series of coke-free DRM catalysts are developed herein by partially substituting Al from CoAl2O4 with other metals.
Mechanically-primed voltage-gated proton channels from angiosperm plants
Authors: Zhao Chang , Webster Parker D. , De Angeli Alexis , Tombola Francesco
Published: November 2023

Voltage-gated and mechanically-gated ion channels are distinct classes of membrane proteins that conduct ions across gated pores and are turned on by electrical or mechanical stimuli, respectively. Here, we describe an Hv channel (a.k.a voltage-dependent H+ channel) from the angiosperm plant A. thaliana that gates with a unique modality as it is turned on by an electrical stimulus only after exposure to a mechanical stimulus, a process that we call priming. The channel localizes in the vascular tissue and has homologs in vascular plants. We find that mechanical priming is not required for activation of non-angiosperm Hvs. Guided by AI-generated structural models of plant Hv homologs, we identify a set of residues playing a crucial role in mechanical priming. We propose that Hvs from angiosperm plants require priming because of a network of hydrophilic/charged residues that locks the channels in a silent resting conformation. Mechanical stimuli destabilize the network allowing the conduction pathway to turn on. In contrast to many other channels and receptors, Hv proteins are not thought to possess mechanisms such as inactivation or desensitization. Our findings demonstrate that angiosperm Hv channels are electrically silent until a mechanical stimulation turns on their voltage-dependent activity.
H3.1K27me1 loss confers Arabidopsis resistance to Geminivirus by sequestering DNA repair proteins onto host genome
Authors: Wang Zhen , Castillo-González Claudia M. , Zhao Changjiang , Tong Chun-Yip , Li Changhao , Zhong Songxiao , Liu Zhiyang , Xie Kaili , Zhu Jiaying , Wu Zhongshou , Peng Xu , Jacob Yannick , Michaels Scott D. , Jacobsen Steven E. , Zhang Xiuren
Published: November 2023

The H3 methyltransferases ATXR5 and ATXR6 deposit H3.1K27me1 to heterochromatin to prevent genomic instability and transposon re-activation. Here, we report that atxr5 atxr6 mutants display robust resistance to Geminivirus. The viral resistance is correlated with activation of DNA repair pathways, but not with transposon re-activation or heterochromatin amplification. We identify RAD51 and RPA1A as partners of virus-encoded Rep protein. The two DNA repair proteins show increased binding to heterochromatic regions and defense-related genes in atxr5 atxr6 vs wild-type plants. Consequently, the proteins have reduced binding to viral DNA in the mutant, thus hampering viral amplification. Additionally, RAD51 recruitment to the host genome arise via BRCA1, HOP2, and CYCB1;1, and this recruitment is essential for viral resistance in atxr5 atxr6. Thus, Geminiviruses adapt to healthy plants by hijacking DNA repair pathways, whereas the unstable genome, triggered by reduced H3.1K27me1, could retain DNA repairing proteins to suppress viral amplification in atxr5 atxr6.
Simultaneous and independent topological control of identical microparticles in non-periodic energy landscapes
Authors: Stuhlmüller Nico C. X. , Farrokhzad Farzaneh , Kuświk Piotr , Stobiecki Feliks , Urbaniak Maciej , Akhundzada Sapida , Ehresmann Arno , Fischer Thomas M. , de las Heras Daniel
Published: November 2023

Topological protection ensures stability of information and particle transport against perturbations. We explore experimentally and computationally the topologically protected transport of magnetic colloids above spatially inhomogeneous magnetic patterns, revealing that transport complexity can be encoded in both the driving loop and the pattern. Complex patterns support intricate transport modes when the microparticles are subjected to simple time-periodic loops of a uniform magnetic field. We design a pattern featuring a topological defect that functions as an attractor or a repeller of microparticles, as well as a pattern that directs microparticles along a prescribed complex trajectory. Using simple patterns and complex loops, we simultaneously and independently control the motion of several identical microparticles differing only in their positions above the pattern. Combining complex patterns and complex loops we transport microparticles from unknown locations to predefined positions and then force them to follow arbitrarily complex trajectories concurrently. Our findings pave the way for new avenues in transport control and dynamic self-assembly in colloidal science.
ZHX2 emerges as a negative regulator of mitochondrial oxidative phosphorylation during acute liver injury
Authors: Zhang Yankun , Fan Yuchen , Hu Huili , Zhang Xiaohui , Wang Zehua , Wu Zhuanchang , Wang Liyuan , Yu Xiangguo , Song Xiaojia , Xiang Peng , Zhang Xiaodong , Wang Tixiao , Tan Siyu , Li Chunyang , Gao Lifen , Liang Xiaohong , Li Shuijie , Li Nailin , Yue Xuetian , Ma Chunhong
Published: November 2023

Mitochondria dysfunction contributes to acute liver injuries, and mitochondrial regulators, such as PGC-1α and MCJ, affect liver regeneration. Therefore, identification of mitochondrial modulators may pave the way for developing therapeutic strategies. Here, ZHX2 is identified as a mitochondrial regulator during acute liver injury. ZHX2 both transcriptionally inhibits expression of several mitochondrial electron transport chain genes and decreases PGC-1α stability, leading to reduction of mitochondrial mass and OXPHOS. Loss of Zhx2 promotes liver recovery by increasing mitochondrial OXPHOS in mice with partial hepatectomy or CCl4-induced liver injury, and inhibition of PGC-1α or electron transport chain abolishes these effects. Notably, ZHX2 expression is higher in liver tissues from patients with drug-induced liver injury and is negatively correlated with mitochondrial mass marker TOM20. Delivery of shRNA targeting Zhx2 effectively protects mice from CCl4-induced liver injury. Together, our data clarify ZHX2 as a negative regulator of mitochondrial OXPHOS and a potential target for developing strategies for improving liver recovery after acute injuries.
Reduced glutathione level in the aqueous humor of patients with primary open-angle glaucoma and normal-tension glaucoma
Authors: Sato Kota , Saigusa Daisuke , Kokubun Taiki , Fujioka Amane , Feng Qiwei , Saito Ritsumi , Uruno Akira , Matsukawa Naomi , Ohno-Oishi Michiko , Kunikata Hiroshi , Yokoyama Yu , Yasuda Masayuki , Himori Noriko , Omodaka Kazuko , Tsuda Satoru , Maekawa Shigeto , Yamamoto Masayuki , Nakazawa Toru
Published: November 2023

Glaucoma is a leading cause of blindness worldwide in older people. Profiling the aqueous humor, including the metabolites it contains, is useful to understand physiological and pathological conditions in the eye. In the current study, we used mass spectrometry (MS) to characterize the aqueous humor metabolomic profile and biological features of patients with glaucoma. Aqueous humor samples were collected during trabeculectomy surgery or cataract surgery and analyzed with global metabolomics. We included 40 patients with glaucoma (32 with POAG, 8 with NTG) and 37 control subjects in a discovery study. VIP analysis revealed five metabolites that were elevated and three metabolites that were reduced in the glaucoma patients. The identified metabolomic profile had an area under the receiver operating characteristic curve of 0.953. Among eight selected metabolites, the glutathione level was significantly decreased in association with visual field defects. Moreover, in a validation study to confirm the reproducibility of our findings, the glutathione level was reduced in NTG and POAG patients compared with a cataract control group. Our findings demonstrate that aqueous humor profiling can help to diagnose glaucoma and that various aqueous humor metabolites are correlated with clinical parameters in glaucoma patients. In addition, glutathione is clearly reduced in the aqueous humor of glaucoma patients with both IOP-dependent and IOP-independent disease subtypes. These findings indicate that antioxidant agents in the aqueous humor reflect glaucomatous optic nerve damage and that excessive oxidative stress may be involved in the pathogenesis of glaucoma.
Approximate symmetries and quantum error correction
Authors: Liu Zi-Wen , Zhou Sisi
Published: November 2023

Quantum error correction (QEC) is a key concept in quantum computation as well as many areas of physics. There are fundamental tensions between continuous symmetries and QEC. One vital situation is unfolded by the Eastin–Knill theorem, which forbids the existence of QEC codes that admit transversal continuous symmetry actions (transformations). Here, we systematically study the competition between continuous symmetries and QEC in a quantitative manner. We first define a series of meaningful measures of approximate symmetries motivated from different perspectives, and then establish a series of trade-off bounds between them and QEC accuracy utilizing multiple different methods. Remarkably, the results allow us to derive general quantitative limitations of transversally implementable logical gates, an important topic in fault-tolerant quantum computation. As concrete examples, we showcase two explicit types of quantum codes, obtained from quantum Reed–Muller codes and thermodynamic codes, respectively, that nearly saturate our bounds. Finally, we discuss several potential applications of our results in physics.
3DSC - a dataset of superconductors including crystal structures
Authors: Sommer Timo , Willa Roland , Schmalian Jörg , Friederich Pascal
Published: November 2023

Data-driven methods, in particular machine learning, can help to speed up the discovery of new materials by finding hidden patterns in existing data and using them to identify promising candidate materials. In the case of superconductors, the use of data science tools is to date slowed down by a lack of accessible data. In this work, we present a new and publicly available superconductivity dataset (‘3DSC’), featuring the critical temperature TC of superconducting materials additionally to tested non-superconductors. In contrast to existing databases such as the SuperCon database which contains information on the chemical composition, the 3DSC is augmented by approximate three-dimensional crystal structures. We perform a statistical analysis and machine learning experiments to show that access to this structural information improves the prediction of the critical temperature TC of materials. Furthermore, we provide ideas and directions for further research to improve the 3DSC. We are confident that this database will be useful in applying state-of-the-art machine learning methods to eventually find new superconductors.
An Australian housing conditions data infrastructure
Authors: Baker Emma , Morey Claire , Daniel Lyrian , Beer Andrew , Bentley Rebecca , Stone Wendy , Rowley Steven , Nygaard Christian A. , London Kerry
Published: November 2023

For the past two decades, researchers and policy makers have known very little about conditions within Australia’s housing stock due to a lack of systematic and reliable data. In 2022, a collaboration of Australian universities and researchers commissioned a large survey of 22,550 private rental, social rental and homeowner households to build a data infrastructure on the household and demographic characteristics, housing quality and conditions in the Australian housing stock. This is the third and largest instalment in a national series of housing conditions data infrastructures.
Prediction of folding patterns for intrinsic disordered protein
Authors: Yang Jiaan , Cheng Wen-xiang , Wu Gang , Sheng Sitong , Zhang Peng
Published: November 2023

The conformation flexibility of natural protein causes both complexity and difficulty to understand the relationship between structure and function. The prediction of intrinsically disordered protein primarily is focusing on to disclose the regions with structural flexibility involving relevant biological functions and various diseases. The order of amino acids in protein sequence determines possible conformations, folding flexibility and biological function. Although many methods provided the information of intrinsically disordered protein (IDP), but the results are mainly limited to determine the locations of regions without knowledge of possible folding conformations. Here, the developed protein folding fingerprint adopted the protein folding variation matrix (PFVM) to reveal all possible folding patterns for the intrinsically disordered protein along its sequence. The PFVM integrally exhibited the intrinsically disordered protein with disordering regions, degree of disorder as well as folding pattern. The advantage of PFVM will not only provide rich information for IDP, but also may promote the study of protein folding problem.
Multispectral multibeam backscatter response of heterogeneous rhodolith beds
Authors: Menandro Pedro S. , Misiuk Benjamin , Brown Craig J. , Bastos Alex C.
Published: November 2023

Acoustic backscatter has been used as a tool to map the seafloor in greater detail and plays an increasingly important role in seafloor mapping to meet multiple ocean management needs. An outstanding challenge to the use of backscatter for seafloor mapping is the distinction between acoustically similar substrates, such as mixed sediments from rhodoliths. Rhodolith beds are a biogenic substrate that provides important ecological services, and are typically classified as a single categorical substrate type—though nodules coverage may be spatially variable. Recently, multispectral acoustic backscatter has demonstrated great potential to improve thematic seafloor mapping compared to single-frequency systems. This work employs multispectral multibeam backscatter and underwater imagery to characterize and map rhodolith beds in the Costa das Algas Marine Protected Area (Brazil). A support vector machine classifier was used to classify multifrequency backscatter mosaics according to rhodolith classes identified from underwater imagery. Results suggest that multispectral backscatter is effective both in providing information for mapping different proportions of rhodolith coverage and in predicting the presence or absence of these nodules. The backscatter of the lowest frequency was the most useful for distinguishing variable proportions of rhodolith coverage, and the two higher frequencies were better predictors of presence and absence.
High-throughput analysis system of interaction kinetics for data-driven antibody design
Authors: Matsunaga Ryo , Ujiie Kan , Inagaki Mayuko , Fernández Pérez Jorge , Yasuda Yoshiki , Mimasu Shinya , Soga Shinji , Tsumoto Kouhei
Published: November 2023

Surface plasmon resonance (SPR) is widely used for antigen–antibody interaction kinetics analysis. However, it has not been used in the screening phase because of the low throughput of measurement and analysis. Herein, we proposed a high-throughput SPR analysis system named “BreviA” using the Brevibacillus expression system. Brevibacillus was transformed using a plasmid library containing various antibody sequences, and single colonies were cultured in 96-well plates. Sequence analysis was performed using bacterial cells, and recombinant antibodies secreted in the supernatant were immobilized on a sensor chip to analyze their interactions with antigens using high-throughput SPR. Using this system, the process from the transformation to 384 interaction analyses can be performed within a week. This system utility was tested using an interspecies specificity design of an anti-human programmed cell death protein 1 (PD-1) antibody. A plasmid library containing alanine and tyrosine mutants of all complementarity-determining region residues was generated. A high-throughput SPR analysis was performed against human and mouse PD-1, showing that the mutation in the specific region enhanced the affinity for mouse PD-1. Furthermore, deep mutational scanning of the region revealed two mutants with > 100-fold increased affinity for mouse PD-1, demonstrating the potential efficacy of antibody design using data-driven approach.
Risk of SARS-CoV-2 infection and hospitalization in individuals with natural, vaccine-induced and hybrid immunity: a retrospective population-based cohort study from Estonia
Authors: Uusküla Anneli , Pisarev Heti , Tisler Anna , Meister Tatjana , Suija Kadri , Huik Kristi , Abroi Aare , Kalda Ruth , Kolde Raivo , Fischer Krista
Published: November 2023

A large proportion of the world’s population has some form of immunity against SARS-CoV-2, through either infection (‘natural’), vaccination or both (‘hybrid’). This retrospective cohort study used data on SARS-CoV-2, vaccination, and hospitalization from national health system from February 2020 to June 2022 and Cox regression modelling to compare those with natural immunity to those with no (Cohort1, n = 94,982), hybrid (Cohort2, n = 47,342), and vaccine (Cohort3, n = 254,920) immunity. In Cohort 1, those with natural immunity were at lower risk for infection during the Delta (aHR 0.17, 95%CI 0.15–0.18) and higher risk (aHR 1.24, 95%CI 1.18–1.32) during the Omicron period than those with no immunity. Natural immunity conferred substantial protection against COVID-19-hospitalization. Cohort 2—in comparison to natural immunity hybrid immunity offered strong protection during the Delta (aHR 0.61, 95%CI 0.46–0.80) but not the Omicron (aHR 1.05, 95%CI 0.93–1.1) period. COVID-19-hospitalization was extremely rare among individuals with hybrid immunity. In Cohort 3, individuals with vaccine-induced immunity were at higher risk than those with natural immunity for infection (Delta aHR 4.90, 95%CI 4.48–5.36; Omicron 1.13, 95%CI 1.06–1.21) and hospitalization (Delta aHR 7.19, 95%CI 4.02–12.84). These results show that risk of infection and severe COVID-19 are driven by personal immunity history and the variant of SARS-CoV-2 causing infection.
Study on correlation between TBM tailings gradation and granitic gneiss surrounding rock stability
Authors: Liu Yuancheng , Deng Ronggui , Yang Bai , Cheng Gang , Wang Tuo , Fu Zhiqian
Published: November 2023

In the process of double-shield TBM excavation, it is difficult to directly observe and test the characteristics of the surrounding rock. In this paper, the screening test of the different type tailings in the wet state was carried out to obtain the gradation curve and curve evaluation index. Combining with the excavation parameters and the surrounding rock characteristics of the tailings, a comprehensive analysis was carried out to establish the evaluation system among with the tailings gradation characteristics, lithology characteristics and excavation parameters. The results showed that: Sparsely fissured rock: the tailings are extensional fractures, the tailings gradation curve is inverse “S” type and gentle, and the evaluation index value: (1.50 > lg(Cu) > 1.35), (1.90 > Cc > 1.10). Broken surrounding rock: the curve is “L” type and steep, the content of coarse particles is much more than that of fine particles and (1.10 > lg(Cu) > 1.00), (2.60 > Cc > 2.40). Fractured rock: the curve is “Step” type, the tailings particles lack the middle particle size, the minerals are mostly weathered, (2.15 > lg(Cu )> 1.95), (0.09 > Cc > 0.07). The research results have good applicability to the surrounding rock stability evaluation of the example tunnel, which verifies the feasibility of the method.
The physiological measurement and evaluation of empathy of video content
Authors: Cho Ayoung , Park Sung , Lee Hyunwoo , Whang Mincheol
Published: November 2023

The COVID-19 pandemic has led to a surge in video content consumption, but measuring viewers' empathy towards the content has been limited to subjective evaluations or attached physiological apparatus. In this study, we introduced a novel non-contact physiological method for measuring empathy towards video content by assessing the synchronization of facial micromovements between the subject and object (i.e., person) within the media. We recorded facial micromovements and heart rate variability (HRV) remotely using a camera while 62 subjects watched one video each, designed and validated to elicit one of four two-dimensional emotions: pleasant-aroused, pleasant-relaxed, unpleasant-aroused, and unpleasant-relaxed. We also collected the subjects' self-assessed emotions and empathy using a questionnaire. The results confirmed that the stimuli effectively induced the intended arousal in the subjects, as evidenced by both self-reported emotions and HRV responses that suggested higher arousal was associated with stronger activity in the sympathetic nervous system. A closer examination of HRV indicators, such as SDNN and Total Power values, showed an amplification during the unpleasant state. We interpret this as the body's dynamic response to stressors, underlining the autonomic nervous system's proactive role in responding to such stimuli. In a broader context, our results emphasized that while subjects showcased augmented empathy during aroused conditions, the introduction of stressors, represented by unpleasant content, led to a dampening of this empathetic response. This findings demonstrate the potential of non-contact physiological methods for measuring empathy toward video content.
Recombinant inbred lines derived from wide crosses in Pisum
Authors: Ellis N. , Hofer J. , Sizer-Coverdale E. , Lloyd D. , Aubert G. , Kreplak J. , Burstin J. , Cheema J. , Bal M. , Chen Y. , Deng S. , Wouters R. H. M. , Steuernagel B. , Chayut N. , Domoney C.
Published: November 2023

Genomic resources are becoming available for Pisum but to link these to phenotypic diversity requires well marked populations segregating for relevant traits. Here we describe two such resources. Two recombinant inbred populations, derived from wide crosses in Pisum are described. One high resolution mapping population involves cv Caméor, for which the first pea whole genome assembly was obtained, crossed to JI0281, a basally divergent P. sativum sativum landrace from Ethiopia. The other is an inter sub-specific cross between P. s. sativum and the independently domesticated P. s. abyssinicum. The corresponding genetic maps provide information on chromosome level sequence assemblies and identify structural differences between the genomes of these two Pisum subspecies. In order to visualise chromosomal translocations that distinguish the mapping parents, we created a simplified version of Threadmapper to optimise it for interactive 3-dimensional display of multiple linkage groups. The genetic mapping of traits affecting seed coat roughness and colour, plant height, axil ring pigmentation, leaflet number and leaflet indentation enabled the definition of their corresponding genomic regions. The consequence of structural rearrangement for trait analysis is illustrated by leaf serration. These analyses pave the way for identification of the underlying genes and illustrate the utility of these publicly available resources. Segregating inbred populations derived from wide crosses in Pisum, together with the associated marker data, are made publicly available for trait dissection. Genetic analysis of these populations is informative about chromosome scale assemblies, structural diversity in the pea genome and has been useful for the fine mapping of several discrete and quantitative traits.
Epidemiological trends of pyogenic spondylodiscitis in Germany: an EANS Spine Section Study
Authors: Kramer Andreas , Thavarajasingam Santhosh G. , Neuhoff Jonathan , Ponniah Hariharan Subbiah , Ramsay Daniele S. C. , Demetriades Andreas K. , Davies Benjamin M. , Shiban Ehab , Ringel Florian
Published: November 2023

Pyogenic spondylodiscitis presents significant diagnostic and therapeutic challenges. In Germany, a comprehensive understanding of its epidemiology and inpatient management outcomes is limited, hindering the optimisation of therapeutic strategies. This study aimed to characterise the evolving epidemiological trends of pyogenic spondylodiscitis in Germany, and concurrently evaluate inpatient management strategies and outcomes. We performed a retrospective population-based study of spondylodiscitis cases in Germany from 2005 to 2021, utilising data from the German Federal Statistical Office database. The parameters assessed were incidence trends, demographic characteristics, inpatient management strategies, and inpatient mortality. The study found a significant rise in the population-adjusted incidence of spondylodiscitis in Germany from 2005 to 2021, increasing by 104% from 5.4 to 11.0 cases per 100,000 individuals (p < 0.001). The highest number of diagnoses was recorded in 2019. Age group-adjusted data revealed the largest relative changes in the “90 + ” age group, followed by the “80–89” and “70–79” age groups. These increases were not solely attributable to population changes but were also confirmed after calculating the age-group-adjusted incidence rates. Additionally, our statistical analysis demonstrated that both age and year significantly influenced the incidence of spondylodiscitis. Over the same period, inpatient mortality also surged significantly by 347% (p < 0.001), with the highest increase recorded in the 90 + age group, observing a 2450% rise (p < 0.001). The mean length of inpatient stay decreased by 15% (p < 0.05). Concurrently, there was a significant increase in surgical interventions using spinal stabilisation procedures (p < 0.001), which might suggest a shift in the treatment paradigm for spondylodiscitis. The results underscore a concerning rise in spondylodiscitis incidence and mortality in Germany, particularly affecting the ageing population. A notable shift towards surgical intervention was observed. The data highlights the urgent necessity for high-level evidence studies comparing surgical versus conservative treatment, thereby guiding optimised therapeutic strategies.
A novel subject-wise dictionary learning approach using multi-subject fMRI spatial and temporal components
Authors: Khalid Muhammad Usman , Nauman Malik Muhammad
Published: November 2023

The conventional dictionary learning (DL) algorithms aim to adapt the dictionary/sparse code to individual functional magnetic resonance imaging (fMRI) data. Thus, lacking the capability to consolidate the spatiotemporal diversities offered by other subjects. Considering that subject-wise (sw) data matrix can be decomposed into the sparse linear combination of multi-subject (MS) time courses and MS spatial maps, two new algorithms, sw sequential DL (swsDL) and sw block DL (swbDL), have been proposed. They are based on the novel framework, defined by the mixing model, where base matrices prepared by operating a computationally fast sparse spatiotemporal blind source separation method over multiple subjects are employed to adapt the mixing matrices to sw training data. They solve the optimization models formulated using $$l_0$$

l
0

/$$l_1$$

l
1

-norm penalization/constraints through dictionary/sparse code pair update and alternating minimization approach. They are unique because no existing sparse DL method can incorporate MS spatiotemporal components while updating sw atoms/sparse codes, which can eventually be assembled using neuroscience knowledge to extract group-level dynamics. Various fMRI datasets are used to evaluate and compare the performance of the proposed algorithms with existing state-of-the-art algorithms. Specifically, overall, a $$14\%$$

14
%

increase in the mean correlation value and $$39\%$$

39
%

reduction in the mean computation time exhibited by swsDL and swbDL, respectively, over the adaptive consistent sequential dictionary algorithm.
Placebo hypoalgesia induced by operant conditioning: a comparative study on the effects of verbal, token-based, and social rewards and punishers
Authors: Bieniek Helena , Bąbel Przemysław
Published: November 2023

Operant conditioning was shown to be a mechanism of placebo hypoalgesia; however, only verbal rewards and punishers were applied in the previous study. We aimed to induce placebo hypoalgesia using more clinically relevant consequences: token-based and social. Participants were divided into three experimental groups (with verbal, social, and token-based rewards and punishers); and two control groups (with and without placebo application). During operant conditioning, participants in the experimental groups received thermal stimuli of equal intensity and were rewarded for reporting lower pain and punished for reporting higher pain compared to their pretest pain levels. The control groups did not receive any consequences. Our results revealed placebo hypoalgesia was induced by operant conditioning only in the experimental groups with social and token-based reinforcement, compared to the control groups. The hypoalgesic effect found in the group that received verbal reinforcement did not differ significantly from the control group with the placebo application. Moreover, expectations about upcoming pain intensity were found to be a mediator, and the number of reinforcers received during conditioning was a predictor of placebo hypoalgesia. These findings highlight the potential benefits of incorporating token-based and social consequences for optimizing treatment outcomes in pain management.