bluuebunny/crossref_metadata_2025_split huggingface dataset:
PeakDecoder enables machine learning-based metabolite annotation and accurate profiling in multidimensional mass spectrometry measurements
Authors: Bilbao Aivett , Munoz Nathalie , Kim Joonhoon , Orton Daniel J. , Gao Yuqian , Poorey Kunal , Pomraning Kyle R. , Weitz Karl , Burnet Meagan , Nicora Carrie D. , Wilton Rosemarie , Deng Shuang , Dai Ziyu , Oksen Ethan , Gee Aaron , Fasani Rick A. , Tsalenko Anya , Tanjore Deepti , Gardner James , Smith Richard D. , Michener Joshua K. , Gladden John M. , Baker Erin S. , Petzold Christopher J. , Kim Young-Mo , Apffel Alex , Magnuson Jon K. , Burnum-Johnson Kristin E. 
Published: April 2023

AbstractMultidimensional measurements using state-of-the-art separations and mass spectrometry provide advantages in untargeted metabolomics analyses for studying biological and environmental bio-chemical processes. However, the lack of rapid analytical methods and robust algorithms for these heterogeneous data has limited its application. Here, we develop and evaluate a sensitive and high-throughput analytical and computational workflow to enable accurate metabolite profiling. Our workflow combines liquid chromatography, ion mobility spectrometry and data-independent acquisition mass spectrometry with PeakDecoder, a machine learning-based algorithm that learns to distinguish true co-elution and co-mobility from raw data and calculates metabolite identification error rates. We apply PeakDecoder for metabolite profiling of various engineered strains ofAspergillus pseudoterreus, Aspergillus niger, Pseudomonas putidaandRhodosporidium toruloides. Results, validated manually and against selected reaction monitoring and gas-chromatography platforms, show that 2683 features could be confidently annotated and quantified across 116 microbial sample runs using a library built from 64 standards.
Pain-causing stinging nettle toxins target TMEM233 to modulate NaV1.7 function
Authors: Jami Sina , Deuis Jennifer R. , Klasfauseweh Tabea , Cheng Xiaoyang , Kurdyukov Sergey , Chung Felicity , Okorokov Andrei L. , Li Shengnan , Zhang Jiangtao , Cristofori-Armstrong Ben , Israel Mathilde R. , Ju Robert J. , Robinson Samuel D. , Zhao Peng , Ragnarsson Lotten , Andersson Åsa , Tran Poanna , Schendel Vanessa , McMahon Kirsten L. , Tran Hue N. T. , Chin Yanni K.-Y. , Zhu Yifei , Liu Junyu , Crawford Theo , Purushothamvasan Saipriyaa , Habib Abdella M. , Andersson David A. , Rash Lachlan D. , Wood John N. , Zhao Jing , Stehbens Samantha J. , Mobli Mehdi , Leffler Andreas , Jiang Daohua , Cox James J. , Waxman Stephen G. , Dib-Hajj Sulayman D. , Neely G. Gregory , Durek Thomas , Vetter Irina 
Published: April 2023

AbstractVoltage-gated sodium (NaV) channels are critical regulators of neuronal excitability and are targeted by many toxins that directly interact with the pore-forming α subunit, typically via extracellular loops of the voltage-sensing domains, or residues forming part of the pore domain. Excelsatoxin A (ExTxA), a pain-causing knottin peptide from the Australian stinging tree Dendrocnide excelsa, is the first reported plant-derived NaV channel modulating peptide toxin. Here we show that TMEM233, a member of the dispanin family of transmembrane proteins expressed in sensory neurons, is essential for pharmacological activity of ExTxA at NaV channels, and that co-expression of TMEM233 modulates the gating properties of NaV1.7. These findings identify TMEM233 as a previously unknown NaV1.7-interacting protein, position TMEM233 and the dispanins as accessory proteins that are indispensable for toxin-mediated effects on NaV channel gating, and provide important insights into the function of NaV channels in sensory neurons.
Navigating surface reconstruction of spinel oxides for electrochemical water oxidation
Authors: Sun Yuanmiao , Wang Jiarui , Xi Shibo , Shen Jingjing , Luo Songzhu , Ge Jingjie , Sun Shengnan , Chen Yubo , Hanna John V. , Li Shuzhou , Wang Xin , Xu Zhichuan J. 
Published: April 2023

AbstractUnderstanding and mastering the structural evolution of water oxidation electrocatalysts lays the foundation to finetune their catalytic activity. Herein, we demonstrate that surface reconstruction of spinel oxides originates from the metal-oxygen covalency polarity in the MT–O–MO backbone. A stronger MO–O covalency relative to MT–O covalency is found beneficial for a more thorough reconstruction towards oxyhydroxides. The structure-reconstruction relationship allows precise prediction of the reconstruction ability of spinel pre-catalysts, based on which the reconstruction degree towards the in situ generated oxyhydroxides can be controlled. The investigations of oxyhydroxides generated from spinel pre-catalysts with the same reconstruction ability provide guidelines to navigate the cation selection in spinel pre-catalysts design. This work reveals the fundamentals for manipulating the surface reconstruction of spinel pre-catalysts for water oxidation.
A point mutation in recC associated with subclonal replacement of carbapenem-resistant Klebsiella pneumoniae ST11 in China
Authors: Zhou Kai , Xue Chun-Xu , Xu Tingting , Shen Ping , Wei Sha , Wyres Kelly L. , Lam Margaret M. C. , Liu Jinquan , Lin Haoyun , Chen Yunbo , Holt Kathryn E. ,   the BRICS Working Group, Chen Yunbo , Ding Hui , Liu Yongyun , Mao Haifeng , Huang Ying , Yang Zhenghai , Dai Yuanyuan , Liao Guolin , Zhu Lisha , Zhang Liping , Li Yanhong , Xu Hongyun , Cao Junmin , Zhang Baohua , Guo Liang , Dong Haixin , Hu Shuyan , Man Sijin , Wang Lu , Liao Zhixiang , Xu Rong , Liu Dan , Jin Yan , Zhou Yizheng , Liao Yiqun , Chen Fenghong , Gu Beiqing , Wang Jiliang , Liang Jinhua , Zheng Lin , Li Aiyun , Shen Jilu , Dong Yinqiao , Zhang Lixia , Hu Hongxia , Quan Bo , Zhu Wencheng , Liang Kunpeng , Liu Qiang , Wang Shifu , Yan Xiaoping , Kang Jiangbang , Xia Xiusan , Ma Lan , Sun Li , Luan Liang , Wang Jianzhong , Lin Haoyun , Li Zhuo , Qiao Dengyan , Zhang Lin , Wan Chuandan , Qi Xiaoyan , Du Fei , Xiao Yonghong 
Published: April 2023

AbstractAdaptation to selective pressures is crucial for clinically important pathogens to establish epidemics, but the underlying evolutionary drivers remain poorly understood. The current epidemic of carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a significant threat to public health. In this study we analyzed the genome sequences of 794 CRKP bloodstream isolates collected in 40 hospitals in China between 2014 and 2019. We uncovered a subclonal replacement in the predominant clone ST11, where the previously prevalent subclone OL101:KL47 was replaced by O2v1:KL64 over time in a stepwise manner. O2v1:KL64 carried a higher load of mobile genetic elements, and a point mutation exclusively detected in the recC of O2v1:KL64 significantly promotes recombination proficiency. The epidemic success of O2v1:KL64 was further associated with a hypervirulent sublineage with enhanced resistance to phagocytosis, sulfamethoxazole-trimethoprim, and tetracycline. The phenotypic alterations were linked to the overrepresentation of hypervirulence determinants and antibiotic genes conferred by the acquisition of an rmpA-positive pLVPK-like virulence plasmid and an IncFII-type multidrug-resistant plasmid, respectively. The dissemination of the sublineage was further promoted by more frequent inter-hospital transmission. The results collectively demonstrate that the expansion of O2v1:KL64 is correlated to a repertoire of genomic alterations convergent in a subpopulation with evolutionary advantages.
Single-atomic platinum on fullerene C60 surfaces for accelerated alkaline hydrogen evolution
Authors: Zhang Ruiling , Li Yaozhou , Zhou Xuan , Yu Ao , Huang Qi , Xu Tingting , Zhu Longtao , Peng Ping , Song Shuyan , Echegoyen Luis , Li Fang-Fang 
Published: April 2023

AbstractThe electrocatalytic hydrogen evolution reaction (HER) is one of the most studied and promising processes for hydrogen fuel generation. Single-atom catalysts have been shown to exhibit ultra-high HER catalytic activity, but the harsh preparation conditions and the low single-atom loading hinder their practical applications. Furthermore, promoting hydrogen evolution reaction kinetics, especially in alkaline electrolytes, remains as an important challenge. Herein, Pt/C60 catalysts with high-loading, high-dispersion single-atomic platinum anchored on C60 are achieved through a room-temperature synthetic strategy. Pt/C60-2 exhibits high HER catalytic performance with a low overpotential (η10) of 25 mV at 10 mA cm−2. Density functional theory calculations reveal that the Pt-C60 polymeric structures in Pt/C60-2 favors water adsorption, and the shell-like charge redistribution around the Pt-bonding region induced by the curved surfaces of two adjacent C60 facilitates the desorption of hydrogen, thus favoring fast reaction kinetics for hydrogen evolution.
An interactive murine single-cell atlas of the lung responses to radiation injury
Authors: Curras-Alonso Sandra , Soulier Juliette , Defard Thomas , Weber Christian , Heinrich Sophie , Laporte Hugo , Leboucher Sophie , Lameiras Sonia , Dutreix Marie , Favaudon Vincent , Massip Florian , Walter Thomas , Mueller Florian , Londoño-Vallejo José-Arturo , Fouillade Charles 
Published: April 2023

AbstractRadiation Induced Lung Injury (RILI) is one of the main limiting factors of thorax irradiation, which can induce acute pneumonitis as well as pulmonary fibrosis, the latter being a life-threatening condition. The order of cellular and molecular events in the progression towards fibrosis is key to the physiopathogenesis of the disease, yet their coordination in space and time remains largely unexplored. Here, we present an interactive murine single cell atlas of the lung response to irradiation, generated from C57BL6/J female mice. This tool opens the door for exploration of the spatio-temporal dynamics of the mechanisms that lead to radiation-induced pulmonary fibrosis. It depicts with unprecedented detail cell type-specific radiation-induced responses associated with either lung regeneration or the failure thereof. A better understanding of the mechanisms leading to lung fibrosis will help finding new therapeutic options that could improve patients’ quality of life.
USP7 controls NGN3 stability and pancreatic endocrine lineage development
Authors: Manea Teodora , Nelson Jessica Kristine , Garrone Cristina Maria , Hansson Karin , Evans Ian , Behrens Axel , Sancho Rocio 
Published: April 2023

AbstractUnderstanding the factors and mechanisms involved in beta-cell development will guide therapeutic efforts to generate fully functional beta cells for diabetes. Neurogenin 3 (NGN3) is the key transcription factor that marks endocrine progenitors and drives beta-cell differentiation. Here we screen for binding partners of NGN3 and identify the deubiquitylating enzyme USP7 as a key regulator of NGN3 stability. Mechanistically, USP7 interacts with, deubiquitinates and stabilizes NGN3. In vivo, conditional knockout of Usp7 in the mouse embryonic pancreas causes a dramatic reduction in islet formation and hyperglycemia in adult mice, due to impaired NGN3-mediated endocrine specification during pancreatic development. Furthermore, pharmacological inhibition of USP7 during endocrine specification in human iPSC models of beta-cell differentiation decreases NGN3 expressing progenitor cell numbers and impairs beta cell differentiation. Thus, the USP7-NGN3 axis is an essential mechanism for driving endocrine development and beta-cell differentiation, which can be therapeutically exploited.
Quantum microscopy of cells at the Heisenberg limit
Authors: He Zhe , Zhang Yide , Tong Xin , Li Lei , Wang Lihong V. 
Published: April 2023

AbstractEntangled biphoton sources exhibit nonclassical characteristics and have been applied to imaging techniques such as ghost imaging, quantum holography, and quantum optical coherence tomography. The development of wide-field quantum imaging to date has been hindered by low spatial resolutions, speeds, and contrast-to-noise ratios (CNRs). Here, we present quantum microscopy by coincidence (QMC) with balanced pathlengths, which enables super-resolution imaging at the Heisenberg limit with substantially higher speeds and CNRs than existing wide-field quantum imaging methods. QMC benefits from a configuration with balanced pathlengths, where a pair of entangled photons traversing symmetric paths with balanced optical pathlengths in two arms behave like a single photon with half the wavelength, leading to a two-fold resolution improvement. Concurrently, QMC resists stray light up to 155 times stronger than classical signals. The low intensity and entanglement features of biphotons in QMC promise nondestructive bioimaging. QMC advances quantum imaging to the microscopic level with significant improvements in speed and CNR toward the bioimaging of cancer cells. We experimentally and theoretically prove that the configuration with balanced pathlengths illuminates an avenue for quantum-enhanced coincidence imaging at the Heisenberg limit.
A visual opsin from jellyfish enables precise temporal control of G protein signalling
Authors: van Wyk Michiel , Kleinlogel Sonja 
Published: April 2023

AbstractPhototransduction is mediated by distinct types of G protein cascades in different animal taxa: bilateral invertebrates typically utilise the Gαq pathway whereas vertebrates typically utilise the Gαt(i/o) pathway. By contrast, photoreceptors in jellyfish (Cnidaria) utilise the Gαs intracellular pathway, similar to olfactory transduction in mammals1. How this habitually slow pathway has adapted to support dynamic vision in jellyfish remains unknown. Here we study a light-sensing protein (rhodopsin) from the box jellyfish Carybdea rastonii and uncover a mechanism that dramatically speeds up phototransduction: an uninterrupted G protein-coupled receptor – G protein complex. Unlike known G protein-coupled receptors (GPCRs), this rhodopsin constitutively binds a single downstream Gαs partner to enable G-protein activation and inactivation within tens of milliseconds. We use this GPCR in a viral gene therapy to restore light responses in blind mice.
Liquid sculpture and curing of bio-inspired polyelectrolyte aqueous two-phase systems
Authors: Zhang Chongrui , Liu Xufei , Gong Jiang , Zhao Qiang 
Published: April 2023

AbstractAqueous two-phase systems (ATPS) provide imperative interfaces and compartments in biology, but the sculpture and conversion of liquid structures to functional solids is challenging. Here, inspired by phase evolution of mussel foot proteins ATPS, we tackle this problem by designing poly(ionic liquids) capable of responsive condensation and phase-dependent curing. When mixed with poly(dimethyl diallyl ammonium chloride), the poly(ionic liquids) formed liquid condensates and ATPS, which were tuned into bicontinuous liquid phases under stirring. Selective, rapid curing of the poly(ionic liquids)-rich phase was facilitated under basic conditions (pH 11), leading to the liquid-to-gel conversion and structure sculpture, i.e., the evolution from ATPS to macroporous sponges featuring bead-and-string networks. This mechanism enabled the selective embedment of carbon nanotubes in the poly(ionic liquids)-rich phase, which showed exceptional stability in harsh conditions (10 wt% NaCl, 80 oC, 3 days) and high (2.5 kg/m2h) solar thermal desalination of concentrated salty water under 1-sun irradiation.
Rational engineering of lung alveolar epithelium
Authors: Leiby Katherine L. , Yuan Yifan , Ng Ronald , Raredon Micha Sam Brickman , Adams Taylor S. , Baevova Pavlina , Greaney Allison M. , Hirschi Karen K. , Campbell Stuart G. , Kaminski Naftali , Herzog Erica L. , Niklason Laura E. 
Published: April 2023

AbstractEngineered whole lungs may one day expand therapeutic options for patients with end-stage lung disease. However, the feasibility of ex vivo lung regeneration remains limited by the inability to recapitulate mature, functional alveolar epithelium. Here, we modulate multimodal components of the alveolar epithelial type 2 cell (AEC2) niche in decellularized lung scaffolds in order to guide AEC2 behavior for epithelial regeneration. First, endothelial cells coordinate with fibroblasts, in the presence of soluble growth and maturation factors, to promote alveolar scaffold population with surfactant-secreting AEC2s. Subsequent withdrawal of Wnt and FGF agonism synergizes with tidal-magnitude mechanical strain to induce the differentiation of AEC2s to squamous type 1 AECs (AEC1s) in cultured alveoli, in situ. These results outline a rational strategy to engineer an epithelium of AEC2s and AEC1s contained within epithelial-mesenchymal-endothelial alveolar-like units, and highlight the critical interplay amongst cellular, biochemical, and mechanical niche cues within the reconstituting alveolus.
Dataset of theoretical multinary perovskite oxides
Authors: Bare Zachary J. L. , Morelock Ryan J. , Musgrave Charles B. 
Published: April 2023

AbstractPerovskite oxides (ternary chemical formula ABO3) are a diverse class of materials with applications including heterogeneous catalysis, solid-oxide fuel cells, thermochemical conversion, and oxygen transport membranes. However, their multicomponent (chemical formula$${A}_{x}{A}_{1-x}^{\text{'}}{B}_{y}{B}_{1-y}^{\text{'}}{O}_{3}$$AxA1−x'ByB1−y'O3) chemical space is underexplored due to the immense number of possible compositions. To expand the number of computed$${A}_{x}{A}_{1-x}^{{\prime} }{B}_{y}{B}_{1-y}^{{\prime} }{O}_{3}$$AxA1−x′ByB1−y′O3compounds we report a dataset of 66,516 theoretical multinary oxides, 59,708 of which are perovskites. First, 69,407$${A}_{0.5}{A}_{0.5}^{{\prime} }{B}_{0.5}{B}_{0.5}^{{\prime} }{O}_{3}$$A0.5A0.5′B0.5B0.5′O3compositions were generated in thea−b+a−Glazer tilting mode using the computationally-inexpensive Structure Prediction and Diagnostic Software (SPuDS) program. Next, we optimized these structures with density functional theory (DFT) using parameters compatible with the Materials Project (MP) database. Our dataset contains these optimized structures and their formation (ΔHf) and decomposition enthalpies (ΔHd) computed relative to MP tabulated elemental references and competing phases, respectively. This dataset can be mined, used to train machine learning models, and rapidly and systematically expanded by optimizing more SPuDS-generated$${A}_{0.5}{A}_{0.5}^{{\prime} }{B}_{0.5}{B}_{0.5}^{{\prime} }{O}_{3}$$A0.5A0.5′B0.5B0.5′O3perovskite structures using MP-compatible DFT calculations.
Gene sequencing and result analysis of balanced translocation carriers by third-generation gene sequencing technology
Authors: Zeng Xiaoqi , Lin Dandan , Liang Danhong , Huang Jingwen , Yi Jinsong , Lin Dianliang , Zhang Zhengmian 
Published: April 2023

AbstractBecause the total gene copy number remains constant and all genes are normally expressed, carriers of balanced chromosomal translocations usually have a normal phenotype but are able to produce many different types of gametes during meiosis, and unbalanced gametes lead to increased risks of infertility, recurrent spontaneous abortion, stillbirth, neonatal death or malformations and intellectual abnormalities in offspring. The key to balanced translocations lies in finding the breakpoints, but current genetic testing techniques are all short-read sequencing, with the disadvantage of procedural complexity and imprecision for precisely identifying the breakpoints. The latest third-generation sequencing technology overcomes these drawbacks and uses robust long-read sequencing to accurately and rapidly detect genome-wide information and identify breakpoint locations. In this paper, we performed whole genome long-read sequencing using an Oxford Nanopore sequencer to detect the breakpoints of 4 balanced chromosomal translocation carriers. The results showed that employing about ~ 10× coverage confirmed 6 of the 8 breakpoints, of which, 2 had microdeletions/insertions identified near the breakpoints and 4 had breakpoints that disrupted the normal gene structure and were simultaneously tested for genome-wide structural variation (SV). The results show that whole genome long-read sequencing is an efficient method for pinpointing translocation breakpoints and providing genome-wide information, which is essential for medical genetics and preimplantation genetic testing.
Establishing the root causes of unsafe behaviors among construction workers: an integrative interpretive structural modeling analysis
Authors: Sathvik S. , Krishnaraj L. , Awuzie Bankole Ostia 
Published: April 2023

AbstractThere has been a significant decline in worker productivity at construction sites globally owing to the increase in accidents and fatalities due to unsafe behavior among workers. Although many studies have explored the incidence of unsafe behaviors among construction workers, limited studies have attempted to evaluate the causal factors and to determine the root causes. An integrative interpretive structural modeling analysis of the interrelationships that exist between these causal factors established from relevant literature was conducted in this study to determine the root factors hence bridging this gap. Fifteen causal factors were identified through literature review, and the nature of interrelationships between them was determined using interpretive structural modeling (ISM) and a Cross-impact matrix multiplication applied to classification (MICMAC) analysis. Data was obtained from a purposively selected cohort of experts using semi-structured interviews. The emergent data was subsequently analyzed using the ISM and MICMAC analysis to ascertain the interrelationships between the causal factors. The results of the study showed that age, sleep quality, degree of interaction and workers’ skillsets were the root causes of unsafe behavior among construction workers. Besides engendering the establishment of the root causes of unsafe behavior among construction workers, the results of this study will facilitate the prioritization of appropriate solutions for tackling the menace.
MasitinibL shows promise as a drug-like analog of masitinib that elicits comparable SARS-Cov-2 3CLpro inhibition with low kinase preference
Authors: Durojaye Olanrewaju Ayodeji , Okoro Nkwachukwu Oziamara , Odiba Arome Solomon , Nwanguma Bennett Chima 
Published: April 2023

AbstractSARS-CoV-2 infection has led to several million deaths worldwide and ravaged the economies of many countries. Hence, developing therapeutics against SARS-CoV-2 remains a core priority in the fight against COVID-19. Most of the drugs that have received emergency use authorization for treating SARS-CoV-2 infection exhibit a number of limitations, including side effects and questionable efficacy. This challenge is further compounded by reinfection after vaccination and the high likelihood of mutations, as well as the emergence of viral escape mutants that render SARS-CoV-2 spike glycoprotein-targeting vaccines ineffective. Employing de novo drug synthesis or repurposing to discover broad-spectrum antivirals that target highly conserved pathways within the viral machinery is a focus of current research. In a recent drug repurposing study, masitinib, a clinically safe drug against the human coronavirus OC43 (HCoV-OC43), was identified as an antiviral agent with effective inhibitory activity against the SARS-CoV-2 3CLpro. Masitinib is currently under clinical trial in combination with isoquercetin in hospitalized patients (NCT04622865). Nevertheless, masitinib has kinase-related side effects; hence, the development of masitinib analogs with lower anti–tyrosine kinase activity becomes necessary. In this study, in an attempt to address this limitation, we executed a comprehensive virtual workflow in silico to discover drug-like compounds matching selected pharmacophore features in the SARS-CoV-2 3CLpro-bound state of masitinib. We identified a novel lead compound, “masitinibL”, a drug-like analog of masitinib that demonstrated strong inhibitory properties against the SARS-CoV-2 3CLpro. In addition, masitinibL further displayed low selectivity for tyrosine kinases, which strongly suggests that masitinibL is a highly promising therapeutic that is preferable to masitinib.