bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiplexed detection of viral antigen and RNA using nanopore sensing and encoded molecular probes
Authors: Ren Ren , Cai Shenglin , Fang Xiaona , Wang Xiaoyi , Zhang Zheng , Damiani Micol , Hudlerova Charlotte , Rosa Annachiara , Hope Joshua , Cook Nicola J. , Gorelkin Peter , Erofeev Alexander , Novak Pavel , Badhan Anjna , Crone Michael , Freemont Paul , Taylor Graham P. , Tang Longhua , Edwards Christopher , Shevchuk Andrew , Cherepanov Peter , Luo Zhaofeng , Tan Weihong , Korchev Yuri , Ivanov Aleksandar P. , Edel Joshua B. 
Published: November 2023

AbstractWe report on single-molecule nanopore sensing combined with position-encoded DNA molecular probes, with chemistry tuned to simultaneously identify various antigen proteins and multiple RNA gene fragments of SARS-CoV-2 with high sensitivity and selectivity. We show that this sensing strategy can directly detect spike (S) and nucleocapsid (N) proteins in unprocessed human saliva. Moreover, our approach enables the identification of RNA fragments from patient samples using nasal/throat swabs, enabling the identification of critical mutations such as D614G, G446S, or Y144del among viral variants. In particular, it can detect and discriminate between SARS-CoV-2 lineages of wild-type B.1.1.7 (Alpha), B.1.617.2 (Delta), and B.1.1.539 (Omicron) within a single measurement without the need for nucleic acid sequencing. The sensing strategy of the molecular probes is easily adaptable to other viral targets and diseases and can be expanded depending on the application required.
CHEX-seq detects single-cell genomic single-stranded DNA with catalytical potential
Authors: Lu Youtao , Lee Jaehee , Li Jifen , Allu Srinivasa Rao , Wang Jinhui , Kim HyunBum , Bullaughey Kevin L. , Fisher Stephen A. , Nordgren C. Erik , Rosario Jean G. , Anderson Stewart A. , Ulyanova Alexandra V. , Brem Steven , Chen H. Isaac , Wolf John A. , Grady M. Sean , Vinogradov Sergei A. , Kim Junhyong , Eberwine James 
Published: November 2023

AbstractGenomic DNA (gDNA) undergoes structural interconversion between single- and double-stranded states during transcription, DNA repair and replication, which is critical for cellular homeostasis. We describe “CHEX-seq” which identifies the single-stranded DNA (ssDNA) in situ in individual cells. CHEX-seq uses 3’-terminal blocked, light-activatable probes to prime the copying of ssDNA into complementary DNA that is sequenced, thereby reporting the genome-wide single-stranded chromatin landscape. CHEX-seq is benchmarked in human K562 cells, and its utilities are demonstrated in cultures of mouse and human brain cells as well as immunostained spatially localized neurons in brain sections. The amount of ssDNA is dynamically regulated in response to perturbation. CHEX-seq also identifies single-stranded regions of mitochondrial DNA in single cells. Surprisingly, CHEX-seq identifies single-stranded loci in mouse and human gDNA that catalyze porphyrin metalation in vitro, suggesting a catalytic activity for genomic ssDNA. We posit that endogenous DNA enzymatic activity is a function of genomic ssDNA.
Pulsed electroreduction of low-concentration nitrate to ammonia
Authors: Huang Yanmei , He Caihong , Cheng Chuanqi , Han Shuhe , He Meng , Wang Yuting , Meng Nannan , Zhang Bin , Lu Qipeng , Yu Yifu 
Published: November 2023

AbstractElectrocatalytic nitrate (NO3−) reduction to ammonia (NRA) has emerged as an alternative strategy for effluent treatment and ammonia production. Despite significant advancements that have been achieved in this field, the efficient conversion of low-concentration nitrate to ammonia at low overpotential remains a formidable challenge. This challenge stems from the sluggish reaction kinetics caused by the limited distribution of negatively charged NO3− in the vicinity of the working electrode and the competing side reactions. Here, a pulsed potential approach is introduced to overcome these issues. A good NRA performance (Faradaic efficiency: 97.6%, yield rate: 2.7 mmol−1 h−1 mgRu−1, conversion rate: 96.4%) is achieved for low-concentration (≤10 mM) nitrate reduction, obviously exceeding the potentiostatic test (Faradaic efficiency: 65.8%, yield rate: 1.1 mmol−1 h−1 mgRu−1, conversion rate: 54.1%). The combined results of in situ characterizations and finite element analysis unveil the performance enhancement mechanism that the periodic appearance of anodic potential can significantly optimize the adsorption configuration of the key *NO intermediate and increase the local NO3− concentration. Furthermore, our research implies an effective approach for the rational design and precise manipulation of reaction processes, potentially extending its applicability to a broader range of catalytic applications.
Cryo-EM structures of the plant anion channel SLAC1 from Arabidopsis thaliana suggest a combined activation model
Authors: Lee Yeongmok , Jeong Hyeon Seong , Jung Seoyeon , Hwang Junmo , Le Chi Truc Han , Jun Sung-Hoon , Du Eun Jo , Kang KyeongJin , Kim Beom-Gi , Lim Hyun-Ho , Lee Sangho 
Published: November 2023

AbstractThe anion channel SLAC1 functions as a crucial effector in the ABA signaling, leading to stomata closure. SLAC1 is activated by phosphorylation in its intracellular domains. Both a binding-activation model and an inhibition-release model for activation have been proposed based on only the closed structures of SLAC1, rendering the structure-based activation mechanism controversial. Here we report cryo-EM structures of Arabidopsis SLAC1 WT and its phosphomimetic mutants in open and closed states. Comparison of the open structure with the closed ones reveals the structural basis for opening of the conductance pore. Multiple phosphorylation of an intracellular domain (ICD) causes dissociation of ICD from the transmembrane domain. A conserved, positively-charged sequence motif in the intracellular loop 2 (ICL2) seems to be capable of sensing of the negatively charged phosphorylated ICD. Interactions between ICL2 and ICD drive drastic conformational changes, thereby widening the pore. From our results we propose that SLAC1 operates by a mechanism combining the binding-activation and inhibition-release models.
Interactome profiling of Crimean-Congo hemorrhagic fever virus glycoproteins
Authors: Dai Shiyu , Min Yuan-Qin , Li Qi , Feng Kuan , Jiang Zhenyu , Wang Zhiying , Zhang Cunhuan , Ren Fuli , Fang Yaohui , Zhang Jingyuan , Zhu Qiong , Wang Manli , Wang Hualin , Deng Fei , Ning Yun-Jia 
Published: November 2023

AbstractCrimean-Congo hemorrhagic fever virus (CCHFV) is a biosafety level-4 pathogen requiring urgent research and development efforts. The glycoproteins of CCHFV, Gn and Gc, are considered to play multiple roles in the viral life cycle by interactions with host cells; however, these interactions remain largely unclear to date. Here, we analyzed the cellular interactomes of CCHFV glycoproteins and identified 45 host proteins as high-confidence Gn/Gc interactors. These host molecules are involved in multiple cellular biological processes potentially associated with the physiological actions of the viral glycoproteins. Then, we elucidated the role of a representative cellular protein, HAX1. HAX1 interacts with Gn by its C-terminus, while its N-terminal region leads to mitochondrial localization. By the strong interaction, HAX1 sequestrates Gn to mitochondria, thus depriving Gn of its normal Golgi localization that is required for functional glycoprotein-mediated progeny virion packaging. Consistently, the inhibitory activity of HAX1 against viral packaging and hence propagation was further elucidated in the contexts of pseudotyped and authentic CCHFV infections in cellular and animal models. Together, the findings provide a systematic CCHFV Gn/Gc-cell protein-protein interaction map, but also unravel a HAX1/mitochondrion-associated host antiviral mechanism, which may facilitate further studies on CCHFV biology and therapeutic approaches.
Functional annotation of enzyme-encoding genes using deep learning with transformer layers
Authors: Kim Gi Bae , Kim Ji Yeon , Lee Jong An , Norsigian Charles J. , Palsson Bernhard O. , Lee Sang Yup 
Published: November 2023

AbstractFunctional annotation of open reading frames in microbial genomes remains substantially incomplete. Enzymes constitute the most prevalent functional gene class in microbial genomes and can be described by their specific catalytic functions using the Enzyme Commission (EC) number. Consequently, the ability to predict EC numbers could substantially reduce the number of un-annotated genes. Here we present a deep learning model, DeepECtransformer, which utilizes transformer layers as a neural network architecture to predict EC numbers. Using the extensively studiedEscherichia coliK-12 MG1655 genome, DeepECtransformer predicted EC numbers for 464 un-annotated genes. We experimentally validated the enzymatic activities predicted for three proteins (YgfF, YciO, and YjdM). Further examination of the neural network’s reasoning process revealed that the trained neural network relies on functional motifs of enzymes to predict EC numbers. Thus, DeepECtransformer is a method that facilitates the functional annotation of uncharacterized genes.
Superior colliculus bidirectionally modulates choice activity in frontal cortex
Authors: Thomas Alyse , Yang Weiguo , Wang Catherine , Tipparaju Sri Laasya , Chen Guang , Sullivan Brennan , Swiekatowski Kylie , Tatam Mahima , Gerfen Charles , Li Nuo 
Published: November 2023

AbstractAction selection occurs through competition between potential choice options. Neural correlates of choice competition are observed across frontal cortex and downstream superior colliculus (SC) during decision-making, yet how these regions interact to mediate choice competition remains unresolved. Here we report that SC can bidirectionally modulate choice competition and drive choice activity in frontal cortex. In the mouse, topographically matched regions of frontal cortex and SC formed a descending motor pathway for directional licking and a re-entrant loop via the thalamus. During decision-making, distinct neuronal populations in both frontal cortex and SC encoded opposing lick directions and exhibited competitive interactions. SC GABAergic neurons encoded ipsilateral choice and locally inhibited glutamatergic neurons that encoded contralateral choice. Activating or suppressing these cell types could bidirectionally drive choice activity in frontal cortex. These results thus identify SC as a major locus to modulate choice competition within the broader action selection network.
Dimension-agnostic and granularity-based spatially variable gene identification using BSP
Authors: Wang Juexin , Li Jinpu , Kramer Skyler T. , Su Li , Chang Yuzhou , Xu Chunhui , Eadon Michael T. , Kiryluk Krzysztof , Ma Qin , Xu Dong 
Published: November 2023

AbstractIdentifying spatially variable genes (SVGs) is critical in linking molecular cell functions with tissue phenotypes. Spatially resolved transcriptomics captures cellular-level gene expression with corresponding spatial coordinates in two or three dimensions and can be used to infer SVGs effectively. However, current computational methods may not achieve reliable results and often cannot handle three-dimensional spatial transcriptomic data. Here we introduce BSP (big-small patch), a non-parametric model by comparing gene expression pattens at two spatial granularities to identify SVGs from two or three-dimensional spatial transcriptomics data in a fast and robust manner. This method has been extensively tested in simulations, demonstrating superior accuracy, robustness, and high efficiency. BSP is further validated by substantiated biological discoveries in cancer, neural science, rheumatoid arthritis, and kidney studies with various types of spatial transcriptomics technologies.
An adaptive stress response that confers cellular resilience to decreased ubiquitination
Authors: Hunt Liam C. , Pagala Vishwajeeth , Stephan Anna , Xie Boer , Kodali Kiran , Kavdia Kanisha , Wang Yong-Dong , Shirinifard Abbas , Curley Michelle , Graca Flavia A. , Fu Yingxue , Poudel Suresh , Li Yuxin , Wang Xusheng , Tan Haiyan , Peng Junmin , Demontis Fabio 
Published: November 2023

AbstractUbiquitination is a post-translational modification initiated by the E1 enzyme UBA1, which transfers ubiquitin to ~35 E2 ubiquitin-conjugating enzymes. While UBA1 loss is cell lethal, it remains unknown how partial reduction in UBA1 activity is endured. Here, we utilize deep-coverage mass spectrometry to define the E1-E2 interactome and to determine the proteins that are modulated by knockdown of UBA1 and of each E2 in human cells. These analyses define the UBA1/E2-sensitive proteome and the E2 specificity in protein modulation. Interestingly, profound adaptations in peroxisomes and other organelles are triggered by decreased ubiquitination. While the cargo receptor PEX5 depends on its mono-ubiquitination for binding to peroxisomal proteins and importing them into peroxisomes, we find that UBA1/E2 knockdown induces the compensatory upregulation of other PEX proteins necessary for PEX5 docking to the peroxisomal membrane. Altogether, this study defines a homeostatic mechanism that sustains peroxisomal protein import in cells with decreased ubiquitination capacity.
Robust and efficient verification of graph states in blind measurement-based quantum computation
Authors: Li Zihao , Zhu Huangjun , Hayashi Masahito 
Published: November 2023

AbstractBlind quantum computation (BQC) is a secure quantum computation method that protects the privacy of clients. Measurement-based quantum computation (MBQC) is a promising approach for realizing BQC. To obtain reliable results in blind MBQC, it is crucial to verify whether the resource graph states are accurately prepared in the adversarial scenario. However, previous verification protocols for this task are too resource-consuming or noise-susceptible to be applied in practice. Here, we propose a robust and efficient protocol for verifying arbitrary graph states with any prime local dimension in the adversarial scenario, which leads to a robust and efficient protocol for verifying the resource state in blind MBQC. Our protocol requires only local Pauli measurements and is thus easy to realize with current technologies. Nevertheless, it can achieve optimal scaling behaviors with respect to the system size and the target precision as quantified by the infidelity and significance level, which has never been achieved before. Notably, our protocol can exponentially enhance the scaling behavior with the significance level.
Improved global 250 m 8-day NDVI and EVI products from 2000–2021 using the LSTM model
Authors: Xiong Changhao , Ma Han , Liang Shunlin , He Tao , Zhang Yufang , Zhang Guodong , Xu Jianglei 
Published: November 2023

AbstractSatellite vegetation index (VI) products, such as normalized difference vegetation index (NDVI) and enhanced vegetation index (EVI), have been widely used. However, they are severely contaminated by clouds and other factors and provide false signals of the surface vegetation conditions. In this study, the new global seamless 250 m, eight-day NDVI and EVI products from 2000–2021 were developed from Moderate Resolution Imaging Spectroradiometer (MODIS) surface reflectance data using a long short-term memory (LSTM) neural network method. High-quality globally representative time series VI samples were constructed to train the model using a combination of the Savitzky-Golay filter (SG), Global LAnd Surface Satellite (GLASS) leaf area index (LAI) fitting and upper envelope methods. To evaluate the proposed method and the 250 m VI products, the MODIS VI product (MOD13Q1) was used for the inter-comparisons using four widely used VI reconstruction methods. Assuming that the MODIS VI data of high quality represents the true values, the root mean square error (RMSE) for NDVI and EVI generated by the LSTM model are 0.0734 and 0.0509, respectively.
Bioactivity properties of hydroxyapatite/clay nanocomposites
Authors: Ofudje Edwin Andrew , Akande James Asamu , Sodiya Ezekiel Folorunso , Ajayi Gabriel O. , Ademoyegun Adeniyi John , Al-Sehemi Abdullah G. , Kavil Yasar N. , Bakheet Ammar M. 
Published: November 2023

AbstractThe need for bioactive and non-toxic biomaterials is on a high demand in tissue engineering applications nowadays. Hydroxyapatite (HAp) is the chief constituent of teeth and bones in mammas. One of the major challenges with the use of HAp in engineering application is its brittleness and to overcome this, it’s important to react it with a material that can enhanced it’s fragility. To this end, HAp and HAp/clay nanocomposites were developed via wet chemical process to mimic natural HAp and to equally confer special properties such as mechanical properties, high surface area, crystallinity, high porosity, and biocompatibility on the biomaterial. The functional groups properties of the as-prepared nanocomposites analyzed by FT-IR showed that the HAp and clay posed reactive centers such as Al–Al–OH, Si–Si–OH, Si–O, PO43−, –OH, and Si–O–Al. The XRD results confirmed the formation of HAp/clay nanocomposite, while SEM and TEM images showed the morphologies of the prepared nanocomposites to be round shape particles. Besides, EDX result revealed the Ca/P ratio of HAp and HAp-C to be lower than that of stoichiometric ratio (1.67) which implies the presence of K, Na, Ca, Mg, Si and Al in the HAp/clay nanocomposite. The mechanical properties of the apatite were greatly enhanced by the addition of clay. The physiological behaviour of the fabricated apatite composites in saline solution showed steady increase in the values of the saline pH of the various biomolecules until day 5 and became fairly constant at day 7 with pH range of 7.30–7.38. Though the saline solution was acidic at the beginning due to dissolved carbon dioxide, the pH of the saline solution containing the nanocomposites gradually became neutral and fairly alkaline over time as a result of the presence of Lewis basis structures in the composites which helps in neutralizing the acidic solution. Furthermore, proliferation of apatites particles onto the surface of the nanocomposites was observed after treatment with simulated body fluids (SBF) media for 7 days. Thus, HAp/clay nanocomposites can be useful biomaterials in bone tissue engineering.
Process based modelling of plants–fungus interactions explains fairy ring types and dynamics
Authors: Salvatori Nicole , Moreno Mauro , Zotti Maurizio , Iuorio Annalisa , Cartenì Fabrizio , Bonanomi Giuliano , Mazzoleni Stefano , Giannino Francesco 
Published: November 2023

AbstractMany mushroom-forming fungi can develop circular colonies affecting the vegetation in a phenomenon named fairy rings. Since the nineteenth century, several hypotheses have been proposed to explain how fairy ring fungi form ring-like shapes instead of disks and why they produce negative or positive effects on the surrounding vegetation. In this context, we present a novel process-based mathematical model aimed at reproducing the mycelial spatial configuration of fairy rings and test different literature-supported hypotheses explaining the suppressive and stimulating effects of fungi on plants. Simulations successfully reproduced the shape of fairy rings through the accumulation of fungal self-inhibitory compounds. Moreover, regarding the negative effects of fungi on vegetation, results suggest that fungal-induced soil hydrophobicity is sufficient to reproduce all observed types of fairy rings, while the potential production of phytotoxins is not. In relation to the positive effects of fungi on plants, results show that the release of phytostimulants is needed to reproduce the vegetation patterns associated to some fairy ring types. Model outputs can guide future experiments and field work to corroborate the considered hypotheses and provide more information for further model improvements.
The effect of similarity perceptions on human cooperation and confrontation
Authors: Fischer Ilan , Savranevski Lior 
Published: November 2023

AbstractBy assuring aversive actions are followed by similarly aversive reactions, legislators of antiquity aimed to reduce belligerence and aggression. In the present study we show how similarity perceptions drive cooperation and confrontation across several strategic decision types. Examining the choices made in three one-shot symmetric conflict games: the prisoner’s dilemma, the chicken, and the battle of the sexes, we show how a short encounter with a stranger accounts for the formation of subjective similarity perceptions, which together with the expected payoffs of the game determine the choice of the preferred alternative. We describe the role of similarity perceptions for all two-by-two games, specifically for a subset of fifty-seven games that are sensitive to similarity perceptions with the opponent. We then suggest that this mechanism, by which individuals maximize expected payoffs, is key to the understanding of the evolution of cooperation and confrontation.
Chest compression quality and patient outcomes with the use of a CPR feedback device: A retrospective study
Authors: Leo Wen Zhe , Chua Damien , Tan Hui Cheng , Ho Vui Kian 
Published: November 2023

AbstractFeedback devices were developed to guide resuscitations as targets recommended by various guidelines are difficult to achieve. Yet, there is limited evidence to support their use for in-hospital cardiac arrests (IHCA), and they did not correlate with patient outcomes. Therefore, this study has investigated the compression quality and patient outcomes in IHCA with the use of a feedback device via a retrospective study of inpatient code blue activations in a Singapore hospital over one year. The primary outcome was compression quality and secondary outcomes were survival, downtime and neurological status. 64 of 110 (58.2%) cases were included. Most resuscitations (71.9%) met the recommended chest compression fraction (CCF, defined as the proportion of time spent on compressions during resuscitation) despite overall quality being suboptimal. Greater survival to discharge and better neurological status in resuscitated patients respectively correlated with higher median CCF (p = 0.040 and 0.026 respectively) and shorter downtime (p < 0.001 and 0.001 respectively); independently, a higher CCF correlated with a shorter downtime (p = 0.014). Overall, this study demonstrated that reducing interruptions is crucial for good outcomes in IHCA. However, compression quality remained suboptimal despite feedback device implementation, possibly requiring further simulation training and coaching. Future multicentre studies incorporating these measures should be explored.
High-confinement alumina waveguides with sub-dB/cm propagation losses at 450 nm
Authors: McKay Elissa , Pruiti Natale G. , May Stuart , Sorel Marc 
Published: November 2023

AbstractAmorphous alumina is highly transparent across the visible spectrum, making it a promising candidate for low-loss waveguiding at short wavelengths. However, previous alumina waveguide demonstrations in the visible region have focused on low- to moderate-confinement waveguides, where the diffuse mode reduces the design flexibility and integration density of photonic integrated circuits. Here, we have developed a high-quality etch mask and a highly selective BCl3 plasma etch, allowing etching of amorphous alumina waveguides up to 800 nm thick. Using this process, we have fabricated waveguides using an alumina film grown by atomic layer deposition (ALD) which are the lowest-loss high-confinement waveguides for blue light to date: we achieve single-mode propagation losses of 0.8 dB/cm at a propagation wavelength of 450 nm.