bluuebunny/crossref_metadata_2025 huggingface dataset:
Bulk-local-density-of-state correspondence in topological insulators
Authors: Xie Biye , Huang Renwen , Jia Shiyin , Lin Zemeng , Hu Junzheng , Jiang Yao , Ma Shaojie , Zhan Peng , Lu Minghui , Wang Zhenlin , Chen Yanfeng , Zhang Shuang
Published: November 2023

In the quest to connect bulk topological quantum numbers to measurable parameters in real materials, current established approaches often necessitate specific conditions, limiting their applicability. Here we propose and demonstrate an approach to link the non-trivial hierarchical bulk topology to the multidimensional partition of local density of states (LDOS), denoted as the bulk-LDOS correspondence. In finite-size topologically nontrivial photonic crystals, we observe the LDOS partitioned into three distinct regions: a two-dimensional interior bulk area, a one-dimensional edge region, and zero-dimensional corner sites. Contrarily, topologically trivial cases exhibit uniform LDOS distribution across the entire two-dimensional bulk area. Our findings provide a general framework for distinguishing topological insulators and uncovering novel aspects of topological directional band-gap materials, even in the absence of in-gap states.
Evidence of an upper ionospheric electric field perturbation correlated with a gamma ray burst
Authors: Piersanti Mirko , Ubertini Pietro , Battiston Roberto , Bazzano Angela , D’Angelo Giulia , Rodi James G. , Diego Piero , Zeren Zhima , Ammendola Roberto , Badoni Davide , Bartocci Simona , Beolè Stefania , Bertello Igor , Burger William J. , Campana Donatella , Cicone Antonio , Cipollone Piero , Coli Silvia , Conti Livio , Contin Andrea , Cristoforetti Marco , De Angelis Fabrizio , De Donato Cinzia , De Santis Cristian , Di Luca Andrea , Fiorenza Emiliano , Follega Francesco Maria , Gebbia Giuseppe , Iuppa Roberto , Lega Alessandro , Lolli Mauro , Martino Bruno , Martucci Matteo , Masciantonio Giuseppe , Mergè Matteo , Mese Marco , Morbidini Alfredo , Neubüser Coralie , Nozzoli Francesco , Nuccilli Fabrizio , Oliva Alberto , Osteria Giuseppe , Palma Francesco , Palmonari Federico , Panico Beatrice , Papini Emanuele , Parmentier Alexandra , Perciballi Stefania , Perfetto Francesco , Perinelli Alessio , Picozza Piergiorgio , Pozzato Michele , Rebustini Gianmaria , Recchiuti Dario , Ricci Ester , Ricci Marco , Ricciarini Sergio B. , Russi Andrea , Sahnoun Zuleika , Savino Umberto , Scotti Valentina , Shen Xuhui , Sotgiu Alessandro , Sparvoli Roberta , Tofani Silvia , Vertolli Nello , Vilona Veronica , Vitale Vincenzo , Zannoni Ugo , Zoffoli Simona , Zuccon Paolo
Published: November 2023

Earth’s atmosphere, whose ionization stability plays a fundamental role for the evolution and endurance of life, is exposed to the effect of cosmic explosions producing high energy Gamma-ray-bursts. Being able to abruptly increase the atmospheric ionization, they might deplete stratospheric ozone on a global scale. During the last decades, an average of more than one Gamma-ray-burst per day were recorded. Nevertheless, measurable effects on the ionosphere were rarely observed, in any case on its bottom-side (from about 60 km up to about 350 km of altitude). Here, we report evidence of an intense top-side (about 500 km) ionospheric perturbation induced by significant sudden ionospheric disturbance, and a large variation of the ionospheric electric field at 500 km, which are both correlated with the October 9, 2022 Gamma-ray-burst (GRB221009A).
A robotic sensory system with high spatiotemporal resolution for texture recognition
Authors: Bai Ningning , Xue Yiheng , Chen Shuiqing , Shi Lin , Shi Junli , Zhang Yuan , Hou Xingyu , Cheng Yu , Huang Kaixi , Wang Weidong , Zhang Jin , Liu Yuan , Guo Chuan Fei
Published: November 2023

Humans can gently slide a finger on the surface of an object and identify it by capturing both static pressure and high-frequency vibrations. Although modern robots integrated with flexible sensors can precisely detect pressure, shear force, and strain, they still perform insufficiently or require multi-sensors to respond to both static and high-frequency physical stimuli during the interaction. Here, we report a real-time artificial sensory system for high-accuracy texture recognition based on a single iontronic slip-sensor, and propose a criterion—spatiotemporal resolution, to corelate the sensing performance with recognition capability. The sensor can respond to both static and dynamic stimuli (0-400 Hz) with a high spatial resolution of 15 μm in spacing and 6 μm in height, together with a high-frequency resolution of 0.02 Hz at 400 Hz, enabling high-precision discrimination of fine surface features. The sensory system integrated on a prosthetic fingertip can identify 20 different commercial textiles with a 100.0% accuracy at a fixed sliding rate and a 98.9% accuracy at random sliding rates. The sensory system is expected to help achieve subtle tactile sensation for robotics and prosthetics, and further be applied to haptic-based virtual reality and beyond.
Targeted suppression of mTORC2 reduces seizures across models of epilepsy
Authors: Okoh James , Mays Jacqunae , Bacq Alexandre , Oses-Prieto Juan A. , Tyanova Stefka , Chen Chien-Ju , Imanbeyev Khalel , Doladilhe Marion , Zhou Hongyi , Jafar-Nejad Paymaan , Burlingame Alma , Noebels Jeffrey , Baulac Stephanie , Costa-Mattioli Mauro
Published: November 2023

Epilepsy is a neurological disorder that poses a major threat to public health. Hyperactivation of mTOR complex 1 (mTORC1) is believed to lead to abnormal network rhythmicity associated with epilepsy, and its inhibition is proposed to provide some therapeutic benefit. However, mTOR complex 2 (mTORC2) is also activated in the epileptic brain, and little is known about its role in seizures. Here we discover that genetic deletion of mTORC2 from forebrain neurons is protective against kainic acid-induced behavioral and EEG seizures. Furthermore, inhibition of mTORC2 with a specific antisense oligonucleotide robustly suppresses seizures in several pharmacological and genetic mouse models of epilepsy. Finally, we identify a target of mTORC2, Nav1.2, which has been implicated in epilepsy and neuronal excitability. Our findings, which are generalizable to several models of human seizures, raise the possibility that inhibition of mTORC2 may serve as a broader therapeutic strategy against epilepsy.
Clinically relevant antibiotic resistance genes are linked to a limited set of taxa within gut microbiome worldwide
Authors: Diebold Peter J. , Rhee Matthew W. , Shi Qiaojuan , Trung Nguyen Vinh , Umrani Fayaz , Ahmed Sheraz , Kulkarni Vandana , Deshpande Prasad , Alexander Mallika , Thi Hoa Ngo , Christakis Nicholas A. , Iqbal Najeeha Talat , Ali Syed Asad , Mathad Jyoti S. , Brito Ilana L.
Published: November 2023

The acquisition of antimicrobial resistance (AR) genes has rendered important pathogens nearly or fully unresponsive to antibiotics. It has been suggested that pathogens acquire AR traits from the gut microbiota, which collectively serve as a global reservoir for AR genes conferring resistance to all classes of antibiotics. However, only a subset of AR genes confers resistance to clinically relevant antibiotics, and, although these AR gene profiles are well-characterized for common pathogens, less is known about their taxonomic associations and transfer potential within diverse members of the gut microbiota. We examined a collection of 14,850 human metagenomes and 1666 environmental metagenomes from 33 countries, in addition to nearly 600,000 isolate genomes, to gain insight into the global prevalence and taxonomic range of clinically relevant AR genes. We find that several of the most concerning AR genes, such as those encoding the cephalosporinase CTX-M and carbapenemases KPC, IMP, NDM, and VIM, remain taxonomically restricted to Proteobacteria. Even cfiA, the most common carbapenemase gene within the human gut microbiome, remains tightly restricted to Bacteroides, despite being found on a mobilizable plasmid. We confirmed these findings in gut microbiome samples from India, Honduras, Pakistan, and Vietnam, using a high-sensitivity single-cell fusion PCR approach. Focusing on a set of genes encoding carbapenemases and cephalosporinases, thus far restricted to Bacteroides species, we find that few mutations are required for efficacy in a different phylum, raising the question of why these genes have not spread more widely. Overall, these data suggest that globally prevalent, clinically relevant AR genes have not yet established themselves across diverse commensal gut microbiota.
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

We 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

Genomic 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

Electrocatalytic 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

The 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

Crimean-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

Functional 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

Action 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

Identifying 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

Ubiquitination 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

Blind 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

Satellite 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

The 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

Many 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

By 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

Feedback 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

Amorphous 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.
3D patient-specific modeling and structural finite element analysis of atherosclerotic carotid artery based on computed tomography angiography
Authors: Curcio Nicoletta , Rosato Antonio , Mazzaccaro Daniela , Nano Giovanni , Conti Michele , Matrone Giulia
Published: November 2023

The assessment of carotid plaque vulnerability is a relevant clinical information that can help prevent adverse cerebrovascular events. To this aim, in this study, we propose a patient-specific computational workflow to quantify the stress distribution in an atherosclerotic carotid artery, by means of geometric modeling and structural simulation of the plaque and vessel wall. Ten patients were involved in our study. Starting with segmentation of the lumen, calcific and lipid plaque components from computed tomography angiography images, the fibrous component and the vessel wall were semi-automatically reconstructed with an ad-hoc procedure. Finite element analyses were performed using local pressure values derived from ultrasound imaging. Simulation outputs were analyzed to assess how mechanical factors influence the stresses within the atherosclerotic wall. The developed reconstruction method was first evaluated by comparing the results obtained using the automatically generated fibrous component model and the one derived from image segmentation. The high-stress regions in the carotid artery wall around plaques suggest areas of possible rupture. In mostly lipidic and heterogeneous plaques, the highest stresses are localized at the interface between the lipidic components and the lumen, in the fibrous cap.
Emerging infectious disease surveillance using a hierarchical diagnosis model and the Knox algorithm
Authors: Wang Mengying , Yang Bingqing , Liu Yunpeng , Yang Yingyun , Ji Hong , Yang Cheng
Published: November 2023

Emerging infectious diseases are a critical public health challenge in the twenty-first century. The recent proliferation of such diseases has raised major social and economic concerns. Therefore, early detection of emerging infectious diseases is essential. Subjects from five medical institutions in Beijing, China, which met the spatial-specific requirements, were analyzed. A quality control process was used to select 37,422 medical records of infectious diseases and 56,133 cases of non-infectious diseases. An emerging infectious disease detection model (EIDDM), a two-layer model that divides the problem into two sub-problems, i.e., whether a case is an infectious disease, and if so, whether it is a known infectious disease, was proposed. The first layer model adopts the binary classification model TextCNN-Attention. The second layer is a multi-classification model of LightGBM based on the one-vs-rest strategy. Based on the experimental results, a threshold of 0.5 is selected. The model results were compared with those of other models such as XGBoost and Random Forest using the following evaluation indicators: accuracy, sensitivity, specificity, positive predictive value, and negative predictive value. The prediction performance of the first-layer TextCNN is better than that of other comparison models. Its average specificity for non-infectious diseases is 97.57%, with an average negative predictive value of 82.63%, indicating a low risk of misdiagnosing non-infectious diseases as infectious (i.e., a low false positive rate). Its average positive predictive value for eight selected infectious diseases is 95.07%, demonstrating the model's ability to avoid misdiagnoses. The overall average accuracy of the model is 86.11%. The average prediction accuracy of the second-layer LightGBM model for emerging infectious diseases reaches 90.44%. Furthermore, the response time of a single online reasoning using the LightGBM model is approximately 27 ms, which makes it suitable for analyzing clinical records in real time. Using the Knox method, we found that all the infectious diseases were within 2000 m in our case, and a clustering feature of spatiotemporal interactions (P < 0.05) was observed as well. Performance testing and model comparison results indicated that the EIDDM is fast and accurate and can be used to monitor the onset/outbreak of emerging infectious diseases in real-world hospitals.
Developmental and foliation changes due to dysregulation of adenosine kinase in the cerebellum
Authors: Gebril Hoda M. , Lai Tho , Fedele Denise E. , Wahba Amir
Published: November 2023

Adenosine kinase (ADK), the major adenosine-metabolizing enzyme, plays a key role in brain development and disease. In humans, mutations in the Adk gene have been linked to developmental delay, stunted growth, and intellectual disability. To better understand the role of ADK in brain development, it is important to dissect the specific roles of the two isoforms of the enzyme expressed in the cytoplasm (ADK-S) and cell nucleus (ADK-L). We, therefore, studied brain development in Adk-tg transgenic mice, which only express ADK-S in the absence of ADK-L throughout development. In the mutant animals, we found a reduction in the overall brain, body size, and weight during fetal and postnatal development. As a major developmental abnormality, we found a profound change in the foliation pattern of the cerebellum. Strikingly, our results indicated aberrant Purkinje cells arborization at P9 and accelerated cell death at P6 and P9. We found defects in cerebellar cell proliferation and migration using a bromodeoxyuridine (BrdU)-based cell proliferation assay at postnatal day 7. Our data demonstrate that dysregulation of ADK expression during brain development profoundly affects brain growth and differentiation.
Estimating the effectiveness of electric vehicles braking when determining the circumstances of a traffic accident
Authors: Kashkanov Andrii , Semenov Andriy , Kashkanova Anastasiia , Kryvinska Natalia , Palchevskyi Oleg , Baraban Serhii
Published: November 2023

In the vast majority of cases, the braking process is used to prevent traffic accidents. The effectiveness of this process depends on the design and functionality of vehicle braking systems (presence of anti-lock braking system, emergency braking system, preventive safety systems, etc.) and is limited by the amount of frictional forces in contact of tires with the road. The improvement of methodical approaches to evaluating the effectiveness of braking of cars contributes to increasing the accuracy and objectivity of establishing the circumstances of the occurrence of emergency situations. The paper analyses existing methods of evaluating the braking parameters of vehicles (including those with an electric drive) and modern methods of evaluating electric vehicle braking parameters and conducting auto-technical investigations of traffic accidents, which relate to using different methodological approaches and digital technologies at all stages of expert research. In contrast to existing models, the proposed mathematical model for estimating the trajectory of two-axle cars during braking allows for considering various types of input parameter uncertainty, reducing the range of possible modeling errors by 39%. Comparing simulation results and experimental data showed that the average relative error is 4.58%, and the maximum error did not exceed 7.82%. The performed study of the stability of the electric vehicles' movement during emergency braking with the help of developed mathematical models in the Mathcad software environment reveals the content of the algorithm of a similar calculation in specialized computer programs of auto technical examination. Conducting such calculations is relevant in the analysis of real accident situations, where specific circumstances and features that cannot be considered during modeling in specialized software must be taken into account. Simultaneously, the probability of type I errors is reduced by 2–19%, and type II errors are reduced by 43–68%.
Enhancing the direct charging performance of an open quantum battery by adjusting its velocity
Authors: Mojaveri B. , Jafarzadeh Bahrbeig R. , Fasihi M. A. , Babanzadeh S.
Published: November 2023

The performance of open quantum batteries (QBs) is severely limited by decoherence due to the interaction with the surrounding environment. So, protecting the charging processes against decoherence is of great importance for realizing QBs. In this work we address this issue by developing a charging process of a qubit-based open QB composed of a qubit-battery and a qubit-charger, where each qubit moves inside an independent cavity reservoir. Our results show that, in both the Markovian and non-Markovian dynamics, the charging characteristics, including the charging energy, efficiency and ergotropy, regularly increase with increasing the speed of charger and battery qubits. Interestingly, when the charger and battery move with higher velocities, the initial energy of the charger is completely transferred to the battery in the Markovian dynamics. In this situation, it is possible to extract the total stored energy as work for a long time. Our findings show that open moving-qubit systems are robust and reliable QBs, thus making them a promising candidate for experimental implementations.
Functionality, physical activity, fatigue and quality of life in patients with acute COVID-19 and Long COVID infection
Authors: Vélez-Santamaría Rodrigo , Fernández-Solana Jessica , Méndez-López Fátima , Domínguez-García Marta , González-Bernal Jerónimo J. , Magallón-Botaya Rosa , Oliván-Blázquez Bárbara , González-Santos Josefa , Santamaría-Peláez Mirian
Published: November 2023

A prominent feature of COVID-19, both in the short and long term, is the reduction in quality of life (QoL) due to low functionality scores and the presence of fatigue, which can hinder daily activities. The main objective of this study is to compare the functional status, level of physical activity, fatigue, and QoL of patients with Long COVID to other COVID-19 patients who did not develop persistent illness, and to determine whether there is a relationship between these variables and QoL. A cross-sectional study was conducted with 170 participants who had been infected with COVID-19 or had developed Long COVID. The main variables studied were functionality, physical activity, QoL and fatigue, measured using the PostCOVID-19 Functional Status Scale (PCFS), International Physical Activity Questionnaire (IPAQ), Short Form 12 (SF-12), and Fatigue Severity Scale (FSS). The main findings show a significant relationship (p < 0.001) between reduced functionality, lower physical activity levels, increased fatigue severity, and poorer QoL in Long COVID patients. Furthermore, these variables are also related to worse QoL, but only functional status predicts it. In conclusion, our results have shown highly significant correlations between the group with COVID-19 and Long COVID regarding functional status, level of physical activity, QoL, and fatigue.
Curcumin enhances elvitegravir concentration and alleviates oxidative stress and inflammatory response
Authors: Godse Sandip , Zhou Lina , Sinha Namita , Kodidela Sunitha , Kumar Asit , Singh Udai P. , Kumar Santosh
Published: November 2023

In this study, we investigated the potential of using curcumin (CUR) as an adjuvant to enhance the delivery of antiretroviral drug elvitegravir (EVG) across the BBB, and alleviate oxidative stress and inflammatory response, which are the major hallmark of HIV neuropathogenesis. In a mouse model, we compared the biodistribution of EVG alone and in combination with CUR using intraperitoneal (IP) and intranasal (IN) routes. IN administration showed a significantly higher accumulation of EVG in the brain, while both IP and IN routes led to increased EVG levels in the lungs and liver. The addition of CUR further enhanced EVG brain delivery, especially when administered via the IN route. The expression of neural marker proteins, synaptophysin, L1CAM, NeuN, and GFAP was not significantly altered by EVG or CUR alone or their combination, indicating preserved neural homeostasis. After establishing improved brain concentration and safety of CUR-adjuvanted EVG in mice in acute treatment, we studied the effect of this treatment in HIV-infected U1 macrophages. In U1 macrophages, we also observed that the addition of CUR enhanced the intracellular concentration of EVG. The total area under the curve (AUCtot) for EVG was significantly higher in the presence of CUR. We also evaluated the effects of CUR on oxidative stress and antioxidant capacity in EVG-treated U1 macrophages. CUR reduced oxidative stress, as evidenced by decreased reactive oxygen species (ROS) levels and elevated antioxidant enzyme expression. Furthermore, the combination of CUR and EVG exhibited a significant reduction in proinflammatory cytokines (TNFα, IL-1β, IL-18) and chemokines (RANTES, MCP-1) in U1 macrophages. Additionally, western blot analysis confirmed the decreased expression of IL-1β and TNF-α in EVG + CUR-treated cells. These findings suggest the potential of CUR to enhance EVG permeability to the brain and subsequent efficacy of EVG, including HIV neuropathogenesis.
Context dependent cognitive development in Bhutanese children
Authors: Gredebäck Gustaf , Dorji Nidup , Sen Umay , Nyström Pär , Hellberg Johanna , Wangchuk
Published: November 2023

We assessed risk/protective factors for cognitive development of Bhutanese children (504 3–5 year-olds, 49% girls, major ethnicities Ngalop 26%, Tshangla 30%, Lhotsampa 34%) using a non-verbal test of cognitive capacity (SON-R) and primary caregiver interviews. Cognitive capacity was related to the family’s SES and whether the family belonged to the primary Buddhist majority ethnic groups (Ngalop or Tshangla) or primarily Hindu minorities (Lhotsampa). In majority families more engagement in Buddhist practices was associated with higher cognitive capacity in children. Minority children were more impacted by parents autonomous-relatedness values. Results demonstrate that cognitive development is dependent on the financial and educational context of the family, societal events, and culture specific risk/protective factors that differ across sub-groups (majority/minority, culture/religion).
Next-generation genetic sexing strain establishment in the agricultural pest Ceratitis capitata
Authors: Davydova Serafima , Liu Junru , Kandul Nikolay P. , Braswell W. Evan , Akbari Omar S. , Meccariello Angela
Published: November 2023

Tephritid fruit fly pests pose an increasing threat to the agricultural industry due to their global dispersion and a highly invasive nature. Here we showcase the feasibility of an early-detection SEPARATOR sex sorting approach through using the non-model Tephritid pest, Ceratitis capitata. This system relies on female-only fluorescent marker expression, accomplished through the use of a sex-specific intron of the highly-conserved transformer gene from C. capitata and Anastrepha ludens. The herein characterized strains have 100% desired phenotype outcomes, allowing accurate male–female separation during early development. Overall, we describe an antibiotic and temperature-independent sex-sorting system in C. capitata, which, moving forward, may be implemented in other non-model Tephritid pest species. This strategy can facilitate the establishment of genetic sexing systems with endogenous elements exclusively, which, on a wider scale, can improve pest population control strategies like sterile insect technique.