bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cryo-EM structures of Thogoto virus polymerase reveal unique RNA transcription and replication mechanisms among orthomyxoviruses
Authors: Xue Lu , Chang Tiancai , Li Zimu , Wang Chenchen , Zhao Heyu , Li Mei , Tang Peng , Wen Xin , Yu Mengmeng , Wu Jiqin , Bao Xichen , Wang Xiaojun , Gong Peng , He Jun , Chen Xinwen , Xiong Xiaoli 
Published: May 2024

AbstractInfluenza viruses and thogotoviruses account for most recognized orthomyxoviruses. Thogotoviruses, exemplified by Thogoto virus (THOV), are capable of infecting humans using ticks as vectors. THOV transcribes mRNA without the extraneous 5′ end sequences derived from cap-snatching in influenza virus mRNA. Here, we report cryo-EM structures to characterize THOV polymerase RNA synthesis initiation and elongation. The structures demonstrate that THOV RNA transcription and replication are able to start with short dinucleotide primers and that the polymerase cap-snatching machinery is likely non-functional. Triggered by RNA synthesis, asymmetric THOV polymerase dimers can form without the involvement of host factors. We confirm that, distinctive from influenza viruses, THOV-polymerase RNA synthesis is weakly dependent of the host factors ANP32A/B/E in human cells. This study demonstrates varied mechanisms in RNA synthesis and host factor utilization among orthomyxoviruses, providing insights into the mechanisms behind thogotoviruses’ broad-infectivity range.
Observation of the photonic Hall effect and photonic magnetoresistance in random lasers
Authors: Du Wenyu , Hu Lei , Xia Jiangying , Zhang Lin , Li Siqi , Kuai Yan , Cao Zhigang , Xu Feng , Liu Yu , Zhou Kaiming , Xie Kang , Yu Benli , Raposo Ernesto P. , Gomes Anderson S. L. , Hu Zhijia 
Published: May 2024

AbstractModulation of scattering in random lasers (RLs) by magnetic fields has attracted much attention due to its rich physical insights. We fabricate magnetic gain polymer optical fiber to generate RLs. From macroscopic experimental phenomena, with the increase of the magnetic field strength, the magnetic transverse photocurrent exists in disordered multiple scattering of RLs and the emission intensity of RLs decreases, which is the experimental observation of photonic Hall effect (PHE) and photonic magnetoresistance (PMR) in RLs. At the microscopic level, based on the field dependence theory of magnetic disorder in scattered nanoparticles and the replica symmetry breaking theory, the magnetic-induced transverse diffusion of photons reduces the scattering disorder, and then decreases the intensity fluctuation disorder of RLs. Our work establishes a connection between the above two effects and RLs, visualizes the influence of magnetic field on RL scattering at the microscopic level, which is crucial for the design of RLs.
An NLR paralog Pit2 generated from tandem duplication of Pit1 fine-tunes Pit1 localization and function
Authors: Li Yuying , Wang Qiong , Jia Huimin , Ishikawa Kazuya , Kosami Ken-ichi , Ueba Takahiro , Tsujimoto Atsumi , Yamanaka Miki , Yabumoto Yasuyuki , Miki Daisuke , Sasaki Eriko , Fukao Yoichiro , Fujiwara Masayuki , Kaneko-Kawano Takako , Tan Li , Kojima Chojiro , Wing Rod A. , Sebastian Alfino , Nishimura Hideki , Fukada Fumi , Niu Qingfeng , Shimizu Motoki , Yoshida Kentaro , Terauchi Ryohei , Shimamoto Ko , Kawano Yoji 
Published: May 2024

AbstractNLR family proteins act as intracellular receptors. Gene duplication amplifies the number of NLR genes, and subsequent mutations occasionally provide modifications to the second gene that benefits immunity. However, evolutionary processes after gene duplication and functional relationships between duplicated NLRs remain largely unclear. Here, we report that the rice NLR protein Pit1 is associated with its paralogue Pit2. The two are required for the resistance to rice blast fungus but have different functions: Pit1 induces cell death, while Pit2 competitively suppresses Pit1-mediated cell death. During evolution, the suppression of Pit1 by Pit2 was probably generated through positive selection on two fate-determining residues in the NB-ARC domain of Pit2, which account for functional differences between Pit1 and Pit2. Consequently, Pit2 lost its plasma membrane localization but acquired a new function to interfere with Pit1 in the cytosol. These findings illuminate the evolutionary trajectory of tandemly duplicated NLR genes after gene duplication.
Structural basis for selectivity and antagonism in extracellular GPCR-nanobodies
Authors: Schlimgen Roman R. , Peterson Francis C. , Heukers Raimond , Smit Martine J. , McCorvy John D. , Volkman Brian F. 
Published: May 2024

AbstractG protein-coupled receptors (GPCRs) are pivotal therapeutic targets, but their complex structure poses challenges for effective drug design. Nanobodies, or single-domain antibodies, have emerged as a promising therapeutic strategy to target GPCRs, offering advantages over traditional small molecules and antibodies. However, an incomplete understanding of the structural features enabling GPCR-nanobody interactions has limited their development. In this study, we investigate VUN701, a nanobody antagonist targeting the atypical chemokine receptor 3 (ACKR3). We determine that an extended CDR3 loop is required for ACKR3 binding. Uncommon in most nanobodies, an extended CDR3 is prevalent in GPCR-targeting nanobodies. Combining experimental and computational approaches, we map an inhibitory ACKR3-VUN701 interface and define a distinct conformational mechanism for GPCR inactivation. Our results provide insights into class A GPCR-nanobody selectivity and suggest a strategy for the development of these new therapeutic tools.
Robotic wireless capsule endoscopy: recent advances and upcoming technologies
Authors: Cao Qing , Deng Runyi , Pan Yue , Liu Ruijie , Chen Yicheng , Gong Guofang , Zou Jun , Yang Huayong , Han Dong 
Published: May 2024

AbstractWireless capsule endoscopy (WCE) offers a non-invasive evaluation of the digestive system, eliminating the need for sedation and the risks associated with conventional endoscopic procedures. Its significance lies in diagnosing gastrointestinal tissue irregularities, especially in the small intestine. However, existing commercial WCE devices face limitations, such as the absence of autonomous lesion detection and treatment capabilities. Recent advancements in micro-electromechanical fabrication and computational methods have led to extensive research in sophisticated technology integration into commercial capsule endoscopes, intending to supersede wired endoscopes. This Review discusses the future requirements for intelligent capsule robots, providing a comparative evaluation of various methods’ merits and disadvantages, and highlighting recent developments in six technologies relevant to WCE. These include near-field wireless power transmission, magnetic field active drive, ultra-wideband/intrabody communication, hybrid localization, AI-based autonomous lesion detection, and magnetic-controlled diagnosis and treatment. Moreover, we explore the feasibility for future “capsule surgeons”.
Structural insights into the DNA topoisomerase II of the African swine fever virus
Authors: Cong Jingyuan , Xin Yuhui , Kang Huiling , Yang Yunge , Wang Chenlong , Zhao Dongming , Li Xuemei , Rao Zihe , Chen Yutao 
Published: May 2024

AbstractType II topoisomerases are ubiquitous enzymes that play a pivotal role in modulating the topological configuration of double-stranded DNA. These topoisomerases are required for DNA metabolism and have been extensively studied in both prokaryotic and eukaryotic organisms. However, our understanding of virus-encoded type II topoisomerases remains limited. One intriguing example is the African swine fever virus, which stands as the sole mammalian-infecting virus encoding a type II topoisomerase. In this work, we use several approaches including cryo-EM, X-ray crystallography, and biochemical assays to investigate the structure and function of the African swine fever virus type II topoisomerase, pP1192R. We determine the structures of pP1192R in different conformational states and confirm its enzymatic activity in vitro. Collectively, our results illustrate the basic mechanisms of viral type II topoisomerases, increasing our understanding of these enzymes and presenting a potential avenue for intervention strategies to mitigate the impact of the African swine fever virus.
Neuronal tuning and population representations of shape and category in human visual cortex
Authors: Bougou Vasiliki , Vanhoyland Michaël , Bertrand Alexander , Van Paesschen Wim , Op De Beeck Hans , Janssen Peter , Theys Tom 
Published: May 2024

AbstractObject recognition and categorization are essential cognitive processes which engage considerable neural resources in the human ventral visual stream. However, the tuning properties of human ventral stream neurons for object shape and category are virtually unknown. We performed large-scale recordings of spiking activity in human Lateral Occipital Complex in response to stimuli in which the shape dimension was dissociated from the category dimension. Consistent with studies in nonhuman primates, the neuronal representations were primarily shape-based, although we also observed category-like encoding for images of animals. Surprisingly, linear decoders could reliably classify stimulus category even in data sets that were entirely shape-based. In addition, many recording sites showed an interaction between shape and category tuning. These results represent a detailed study on shape and category coding at the neuronal level in the human ventral visual stream, furnishing essential evidence that reconciles human imaging and macaque single-cell studies.
Systematic assessment of ISWI subunits shows that NURF creates local accessibility for CTCF
Authors: Iurlaro Mario , Masoni Francesca , Flyamer Ilya M. , Wirbelauer Christiane , Iskar Murat , Burger Lukas , Giorgetti Luca , Schübeler Dirk 
Published: May 2024

AbstractCatalytic activity of the imitation switch (ISWI) family of remodelers is critical for nucleosomal organization and DNA binding of certain transcription factors, including the insulator protein CTCF. Here we define the contribution of individual subcomplexes by deriving a panel of isogenic mouse stem cell lines, each lacking one of six ISWI accessory subunits. Individual deletions of subunits of either CERF, RSF, ACF, WICH or NoRC subcomplexes only moderately affect the chromatin landscape, while removal of the NURF-specific subunit BPTF leads to a strong reduction in chromatin accessibility and SNF2H ATPase localization around CTCF sites. This affects adjacent nucleosome occupancy and CTCF binding. At a group of sites with reduced chromatin accessibility, CTCF binding persists but cohesin occupancy is reduced, resulting in decreased insulation. These results suggest that CTCF binding can be separated from its function as an insulator in nuclear organization and identify a specific role for NURF in mediating SNF2H localization and chromatin opening at bound CTCF sites.
Research on the interaction between trench material and pipeline under fault displacement
Authors: Yang Ming , Wang Dongyuan , Jia Haidong , Hu Wenjun , Zhao Yu , Tang Jungfeng 
Published: May 2024

AbstractWith the large-scale construction of oil and gas pipelines, the safety issues of long-distance buried pipelines in the service and construction have become increasingly prominent. The complex geological and topographical conditions of the special zone will put forwards extremely high requirements on pipe trench laying backfill materials and construction technology. For example, pipelines are inevitable to cross the active fault, while the trench backfilled with soil has limitations in protecting them from failure under the active fault displacement caused by the earthquake. Therefore, it is necessary to study the pipe–soil interaction mechanism, determine the stress state of the pipeline and propose a new backfilling material that can protect the pipeline from failure. Foam concrete (FC) provides a new choice to backfill the buried pipeline trench due to its high-homogeneity, lightweight, controllable-strength, and self-compacting. To further determine the applicability of the FC, the pipe-FC interaction mechanism is studied. Then, a FE model of the FC-pipeline-soil interaction system is established by Abaqus to quantitatively analyze the applicability of the FC based on the experimental data of the mechanical performance of the FC. It proves that using FC as trench backfill material has a noticeable protective effect on the pipeline under the earthquake-induced displacement of the normal fault. Furthermore, FC has a better protective effect on the pipeline subjected to compressive than tensile. Therefore, the reference for applying FC in trench backfilling of pipelines crossing normal fault is provided.
Mechanisms of cordycepin in the treatment of pulmonary arterial hypertension in rats based on metabonomics and transcriptomics
Authors: Lin Jiangpeng , Chen Riken , Liao Huizhao , Zhang Yuzhuo , Zheng Zhenzhen , Hong Cheng 
Published: May 2024

AbstractPulmonary arterial hypertension (PAH) is a fatal disease featured by high morbidity and mortality. Although Cordycepin is known for its anti-inflammatory, antioxidant and immune-enhancing effects, its role in PAH treatment and the underlying mechanisms remain unclear. The therapeutic effects of Cordycepin on rats with PAH were investigated using a monocrotaline (MCT)-induced rat model. The metabolic effects of Cordycepin were assessed based on the plasma metabolome. The potential mechanisms of Cordycepin in PAH treatment were investigated through transcriptome sequencing and validated in pulmonary artery smooth muscle cells (PASMC). Evaluations included hematoxylin and eosin staining for pulmonary vascular remodeling, CCK-8 assay, EDU, and TUNEL kits for cell viability, proliferation, and apoptosis, respectively, and western blot for protein expression. Cordycepin significantly reduced right ventricular systolic pressure (RVSP) and right ventricular hypertrophy index (RVHI) in PAH rats, and mitigated pulmonary vascular remodeling. Plasma metabolomics showed that Cordycepin could reverse the metabolic disorders in the lungs of MCT-induced PAH rats, particularly impacting linoleic acid and alpha-linolenic acid metabolism pathways. Transcriptomics revealed that the P53 pathway might be the primary pathway involved, and western blot results showed that Cordycepin significantly increased P53 and P21 protein levels in lung tissues. Integrated analysis of transcriptomics and metabolomics suggested that these pathways were mainly enriched in linoleic acid metabolism and alpha-linolenic acid metabolism pathway. In vitro experiments demonstrated that Cordycepin significantly inhibited the PDGFBB (PD)-induced abnormal proliferation and migration of PASMC and promoted PD-induced apoptosis. Meanwhile, Cordycepin enhanced the expression levels of P53 and P21 proteins in PD-insulted PASMC. However, inhibitors of P53 and P21 eliminated these effects of Cordycepin. Cordycepin may activate the P53–P21 pathway to inhibit abnormal proliferation and migration of PASMC and promote apoptosis, offering a potential approach for PAH treatment.
Exploring the transcriptome of immature stages of Ornithodoros hermsi, the soft-tick vector of tick-borne relapsing fever
Authors: de Sousa-Paula Lucas C. , Berger Markus , Talyuli Octavio A. C. , Schwartz Cindi L. , Saturday Greg A. , Ribeiro José M. C. , Tirloni Lucas 
Published: May 2024

AbstractBlood-feeding behavior has independently evolved in arthropods multiple times. Unlike hard ticks, soft ticks employ a rapid-feeding strategy for hematophagy, and there are comparatively limited studies on the transcriptomes of these organisms. This study investigates the soft tick Ornithodoros hermsi, conducting histopathological examinations at bitten skin sites and tick whole-body transcriptomic analyses across various developmental and feeding stages, including larvae, 1st-nymphal, and 2nd-nymphal stages. The results revealed the ability of O. hermsi to induce skin hemorrhage at the bite sites. Transcriptomic analyses identified three consistent transcriptional profiles: unfed, early-fed (6 h, 12 h, 24 h), and late-fed (5 days). The unfed profile exhibited high transcriptional activity across most of the functional classes annotated. In contrast, early-fed stages exhibited decreased expression of most functional classes, except for the unknown, which is highly expressed. Finally, transcriptional expression of most functional classes increased in the late-fed groups, resembling the baseline expression observed in the unfed groups. These findings highlight intense pre-feeding transcriptional activity in O. hermsi ticks, aligning with their rapid-feeding strategy. Moreover, besides shedding light on the temporal dynamics of key pathways during blood meal processing and tick development, this study contributes significantly to the transcriptome repertoire of a medically relevant soft tick species with relatively limited prior knowledge.
Metformin is a potential therapeutic for COVID-19/LUAD by regulating glucose metabolism
Authors: Hou Yongwang , Yang Zhicong , Xiang Baoli , Liu Jiangmin , Geng Lina , Xu Dandan , Zhan Minghua , Xu Yuhuan , Zhang Bin 
Published: May 2024

AbstractLung adenocarcinoma (LUAD) is the most common and aggressive subtype of lung cancer, and coronavirus disease 2019 (COVID-19) has become a serious public health threat worldwide. Patients with LUAD and COVID-19 have a poor prognosis. Therefore, finding medications that can be used to treat COVID-19/LUAD patients is essential. Bioinformatics analysis was used to identify 20 possible metformin target genes for the treatment of COVID-19/LUAD. PTEN and mTOR may serve as hub target genes of metformin. Metformin may be able to cure COVID-19/LUAD comorbidity through energy metabolism, oxidoreductase NADH activity, FoxO signalling pathway, AMPK signalling system, and mTOR signalling pathway, among other pathways, according to the results of bioinformatic research. Metformin has ability to inhibit the proliferation of A549 cells, according to the results of colony formation and proliferation assays. In A549 cells, metformin increased glucose uptake and lactate generation, while decreasing ATP synthesis and the NAD+/NADH ratio. In summary, PTEN and mTOR may be potential targets of metformin for the treatment of COVID-19/LUAD. The mechanism by which metformin inhibits lung adenocarcinoma cell proliferation may be related to glucose metabolism regulated by PI3K/AKT signalling and mTOR signalling pathways. Our study provides a new theoretical basis for the treatment of COVID-19/LUAD.
Selecting EEG channels and features using multi-objective optimization for accurate MCI detection: validation using leave-one-subject-out strategy
Authors: Aljalal Majid , Aldosari Saeed A. , Molinas Marta , Alturki Fahd A. 
Published: May 2024

AbstractEffective management of dementia requires the timely detection of mild cognitive impairment (MCI). This paper introduces a multi-objective optimization approach for selecting EEG channels (and features) for the purpose of detecting MCI. Firstly, each EEG signal from each channel is decomposed into subbands using either variational mode decomposition (VMD) or discrete wavelet transform (DWT). A feature is then extracted from each subband using one of the following measures: standard deviation, interquartile range, band power, Teager energy, Katz's and Higuchi's fractal dimensions, Shannon entropy, sure entropy, or threshold entropy. Different machine learning techniques are used to classify the features of MCI cases from those of healthy controls. The classifier's performance is validated using leave-one-subject-out (LOSO) cross-validation (CV). The non-dominated sorting genetic algorithm (NSGA)-II is designed with the aim of minimizing the number of EEG channels (or features) and maximizing classification accuracy. The performance is evaluated using a publicly available online dataset containing EEGs from 19 channels recorded from 24 participants. The results demonstrate a significant improvement in performance when utilizing the NSGA-II algorithm. By selecting only a few appropriate EEG channels, the LOSO CV-based results show a significant improvement compared to using all 19 channels. Additionally, the outcomes indicate that accuracy can be further improved by selecting suitable features from different channels. For instance, by combining VMD and Teager energy, the SVM accuracy obtained using all channels is 74.24%. Interestingly, when only five channels are selected using NSGA-II, the accuracy increases to 91.56%. The accuracy is further improved to 95.28% when using only 8 features selected from 7 channels. This demonstrates that by choosing informative features or channels while excluding noisy or irrelevant information, the impact of noise is reduced, resulting in improved accuracy. These promising findings indicate that, with a limited number of channels and features, accurate diagnosis of MCI is achievable, which opens the door for its application in clinical practice.
External auricle temperature enhances ear-based wearable accuracy during physiological strain monitoring in the heat
Authors: Tan Shawn Chee Chong , Tran Trinh Canh Khanh , Chiang Charis Yi Ning , Pan Jieming , Low Ivan Cherh Chiet 
Published: May 2024

AbstractBody core temperature (Tc) monitoring is crucial for minimizing heat injury risk. However, validated strategies are invasive and expensive. Although promising, aural canal temperature (Tac) is susceptible to environmental influences. This study investigated whether incorporation of external auricle temperature (Tea) into an ear-based Tc algorithm enhances its accuracy during multiple heat stress conditions. Twenty males (mean ± SD; age = 25 ± 3 years, BMI = 21.7 ± 1.8, body fat = 12 ± 3%, maximal aerobic capacity (VO2max) = 64 ± 7 ml/kg/min) donned an ear-based wearable and performed a passive heating (PAH), running (RUN) and brisk walking trial (WALK). PAH comprised of immersion in hot water (42.0 ± 0.3 °C). RUN (70 ± 3%VO2max) and WALK (50 ± 10%VO2max) were conducted in an environmental chamber (Tdb = 30.0 ± 0.2 °C, RH = 71 ± 2%). Several Tc models, developed using Tac, Tea and heart rate, were validated against gastrointestinal temperature. Inclusion of Tea as a model input improved the accuracy of the ear-based Tc algorithm. Our best performing model (Trf3) displayed good group prediction errors (mean bias error = − 0.02 ± 0.26 °C) but exhibited individual prediction errors (percentage target attainment ± 0.40 °C = 88%) that marginally exceeded our validity criterion. Therefore, Trf3 demonstrates potential utility for group-based Tc monitoring, with additional refinement needed to extend its applicability to personalized heat strain monitoring.