bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimal storage and recall with biologically plausible synapses
Authors: Savin Cristina , Lengyel Mate 
Published: January 2023

AbstractSynaptic plasticity is widely accepted to underlie learning and memory. Yet, models of associative networks with biologically plausible synapses fail to match brain performance: memories stored in such networks are quickly overwritten by ongoing plasticity (Amit & Fusi 1996, Fusi et al 2007). Metaplasticity - the process by which neural activity changes the ability of synapses to exhibit further plasticity - is believed to increase memory capacity (Fusi et al 2005). However, it remains unclear if neurons can make use of this additional information during recall. In particular, previous attempts at reading out information in metaplastic synapses using heuristic recall dynamics led to rather poor performance (Huang & Amit 2010).Here, we developed a theoretical framework for storage and recall with finite-state synapses that allowed us to find neural and synaptic dynamics that maximize the efficiency of autoassociative recall.Since information storage by synaptic plasticity is lossy, we formulated the problem of recalling a previously stored pattern from a noisy cue as probabilistic inference (Lengyel et al 2005) and derived neural dynamics efficiently implementing such inferences. Our approach is general and can be applied to any synaptic plasticity model which involves stochastic transitions between a finite set of states.We show how synaptic plasticity rules need to be matched to the statistics of stored patterns, and how recall dynamics need to be matched both to input statistics and to the plasticity rule itself in order to achieve optimal performance. In particular, for binary synapses with metastates we demonstrate for the first time that memories can be efficiently read out with biologically plausible network dynamics that we derive directly from the synaptic metaplasticity rule with virtually no free parameters.
Implantable intracortical microelectrodes: reviewing the present with a focus on the future
Authors: Wang Yang , Yang Xinze , Zhang Xiwen , Wang Yijun , Pei Weihua 
Published: January 2023

AbstractImplantable intracortical microelectrodes can record a neuron’s rapidly changing action potentials (spikes). In vivo neural activity recording methods often have either high temporal or spatial resolution, but not both. There is an increasing need to record more neurons over a longer duration in vivo. However, there remain many challenges to overcome before achieving long-term, stable, high-quality recordings and realizing comprehensive, accurate brain activity analysis. Based on the vision of an idealized implantable microelectrode device, the performance requirements for microelectrodes are divided into four aspects, including recording quality, recording stability, recording throughput, and multifunctionality, which are presented in order of importance. The challenges and current possible solutions for implantable microelectrodes are given from the perspective of each aspect. The current developments in microelectrode technology are analyzed and summarized.
Mesenchymal stem cell-derived extracellular vesicles transfer miR-598 to inhibit the growth and metastasis of non-small-cell lung cancer by targeting THBS2
Authors: Li Xuebo , Wu Fan 
Published: January 2023

AbstractNon-small-cell lung cancer (NSCLC) is the subtype of lung cancer, which accounts for about 85% of diagnosed lung cancer cases, and is without any effective therapy. Emerging evidence has revealed microRNA-598 (miR-598) as potential therapeutic target and diagnostic marker of NSCLC. In the present study, we sought to define the role of mesenchymal stem cells (MSCs)-derived extracellular vesicles (EVs) containing miR-598 in NSCLC. Co-culture experiments were conducted to examine the secretion of miR-598 by MSCs and the uptake of EVs by NSCLC cells. The expression of miR-598 in NSCLC cell lines, tissues, and MSC-derived EVs was detected by the RT-qPCR. After treatment with MSCs-EVs, CCK-8 and Transwell assays were adopted to evaluate the effects of miR-598 on proliferation, migration, and invasion capacities of NSCLC cells. Finally, the effects of miR-598 on tumor growth and metastasis were further validated in vivo through subcutaneous tumorigenesis and experimental pulmonary metastasis in nude mice. We found that MSCs-derived EVs could deliver miR-598 into NSCLC cells, where miR-598 specifically targeted and bound with mRNA of THBS2 to inhibit its translational process. By suppressing the promoting effects of THBS2 on the proliferation, migration, and invasion of NSCLC cells, the EV treatment reduced the progression of NSCLC. Notably, these inhibitory effects were reversed by concomitantly overexpressing THBS2. Overall, we find that MSCs-derived EVs containing miR-598 targets THBS2 to inhibit the proliferation and migration of NSCLC cells in vivo and in vitro.
Targeted systematic evolution of an RNA platform neutralizing DNMT1 function and controlling DNA methylation
Authors: Esposito Carla L. , Autiero Ida , Sandomenico Annamaria , Li H. , Bassal Mahmoud A. , Ibba Maria L. , Wang Dongfang , Rinaldi Lucrezia , Ummarino Simone , Gaggi Giulia , Borchiellini Marta , Swiderski Piotr , Ruvo Menotti , Catuogno Silvia , Ebralidze Alexander K. , Kortylewski Marcin , de Franciscis Vittorio , Di Ruscio Annalisa 
Published: January 2023

AbstractDNA methylation is a fundamental epigenetic modification regulating gene expression. Aberrant DNA methylation is the most common molecular lesion in cancer cells. However, medical intervention has been limited to the use of broadly acting, small molecule-based demethylating drugs with significant side-effects and toxicities. To allow for targeted DNA demethylation, we integrated two nucleic acid-based approaches: DNMT1 interacting RNA (DiR) and RNA aptamer strategy. By combining the RNA inherent capabilities of inhibiting DNMT1 with an aptamer platform, we generated a first-in-class DNMT1-targeted approach – aptaDiR. Molecular modelling of RNA-DNMT1 complexes coupled with biochemical and cellular assays enabled the identification and characterization of aptaDiR. This RNA bio-drug is able to block DNA methylation, impair cancer cell viability and inhibit tumour growth in vivo. Collectively, we present an innovative RNA-based approach to modulate DNMT1 activity in cancer or diseases characterized by aberrant DNA methylation and suggest the first alternative strategy to overcome the limitations of currently approved non-specific hypomethylating protocols, which will greatly improve clinical intervention on DNA methylation.
Hidden heatwaves and severe coral bleaching linked to mesoscale eddies and thermocline dynamics
Authors: Wyatt Alex S. J. , Leichter James J. , Washburn Libe , Kui Li , Edmunds Peter J. , Burgess Scott C. 
Published: January 2023

AbstractThe severity of marine heatwaves (MHWs) that are increasingly impacting ocean ecosystems, including vulnerable coral reefs, has primarily been assessed using remotely sensed sea-surface temperatures (SSTs), without information relevant to heating across ecosystem depths. Here, using a rare combination of SST, high-resolution in-situ temperatures, and sea level anomalies observed over 15 years near Moorea, French Polynesia, we document subsurface MHWs that have been paradoxical in comparison to SST metrics and associated with unexpected coral bleaching across depths. Variations in the depth range and severity of MHWs was driven by mesoscale (10s to 100s of km) eddies that altered sea levels and thermocline depths and decreased (2007, 2017 and 2019) or increased (2012, 2015, 2016) internal-wave cooling. Pronounced eddy-induced reductions in internal waves during early 2019 contributed to a prolonged subsurface MHW and unexpectedly severe coral bleaching, with subsequent mortality offsetting almost a decade of coral recovery. Variability in mesoscale eddy fields, and thus thermocline depths, is expected to increase with climate change, which, along with strengthening and deepening stratification, could increase the occurrence of subsurface MHWs over ecosystems historically insulated from surface ocean heating by the cooling effects of internal waves.
Amazon windthrow disturbances are likely to increase with storm frequency under global warming
Authors: Feng Yanlei , Negrón-Juárez Robinson I. , Romps David M. , Chambers Jeffrey Q. 
Published: January 2023

AbstractForest mortality caused by convective storms (windthrow) is a major disturbance in the Amazon. However, the linkage between windthrows at the surface and convective storms in the atmosphere remains unclear. In addition, the current Earth system models (ESMs) lack mechanistic links between convective wind events and tree mortality. Here we find an empirical relationship that maps convective available potential energy, which is well simulated by ESMs, to the spatial pattern of large windthrow events. This relationship builds connections between strong convective storms and forest dynamics in the Amazon. Based on the relationship, our model projects a 51 ± 20% increase in the area favorable to extreme storms, and a 43 ± 17% increase in windthrow density within the Amazon by the end of this century under the high-emission scenario (SSP 585). These results indicate significant changes in tropical forest composition and carbon cycle dynamics under climate change.
Adaptive coding across visual features during free-viewing and fixation conditions
Authors: Nigam Sunny , Milton Russell , Pojoga Sorin , Dragoi Valentin 
Published: January 2023

AbstractTheoretical studies have long proposed that adaptation allows the brain to effectively use the limited response range of sensory neurons to encode widely varying natural inputs. However, despite this influential view, experimental studies have exclusively focused on how the neural code adapts to a range of stimuli lying along a single feature axis, such as orientation or contrast. Here, we performed electrical recordings in macaque visual cortex (area V4) to reveal significant adaptive changes in the neural code of single cells and populations across multiple feature axes. Both during free viewing and passive fixation, populations of cells improved their ability to encode image features after rapid exposure to stimuli lying on orthogonal feature axes even in the absence of initial tuning to these stimuli. These results reveal a remarkable adaptive capacity of visual cortical populations to improve network computations relevant for natural viewing despite the modularity of the functional cortical architecture.
Quantum interference between dark-excitons and zone-edged acoustic phonons in few-layer WS2
Authors: Tan Qing-Hai , Li Yun-Mei , Lai Jia-Min , Sun Yu-Jia , Zhang Zhe , Song Feilong , Robert Cedric , Marie Xavier , Gao Weibo , Tan Ping-Heng , Zhang Jun 
Published: January 2023

AbstractFano resonance which describes a quantum interference between continuum and discrete states, provides a unique method for studying strongly interacting physics. Here, we report a Fano resonance between dark excitons and zone-edged acoustic phonons in few-layer WS2 by using the resonant Raman technique. The discrete phonons with large momentum at the M-point of the Brillouin zone and the continuum dark exciton states related to the optically forbidden transition at K and Q valleys are coupled by the exciton-phonon interactions. We observe rich Fano resonance behaviors across layers and modes defined by an asymmetry-parameter q: including constructive interference with two mirrored asymmetry Fano peaks (weak coupling, q > 1 and q < − 1), and destructive interference with Fano dip (strong coupling, ∣q∣ < < 1). Our results provide new insight into the exciton-phonon quantum interference in two-dimensional semiconductors, where such interferences play a key role in their transport, optical, and thermodynamic properties.
Computational conjugate adaptive optics microscopy for longitudinal through-skull imaging of cortical myelin
Authors: Kwon Yongwoo , Hong Jin Hee , Kang Sungsam , Lee Hojun , Jo Yonghyeon , Kim Ki Hean , Yoon Seokchan , Choi Wonshik 
Published: January 2023

AbstractMyelination processes are closely related to higher brain functions such as learning and memory. While their longitudinal observation has been crucial to understanding myelin-related physiology and various brain disorders, skull opening or thinning has been required to secure clear optical access. Here we present a high-speed reflection matrix microscope using a light source with a wavelength of 1.3 μm to reduce tissue scattering and aberration. Furthermore, we develop a computational conjugate adaptive optics algorithm designed for the recorded reflection matrix to optimally compensate for the skull aberrations. These developments allow us to realize label-free longitudinal imaging of cortical myelin through an intact mouse skull. The myelination processes of the same mice were observed from 3 to 10 postnatal weeks to the depth of cortical layer 4 with a spatial resolution of 0.79 μm. Our system will expedite the investigations on the role of myelination in learning, memory, and brain disorders.
Brucella effectors NyxA and NyxB target SENP3 to modulate the subcellular localisation of nucleolar proteins
Authors: Louche Arthur , Blanco Amandine , Lacerda Thais Lourdes Santos , Cancade-Veyre Lison , Lionnet Claire , Bergé Célia , Rolando Monica , Lembo Frédérique , Borg Jean-Paul , Buchrieser Carmen , Nagahama Masami , Gérard Francine C. A. , Gorvel Jean-Pierre , Gueguen-Chaignon Virginie , Terradot Laurent , Salcedo Suzana P. 
Published: January 2023

AbstractThe cell nucleus is a primary target for intracellular bacterial pathogens to counteract immune responses and hijack host signalling pathways to cause disease. Here we identify two Brucella abortus effectors, NyxA and NyxB, that interfere with host protease SENP3, and this facilitates intracellular replication of the pathogen. The translocated Nyx effectors directly interact with SENP3 via a defined acidic patch (identified from the crystal structure of NyxB), preventing nucleolar localisation of SENP3 at late stages of infection. By sequestering SENP3, the effectors promote cytoplasmic accumulation of nucleolar AAA-ATPase NVL and ribosomal protein L5 (RPL5) in effector-enriched structures in the vicinity of replicating bacteria. The shuttling of ribosomal biogenesis-associated nucleolar proteins is inhibited by SENP3 and requires the autophagy-initiation protein Beclin1 and the SUMO-E3 ligase PIAS3. Our results highlight a nucleomodulatory function of two Brucella effectors and reveal that SENP3 is a crucial regulator of the subcellular localisation of nucleolar proteins during Brucella infection, promoting intracellular replication of the pathogen.
Searching for chromate replacements using natural language processing and machine learning algorithms
Authors: Zhao Shujing , Birbilis Nick 
Published: January 2023

AbstractThe past few years have seen the application of machine learning utilised in the exploration of materials. As in many fields of research—the vast majority of knowledge is published as text, which poses challenges in either a consolidated or statistical analysis across studies and reports. To address this issue, the application of natural language processing (NLP) has been explored in several studies to date. In the present work, we have employed the Word2Vec model, previously explored by others, and the BERT model—applying them towards the search for chromate replacements in the field of corrosion protection. From a database of over 80 million records, a down-selection of 5990 papers focused on the topic of corrosion protection were examined using NLP. This study demonstrates it is possible to extract knowledge from the automated interpretation of the scientific literature and achieve expert human-level insights.
Metavirome of 31 tick species provides a compendium of 1,801 RNA virus genomes
Authors: Ni Xue-Bing , Cui Xiao-Ming , Liu Jin-Yue , Ye Run-Ze , Wu Yu-Qian , Jiang Jia-Fu , Sun Yi , Wang Qian , Shum Marcus Ho-Hin , Chang Qiao-Cheng , Zhao Lin , Han Xiao-Hu , Ma Ke , Shen Shi-Jing , Zhang Ming-Zhu , Guo Wen-Bin , Zhu Jin-Guo , Zhan Lin , Li Liang-Jing , Ding Shu-Jun , Zhu Dai-Yun , Zhang Jie , Xia Luo-Yuan , Oong Xiang-Yong , Ruan Xiang-Dong , Shao Hong-Ze , Que Teng-Cheng , Liu Guang-Yuan , Du Chun-Hong , Huang En-Jiong , Wang Xin , Du Li-Feng , Wang Chong-Cai , Shi Wen-Qiang , Pan Yu-Sheng , Zhou Yu-Hao , Qu Jiang-Li , Ma Jiang , Gong Cai-Wei , Chen Qi-Qing , Qin Qian ,   Tick Genome and Microbiome Consortium (TIGMIC), Lam Tommy Tsan-Yuk , Jia Na , Cao Wu-Chun 
Published: January 2023

AbstractThe increasing prevalence and expanding distribution of tick-borne viruses globally have raised health concerns, but the full repertoire of the tick virome has not been assessed. We sequenced the meta-transcriptomes of 31 different tick species in the Ixodidae and Argasidae families from across mainland China, and identified 724 RNA viruses with distinctive virome compositions among genera. A total of 1,801 assembled and complete or nearly complete viral genomes revealed an extensive diversity of genome architectures of tick-associated viruses, highlighting ticks as a reservoir of RNA viruses. We examined the phylogenies of different virus families to investigate virome evolution and found that the most diverse tick-associated viruses are positive-strand RNA virus families that demonstrate more ancient divergence than other arboviruses. Tick-specific viruses are often associated with only a few tick species, whereas virus clades that can infect vertebrates are found in a wider range of tick species. We hypothesize that tick viruses can exhibit both ‘specialist’ and ‘generalist’ evolutionary trends. We hope that our virome dataset will enable much-needed research on vertebrate-pathogenic tick-associated viruses.
Gene gain facilitated endosymbiotic evolution of Chlamydiae
Authors: Dharamshi Jennah E. , Köstlbacher Stephan , Schön Max E. , Collingro Astrid , Ettema Thijs J. G. , Horn Matthias 
Published: January 2023

AbstractChlamydiae is a bacterial phylum composed of obligate animal and protist endosymbionts. However, other members of the Planctomycetes–Verrucomicrobia–Chlamydiae superphylum are primarily free living. How Chlamydiae transitioned to an endosymbiotic lifestyle is still largely unresolved. Here we reconstructed Planctomycetes–Verrucomicrobia–Chlamydiae species relationships and modelled superphylum genome evolution. Gene content reconstruction from 11,996 gene families suggests a motile and facultatively anaerobic last common Chlamydiae ancestor that had already gained characteristic endosymbiont genes. Counter to expectations for genome streamlining in strict endosymbionts, we detected substantial gene gain within Chlamydiae. We found that divergence in energy metabolism and aerobiosis observed in extant lineages emerged later during chlamydial evolution. In particular, metabolic and aerobic genes characteristic of the more metabolically versatile protist-infecting chlamydiae were gained, such as respiratory chain complexes. Our results show that metabolic complexity can increase during endosymbiont evolution, adding an additional perspective for understanding symbiont evolutionary trajectories across the tree of life.
Effects of syllable boundaries in Tibetan reading
Authors: Wang Danhui , Zeng Man , Zhao Han , Gao Lei , Li Shan , Niu Zibei , Bai Xuejun , Gao Xiaolei 
Published: January 2023

AbstractInterword spaces exist in the texts of many languages that use alphabetic writing systems. In most cases, interword spaces, as a kind of word boundary information, play an important role in the reading process of readers. Tibetan also uses alphabetic writing, its text has no spaces between words as word boundary markers. Instead, there are intersyllable tshegs (“
”), which are superscript dots. Interword spaces play an important role in reading as word boundary information. Therefore, it is interesting to investigate the role of tshegs and what effect replacing tshegs with spaces will have on Tibetan reading. To answer these questions, Experiment 1 was conducted in which 72 Tibetan undergraduates read three-syllable-boundary conditions (normal, spaced, and untsheged). However, in Experiment 1, because we performed the experimental operations of deleting tshegs and replacing tshegs, the spatial information distribution of Tibetan sentences under different operating conditions was different, which may have a certain potential impact on the experimental results. To rule out the underlying confounding factor, in Experiment 2, 58 undergraduates read sentences for both untsheged and alternating-color conditions. Overall, the global and local analyses revealed that tshegs, spaces, and alternating-color markers as syllable boundaries can help readers segment syllables in Tibetan reading. In Tibetan reading, both spaces and tshegs are effective visual syllable segmentation cues, and spaces are more effective visual syllable segmentation cues than tshegs.
Predictive modeling of optimism bias using gray matter cortical thickness
Authors: Kotikalapudi Raviteja , Moser Dominik A. , Dricu Mihai , Spisak Tamas , Aue Tatjana 
Published: January 2023

AbstractPeople have been shown to be optimistically biased when their future outcome expectancies are assessed. In fact, we display optimism bias (OB) toward our own success when compared to a rival individual’s (personal OB [POB]). Similarly, success expectancies for social groups we like reliably exceed those we mention for a rival group (social OB [SOB]). Recent findings suggest the existence of neural underpinnings for OB. Mostly using structural/functional MRI, these findings rely on voxel-based mass-univariate analyses. While these results remain associative in nature, an open question abides whether MRI information can accurately predict OB. In this study, we hence used predictive modelling to forecast the two OBs. The biases were quantified using a validated soccer paradigm, where personal (self versus rival) and social (in-group versus out-group) forms of OB were extracted at the participant level. Later, using gray matter cortical thickness, we predicted POB and SOB via machine-learning. Our model explained 17% variance (R2 = 0.17) in individual variability for POB (but not SOB). Key predictors involved the rostral-caudal anterior cingulate cortex, pars orbitalis and entorhinal cortex—areas that have been associated with OB before. We need such predictive models on a larger scale, to help us better understand positive psychology and individual well-being.
National-scale simulation of human movement in a spatially coupled individual-based model of malaria in Burkina Faso
Authors: Zupko Robert J. , Nguyen Tran Dang , Wesolowski Amy , Gerardin Jaline , Boni Maciej F. 
Published: January 2023

AbstractMalaria due to the Plasmodium falciparum parasite remains a threat to human health despite eradication efforts and the development of anti-malarial treatments, such as artemisinin combination therapies. Human movement and migration have been linked to the propagation of malaria on national scales, highlighting the need for the incorporation of human movement in modeling efforts. Spatially couped individual-based models have been used to study how anti-malarial resistance evolves and spreads in response to drug policy changes; however, as the spatial scale of the model increases, the challenges associated with modeling of movement also increase. In this paper we discuss the development, calibration, and validation of a movement model in the context of a national-scale, spatial, individual-based model used to study the evolution of drug resistance in the malaria parasite.