bluuebunny/crossref_metadata_2025_split huggingface dataset:
GMSK Demodulation Combining 1D‐CNN and Bi‐LSTM Network Over Strong Solar Wind Turbulence Channel
Authors: Zhu Manqin , Hu Shengbo , Yang Kai , Yan Tingting , Ye Lv , Li Hongjuan , Jin Yang 
Published: January 2023

AbstractTo solve the problem of bit error rate (BER) performance degradation over strong solar wind turbulence channel, this paper addresses to Gaussian minimum frequency shift keying (GMSK) demodulation using machine learning. First, by analyzing the scintillation characteristics of the telemetry signal caused by solar wind turbulence during the solar superior conjunction, the K distribution channel model is innovatively established over strong solar wind turbulence channel. Then, the approximate probability density function of the K distribution of the established channel is studied by using Laguerre orthogonal polynomial for convenience. Additionally, the BER performance of GMSK over strong solar wind turbulence channel is analyzed. Second, using a one‐dimensional convolutional neural network (1D‐CNN) and bidirectional long short‐term memory network (Bi‐LSTM), two demodulators for GMSK are proposed. By integrating the 1D‐CNN and LSTM to extract local features and process the dynamic information of GMSK signals, we propose a novel GMSK demodulator over strong solar wind turbulence channel with combining 1D‐CNN and Bi‐LSTM. The simulation results show that, even if the solar wind turbulence has serious effects on the signal at a low signal‐to‐noise ratio, the proposed combining neural network demodulation can obtain better BER performance than the classical Viterbi algorithm, demodulation using only a single 1D‐CNN or Bi‐LSTM. The proposed GMSK demodulator is more suitable for the deep space exploration of the solar system.
Lineage tracking to reveal the fate of hematopoietic stem cells influenced by Flk2− multipotent progenitors after transplantation
Authors: Wang Zheng , Jiang Du , Vergel-Rodriguez Mary , Nogalska Anna , Lu Rong 
Published: January 2023

AbstractAfter transplantation, hematopoietic stem cells (HSCs) sustain blood cell regeneration throughout the patient’s life. Recent studies suggest that several types of mature blood cells provide feedback signals to regulate HSC fate. However, the potential feedback effect of hematopoietic progenitor cells has not been characterized to date. The present investigation demonstrated that multipotent progenitors (MPPs) promoted T cell production of HSCs when both cell types were cotransplanted in mice. Using genetic barcodes to track individual HSCs in mice, we found that the increased T cell production by HSCs was associated with the combined effects of altered lineage bias and clonal expansion during HSC differentiation. We showed that MPP and HSC co-transplantation promoted the multilineage differentiation of HSCs in the short term while preserving lymphoid-specialized HSC differentiation in the long term. Our findings indicate that MPPs derived from HSCs regulate the fate of HSCs after bone marrow transplantation.
Gene loss and symbiont switching during adaptation to the deep sea in a globally distributed symbiosis
Authors: Osvatic Jay T , Yuen Benedict , Kunert Martin , Wilkins Laetitia , Hausmann Bela , Girguis Peter , Lundin Kennet , Taylor John , Jospin Guillaume , Petersen Jillian M 
Published: January 2023

Abstract
Chemosynthetic symbioses between bacteria and invertebrates occur worldwide from coastal sediments to the deep sea. Most host groups are restricted to either shallow or deep waters. In contrast, Lucinidae, the most species-rich family of chemosymbiotic invertebrates, has both shallow- and deep-sea representatives. Multiple lucinid species have independently colonized the deep sea, which provides a unique framework for understanding the role microbial symbionts play in evolutionary transitions between shallow and deep waters. Lucinids acquire their symbionts from their surroundings during early development, which may allow them to flexibly acquire symbionts that are adapted to local environments. Via metagenomic analyses of museum and other samples collected over decades, we investigated the biodiversity and metabolic capabilities of the symbionts of 22 mostly deep-water lucinid species. We aimed to test the theory that the symbiont played a role in adaptation to life in deep-sea habitats. We identified 16 symbiont species, mostly within the previously described genus Ca. Thiodiazotropha. Most genomic functions were shared by both shallow-water and deep-sea Ca. Thiodiazotropha, though nitrogen fixation was exclusive to shallow-water species. We discovered multiple cases of symbiont switching near deep-sea hydrothermal vents and cold seeps, where distantly related hosts convergently acquired novel symbionts from a different bacterial order. Finally, analyses of selection revealed consistently stronger purifying selection on symbiont genomes in two extreme habitats - hydrothermal vents and an oxygen-minimum zone. Our findings reveal that shifts in symbiont metabolic capability and, in some cases, acquisition of a novel symbiont accompanied adaptation of lucinids to challenging deep-sea habitats.
The ‘stealth-bomber’ paradigm for deciphering the tumour response to carbon-ion irradiation
Authors: Wozny Anne-Sophie , Rodriguez-Lafrasse Claire 
Published: January 2023

AbstractNumerous studies have demonstrated the higher biological efficacy of carbon-ion irradiation (C-ions) and their ballistic precision compared with photons. At the nanometre scale, the reactive oxygen species (ROS) produced by radiation and responsible for the indirect effects are differentially distributed according to the type of radiation. Photon irradiation induces a homogeneous ROS distribution, whereas ROS remain condensed in clusters in the C-ions tracks. Based on this linear energy transfer-dependent differential nanometric ROS distribution, we propose that the higher biological efficacy and specificities of the molecular response to C-ions rely on a ‘stealth-bomber’ effect. When biological targets are on the trajectories of the particles, the clustered radicals in the tracks are responsible for a ‘bomber’ effect. Furthermore, the low proportion of ROS outside the tracks is not able to trigger the cellular mechanisms of defence and proliferation. The ability of C-ions to deceive the cellular defence of the cancer cells is then categorised as a ‘stealth’ effect. This review aims to classify the biological arguments supporting the paradigm of the ‘stealth-bomber’ as responsible for the biological superiority of C-ions compared with photons. It also explains how and why C-ions will always be more efficient for treating patients with radioresistant cancers than conventional radiotherapy.
The U2AF65/circNCAPG/RREB1 feedback loop promotes malignant phenotypes of glioma stem cells through activating the TGF-β pathway
Authors: Li Hao , Jiang Yang , Hu Jinpeng , Xu Jinkun , Chen Lian , Zhang Guoqing , Zhao Junshuang , Zong Shengliang , Guo Zhengting , Li Xinqiao , Zhao Xiang , Jing Zhitao 
Published: January 2023

AbstractGlioma is the most aggressive and common malignant neoplasms in human brain tumors. Numerous studies have showed that glioma stem cells (GSCs)drive the malignant progression of gliomas. Recent studies have revealed that circRNAs can maintain stemness and promote malignant progression of glioma stem cells. We used bioinformatics analysis to identify circRNAs and potential RNA-binding proteins (RBPs) in glioma. qRT-PCR, western blotting, RNA FISH, RNA pull-down, RNA immunoprecipitation assay, ChIP, immunohistochemistry, and immunofluorescence methods were used to quantified the expression of circNCAPG, U2AF65, RREB1 and TGF-β1, and the underlying mechanisms between them. MTS, EDU, neurosphere formation, limiting dilution neurosphere formation and transwell assays examined the proliferation and invasive capability of GSCs, respectively. We identified a novel circRNA named circNCAPG was overexpressed and indicated the poor prognosis in glioma patients. Upregulating circNCAPG promoted the malignant progression of GSCs. RNA binding protein U2AF65 could stabilize circNCAPG by direct binding. Mechanically, circNCAPG interacted with and stabilized RREB1, as well as stimulated RREB1 nuclear translocation to activate TGF-β1 signaling pathway. Furthermore, RREB1 transcriptionally upregulated U2AF65 expression to improve the stability of circNCAPG in GSCs, which established a feedback loop involving U2AF65, circNCAPG and RREB1. Since circRNA is more stable than mRNA and can execute its function continuously, targeting circNCAPG in glioma may be a novel promising therapeutic.
RBM4 regulates cellular senescence via miR1244/SERPINE1 axis
Authors: Wang Luning , Zhang Xiaohong , Sheng Junxiu , Chen Lei , Zhi Lili , Zheng Qianqian , Qi Yangfan , Wang Linlin , Zhang Jinrui , Zhao Jinyao , Wang Yang , Liu Shu-Xin , Sun Ming-Zhong , Zhang Wenjing 
Published: January 2023

AbstractCellular senescence serves as a powerful tumor suppressing mechanism that inhibits the proliferation of cancer cells bearing oncogenic mutations at the initial stage of cancer development. RNA-binding proteins (RBPs) play important roles in cancer progression and treatment through distinct functions. However, functions and mechanisms of RNA binding proteins in regulating senescence remain elusive. Here we reported that the RNA binding protein RBM4 contributed to cellular senescence. Depletion of RBM4 induced senescence in different types of cells, including multiple cancer cells. Meanwhile, RBM4 ablation inhibited cancer cell progression both in vitro and in vivo. Specifically, knockdown of RBM4 significantly increased the level of SERPINE1, a known promoter of senescence, thereby inducing the senescence of lung cancer cells. Mechanistically, miR-1244 bound to the 3ʹ-UTR of SERPINE1 to suppress its expression, whereas depletion of RBM4 reduced the level of miR-1244 by promoting the degradation of primary miR-1244 transcripts (pri-miR1244), thus increasing the expression of SERPINE1 and inducing subsequent senescence. Moreover, either SERPINE1 inhibitor or miR-1244 mimics attenuated the RBM4 depletion-induced senescence. Altogether, our study revealed a novel mechanism of RBM4 in the regulation of cancer progression through controlling senescence, providing a new avenue for targeting RBM4 in cancer therapeutics.
A photothermal-response oxygen release platform based on a hydrogel for accelerating wound healing
Authors: Li Chunyang , He Xiaojun , Li Qingfeng , Lv Mingzhi , Shen Jianliang , Jin Lin , He Deyan 
Published: January 2023

AbstractDuring wound healing, oxygen availability and the anti-inflammatory microenvironment play an important role in the formation of new tissue. However, providing continuous and controllable oxygen around the injured tissue while inhibiting inflammation and realizing the synergistic effect of oxygen supply and anti-inflammation is still a major problem affecting the regeneration and repair of wound tissue. Inspired by skin wound pathology and the inflammatory microenvironment, a photothermal response-assisted strategy was developed in this study. We prepared a composite hydrogel system of polydopamine-hyaluronic acid (PDA-HA) hydrogel-loaded calcium peroxide-indocyanine green combined with lauric acid and manganese dioxide (CaO2-ICG@LA@MnO2) nanoparticles that showed excellent photothermal performance under near-infrared (NIR) irradiation and realized the on-off release of oxygen and reactive oxygen species (ROS). Controllable and sustainable oxygen release can promote the regeneration and repair of damaged tissue, and the generated ROS can effectively inhibit the outbreak of inflammation at the initial stage of wound healing. We believe that the system we have developed can be used in a new approach for treating chronic wounds.
EPS8 variant causes deafness, autosomal recessive 102 (DFNB102) and literature review
Authors: Abbasi Zahra , Jafari Khamirani Hossein , Tabei Seyed Mohammad Bagher , Manoochehri Jamal , Dianatpour Mehdi , Dastgheib Seyed Alireza 
Published: January 2023

AbstractPathogenic variants in the EPS8 gene result in nonsyndromic hearing loss. This gene encodes the EPS8 protein in cochlear inner hair cells and performs critical roles in stimulating actin polymerization and bundling. Thus far, only four pathogenic variations in EPS8 have been described. In this study, we report the fifth pathogenic variant in the EPS8 gene in an Iranian patient with DFNB102. Furthermore, we review literature cases with EPS8 mutations.
GALA: a computational framework for de novo chromosome-by-chromosome assembly with long reads
Authors: Awad Mohamed , Gan Xiangchao 
Published: January 2023

AbstractHigh-quality genome assembly has wide applications in genetics and medical studies. However, it is still very challenging to achieve gap-free chromosome-scale assemblies using current workflows for long-read platforms. Here we report on GALA (Gap-free long-read Assembly tool), a computational framework for chromosome-based sequencing data separation and de novo assembly implemented through a multi-layer graph that identifies discordances within preliminary assemblies and partitions the data into chromosome-scale scaffolding groups. The subsequent independent assembly of each scaffolding group generates a gap-free assembly likely free from the mis-assembly errors which usually hamper existing workflows. This flexible framework also allows us to integrate data from various technologies, such as Hi-C, genetic maps, and even motif analyses to generate gap-free chromosome-scale assemblies. As a proof of principle we de novo assemble the C. elegans genome using combined PacBio and Nanopore sequencing data and a rice cultivar genome using Nanopore sequencing data from publicly available datasets. We also demonstrate the proposed method’s applicability with a gap-free assembly of the human genome using PacBio high-fidelity (HiFi) long reads. Thus, our method enables straightforward assembly of genomes with multiple data sources and overcomes barriers that at present restrict the application of de novo genome assembly technology.
Control of protein stability by post-translational modifications
Authors: Lee Ji Min , Hammarén Henrik M. , Savitski Mikhail M. , Baek Sung Hee 
Published: January 2023

AbstractPost-translational modifications (PTMs) can occur on specific amino acids localized within regulatory domains of target proteins, which control a protein’s stability. These regions, called degrons, are often controlled by PTMs, which act as signals to expedite protein degradation (PTM-activated degrons) or to forestall degradation and stabilize a protein (PTM-inactivated degrons). We summarize current knowledge of the regulation of protein stability by various PTMs. We aim to display the variety and breadth of known mechanisms of regulation as well as highlight common themes in PTM-regulated degrons to enhance potential for identifying novel drug targets where druggable targets are currently lacking.
Interleukin-13 and its receptor are synaptic proteins involved in plasticity and neuroprotection
Authors: Li Shun , olde Heuvel Florian , Rehman Rida , Aousji Oumayma , Froehlich Albrecht , Li Zhenghui , Jark Rebecca , Zhang Wanhong , Conquest Alison , Woelfle Sarah , Schoen Michael , O´Meara Caitlin C. , Reinhardt Richard Lee , Voehringer David , Kassubek Jan , Ludolph Albert , Huber-Lang Markus , Knöll Bernd , Morganti-Kossmann Maria Cristina , Brockmann Marisa M. , Boeckers Tobias , Roselli Francesco 
Published: January 2023

AbstractImmune system molecules are expressed by neurons, yet their functions are often unknown. We have identified IL-13 and its receptor IL-13Ra1 as neuronal, synaptic proteins in mouse, rat, and human brains, whose engagement upregulates the phosphorylation of NMDAR and AMPAR subunits and, in turn, increases synaptic activity and CREB-mediated transcription. We demonstrate that increased IL-13 is a hallmark of traumatic brain injury (TBI) in male mice as well as in two distinct cohorts of human patients. We also provide evidence that IL-13 upregulation protects neurons from excitotoxic death. We show IL-13 upregulation occurring in several cohorts of human brain samples and in cerebrospinal fluid (CSF). Thus, IL-13 is a physiological modulator of synaptic physiology of neuronal origin, with implications for the establishment of synaptic plasticity and the survival of neurons under injury conditions. Furthermore, we suggest that the neuroprotection afforded through the upregulation of IL-13 represents an entry point for interventions in the pathophysiology of TBI.
Resolving the intrinsic short-range ordering of K+ ions on cleaved muscovite mica
Authors: Franceschi Giada , Kocán Pavel , Conti Andrea , Brandstetter Sebastian , Balajka Jan , Sokolović Igor , Valtiner Markus , Mittendorfer Florian , Schmid Michael , Setvín Martin , Diebold Ulrike 
Published: January 2023

AbstractMuscovite mica, KAl2(Si3Al)O10(OH)2, is a common layered phyllosilicate with perfect cleavage planes. The atomically flat surfaces obtained through cleaving lend themselves to scanning probe techniques with atomic resolution and are ideal to model minerals and clays. Despite the importance of the cleaved mica surfaces, several questions remain unresolved. It is established that K+ ions decorate the cleaved surface, but their intrinsic ordering – unaffected by the interaction with the environment – is not known. This work presents clear images of the K+ distribution of cleaved mica obtained with low-temperature non-contact atomic force microscopy (AFM) under ultra-high vacuum (UHV) conditions. The data unveil the presence of short-range ordering, contrasting previous assumptions of random or fully ordered distributions. Density functional theory (DFT) calculations and Monte Carlo simulations show that the substitutional subsurface Al3+ ions have an important role for the surface K+ ion arrangement.
ChIATAC is an efficient strategy for multi-omics mapping of 3D epigenomes from low-cell inputs
Authors: Chai Haoxi , Tjong Harianto , Li Peng , Liao Wei , Wang Ping , Wong Chee Hong , Ngan Chew Yee , Leonard Warren J. , Wei Chia-Lin , Ruan Yijun 
Published: January 2023

AbstractConnecting genes to their cis-regulatory elements has been enabled by genome-wide mapping of chromatin interactions using proximity ligation in ChIA-PET, Hi-C, and their derivatives. However, these methods require millions of input cells for high-quality data and thus are unsuitable for many studies when only limited cells are available. Conversely, epigenomic profiling via transposase digestion in ATAC-seq requires only hundreds to thousands of cells to robustly map open chromatin associated with transcription activity, but it cannot directly connect active genes to their distal enhancers. Here, we combine proximity ligation in ChIA-PET and transposase accessibility in ATAC-seq into ChIATAC to efficiently map interactions between open chromatin loci in low numbers of input cells. We validate ChIATAC in Drosophila cells and optimize it for mapping 3D epigenomes in human cells robustly. Applying ChIATAC to primary human T cells, we reveal mechanisms that topologically regulate transcriptional programs during T cell activation.
Arabidopsis DXO1 activates RNMT1 to methylate the mRNA guanosine cap
Authors: Xiao Chen , Li Kaien , Hua Jingmin , He Zhao , Zhang Feng , Li Qiongfang , Zhang Hailei , Yang Lei , Pan Shuying , Cai Zongwei , Yu Zhiling , Wong Kam-Bo , Xia Yiji 
Published: January 2023

AbstractEukaryotic messenger RNA (mRNA) typically contains a methylated guanosine (m7G) cap, which mediates major steps of mRNA metabolism. Recently, some RNAs in both prokaryotic and eukaryotic organisms have been found to carry a non-canonical cap such as the NAD cap. Here we report that Arabidopsis DXO family protein AtDXO1, which was previously known to be a decapping enzyme for NAD-capped RNAs (NAD-RNA), is an essential component for m7G capping. AtDXO1 associates with and activates RNA guanosine-7 methyltransferase (AtRNMT1) to catalyze conversion of the guanosine cap to the m7G cap. AtRNMT1 is an essential gene. Partial loss-of-function mutations of AtRNMT1 and knockout mutation of AtDXO1 reduce m7G-capped mRNA but increase G-capped mRNAs, leading to similar pleiotropic phenotypes, whereas overexpression of AtRNMT1 partially restores the atdxo1 phenotypes. This work reveals an important mechanism in m7G capping in plants by which the NAD-RNA decapping enzyme AtDXO1 is required for efficient guanosine cap methylation.
In-plane ferroelectric tunnel junctions based on 2D α-In2Se3/semiconductor heterostructures
Authors: Liu Zifang , Hou Pengfei , Sun Lizhong , Tsymbal Evgeny Y. , Jiang Jie , Yang Qiong 
Published: January 2023

AbstractFerroelectric tunnel junctions (FTJs) have great potential for application in high-density non-volatile memories. Recently, α-In2Se3 was found to exhibit robust in-plane and out-of-plane ferroelectric polarizations at a monolayer thickness, which is ideal to serve as a ferroelectric component in miniaturized electronic devices. In this work, we design two-dimensional van der Waals heterostructures composed of an α-In2Se3 ferroelectric and a hexagonal IV–VI semiconductor and propose an in-plane FTJ based on these heterostructures. Our first-principles calculations show that the electronic band structure of the designed heterostructures can be switched between insulating and metallic states by ferroelectric polarization. We demonstrate that the in-plane FTJ exhibits two distinct transport regimes, tunneling and metallic, for OFF and ON states, respectively, leading to a giant tunneling electroresistance effect with the OFF/ON resistance ratio exceeding 1 × 104. Our results provide a promising approach for the high-density ferroelectric memory based on the 2D ferroelectric/semiconductor heterostructures.
Combined EEG and immersive virtual reality unveil dopaminergic modulation of error monitoring in Parkinson’s Disease
Authors: Pezzetta R. , Ozkan D. G. , Era V. , Tieri G. , Zabberoni S. , Taglieri S. , Costa A. , Peppe A. , Caltagirone C. , Aglioti S. M. 
Published: January 2023

AbstractDetecting errors in your own and others’ actions is associated with discrepancies between intended and expected outcomes. The processing of salient events is associated with dopamine release, the balance of which is altered in Parkinson’s disease (PD). Errors in observed actions trigger various electrocortical indices (e.g. mid-frontal theta, error-related delta, and error positivity [oPe]). However, the impact of dopamine depletion to observed errors in the same individual remains unclear. Healthy controls (HCs) and PD patients observed ecological reach-to-grasp-a-glass actions performed by a virtual arm from a first-person perspective. PD patients were tested under their dopaminergic medication (on-condition) and after dopaminergic withdrawal (off-condition). Analyses of oPe, delta, and theta-power increases indicate that while the formers were elicited after incorrect vs. correct actions in all groups, the latter were observed in on-condition but altered in off-condition PD. Therefore, different EEG error signatures may index the activity of distinct mechanisms, and error-related theta power is selectively modulated by dopamine depletion. Our findings may facilitate discovering dopamine-related biomarkers for error-monitoring dysfunctions that may have crucial theoretical and clinical implications.