bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phanerozoic Evolution of Lithospheric Structures of the North China Craton
Authors: Xu Yixian , Zhang Yi , Yang Bo , Bao Xuewei 
Published: March 2022

AbstractModification of the cratonic lithosphere remains no consensus on the mechanisms. We here presented a method to reconstruct the Paleozoic‐lithospheric structures of the North China Craton (NCC) from its current structures. The results show that, after the Paleozoic, massive thinning only occurred in the eastern East Block (EB) but thickening presented in the northern Ordos Basin and the region from the Weibei uplift to South Taihang Mountains uplift. We also calculated the self‐sustaining oscillation periods of three parts in the NCC during the course of feedback between the thermal and mechanical equilibrium. The periods are in good agreement with the periodicity reflected in the sedimentation rate of the Ordos Basin and basaltic underplating events in the Trans‐North China Orogen. Based on the presenting results, we argue that, except the EB, the Phanerozoic lithospheric modification of the NCC is mainly controlled by heat conduction and dissipation through the cratonic lithosphere.
Network analysis of depressive and anxiety symptoms in adolescents during the later stage of the COVID-19 pandemic
Authors: Cai Hong , Bai Wei , Liu Huanzhong , Chen Xu , Qi Han , Liu Rui , Cheung Teris , Su Zhaohui , Lin Jingxia , Tang Yi-lang , Jackson Todd , Zhang Qinge , Xiang Yu-Tao 
Published: March 2022

AbstractNetwork analysis is an effective approach for examining complex relationships between psychiatric symptoms. This study was designed to examine item-level relationships between depressive and anxiety symptoms using network analysis in an adolescent sample and identified the most central symptoms within the depressive-anxiety symptoms network model. Depressive and anxiety symptoms were assessed using the Patient Health Questionire-9 (PHQ-9) and Generalized Anxiety Disorder Screener (GAD-7), respectively. The structure of depressive and anxiety symptoms was characterized using “Strength” and “Bridge Strength” as centrality indices in the symptom network. Network stability was tested using a case-dropping bootstrap procedure. Finally, a Network Comparison Test (NCT) was conducted to examine whether network characteristics differed on the basis of gender, school grade and residence. Network analysis revealed that nodes PHQ2 (“Sad mood”), GAD6 (“Irritability”), GAD3 (“Worry too much”), and PHQ6 (“Guilty”) were central symptoms in the network model of adolescents. Additionally, bridge symptoms linking anxiety and depressive symptoms in this sample were nodes PHQ6 (“Guilty”), PHQ2 (“Sad mood”), and PHQ9 (“Suicide ideation”). Gender, school grade and residence did not significantly affect the network structure. Central symptoms (e.g., Sad mood, Irritability, Worry too much, and Guilty) and key bridge symptoms (e.g., Guilty, Sad mood, and Suicide ideation) in the depressive and anxiety symptoms network may be useful as potential targets for intervention among adolescents who are at risk for or suffer from depressive and anxiety symptoms.
Circulating tumour cells in the -omics era: how far are we from achieving the ‘singularity’?
Authors: Visal Tanvi H. , den Hollander Petra , Cristofanilli Massimo , Mani Sendurai A. 
Published: March 2022

AbstractOver the past decade, cancer diagnosis has expanded to include liquid biopsies in addition to tissue biopsies. Liquid biopsies can result in earlier and more accurate diagnosis and more effective monitoring of disease progression than tissue biopsies as samples can be collected frequently. Because of these advantages, liquid biopsies are now used extensively in clinical care. Liquid biopsy samples are analysed for circulating tumour cells (CTCs), cell-free DNA, RNA, proteins and exosomes. CTCs originate from the tumour, play crucial roles in metastasis and carry information on tumour heterogeneity. Multiple single-cell omics approaches allow the characterisation of the molecular makeup of CTCs. It has become evident that CTCs are robust biomarkers for predicting therapy response, clinical development of metastasis and disease progression. This review describes CTC biology, molecular heterogeneity within CTCs and the involvement of EMT in CTC dynamics. In addition, we describe the single-cell multi-omics technologies that have provided insights into the molecular features within therapy-resistant and metastasis-prone CTC populations. Functional studies coupled with integrated multi-omics analyses have the potential to identify therapies that can intervene the functions of CTCs.
Downregulation of TPX2 impairs the antitumor activity of CD8+ T cells in hepatocellular carcinoma
Authors: Wang Xiaochen , Wang Jianchu , Shen Haiyuan , Luo Zongjiang , Lu Xiaojie 
Published: March 2022

AbstractTargeting key genes that play dominant roles in T cell dysfunction is an efficient strategy for cancer immunotherapy. Here, we aimed to investigate the role of TPX2 in the antitumor effect of CD8 + T cells in hepatocellular carcinoma (HCC). Flow cytometry was used to assay the level of cell surface markers and cytokines in T cells, through which we found that TPX2 was downregulated in HCC-infiltrating CD8 + T cells. TPX2 depletion restricted the antitumor activity of CD8 + T cells, and TPX2 overexpression increased the antitumor effect of CD8 + T cells in tumor-bearing Cd8−/− mice. TPX2 overexpression improved the antitumor function of human CD8 + T cells and response to anti-PD-1 therapy in an HCC patient-derived xenograft (PDX) mouse model with or without anti-PD-1 therapy. In mechanism, TPX2 promotes the phosphorylation of P65, thus increases the level of p-P65 in nuclear, and p-P65 binds to the promoter of CXCR5, activates its transcription, and increases the level of CXCR5 on CD8 + T cells in a TPX2-dependent way. In conclusion, TPX2 maintains the antitumor effect of CD8 + T cells in HCC by regulating CXCR5 via the NF-κB signaling pathway. Increased TPX2 expression in CD8 + T cells exerts synergistic effects with anti-PD-1 therapy, suggesting a promising immunotherapeutic method in HCC.
Introgressive hybridisation between domestic pigs (Sus scrofa domesticus) and endemic Corsican wild boars (S. s. meridionalis): effects of human-mediated interventions
Authors: Schleimer Anna , Richart Lorraine , Drygala Frank , Casabianca François , Maestrini Oscar , Weigand Hannah , Schwartz Chantal , Mittelbronn Michel , Frantz Alain C. 
Published: March 2022

AbstractOwing to the intensified domestication process with artificial trait selection, introgressive hybridisation between domestic and wild species poses a management problem. Traditional free-range livestock husbandry, as practiced in Corsica and Sardinia, is known to facilitate hybridisation between wild boars and domestic pigs (Sus scrofa). Here, we assessed the genetic distinctness and genome-wide domestic pig ancestry levels of the Corsican wild boar subspeciesS. s. meridionalis, with reference to its Sardinian conspecifics, employing a genome-wide single nucleotide polymorphism (SNP) assay and mitochondrial control region (mtCR) haplotypes. We also assessed the reliance of morphological criteria and the melanocortin-1 receptor (MC1R) coat colour gene to identify individuals with domestic introgression. While Corsican wild boars showed closest affinity to Sardinian and Italian wild boars compared to other European populations based on principal component analysis, the observation of previously undescribed mtCR haplotypes and high levels of nuclear divergence (Weir’sθ > 0.14) highlighted the genetic distinctness of CorsicanS. s. meridionalis. Across three complementary analyses of mixed ancestry (i.e., STRUCTURE, PCADMIX, and ELAI), proportions of domestic pig ancestry were estimated at 9.5% in Corsican wild boars, which was significantly higher than in wild boars in Sardinia, where free-range pig keeping was banned in 2012. Comparison of morphologically pure- and hybrid-looking Corsican wild boars suggested a weak correlation between morphological criteria and genome-wide domestic pig ancestry. The study highlights the usefulness of molecular markers to assess the direct impacts of management practices on gene flow between domestic and wild species.
Uptake of N2O5 by aqueous aerosol unveiled using chemically accurate many-body potentials
Authors: Cruzeiro Vinícius Wilian D. , Galib Mirza , Limmer David T. , Götz Andreas W. 
Published: March 2022

AbstractThe reactive uptake of N2O5to aqueous aerosol is a major loss channel for nitrogen oxides in the troposphere. Despite its importance, a quantitative picture of the uptake mechanism is missing. Here we use molecular dynamics simulations with a data-driven many-body model of coupled-cluster accuracy to quantify thermodynamics and kinetics of solvation and adsorption of N2O5in water. The free energy profile highlights that N2O5is selectively adsorbed to the liquid–vapor interface and weakly solvated. Accommodation into bulk water occurs slowly, competing with evaporation upon adsorption from gas phase. Leveraging the quantitative accuracy of the model, we parameterize and solve a reaction–diffusion equation to determine hydrolysis rates consistent with experimental observations. We find a short reaction–diffusion length, indicating that the uptake is dominated by interfacial features. The parameters deduced here, including solubility, accommodation coefficient, and hydrolysis rate, afford a foundation for which to consider the reactive loss of N2O5in more complex solutions.
Atomic structure of the predominant GII.4 human norovirus capsid reveals novel stability and plasticity
Authors: Hu Liya , Salmen Wilhelm , Chen Rong , Zhou Yi , Neill Frederick , Crowe James E. , Atmar Robert L. , Estes Mary K. , Prasad B. V. Venkataram 
Published: March 2022

AbstractHuman noroviruses (HuNoVs) cause sporadic and epidemic viral gastroenteritis worldwide. The GII.4 variants are responsible for most HuNoV infections, and GII.4 virus-like particles (VLPs) are being used in vaccine development. The atomic structure of the GII.4 capsid in the native T = 3 state has not been determined. Here we present the GII.4 VLP structure with T = 3 symmetry determined using X-ray crystallography and cryo-EM at 3.0 Å and 3.8 Å resolution, respectively, which reveals unanticipated novel features. A novel aspect in the crystal structure determined without imposing icosahedral symmetry is the remarkable adaptability of the capsid protein VP1 driven by the flexible hinge between the shell and the protruding domains. In both crystal and cryo-EM structures, VP1 adopts a stable conformation with the protruding domain resting on the shell domain, in contrast to the ‘rising’ conformation observed in recent cryo-EM structures of other GII.4 VLPs. Our studies further revealed that the resting state of VP1 dimer is stabilized by a divalent ion, and chelation using EDTA increases capsid diameter, exposing new hydrophobic and antigenic sites and suggesting a transition to the rising conformation. These novel insights into GII.4 capsid structure, stability, and antigen presentation may be useful for ongoing vaccine development.
Attosecond photoionisation time delays reveal the anisotropy of the molecular potential in the recoil frame
Authors: Ahmadi H. , Plésiat E. , Moioli M. , Frassetto F. , Poletto L. , Decleva P. , Schröter C. D. , Pfeifer T. , Moshammer R. , Palacios A. , Martin F. , Sansone G. 
Published: March 2022

AbstractPhotoionisation time delays carry structural and dynamical information on the target system, including electronic correlation effects in atoms and molecules and electron transport properties at interfaces. In molecules, the electrostatic potential experienced by an outgoing electron depends on the emission direction, which should thus lead to anisotropic time delays. To isolate this effect, information on the orientation of the molecule at the photoionisation instant is required. Here we show how attosecond time delays reflect the anisotropic molecular potential landscape in CF4 molecules. The variations in the measured delays can be directly related to the different heights of the potential barriers that the outgoing electrons see in the vicinity of shape resonances. Our results indicate the possibility to investigate the spatial characteristics of the molecular potential by mapping attosecond photoionisation time delays in the recoil-frame.
Fully-automated and ultra-fast cell-type identification using specific marker combinations from single-cell transcriptomic data
Authors: Ianevski Aleksandr , Giri Anil K. , Aittokallio Tero 
Published: March 2022

AbstractIdentification of cell populations often relies on manual annotation of cell clusters using established marker genes. However, the selection of marker genes is a time-consuming process that may lead to sub-optimal annotations as the markers must be informative of both the individual cell clusters and various cell types present in the sample. Here, we developed a computational platform, ScType, which enables a fully-automated and ultra-fast cell-type identification based solely on a given scRNA-seq data, along with a comprehensive cell marker database as background information. Using six scRNA-seq datasets from various human and mouse tissues, we show how ScType provides unbiased and accurate cell type annotations by guaranteeing the specificity of positive and negative marker genes across cell clusters and cell types. We also demonstrate how ScType distinguishes between healthy and malignant cell populations, based on single-cell calling of single-nucleotide variants, making it a versatile tool for anticancer applications. The widely applicable method is deployed both as an interactive web-tool (https://sctype.app), and as an open-source R-package.
Engineered assembly of water-dispersible nanocatalysts enables low-cost and green CO2 capture
Authors: Alivand Masood S. , Mazaheri Omid , Wu Yue , Zavabeti Ali , Christofferson Andrew J. , Meftahi Nastaran , Russo Salvy P. , Stevens Geoffrey W. , Scholes Colin A. , Mumford Kathryn A. 
Published: March 2022

AbstractCatalytic solvent regeneration has attracted broad interest owing to its potential to reduce energy consumption in CO2 separation, enabling industry to achieve emission reduction targets of the Paris Climate Accord. Despite recent advances, the development of engineered acidic nanocatalysts with unique characteristics remains a challenge. Herein, we establish a strategy to tailor the physicochemical properties of metal-organic frameworks (MOFs) for the synthesis of water-dispersible core-shell nanocatalysts with ease of use. We demonstrate that functionalized nanoclusters (Fe3O4-COOH) effectively induce missing-linker deficiencies and fabricate mesoporosity during the self-assembly of MOFs. Superacid sites are created by introducing chelating sulfates on the uncoordinated metal clusters, providing high proton donation capability. The obtained nanomaterials drastically reduce the energy consumption of CO2 capture by 44.7% using only 0.1 wt.% nanocatalyst, which is a ∽10-fold improvement in efficiency compared to heterogeneous catalysts. This research represents a new avenue for the next generation of advanced nanomaterials in catalytic solvent regeneration.
Fusobacterium nucleatum reduces METTL3-mediated m6A modification and contributes to colorectal cancer metastasis
Authors: Chen, Shujie , Zhang Lu , Li Mengjie , Zhang Ying , Sun Meng , Wang Lingfang , Lin Jiebo , Cui Yun , Chen Qian , Jin Chenqi , Li Xiang , Wang Boya , Chen Hao , Zhou Tianhua , Wang Liangjing , Hsu Chih-Hung , Zhuo Wei 
Published: March 2022

AbstractMicrobiota-host interactions play critical roles in colorectal cancer (CRC) progression, however, the underlying mechanisms remain elusive. Here, we uncover that Fusobacterium nucleatum (F. nucleatum) induces a dramatic decline of m6A modifications in CRC cells and patient-derived xenograft (PDX) tissues by downregulation of an m6A methyltransferase METTL3, contributing to inducation of CRC aggressiveness. Mechanistically, we characterized forkhead box D3 (FOXD3) as a transcription factor for METTL3. F. nucleatum activates YAP signaling, inhibits FOXD3 expression, and subsequently reduces METTL3 transcription. Downregulation of METTL3 promotes its target kinesin family member 26B (KIF26B) expression by reducing its m6A levels and diminishing YTHDF2-dependent mRNA degradation, which contributes to F. nucleatum-induced CRC metastasis. Moreover, METTL3 expression is negatively correlated with F. nucleatum and KIF26B levels in CRC tissues. A high expression of KIF26B is also significantly correlated with a shorter survival time of CRC patients. Together, our findings provide insights into modulating human m6A epitranscriptome by gut microbiota, and its significance in CRC progression.
A comprehensive temporal patterning gene network in Drosophila medulla neuroblasts revealed by single-cell RNA sequencing
Authors: Zhu Hailun , Zhao Sihai Dave , Ray Alokananda , Zhang Yu , Li Xin 
Published: March 2022

AbstractDuring development, neural progenitors are temporally patterned to sequentially generate a variety of neural types. In Drosophila neural progenitors called neuroblasts, temporal patterning is regulated by cascades of Temporal Transcription Factors (TTFs). However, known TTFs were mostly identified through candidate approaches and may not be complete. In addition, many fundamental questions remain concerning the TTF cascade initiation, progression, and termination. In this work, we use single-cell RNA sequencing of Drosophila medulla neuroblasts of all ages to identify a list of previously unknown TTFs, and experimentally characterize their roles in temporal patterning and neuronal specification. Our study reveals a comprehensive temporal gene network that patterns medulla neuroblasts from start to end. Furthermore, the speed of the cascade progression is regulated by Lola transcription factors expressed in all medulla neuroblasts. Our comprehensive study of the medulla neuroblast temporal cascade illustrates mechanisms that may be conserved in the temporal patterning of neural progenitors.
Bacteria eat nanoprobes for aggregation-enhanced imaging and killing diverse microorganisms
Authors: Yang Yunmin , Chu Binbin , Cheng Jiayi , Tang Jiali , Song Bin , Wang Houyu , He Yao 
Published: March 2022

AbstractCurrently optical-based techniques for in vivo microbial population imaging are limited by low imaging depth and highly light-scattering tissue; and moreover, are generally effective against only one specific group of bacteria. Here, we introduce an imaging and therapy strategy, in which different bacteria actively eat the glucose polymer (GP)-modified gold nanoparticles through ATP-binding cassette (ABC) transporter pathway, followed by laser irradiation-mediated aggregation in the bacterial cells. As a result, the aggregates display ~15.2-fold enhancement in photoacoustic signals and ~3.0-fold enhancement in antibacterial rate compared with non-aggregated counterparts. Significantly, the developed strategy allows ultrasensitive imaging of bacteria in vivo as low ~105 colony-forming unit (CFU), which is around two orders of magnitude lower than most optical contrast agents. We further demonstrate the developed strategy enables the detection of ~107 CFU bacteria residing within tumour or gut. This technique enables visualization and treatment of diverse bacteria, setting the crucial step forward the study of microbial ecosystem.
iRhom pseudoproteases regulate ER stress-induced cell death through IP3 receptors and BCL-2
Authors: Dulloo Iqbal , Atakpa-Adaji Peace , Yeh Yi-Chun , Levet Clémence , Muliyil Sonia , Lu Fangfang , Taylor Colin W. , Freeman Matthew 
Published: March 2022

AbstractThe folding capacity of membrane and secretory proteins in the endoplasmic reticulum (ER) can be challenged by physiological and pathological perturbations, causing ER stress. If unresolved, this leads to cell death. We report a role for iRhom pseudoproteases in controlling apoptosis due to persistent ER stress. Loss of iRhoms causes cells to be resistant to ER stress-induced apoptosis. iRhom1 and iRhom2 interact with IP3receptors, critical mediators of intracellular Ca2+signalling, and regulate ER stress-induced transport of Ca2+into mitochondria, a primary trigger of mitochondrial membrane depolarisation and cell death. iRhoms also bind to the anti-apoptotic regulator BCL-2, attenuating the inhibitory interaction between BCL-2 and IP3receptors, which promotes ER Ca2+release. The discovery of the participation of iRhoms in the control of ER stress-induced cell death further extends their potential pathological significance to include diseases dependent on protein misfolding and aggregation.
Parallel detection and spatial mapping of large nuclear spin clusters
Authors: Cujia K. S. , Herb K. , Zopes J. , Abendroth J. M. , Degen C. L. 
Published: March 2022

AbstractNuclear magnetic resonance imaging (MRI) at the atomic scale offers exciting prospects for determining the structure and function of individual molecules and proteins. Quantum defects in diamond have recently emerged as a promising platform towards reaching this goal, and allowed for the detection and localization of single nuclear spins under ambient conditions. Here, we present an efficient strategy for extending imaging to large nuclear spin clusters, fulfilling an important requirement towards a single-molecule MRI technique. Our method combines the concepts of weak quantum measurements, phase encoding and simulated annealing to detect three-dimensional positions from many nuclei in parallel. Detection is spatially selective, allowing us to probe nuclei at a chosen target radius while avoiding interference from strongly-coupled proximal nuclei. We demonstrate our strategy by imaging clusters containing more than 20 carbon-13 nuclear spins within a radius of 2.4 nm from single, near-surface nitrogen–vacancy centers at room temperature. The radius extrapolates to 5–6 nm for 1H. Beside taking an important step in nanoscale MRI, our experiment also provides an efficient tool for the characterization of large nuclear spin registers in the context of quantum simulators and quantum network nodes.
Tunable and scalable fabrication of block copolymer-based 3D polymorphic artificial cell membrane array
Authors: Kang Dong-Hyun , Han Won Bae , Il Ryu Hyun , Kim Nam Hyuk , Kim Tae Young , Choi Nakwon , Kang Ji Yoon , Yu Yeon Gyu , Kim Tae Song 
Published: March 2022

AbstractOwing to their excellent durability, tunable physical properties, and biofunctionality, block copolymer-based membranes provide a platform for various biotechnological applications. However, conventional approaches for fabricating block copolymer membranes produce only planar or suspended polymersome structures, which limits their utilization. This study is the first to demonstrate that an electric-field-assisted self-assembly technique can allow controllable and scalable fabrication of 3-dimensional block copolymer artificial cell membranes (3DBCPMs) immobilized on predefined locations. Topographically and chemically structured microwell array templates facilitate uniform patterning of block copolymers and serve as reactors for the effective growth of 3DBCPMs. Modulating the concentration of the block copolymer and the amplitude/frequency of the electric field generates 3DBCPMs with diverse shapes, controlled sizes, and high stability (100% survival over 50 days). In vitro protein–membrane assays and mimicking of human intestinal organs highlight the potential of 3DBCPMs for a variety of biological applications such as artificial cells, cell-mimetic biosensors, and bioreactors.