bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multistage Nucleation of the 2021 Yangbi MS 6.4 Earthquake, Yunnan, China and Its Foreshocks
Authors: Liu Min , Li Hongyi , Li Lu , Zhang Miao , Wang Weitao 
Published: April 2022

AbstractOn 21 May 2021, an MS 6.4 earthquake occurred in Yangbi, Yunnan province, China. A significant foreshock sequence occurred 3 days before the mainshock, which provides an opportunity to study earthquake nucleation. In this study, we adopt a template matching technique and a double‐difference location method to build a catalog for the foreshock sequence of the 2021 Yangbi MS 6.4 earthquake, which contains 1,086 events with high‐precision locations. The whole foreshock sequence can be grouped into four episodes, each with one MW > 3.7 principal foreshock. The foreshocks within the first episode initiated on a NW‐trending small fault, whereas the subsequent foreshocks within episodes 2–4 jumped onto a nearby major fault to gradually rupture toward NW direction. We identify three MW > 3.4 repeating earthquakes on the NW‐trending small fault in episode 1, implying that aseismic slip occurred in the early stage of the mainshock nucleation. Meanwhile, the rupture dimension estimation and stress disturbance analysis of the later foreshocks in episodes 2–4 reveal a cascading rupture process on the major fault, indicating that stress transfer may dominate the later stage of the mainshock nucleation. Hence, our study suggests that the two end‐member mechanisms of aseismic slip and stress transfer may be compossible in the nucleation process of the 2021 Yangbi MS 6.4 mainshock.
Functional analysis of circulating tumour cells: the KEY to understand the biology of the metastatic cascade
Authors: Eslami-S Zahra , Cortés-Hernández Luis Enrique , Thomas Frédéric , Pantel Klaus , Alix-Panabières Catherine 
Published: April 2022

AbstractMetastasis formation is the main cause of cancer-related death in patients with solid tumours. At the beginning of this process, cancer cells escape from the primary tumour to the blood circulation where they become circulating tumour cells (CTCs). Only a small subgroup of CTCs will survive during the harsh journey in the blood and colonise distant sites. The in-depth analysis of these metastasis-competent CTCs is very challenging because of their extremely low concentration in peripheral blood. So far, only few groups managed to expand in vitro and in vivo CTCs to be used as models for large-scale descriptive and functional analyses of CTCs. These models have shown already the high variability and complexity of the metastatic cascade in patients with cancer, and open a new avenue for the development of new diagnostic and therapeutic approaches.
A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments
Authors: Pan Shaojun , Zhu Chengkai , Zhao Xing-Ming , Coelho Luis Pedro 
Published: April 2022

AbstractMetagenomic binning is the step in building metagenome-assembled genomes (MAGs) when sequences predicted to originate from the same genome are automatically grouped together. The most widely-used methods for binning are reference-independent, operating de novo and enable the recovery of genomes from previously unsampled clades. However, they do not leverage the knowledge in existing databases. Here, we introduce SemiBin, an open source tool that uses deep siamese neural networks to implement a semi-supervised approach, i.e. SemiBin exploits the information in reference genomes, while retaining the capability of reconstructing high-quality bins that are outside the reference dataset. Using simulated and real microbiome datasets from several different habitats from GMGCv1 (Global Microbial Gene Catalog), including the human gut, non-human guts, and environmental habitats (ocean and soil), we show that SemiBin outperforms existing state-of-the-art binning methods. In particular, compared to other methods, SemiBin returns more high-quality bins with larger taxonomic diversity, including more distinct genera and species.
Magnesium galvanic cells produce hydrogen and modulate the tumor microenvironment to inhibit cancer growth
Authors: Yang Nailin , Gong Fei , Liu Bo , Hao Yu , Chao Yu , Lei Huali , Yang Xiaoyuan , Gong Yuehan , Wang Xianwen , Liu Zhuang , Cheng Liang 
Published: April 2022

AbstractHydrogen can be used as an anti-cancer treatment. However, the continuous generation of H2 molecules within the tumor is challenging. Magnesium (Mg) and its alloys have been extensively used in the clinic as implantable metals. Here we develop, by decorating platinum on the surface of Mg rods, a Mg-based galvanic cell (MgG), which allows the continuous generation of H2 in an aqueous environment due to galvanic-cell-accelerated water etching of Mg. By implanting MgG rods into a tumor, H2 molecules can be generated within the tumor, which induces mitochondrial dysfunction and intracellular redox homeostasis destruction. Meanwhile, the Mg(OH)2 residue can neutralize the acidic tumor microenvironment (TME). Such MgG rods with the micro-galvanic cell structure enable hydrogen therapy to inhibit the growth of tumors, including murine tumor models, patient-derived xenografts (PDX), as well as VX2 tumors in rabbits. Our research suggests that the galvanic cells for hydrogen therapy based on implantable metals may be a safe and effective cancer treatment.
Reactant-induced photoactivation of in situ generated organogold intermediates leading to alkynylated indoles via Csp2-Csp cross-coupling
Authors: Zhao Fen , Abdellaoui Mehdi , Hagui Wided , Ballarin-Marion Maria , Berthet Jérôme , Corcé Vincent , Delbaere Stéphanie , Dossmann Héloïse , Espagne Agathe , Forté Jérémy , Jullien Ludovic , Le Saux Thomas , Mouriès-Mansuy Virginie , Ollivier Cyril , Fensterbank Louis 
Published: April 2022

AbstractPhotosensitization of organogold intermediates is an emerging field in catalysis. In this context, an access to 2,3-disubstituted indoles from o-alkynyl aniline and iodoalkyne derivatives via a gold-catalyzed sequence under visible-light irradiation and in the absence of an exogenous photocatalyst was uncovered. A wide scope of the process is observed. Of note, 2-iodo-ynamides can be used as electrophiles in this cross-coupling reaction. The resulting N-alkynyl indoles lend themselves to post-functionalization affording valuable scaffolds, notably benzo[a]carbazoles. Mechanistic studies converge on the fact that a potassium sulfonyl amide generates emissive aggregates in the reaction medium. Static quenching of these aggregates by a vinylgold(I) intermediate yields to an excited state of the latter, which can react with an electrophile via oxidative addition and reductive elimination to forge the key C-C bond. This reactant-induced photoactivation of an organogold intermediate opens rich perspectives in the field of cross-coupling reactions.
A systems genomics approach to uncover patient-specific pathogenic pathways and proteins in ulcerative colitis
Authors: Brooks-Warburton Johanne , Modos Dezso , Sudhakar Padhmanand , Madgwick Matthew , Thomas John P. , Bohar Balazs , Fazekas David , Zoufir Azedine , Kapuy Orsolya , Szalay-Beko Mate , Verstockt Bram , Hall Lindsay J. , Watson Alastair , Tremelling Mark , Parkes Miles , Vermeire Severine , Bender Andreas , Carding Simon R. , Korcsmaros Tamas 
Published: April 2022

AbstractWe describe a precision medicine workflow, the integrated single nucleotide polymorphism network platform (iSNP), designed to determine the mechanisms by which SNPs affect cellular regulatory networks, and how SNP co-occurrences contribute to disease pathogenesis in ulcerative colitis (UC). Using SNP profiles of 378 UC patients we map the regulatory effects of the SNPs to a human signalling network containing protein-protein, miRNA-mRNA and transcription factor binding interactions. With unsupervised clustering algorithms we group these patient-specific networks into four distinct clusters driven by PRKCB, HLA, SNAI1/CEBPB/PTPN1 and VEGFA/XPO5/POLH hubs. The pathway analysis identifies calcium homeostasis, wound healing and cell motility as key processes in UC pathogenesis. Using transcriptomic data from an independent patient cohort, with three complementary validation approaches focusing on the SNP-affected genes, the patient specific modules and affected functions, we confirm the regulatory impact of non-coding SNPs. iSNP identified regulatory effects for disease-associated non-coding SNPs, and by predicting the patient-specific pathogenic processes, we propose a systems-level way to stratify patients.
ERK1/2 is an ancestral organising signal in spiral cleavage
Authors: Seudre Océane , Carrillo-Baltodano Allan M. , Liang Yan , Martín-Durán José M. 
Published: April 2022

AbstractAnimal development is classified as conditional or autonomous based on whether cell fates are specified through inductive signals or maternal determinants, respectively. Yet how these two major developmental modes evolved remains unclear. During spiral cleavage—a stereotypic embryogenesis ancestral to 15 invertebrate groups, including molluscs and annelids—most lineages specify cell fates conditionally, while some define the primary axial fates autonomously. To identify the mechanisms driving this change, we studyOwenia fusiformis, an early-branching, conditional annelid. InOwenia, ERK1/2-mediated FGF receptor signalling specifies the endomesodermal progenitor. This cell likely acts as an organiser, inducing mesodermal and posterodorsal fates in neighbouring cells and repressing anteriorising signals. The organising role of ERK1/2 inOweniais shared with molluscs, but not with autonomous annelids. Together, these findings suggest that conditional specification of an ERK1/2+embryonic organiser is ancestral in spiral cleavage and was repeatedly lost in annelid lineages with autonomous development.
Discovery of quantum phases in the Shastry-Sutherland compound SrCu2(BO3)2 under extreme conditions of field and pressure
Authors: Shi Zhenzhong , Dissanayake Sachith , Corboz Philippe , Steinhardt William , Graf David , Silevitch D. M. , Dabkowska Hanna A. , Rosenbaum T. F. , Mila Frédéric , Haravifard Sara 
Published: April 2022

AbstractThe 2-dimensional layered oxide material SrCu2(BO3)2, long studied as a realization of the Shastry-Sutherland spin topology, exhibits a range of intriguing physics as a function of both hydrostatic pressure and magnetic field, with a still debated intermediate plaquette phase appearing at approximately 20 kbar and a possible deconfined critical point at higher pressure. Here, we employ a tunnel diode oscillator (TDO) technique to probe the behavior in the combined extreme conditions of high pressure, high magnetic field, and low temperature. We reveal an extensive phase space consisting of multiple magnetic analogs of the elusive supersolid phase and a magnetization plateau. In particular, a 10 × 2 supersolid and a 1/5 plateau, identified by infinite Projected Entangled Pair States (iPEPS) calculations, are found to rely on the presence of both magnetic and non-magnetic particles in the sea of dimer singlets. These states are best understood as descendants of the full-plaquette phase, the leading candidate for the intermediate phase of SrCu2(BO3)2.
Crystal structures and insights into precursor tRNA 5’-end processing by prokaryotic minimal protein-only RNase P
Authors: Li Yangyang , Su Shichen , Gao Yanqing , Lu Guoliang , Liu Hehua , Chen Xi , Shao Zhiwei , Zhang Yixi , Shao Qiyuan , Zhao Xin , Yang Jie , Cao Chulei , Lin Jinzhong , Ma Jinbiao , Gan Jianhua 
Published: April 2022

AbstractBesides the canonical RNA-based RNase P, pre-tRNA 5’-end processing can also be catalyzed by protein-only RNase P (PRORP). To date, various PRORPs have been discovered, but the basis underlying substrate binding and cleavage by HARPs (homolog of Aquifex RNase P) remains elusive. Here, we report structural and biochemical studies of HARPs. Comparison of the apo- and pre-tRNA-complexed structures showed that HARP is able to undergo large conformational changes that facilitate pre-tRNA binding and catalytic site formation.Planctomycetes bacteriumHARP exists as dimer in vitro, but gel filtration and electron microscopy analysis confirmed that HARPs fromThermococcus celer,Thermocrinis minervaeandThermocrinis rubercan assemble into larger oligomers. Structural analysis, mutagenesis and in vitro biochemical studies all supported one cooperative pre-tRNA processing mode, in which one HARP dimer binds pre-tRNA at the elbow region whereas 5’-end removal is catalyzed by the partner dimer. Our studies significantly advance our understanding on pre-tRNA processing by PRORPs.
A high-resolution 4D terrestrial laser scan dataset of the Kijkduin beach-dune system, The Netherlands
Authors: Vos Sander , Anders Katharina , Kuschnerus Mieke , Lindenbergh Roderik , Höfle Bernhard , Aarninkhof Stefan , de Vries Sierd 
Published: April 2022

AbstractSandy coasts form the interface between land and sea and their morphologies are highly dynamic. A combination of human and natural forcing results in morphologic changes affecting both nature values and coastal safety. Terrestrial laser scanning (TLS) is a technique enabling near-continuous monitoring of the changing morphology of a sandy beach-dune system with centimetre-order accuracy. In Kijkduin, The Netherlands, a laser scanner sampled one kilometre of coast at hourly intervals for about six months. This resulted in over 4,000 consecutive topographic scans of around one million points each, at decimetre-order point spacing. Analysis of the resulting dataset will offer new insights into the morphological behaviour of the beach-dune system at hourly to monthly time scales, ultimately increasing our fundamental scientific understanding of these complex geographic systems. It further provides the basis for developing novel algorithms to extract morphodynamic and geodetic information from this unique 4D spatiotemporal dataset. Finally, experiences from this TLS setup support the development of improved near-continuous 3D observation of both natural and anthropogenic scenes in general.
MiR-26a-5p as a useful therapeutic target for upper tract urothelial carcinoma by regulating WNT5A/β-catenin signaling
Authors: Chung Yueh-Hua , Cheng Yuan-Tso , Kao Ying-Hsien , Tsai Wan-Chi , Huang Gong-Kai , Chen Yen-Ta , Shen Yuan-Chi , Tai Ming-Hong , Chiang Po-Hui 
Published: April 2022

AbstractThe role of miRNAs in cancer and their possible function as therapeutic agents are interesting and needed further investigation. The miR-26a-5p had been demonstrated as a tumor suppressor in various cancers. However, the importance of miR-26a-5p regulation in upper tract urothelial carcinoma (UTUC) remains unclear. Here, we aimed to explore the miR-26a-5p expression in UTUC tissues and to identify its regulatory targets and signal network involved in UTUC tumorigenesis. The miR-26a-5p expression was validated by quantitative real-time polymerase chain reaction (qPCR) using renal pelvis tissue samples from 22 patients who were diagnosed with UTUC and 64 cases of renal pelvis tissue microarray using in situ hybridization staining. BFTC-909 UTUC cells were used to examine the effects of miR-26a-5p genetic delivery on proliferation, migration and expression of epithelial-to-mesenchymal transition (EMT) markers. MiR-26a-5p was significantly down-regulated in UTUC tumors compared to adjacent normal tissue and was decreased with histological grades. Moreover, restoration of miR-26a-5p showed inhibition effects on proliferation and migration of BFTC-909 cells. In addition, miR-26a-5p delivery regulated the EMT marker expression and inhibited WNT5A/β-catenin signaling and expression of downstream molecules including NF-κB and MMP-9 in BFTC-909 cells. This study demonstrated that miR-26a-5p restoration may reverse EMT process and regulate WNT5A/β-catenin signaling in UTUC cells. Further studies warranted to explore the potential roles in biomarkers for diagnostics and prognosis, as well as novel therapeutics targets for UTUC treatment.
Reservoir computing with dielectric relaxation at an electrode–ionic liquid interface
Authors: Koh Sang-Gyu , Shima Hisashi , Naitoh Yasuhisa , Akinaga Hiroyuki , Kinoshita Kentaro 
Published: April 2022

AbstractA physical reservoir device with tunable transient dynamics is strongly required to process time-series data with various timescales generated in the edge region. In this study, we proposed using the dielectric relaxation at an electrode–ionic liquid (IL) interface as the physical reservoir by making the most of designable physicochemical properties of ILs. The transient dynamics of a Au/IL/Au reservoir device were characterized as a function of the alkyl chain length of cations in the IL (1-alkyl-3-methylimidazolium bis(trifluoromethane sulfonyl)imide). By considering a weighted sum of exponentials expressing a superposition of Debye-type relaxations, the transient dynamics were well reconstructed. Although such complex dynamics governed by multiple relaxation processes were observed, each extracted relaxation time scales with a power law as a function of IL’s viscosity determined by the alkyl chain length of cations. This indicates that the relaxation processes are characterized by bulk properties of the ILs that obey the widely received Vogel-Fulcher-Tammann law. We demonstrated that the 4-bit time-series signals were transformed into the 16 classifiable data, and the data transformation, which enables to achieve higher accuracy in an image classification task, can be easily optimized according to the features of the input signals by controlling the IL’s viscosity.
The role of neurotrophin genes involved in the vulnerability to gambling disorder
Authors: Solé-Morata Neus , Baenas Isabel , Etxandi Mikel , Granero Roser , Forcales Sonia V. , Gené Manel , Barrot Carme , Gómez-Peña Mónica , Menchón José M. , Ramoz Nicolás , Gorwood Philip , Fernández-Aranda Fernando , Jiménez-Murcia Susana 
Published: April 2022

AbstractEvidence about the involvement of genetic factors in the development of gambling disorder (GD) has been assessed. Among studies assessing heritability and biological vulnerability for GD, neurotrophin (NTF) genes have emerged as promising targets, since a growing literature showed a possible link between NTF and addiction-related disorders. Thus, we aimed to explore the role of NTF genes and GD with the hypothesis that some NTF gene polymorphisms could constitute biological risk factors. The sample included 166 patients with GD and 191 healthy controls. 36 single nucleotide polymorphisms (SNPs) from NTFs (NGF, NGFR, NTRK1, BDNF, NTRK2, NTF3, NTRK3, NTF4, CNTF and CNTFR) were selected and genotyped. Linkage disequilibrium (LD) and haplotype constructions were analyzed, in relationship with the presence of GD. Finally, regulatory elements overlapping the identified SNPs variants associated with GD were searched. The between groups comparisons of allele frequencies indicated that 6 SNPs were potentially associated with GD. Single and multiple-marker analyses showed a strong association between both NTF3 and NTRK2 genes, and GD. The present study supports the involvement of the NTF family in the aetiopathogenesis of GD. An altered cross-regulation of different NTF members signalling pathways might be considered as a biological vulnerability factor for GD.
A randomised study to assess the nicotine pharmacokinetics of an oral nicotine pouch and two nicotine replacement therapy products
Authors: Azzopardi David , Ebajemito James , McEwan Michael , Camacho Oscar M. , Thissen Jesse , Hardie George , Voisine Richard , Mullard Gavin , Cohen Zvi , Murphy James 
Published: April 2022

AbstractNicotine replacement therapies (NRTs) are intended for short-term use to help cigarette smokers to quit. Some smokers find NRTs ineffective or seek a more satisfactory source of nicotine. Tobacco-free oral nicotine pouch (NP) products have emerged as a potential reduced risk product compared with cigarettes and other tobacco products. In a randomised crossover clinical study, thirty-four healthy adult smokers were enrolled and their nicotine Cmax and AUC0-T determined for three 4 mg nicotine products (NP, gum, lozenge) under fasting conditions. The NP, lozenge and gum mean Cmax values were 8.5, 8.3 and 4.4 ng/mL, AUC0-T values were 30.6, 31.5 and 14.3 ng*h/mL, respectively. The NP showed similar nicotine bioavailability to the lozenge (p = 0.6526 (Cmax), p = 1.0000 (AUC0-T)), and superior bioavailability to the gum (p  < 0.0001 for Cmax and AUC0-T). Compared with the lozenge, the NP demonstrated greater product satisfaction with a higher number of positive responses to subjective satisfaction questions. All products were judged to be well-tolerated; the incidence of minor adverse events was lower for the NP (18.2%) than the lozenge (33.3%) or gum (18.8%). In summary, NPs may provide smokers with a more satisfying alternative nicotine source as compared to the reference NRTs.Study Registry/Registered Trial No: ISRCTN/ISRCTN65708311.
Controlling synchronization of gamma oscillations by astrocytic modulation in a model hippocampal neural network
Authors: Makovkin Sergey , Kozinov Evgeny , Ivanchenko Mikhail , Gordleeva Susanna 
Published: April 2022

AbstractRecent in vitro and in vivo experiments demonstrate that astrocytes participate in the maintenance of cortical gamma oscillations and recognition memory. However, the mathematical understanding of the underlying dynamical mechanisms remains largely incomplete. Here we investigate how the interplay of slow modulatory astrocytic signaling with fast synaptic transmission controls coherent oscillations in the network of hippocampal interneurons that receive inputs from pyramidal cells. We show that the astrocytic regulation of signal transmission between neurons improves the firing synchrony and extends the region of coherent oscillations in the biologically relevant values of synaptic conductance. Astrocyte-mediated potentiation of inhibitory synaptic transmission markedly enhances the coherence of network oscillations over a broad range of model parameters. Astrocytic regulation of excitatory synaptic input improves the robustness of interneuron network gamma oscillations induced by physiologically relevant excitatory model drive. These findings suggest a mechanism, by which the astrocytes become involved in cognitive function and information processing through modulating fast neural network dynamics.
Time-dependent power laws in the oxidation and corrosion of metals and alloys
Authors: Itoh Makoto 
Published: April 2022

AbstractUsing the equations which describe the oxide thickness as a function of the oxidation time and temperature in the thermal oxidation of Si, various experimental results on the oxidation and corrosion of metals and alloys available in the literature are analyzed. By the analyses, it is found that the weight loss of copper by atmospheric corrosion and the weight gains of austenitic stainless steel and Ni–Cr alloy by high temperature oxidation follow a time-dependent power law in which both diffusion and reaction are involved. It is also found that the pitting corrosion of aluminum alloys by the immersion with seawater and the high-temperature oxidation of Al(431) follow a time-dependent power law of a reaction-limited kind. In addition, an estimation is given of the activation energy for the pitting corrosion of mild steel by the immersion with seawater.