bluuebunny/crossref_metadata_2025 huggingface dataset:
VE-Cadherin modulates β-catenin/TCF-4 to enhance Vasculogenic Mimicry
Authors: Delgado-Bellido Daniel , Zamudio-Martínez Esteban , Fernández-Cortés Mónica , Herrera-Campos Ana Belén , Olmedo-Pelayo Joaquin , Perez Carmen Jordán , Expósito José , de Álava Enrique , Amaral Ana Teresa , Valle Francisco O’ , Diaz Angel Garcia , Oliver F. J.
Published: February 2023

Vasculogenic Mimicry (VM) refers to the capacity to form a blood network from aggressive cancer cells in an independent way of endothelial cells, to provide nutrients and oxygen leading to enhanced microenvironment complexity and treatment failure. In a previous study, we demonstrated that VE-Cadherin and its phosphorylation at Y658 modulated kaiso-dependent gene expression (CCND1 and Wnt 11) through a pathway involving Focal Adhesion kinase (FAK). In the present research, using a proteomic approach, we have found that β-catenin/TCF-4 is associated with nuclear VE-cadherin and enhances the capacity of malignant melanoma cells to undergo VM in cooperation with VE-Cadherin; in addition, preventing the phosphorylation of Y658 of VE-cadherin upon FAK disabling resulted in VE-Cadherin/β-catenin complex dissociation, increased β-catenin degradation while reducing TCF-4-dependent genes transcription (C-Myc and Twist-1). Uveal melanoma cells knockout for VE-Cadherin loses β-catenin expression while the rescue of VE-Cadherin (but not of the phosphorylation defective VE-Cadherin Y658F mutant) permits stabilization of β-catenin and tumor growth reduction in vivo experiments. In vivo, the concomitant treatment with the FAK inhibitor PF-271 and the anti-angiogenic agent bevacizumab leads to a strong reduction in tumor growth concerning the single treatment. In conclusion, the anomalous expression of VE-Cadherin in metastatic melanoma cells (from both uveal and cutaneous origins), together with its permanent phosphorylation at Y658, favors the induction of the aggressive VM phenotype through the cooperation of β-catenin with VE-Cadherin and by enhancing TCF-4 genes-dependent transcription.
PLK1 inhibition promotes apoptosis and DNA damage in glioma stem cells by regulating the nuclear translocation of YBX1
Authors: Li Xuetao , Chen Guangliang , Liu Bin , Tao Zhennan , Wu Yue , Zhang Kai , Feng Zibin , Huang Yulun , Wang Hao
Published: February 2023

Glioma stem cells (GSCs) are the important cause of tumorigenesis, recurrence, and chemo(radio)resistance in glioma. Targeting GSCs helps improve the outcomes of glioma treatment. Polo-like kinase 1 (PLK1) is a member of the serine/threonine protein kinase family, which is highly conserved. In recent years, it has been suggested that increased levels of PLK1 and its activity are associated with tumor progression and poor prognosis. We aimed to identify whether PLK1 plays a critical role in stemness maintenance and apoptosis regulation in GSCs. Here we identify that PLK1 inhibition can induce apoptosis and DNA damage of GSCs, we have also delineat the possible underlying molecular mechanisms: PLK1 interacts with YBX1 and directly phosphorylates serine 174 and serine 176 of YBX1. Inhibition of PLK1 reduces the phosphorylation level of YBX1, and decreased phosphorylation of YBX1 prevents its nuclear translocation, thereby inducing apoptosis and DNA damage of GSCs. We confirmed that YBX1 knockdown resulted in the apoptosis and DNA damage of GSCs. These findings uncover that PLK1 inhibition induces cell apoptosis and DNA damage in GSCs through YBX1 phosphorylation, providing new insights into the mechanism by which PLK1 inhibition contributes to the apoptosis of and DNA damage in gliomas.
Separation of scales and a thermodynamic description of feature learning in some CNNs
Authors: Seroussi Inbar , Naveh Gadi , Ringel Zohar
Published: February 2023

Deep neural networks (DNNs) are powerful tools for compressing and distilling information. Their scale and complexity, often involving billions of inter-dependent parameters, render direct microscopic analysis difficult. Under such circumstances, a common strategy is to identify slow variables that average the erratic behavior of the fast microscopic variables. Here, we identify a similar separation of scales occurring in fully trained finitely over-parameterized deep convolutional neural networks (CNNs) and fully connected networks (FCNs). Specifically, we show that DNN layers couple only through the second cumulant (kernels) of their activations and pre-activations. Moreover, the latter fluctuates in a nearly Gaussian manner. For infinite width DNNs, these kernels are inert, while for finite ones they adapt to the data and yield a tractable data-aware Gaussian Process. The resulting thermodynamic theory of deep learning yields accurate predictions in various settings. In addition, it provides new ways of analyzing and understanding DNNs in general.
Universal diamond edge Raman scale to 0.5 terapascal and implications for the metallization of hydrogen
Authors: Eremets M. I. , Minkov V. S. , Kong P. P. , Drozdov A. P. , Chariton S. , Prakapenka V. B.
Published: February 2023

The recent progress in generating static pressures up to terapascal values opens opportunities for studying novel materials with unusual properties, such as metallization of hydrogen and high-temperature superconductivity. However, an evaluation of pressure above ~0.3 terapascal is a challenge. We report a universal high-pressure scale up to ~0.5 terapascal, which is based on the shift of the Raman edge of stressed diamond anvils correlated with the equation of state of Au and does not require an additional pressure sensor. According to the new scale, the pressure values are substantially lower by 20% at ~0.5 terapascal compared to the extrapolation of the existing scales. We compare the available data of H2at the highest static pressures. We show that the onset of the proposed metallization of molecular hydrogen reported by different groups is consistent when corrected with the new scale and can be compared with various theoretical predictions.
Lipopolysaccharide biosynthesis and traffic in the envelope of the pathogen Brucella abortus
Authors: Servais Caroline , Vassen Victoria , Verhaeghe Audrey , Küster Nina , Carlier Elodie , Phégnon Léa , Mayard Aurélie , Auberger Nicolas , Vincent Stéphane , De Bolle Xavier
Published: February 2023

Lipopolysaccharide is essential for most Gram-negative bacteria as it is a main component of the outer membrane. In the pathogen Brucella abortus, smooth lipopolysaccharide containing the O-antigen is required for virulence. Being part of the Rhizobiales, Brucella spp. display unipolar growth and lipopolysaccharide was shown to be incorporated at the active growth sites, i.e. the new pole and the division site. By localizing proteins involved in the lipopolysaccharide transport across the cell envelope, from the inner to the outer membrane, we show that the lipopolysaccharide incorporation sites are determined by the inner membrane complex of the lipopolysaccharide transport system. Moreover, we identify the main O-antigen ligase of Brucella spp. involved in smooth lipopolysaccharide synthesis. Altogether, our data highlight a layer of spatiotemporal organization of the lipopolysaccharide biosynthesis pathway and identify an original class of bifunctional O-antigen ligases.
A versatile, high-efficiency platform for CRISPR-based gene activation
Authors: Heidersbach Amy J. , Dorighi Kristel M. , Gomez Javier A. , Jacobi Ashley M. , Haley Benjamin
Published: February 2023

CRISPR-mediated transcriptional activation (CRISPRa) is a powerful technology for inducing gene expression from endogenous loci with exciting applications in high throughput gain-of-function genomic screens and the engineering of cell-based models. However, current strategies for generating potent, stable, CRISPRa-competent cell lines present limitations for the broad utility of this approach. Here, we provide a high-efficiency, self-selecting CRISPRa enrichment strategy, which combined with piggyBac transposon technology enables rapid production of CRISPRa-ready cell populations compatible with a variety of downstream assays. We complement this with an optimized guide RNA scaffold that significantly enhances CRISPRa functionality. Finally, we describe a synthetic guide RNA tool set that enables transient, population-wide gene activation when used with the self-selecting CRISPRa system. Taken together, this versatile platform greatly enhances the potential for CRISPRa across a wide variety of cellular contexts.
Watching the release of a photopharmacological drug from tubulin using time-resolved serial crystallography
Authors: Wranik Maximilian , Weinert Tobias , Slavov Chavdar , Masini Tiziana , Furrer Antonia , Gaillard Natacha , Gioia Dario , Ferrarotti Marco , James Daniel , Glover Hannah , Carrillo Melissa , Kekilli Demet , Stipp Robin , Skopintsev Petr , Brünle Steffen , Mühlethaler Tobias , Beale John , Gashi Dardan , Nass Karol , Ozerov Dmitry , Johnson Philip J. M. , Cirelli Claudio , Bacellar Camila , Braun Markus , Wang Meitian , Dworkowski Florian , Milne Chris , Cavalli Andrea , Wachtveitl Josef , Steinmetz Michel O. , Standfuss Jörg
Published: February 2023

The binding and release of ligands from their protein targets is central to fundamental biological processes as well as to drug discovery. Photopharmacology introduces chemical triggers that allow the changing of ligand affinities and thus biological activity by light. Insight into the molecular mechanisms of photopharmacology is largely missing because the relevant transitions during the light-triggered reaction cannot be resolved by conventional structural biology. Using time-resolved serial crystallography at a synchrotron and X-ray free-electron laser, we capture the release of the anti-cancer compound azo-combretastatin A4 and the resulting conformational changes in tubulin. Nine structural snapshots from 1 ns to 100 ms complemented by simulations show how cis-to-trans isomerization of the azobenzene bond leads to a switch in ligand affinity, opening of an exit channel, and collapse of the binding pocket upon ligand release. The resulting global backbone rearrangements are related to the action mechanism of microtubule-destabilizing drugs.
Mechanisms of the RNA helicases DDX42 and DDX46 in human U2 snRNP assembly
Authors: Yang Fenghua , Bian Tong , Zhan Xiechao , Chen Zhe , Xing Zhihan , Larsen Nicolas A. , Zhang Xiaofeng , Shi Yigong
Published: February 2023

Three RNA helicases – DDX42, DDX46 and DHX15 – are found to be associated with human U2 snRNP, but their roles and mechanisms in U2 snRNP and spliceosome assembly are insufficiently understood. Here we report the cryo-electron microscopy (cryo-EM) structures of the DDX42-SF3b complex and a putative assembly precursor of 17S U2 snRNP that contains DDX42 (DDX42-U2 complex). DDX42 is anchored on SF3B1 through N-terminal sequences, with its N-plug occupying the RNA path of SF3B1. The binding mode of DDX42 to SF3B1 is in striking analogy to that of DDX46. In the DDX42-U2 complex, the N-terminus of DDX42 remains anchored on SF3B1, but the helicase domain has been displaced by U2 snRNA and TAT-SF1. Through in vitro assays, we show DDX42 and DDX46 are mutually exclusive in terms of binding to SF3b. Cancer-driving mutations of SF3B1 target the residues in the RNA path that directly interact with DDX42 and DDX46. These findings reveal the distinct roles of DDX42 and DDX46 in assembly of 17S U2 snRNP and provide insights into the mechanisms of SF3B1 cancer mutations.
Structure of a monomeric photosystem I core associated with iron-stress-induced-A proteins from Anabaena sp. PCC 7120
Authors: Nagao Ryo , Kato Koji , Hamaguchi Tasuku , Ueno Yoshifumi , Tsuboshita Naoki , Shimizu Shota , Furutani Miyu , Ehira Shigeki , Nakajima Yoshiki , Kawakami Keisuke , Suzuki Takehiro , Dohmae Naoshi , Akimoto Seiji , Yonekura Koji , Shen Jian-Ren
Published: February 2023

Iron-stress-induced-A proteins (IsiAs) are expressed in cyanobacteria under iron-deficient conditions. The cyanobacterium Anabaena sp. PCC 7120 has four isiA genes; however, their binding property and functional roles in PSI are still missing. We analyzed a cryo-electron microscopy structure of a PSI-IsiA supercomplex isolated from Anabaena grown under an iron-deficient condition. The PSI-IsiA structure contains six IsiA subunits associated with the PsaA side of a PSI core monomer. Three of the six IsiA subunits were identified as IsiA1 and IsiA2. The PSI-IsiA structure lacks a PsaL subunit; instead, a C-terminal domain of IsiA2 occupies the position of PsaL, which inhibits the oligomerization of PSI, leading to the formation of a PSI monomer. Furthermore, excitation-energy transfer from IsiAs to PSI appeared with a time constant of 55 ps. These findings provide insights into both the molecular assembly of the Anabaena IsiA family and the functional roles of IsiAs.
Widespread perturbation of ETS factor binding sites in cancer
Authors: Carrasco Pro Sebastian , Hook Heather , Bray David , Berenzy Daniel , Moyer Devlin , Yin Meimei , Labadorf Adam Thomas , Tewhey Ryan , Siggers Trevor , Fuxman Bass Juan Ignacio
Published: February 2023

Although >90% of somatic mutations reside in non-coding regions, few have been reported as cancer drivers. To predict driver non-coding variants (NCVs), we present a transcription factor (TF)-aware burden test based on a model of coherent TF function in promoters. We apply this test to NCVs from the Pan-Cancer Analysis of Whole Genomes cohort and predict 2555 driver NCVs in the promoters of 813 genes across 20 cancer types. These genes are enriched in cancer-related gene ontologies, essential genes, and genes associated with cancer prognosis. We find that 765 candidate driver NCVs alter transcriptional activity, 510 lead to differential binding of TF-cofactor regulatory complexes, and that they primarily impact the binding of ETS factors. Finally, we show that different NCVs within a promoter often affect transcriptional activity through shared mechanisms. Our integrated computational and experimental approach shows that cancer NCVs are widespread and that ETS factors are commonly disrupted.
Differential regulation of mRNA stability modulates transcriptional memory and facilitates environmental adaptation
Authors: Li Bingnan , Zeis Patrice , Zhang Yujie , Alekseenko Alisa , Fürst Eliska , Sanchez Yerma Pareja , Lin Gen , Tekkedil Manu M. , Piazza Ilaria , Steinmetz Lars M. , Pelechano Vicent
Published: February 2023

Transcriptional memory, by which cells respond faster to repeated stimuli, is key for cellular adaptation and organism survival. Chromatin organization has been shown to play a role in the faster response of primed cells. However, the contribution of post-transcriptional regulation is not yet explored. Here we perform a genome-wide screen to identify novel factors modulating transcriptional memory in S. cerevisiae in response to galactose. We find that depletion of the nuclear RNA exosome increases GAL1 expression in primed cells. Our work shows that gene-specific differences in intrinsic nuclear surveillance factor association can enhance both gene induction and repression in primed cells. Finally, we show that primed cells present altered levels of RNA degradation machinery and that both nuclear and cytoplasmic mRNA decay modulate transcriptional memory. Our results demonstrate that mRNA post-transcriptional regulation, and not only transcription regulation, should be considered when investigating gene expression memory.
Cryo-EM captures early ribosome assembly in action
Authors: Qin Bo , Lauer Simon M. , Balke Annika , Vieira-Vieira Carlos H. , Bürger Jörg , Mielke Thorsten , Selbach Matthias , Scheerer Patrick , Spahn Christian M. T. , Nikolay Rainer
Published: February 2023

Ribosome biogenesis is a fundamental multi-step cellular process in all domains of life that involves the production, processing, folding, and modification of ribosomal RNAs (rRNAs) and ribosomal proteins. To obtain insights into the still unexplored early assembly phase of the bacterial 50S subunit, we exploited a minimal in vitro reconstitution system using purified ribosomal components and scalable reaction conditions. Time-limited assembly assays combined with cryo-EM analysis visualizes the structurally complex assembly pathway starting with a particle consisting of ordered density for only ~500 nucleotides of 23S rRNA domain I and three ribosomal proteins. In addition, our structural analysis reveals that early 50S assembly occurs in a domain-wise fashion, while late 50S assembly proceeds incrementally. Furthermore, we find that both ribosomal proteins and folded rRNA helices, occupying surface exposed regions on pre-50S particles, induce, or stabilize rRNA folds within adjacent regions, thereby creating cooperativity.
Similarities and differences between multivariate patterns of cognitive and socio-cognitive deficits in schizophrenia, bipolar disorder and related risk
Authors: Raio Alessandra , Pergola Giulio , Rampino Antonio , Russo Marianna , D’Ambrosio Enrico , Selvaggi Pierluigi , De Chiara Valerie , Altamura Mario , Brudaglio Flora , Saponaro Alessandro , Semisa Domenico , Bertolino Alessandro , Antonucci Linda A. , Blasi Giuseppe ,   the Apulian Network on Risk for Psychosis, Manzari Anna , Carofiglio Angela , Barrasso Giuseppe , Bellomo Antonello , Leccisotti Ivana , Di Fino Melania , Andriola Ileana , Pennacchio Teresa Claudia
Published: February 2023

Cognition and social cognition anomalies in patients with bipolar disorder (BD) and schizophrenia (SCZ) have been largely documented, but the degree of overlap between the two disorders remains unclear in this regard. We used machine learning to generate and combine two classifiers based on cognitive and socio-cognitive variables, thus delivering unimodal and multimodal signatures aimed at discriminating BD and SCZ from two independent groups of Healthy Controls (HC1 and HC2 respectively). Multimodal signatures discriminated well between patients and controls in both the HC1-BD and HC2-SCZ cohorts. Although specific disease-related deficits were characterized, the HC1 vs. BD signature successfully discriminated HC2 from SCZ, and vice-versa. Such combined signatures allowed to identify also individuals at First Episode of Psychosis (FEP), but not subjects at Clinical High Risk (CHR), which were classified neither as patients nor as HC. These findings suggest that both trans-diagnostic and disease-specific cognitive and socio-cognitive deficits characterize SCZ and BD. Anomalous patterns in these domains are also relevant to early stages of disease and offer novel insights for personalized rehabilitative programs.
Global long term daily 1 km surface soil moisture dataset with physics informed machine learning
Authors: Han Qianqian , Zeng Yijian , Zhang Lijie , Wang Chao , Prikaziuk Egor , Niu Zhenguo , Su Bob
Published: February 2023

Although soil moisture is a key factor of hydrologic and climate applications, global continuous high resolution soil moisture datasets are still limited. Here we use physics-informed machine learning to generate a global, long-term, spatially continuous high resolution dataset of surface soil moisture, using International Soil Moisture Network (ISMN), remote sensing and meteorological data, guided with the knowledge of physical processes impacting soil moisture dynamics. Global Surface Soil Moisture (GSSM1 km) provides surface soil moisture (0–5 cm) at 1 km spatial and daily temporal resolution over the period 2000–2020. The performance of the GSSM1 km dataset is evaluated with testing and validation datasets, and via inter-comparisons with existing soil moisture products. The root mean square error of GSSM1 km in testing set is 0.05 cm3/cm3, and correlation coefficient is 0.9. In terms of the feature importance, Antecedent Precipitation Evaporation Index (APEI) is the most important significant predictor among 18 predictors, followed by evaporation and longitude. GSSM1 km product can support the investigation of large-scale climate extremes and long-term trend analysis.
Entanglement and quantum correlation measures for quantum multipartite mixed states
Authors: Vesperini Arthur , Bel-Hadj-Aissa Ghofrane , Franzosi Roberto
Published: February 2023

Entanglement, and quantum correlation, are precious resources for quantum technologies implementation based on quantum information science, such as quantum communication, quantum computing, and quantum interferometry. Nevertheless, to our best knowledge, a directly or numerically computable measure for the entanglement of multipartite mixed states is still lacking. In this work, (i) we derive a measure of the degree of quantum correlation for mixed multipartite states. The latter possesses a closed-form expression valid in the general case unlike, to our best knowledge, all other known measures of quantum correlation. (ii) We further propose an entanglement measure, derived from this quantum correlation measure using a novel regularization procedure for the density matrix. Therefore, a comparison of the proposed measures, of quantum correlation and entanglement, allows one to distinguish between quantum correlation detached from entanglement and the one induced by entanglement and, hence, to identify separable but non-classical states. We have tested our quantum correlation and entanglement measures, on states well-known in literature: a general Bell diagonal state and the Werner states, which are easily tractable with our regularization procedure, and we have verified the accordance between our measures and the expected results for these states. Finally, we validate the two measures in two cases of multipartite states. The first is a generalization to three qubits of the Werner state, the second is a one-parameter three qubits mixed state interpolating between a bi-separable state and a genuine multipartite state, passing through a fully separable state.
Atypical changes in Candida albicans cells treated with the Venetin-1 complex from earthworm coelomic fluid
Authors: Wójcik-Mieszawska Sylwia , Lewtak Kinga , Sofińska-Chmiel Weronika , Wydrych Jerzy , Fiołka Marta J.
Published: February 2023

In the present research, the effect of a protein-polysaccharide complex Venetin-1 obtained from the coelomic fluid of Dendrobaena veneta earthworm on Candida albicans cells was characterized. The compound destroyed fungal cells without showing cytotoxicity to human skin fibroblasts, which was demonstrated in earlier studies. Since it had an effect on the fungal cell wall and membrane, this complex was compared with the known antifungal antibiotic fluconazole. Both preparations disturbed the division of yeast cells and resulted in the formation of aggregates and chains of unseparated cells, which was illustrated by staining with fluorochromes. Fluorescent staining of the cell wall with Calcofluor white facilitated comparison of the types of aggregates formed after the action of both substances. The analysis performed with the use of Congo red showed that Venetin-1 exposed deeper layers of the cell wall, whereas no such effect was visible after the use of fluconazole. The FTIR analysis confirmed changes in the mannoprotein layer of the cell wall after the application of the Venetin-1 complex. Staining with Rhodamine 123 and the use of flow cytometry allowed comparison of changes in the mitochondria. Significantly elongated mitochondria were observed after the Venetin-1 application, but not after the application of the classic antibiotic. Phase contrast microscopy revealed vacuole enlargement after the Venetin-1 application. The flow cytometry analysis of C. albicans cells treated with Venetin-1 and fluconazole showed that both substances caused a significant decrease in cell viability.
Electrically conductive scaffolds mimicking the hierarchical structure of cardiac myofibers
Authors: Ul Haq Arsalan , Montaina Luca , Pescosolido Francesca , Carotenuto Felicia , Trovalusci Federica , De Matteis Fabio , Tamburri Emanuela , Di Nardo Paolo
Published: February 2023

Electrically conductive scaffolds, mimicking the unique directional alignment of muscle fibers in the myocardium, are fabricated using the 3D printing micro-stereolithography technique. Polyethylene glycol diacrylate (photo-sensitive polymer), Irgacure 819 (photo-initiator), curcumin (dye) and polyaniline (conductive polymer) are blended to make the conductive ink that is crosslinked using free radical photo-polymerization reaction. Curcumin acts as a liquid filter and prevents light from penetrating deep into the photo-sensitive solution and plays a central role in the 3D printing process. The obtained scaffolds demonstrate well defined morphology with an average pore size of 300 ± 15 μm and semi-conducting properties with a conductivity of ~ 10–6 S/m. Cyclic voltammetry analyses detect the electroactivity and highlight how the electron transfer also involve an ionic diffusion between the polymer and the electrolyte solution. Scaffolds reach their maximum swelling extent 30 min after immersing in the PBS at 37 °C and after 4 weeks they demonstrate a slow hydrolytic degradation rate typical of polyethylene glycol network. Conductive scaffolds display tunable conductivity and provide an optimal environment to the cultured mouse cardiac progenitor cells.
Transcranial direct current stimulation (tDCS) in depression induces structural plasticity
Authors: Jog Mayank A , Anderson Cole , Kubicki Antoni , Boucher Michael , Leaver Amber , Hellemann Gerhard , Iacoboni Marco , Woods Roger , Narr Katherine
Published: February 2023

Transcranial direct current stimulation (tDCS) is a non-invasive neuromodulation technique involving administration of well-tolerated electrical current to the brain through scalp electrodes. TDCS may improve symptoms in neuropsychiatric disorders, but mixed results from recent clinical trials underscore the need to demonstrate that tDCS can modulate clinically relevant brain systems over time in patients. Here, we analyzed longitudinal structural MRI data from a randomized, double-blind, parallel-design clinical trial in depression (NCT03556124, N = 59) to investigate whether serial tDCS individually targeted to the left dorso-lateral prefrontal cortex (DLPFC) can induce neurostructural changes. Significant (FWEc p < 0.05) treatment-related gray matter changes were observed with active high-definition (HD) tDCS relative to sham tDCS within the left DLPFC stimulation target. No changes were observed with active conventional tDCS. A follow-up analysis within individual treatment groups revealed significant gray matter increases with active HD-tDCS in brain regions functionally connected with the stimulation target, including the bilateral DLPFC, bilateral posterior cingulate cortex, subgenual anterior cingulate cortex, and the right hippocampus, thalamus and left caudate brain regions. Integrity of blinding was verified, no significant differences in stimulation-related discomfort were observed between treatment groups, and tDCS treatments were not augmented by any other adjunct treatments. Overall, these results demonstrate that serial HD-tDCS leads to neurostructural changes at a predetermined brain target in depression and suggest that such plasticity effects may propagate over brain networks.
Effect of enzymatic treatment on Eucalyptus globulus vessels passivation
Authors: Vaz Álvaro , Coelho João , Costa Vera , Maloney Thaddeus , Phiri Josphat , Pinto Paula , de Sousa António Mendes , Simões Rogério
Published: February 2023

Hardwood vessel elements generate problems in industrial uncoated wood-free printing paper operation, causing vessel picking and ink refusal. These problems are mitigated using mechanical refining at the cost of paper quality. Vessel enzymatic passivation, altering its adhesion to the fiber network and reducing its hydrophobicity is a way of improving paper quality. The object of this paper is to study how the enzymatic treatment by xylanase and by an enzymatic cocktail containing cellulases and laccases affect elemental chlorine free bleached Eucalyptus globulus vessel and fiber porosities, bulk, and surface chemical compositions. Thermoporosimetry revealed the vessel structure to be more porous, surface analysis showed its lower O/C ratio and bulk chemistry analysis its higher hemicellulose content. Enzymes had different effects on porosity, bulk and surface composition of fibers and vessels, affecting vessel adhesion and hydrophobicity. Vessel picking count decreased 76% for papers containing vessels treated with xylanase and 94% for the papers with vessels treated with the enzymatic cocktail. Fiber sheet samples had lower water contact angle (54.1º) than vessels rich sheets (63.7º), that reduced with xylanase (62.1º) and cocktail (58.4º). It is proposed that differences in vessel and fiber porosity structures affect the enzymatic attacks, eventually causing vessel passivation.
Transcriptomic profiling of programmed cell death 1 (PD-1) expressing T cells in early rheumatoid arthritis identifies a decreased CD4 + PD-1 + signature post-treatment
Authors: Lowe Katie , Small Annabelle , Song Qingxuan , Hao Ling-Yang , Murray-Brown William , Proudman Susanna , Smith Malcolm D. , Nagpal Sunil , Wechalekar Mihir D.
Published: February 2023

Programmed cell death protein 1 (PD-1)-expressing T cells are expanded in individuals with established rheumatoid arthritis (RA). However, little is known about their functional role in the pathogenesis of early RA. To address this, we investigated the transcriptomic profiles of circulating CD4+ and CD8+ PD-1+ lymphocytes from patients with early RA (n = 5) using fluorescence activated cell sorting in conjunction with total RNA sequencing. Additionally, we assessed for alterations in CD4+PD-1+ gene signatures in previously published synovial tissue (ST) biopsy data (n = 19) (GSE89408, GSE97165) before and after six-months of triple disease modifying anti-rheumatic drug (tDMARD) treatment. Comparisons of gene signatures between CD4+PD-1+ vs. PD-1− cells identified significant upregulation of genes including CXCL13 and MAF, and in pathways including Th1 and Th2, cross talk between dendritic cells and NK cells, B cell development and antigen presentation. Gene signatures from early RA ST before and after six-month tDMARD treatment revealed downregulation of the CD4+PD-1+ signatures following treatment, identifying a mechanism through which tDMARDs exert their effect by influencing T cell populations. Furthermore, we identify factors associated with B cell help that are enhanced in the ST compared with PBMCs, highlighting their importance in driving synovial inflammation.
Phase-sensitive optical time domain reflectometry based on geometric phase measurement
Authors: Shaheen Sabahat , Hicke Konstantin , Krebber Katerina
Published: February 2023

A phase-sensitive optical time domain reflectometer based on coherent heterodyne detection of geometric phase in the beat signal of light, is reported for the first time to our knowledge. The use of the geometric phase to extract strain makes it immune to polarisation diversity fading. This is because a polarisation mismatch between the interfering beams is not a hindrance to its measurement. The geometric phase is calculated using the amplitude of the beat signal and individual beam intensities without any need for phase unwrapping. It is measured per beat period and can be equated with the traditionally measured dynamic phase with appropriate scaling. The results show that the system based on the geometric phase successfully measures strain, free from polarisation mismatch fading and phase unwrapping errors, providing a completely novel solution to these problems.
Sensitivity and performance of three novel quantitative assays of SARS-CoV-2 nucleoprotein in blood
Authors: Hillig Thore , Kristensen Josephine R. , Brasen Claus L. , Brandslund Ivan , Olsen Dorte A. , Davidsen Camilla , Madsen Jonna S. , Jensen Claus A. , Hansen Young B. L. , Friis-Hansen Lennart
Published: February 2023

To assess if SARS-CoV-2 (COVID-19) systemic disease can be determined by available nucleoprotein assays, we compared the performance of three commercial SARS-CoV-2 nucleoprotein (N) assays in plasma. A total of 272 plasma samples collected in the period November–December 2021 were analyzed by the methods Simoa SARS CoV‐2 N Protein Advantage Kit [Quanterix Simoa], Solsten SARS-CoV-2 Antigen enzyme immunosorbent assay (ELISA) [Solsten ELISA], and Elecsys SARS‐CoV‐2 Antigen electrochemiluminescence immunoassay [Elecsys ECLIA]. Additionally, a dilution series of inactivated virus culture was analyzed by the three assays. The SARS CoV-2 PCR-status was not known for the patients. Linear correlation in the pairwise correlation between assays as well as linearity of dilution series of inactivated virus culture was estimated by Spearman score. Sensitivity and specificity were estimated by pairwise comparison. The three assays showed poor agreement on patient samples with regards to concentration. Performance on virus culture was excellent but with different level of detection (LOD). Positive vs negative results show comparable sensitivity and specificity of Quanterix Simoa and Solsten ELISA, with a higher LOD in Elecsys ECLIA and thus lower sensitivity and high specificity. N by all tested assays can be used as a marker for systemic COVID-19 disease.
Network coevolution drives segregation and enhances Pareto optimal equilibrium selection in coordination games
Authors: González Casado Miguel A. , Sánchez Angel , San Miguel Maxi
Published: February 2023

In this work we assess the role played by the dynamical adaptation of the interactions network, among agents playing Coordination Games, in reaching global coordination and in the equilibrium selection. Specifically, we analyze a coevolution model that couples the changes in agents’ actions with the network dynamics, so that while agents play the game, they are able to sever some of their current connections and connect with others. We focus on two action update rules: Replicator Dynamics (RD) and Unconditional Imitation (UI), and we define a coevolution rule in which, apart from action updates, with a certain rewiring probability p, agents unsatisfied with their current connections are able to eliminate a link and connect with a randomly chosen neighbor. We call this probability to rewire links the ‘network plasticity’. We investigate a Pure Coordination Game (PCG), in which choices are equivalent, and on a General Coordination Game (GCG), for which there is a risk-dominant action and a payoff-dominant one. Changing the plasticity parameter, there is a transition from a regime in which the system fully coordinates on a single connected component to a regime in which the system fragments in two connected components, each one coordinated on a different action (either if both actions are equivalent or not). The nature of this fragmentation transition is different for different update rules. Second, we find that both for RD and UI in a GCG, there is a regime of intermediate values of plasticity, before the fragmentation transition, for which the system is able to fully coordinate on a single component network on the payoff-dominant action, i.e., coevolution enhances payoff-dominant equilibrium selection for both update rules.
Unprecedented 21st century heat across the Pacific Northwest of North America
Authors: Heeter Karen J. , Harley Grant L. , Abatzoglou John T. , Anchukaitis Kevin J. , Cook Edward R. , Coulthard Bethany L. , Dye Laura A. , Homfeld Inga K.
Published: February 2023

Extreme summer temperatures are increasingly common across the Northern Hemisphere and inflict severe socioeconomic and biological consequences. In summer 2021, the Pacific Northwest region of North America (PNW) experienced a 2-week-long extreme heatwave, which contributed to record-breaking summer temperatures. Here, we use tree-ring records to show that summer temperatures in 2021, as well as the rate of summertime warming during the last several decades, are unprecedented within the context of the last millennium for the PNW. In the absence of committed efforts to curtail anthropogenic emissions below intermediate levels (SSP2–4.5), climate model projections indicate a rapidly increasing risk of the PNW regularly experiencing 2021-like extreme summer temperatures, with a 50% chance of yearly occurrence by 2050. The 2021 summer temperatures experienced across the PNW provide a benchmark and impetus for communities in historically temperate climates to account for extreme heat-related impacts in climate change adaptation strategies.
Heterologous mogrosides biosynthesis in cucumber and tomato by genetic manipulation
Authors: Liao Jingjing , Liu Tingyao , Xie Lei , Mo Changming , Qiao Jing , Huang Xiyang , Cui Shengrong , Jia Xunli , Luo Zuliang , Ma Xiaojun
Published: February 2023

Mogrosides are widely used as high-value natural zero-calorie sweeteners that exhibit an array of biological activities and allow for vegetable flavour breeding by modern molecular biotechnology. In this study, we developed an In-fusion based gene stacking strategy for transgene stacking and a multi-gene vector harbouring 6 mogrosides biosynthesis genes and transformed it into Cucumis sativus and Lycopersicon esculentum. Here we show that transgenic cucumber can produce mogroside V and siamenoside I at 587 ng/g FW and 113 ng/g FW, respectively, and cultivated transgenic tomato with mogroside III. This study provides a strategy for vegetable flavour improvement, paving the way for heterologous biosynthesis of mogrosides.
Glucocorticoids increase tissue cell protection against pore-forming toxins from pathogenic bacteria
Authors: Ormsby Thomas J. R. , Owens Sian E. , Turner Matthew L. , Cronin James G. , Bromfield John J. , Sheldon I. Martin
Published: February 2023

Many species of pathogenic bacteria damage tissue cells by secreting toxins that form pores in plasma membranes. Here we show that glucocorticoids increase the intrinsic protection of tissue cells against pore-forming toxins. Dexamethasone protected several cell types against the cholesterol-dependent cytolysin, pyolysin, from Trueperella pyogenes. Dexamethasone treatment reduced pyolysin-induced leakage of potassium and lactate dehydrogenase, limited actin cytoskeleton alterations, reduced plasma membrane blebbing, and prevented cytolysis. Hydrocortisone and fluticasone also protected against pyolysin-induced cell damage. Furthermore, dexamethasone protected HeLa and A549 cells against the pore-forming toxins streptolysin O from Streptococcus pyogenes, and alpha-hemolysin from Staphylococcus aureus. Dexamethasone cytoprotection was not associated with changes in cellular cholesterol or activating mitogen-activated protein kinase (MAPK) cell stress responses. However, cytoprotection was dependent on the glucocorticoid receptor and 3-hydroxy-3-methyl-glutaryl-coenzyme A reductase (HMGCR). Collectively, our findings imply that glucocorticoids could be exploited to limit tissue damage caused by pathogens secreting pore-forming toxins.
A multi-timescale synaptic weight based on ferroelectric hafnium zirconium oxide
Authors: Halter Mattia , Bégon-Lours Laura , Sousa Marilyne , Popoff Youri , Drechsler Ute , Bragaglia Valeria , Offrein Bert Jan
Published: February 2023

Brain-inspired computing emerged as a forefront technology to harness the growing amount of data generated in an increasingly connected society. The complex dynamics involving short- and long-term memory are key to the undisputed performance of biological neural networks. Here, we report on sub-µm-sized artificial synaptic weights exploiting a combination of a ferroelectric space charge effect and oxidation state modulation in the oxide channel of a ferroelectric field effect transistor. They lead to a quasi-continuous resistance tuning of the synapse by a factor of $$60$$
60
and a fine-grained weight update of more than $$200$$
200
resistance values. We leverage a fast, saturating ferroelectric effect and a slow, ionic drift and diffusion process to engineer a multi-timescale artificial synapse. Our device demonstrates an endurance of more than $${10}^{10}$$

10

10

cycles, a ferroelectric retention of more than $$10$$
10
years, and various types of volatility behavior on distinct timescales, making it well suited for neuromorphic and cognitive computing.
Interaction of N-nitrosamines with binuclear copper complexes for luminescent detection
Authors: Feng Haosheng , Luo Shao-Xiong Lennon , Croy Robert G. , Essigmann John M. , Swager Timothy M.
Published: February 2023

Binuclear Cu(i) complexes bearing N-heterocycles-containing phosphines function as luminescent sensors for N-nitrosamines.
Visible light sensing of ions by a cyanoquinoxaline 1,4-dioxide-based probe and its applications
Authors: Savita  , Nandikolla Adinarayana , Shukla Adarash Kumar , Chandra Sekhar Kondapalli Venkata Gowri , Bhattacharya Anupam
Published: February 2023

Inducting newer fluorophores for colourimetry/fluorimetry-assisted analyte sensing is of great importance.
Inulin: properties and health benefits
Authors: Qin Yu-Qing , Wang Liu-Yan , Yang Xin-Yu , Xu Yi-Jie , Fan Gang , Fan Yan-Ge , Ren Jing-Nan , An Qi , Li Xiao
Published: February 2023

Inulin shows great health benefits in regulating gut flora, regulating glycolipid metabolism, weight loss, anti-inflammatory, reducing the risk of colon cancer, enhancing mineral absorption, improving constipation, and relieving depression.
Organocatalytic asymmetric synthesis of oxazolidino spiropyrazolinonesvia N,O-acetalization/aza Michael addition domino reaction betweenN-Boc pyrazolinone ketimines and γ-hydroxyenones
Authors: Gil-Ordóñez Marta , Martín Laura , Maestro Alicia , Andrés José M.
Published: February 2023

The first organocatalytic asymmetric synthesis of oxazolidino spiropyrazolinones fromN-Boc pyrazolinone ketimines is reported.
A nanozyme composite with high near-infrared photothermal ability for synergistic bacterial elimination
Authors: Liu Jing , Wang Ruke , Zhai Fenfen , Zhang Wengan , Wang Bo , Zhou Hong
Published: February 2023

A nanozyme composite with high near-infrared photothermal ability is synthesized for synergistic bacterial elimination.
Low-cost diatomite supported binary transition metal sulfates: an efficient reusable solid catalyst for biodiesel synthesis
Authors: Chen Weiqing , Wu Zhaoji , Peng Ruoxue , Wu Wenjuan , Li Xiaonan , Cao Dan , Zhang Zhigang , Niu Kui
Published: February 2023

A new catalyst: diatomite supported binary transition metal sulfates (Fe2(SO4)3 and Zr(SO4)2) was prepared. It exhibited excellent catalytic activity in the synthesis of biodiesel from waste fatty acids (conversion close to 100%).
One-step potentiostatic electrodeposition of NiS–NiS2 on sludge-based biochar and its application for a non-enzymatic glucose sensor
Authors: Luo Suxing , Yang Meizhi , Li Jiang , Wu Yuanhui
Published: February 2023

NiS–NiS2/sludge-based biochar/GCE was fabricated by one-step potentiostatic electrodeposition on biochar and used as an interface material for non-enzymatic sensing of glucose with a lower detection limit of 1.5 μM.
Transesterification of cellulose with unactivated esters in superbase–acid conjugate ionic liquids
Authors: Todorov Aleksandar R. , King Alistair W. T. , Kilpeläinen Ilkka
Published: February 2023

Controllable homogeneous cellulose transesterification with unactivated methyl esters.
Towards economic processing of high performance garnets – case study on zero Li excess Ga-substituted LLZO
Authors: Schwab Christian , Häuschen Grit , Mann Markus , Roitzheim Christoph , Guillon Olivier , Fattakhova-Rohlfing Dina , Finsterbusch Martin
Published: February 2023

In this processing study we systematically investigate the impact of lithium excess and dwell time on Ga-substituted LLZO:Ga and show that Li-excess during synthesis and processing is a critical parameter to obtain peak performance.
Recent developments, challenges and future prospects of magnetic field effects in supercapacitors
Authors: Raj K A Sree , Rout Chandra Sekhar
Published: February 2023

This review article covers the scientific discussion on some of the recent advancements in magnetic field controlled effects in supercapacitors and analyzes these effects in detail based on their energy storage mechanisms.
Dicarboxylate-containing and fully substituted ferrocene with rapid dissolvability, high solubility, good stability, and moderate formal potential for mediated electrochemical detection
Authors: Lee Woohyeong , Bhatia Aman , Nandhakumar Ponnusamy , Kim Gyeongho , Joo Jung Min , Yang Haesik
Published: February 2023

A dicarboxylate-containing and fully substituted ferrocene compound exhibits rapid dissolvability, high solubility, good stability, and moderate along with its high electron-mediation rate, and it was applied to mediated glucose detection.
Dual functionalized brush copolymers as versatile antifouling coatings
Authors: Kil Jihyo , Rahman Rafia Tasnim , Wang Wenxuan , Choi Saehan , Nam Yoon Sung , Li Sheng
Published: February 2023

PPFPA-g-PEG-g-PDMS brush copolymers with varying compositions are prepared and then tested against biofoulants. All copolymer coatings show enhanced antifouling properties, and the composition for the best performance differs for proteins and cells.
Remarkable performance recovery in highly defective perovskite solar cells by photo-oxidation
Authors: Goetz Katelyn P. , Thome Fabian T. F. , An Qingzhi , Hofstetter Yvonne J. , Schramm Tim , Yangui Aymen , Kiligaridis Alexander , Loeffler Markus , Taylor Alexander D. , Scheblykin Ivan G. , Vaynzof Yana
Published: February 2023

Exposure to oxygen and light leads to a remarkable performance improvement in the case of highly-defective metal halide perovskite solar cells.
Dual-wavelength enhanced upconversion luminescence properties of Li+-doped NaYF4:Er,Yb glass-ceramic for all-optical logic operations
Authors: Zhang Yanxin , Ying Weitao , He Jingyi , Fan Xuemei , Xu Shiqing , Gu Jianmin , Liu Shimin
Published: February 2023

A strategy by combining Li+ ion doping with dual-wavelength excitation to enhance upconversion luminescence intensity is demonstrated for all-optical logic gate operations.
Sex-dependent colonic microbiota modulation by hazelnut (Corylus avellana L.) dietary fiber
Authors: Daştan Elanur , Çelik Ömer F. , Baş Orhan , Bulut Zafer , Lindemann Stephen R. , Tugay Mehmet İ. , Değermenci Muhammet , Suvarıklı-Alan Beyza , Nizamlıoğlu Mehmet , Tunçil Yunus E.
Published: February 2023

Hazelnut dietary fibers impact colonic microbiota composition and microbial metabolites in a sex-dependent way.
Recent advances in carbon-based materials for high-performance perovskite solar cells: gaps, challenges and fulfillment
Authors: Pandey Sandeep , Karakoti Manoj , Bhardwaj Dinesh , Tatrari Gaurav , Sharma Richa , Pandey Lata , Lee Man-Jong , Sahoo Nanda Gopal
Published: February 2023

Recent advances on the carbon-based materials for efficient and stable perovskite solar cells (PSCs) is deeply analysed. Present review discussed about gaps, challenges, and potential fulfilment towards the possible commercialization of carbon-PSCs.
Visible-light-induced C(sp3)−H thiocyanation of pyrazolin-5-ones: a practical synthesis of 4-thiocyanated 5-hydroxy-1H-pyrazoles
Authors: Hu Xiurong , Guo Haichang , Jiang Huajiang , Zheng Renhua , Zhou Yaqin , Wang Lei
Published: February 2023

A direct, aerobic and visible light photocatalytic approach to synthesize 4-thiocyanated 5-hydroxy-1H-pyrazoles via cross-coupling of pyrazolin-5-ones with ammonium thiocyanate is described.
Abundant metal-catalyzed carbonylation of alkyl bromides and alkyl chlorides
Authors: Gu Xing-Wei , Wu Xiao-Feng
Published: February 2023

Our recent studies on abundant metal (Fe, Cu, and Mn) catalyzed carbonylative transformation of alkyl bromides and alkyl chlorides have been discussed here.
Interface engineering of InP/ZnS core/shell quantum dots by the buffer monolayer for exceptional photocatalytic H2 evolution
Authors: Huang Rong-Jin , Qin Zhi-Kai , Shen Li-Lei , Lv Guangqiang , Tao Furong , Wang Jingui , Gao Yu-Ji
Published: February 2023

Remarkable enhancement of photocatalytic hydrogen evolution from quantum dots by introducing buffer layer between the InP core and ZnS shell.
Tuning the mechanoresponsive luminescence of rotaxane mechanophores by varying the stopper size
Authors: Hiratsuka Keiko , Muramatsu Tatsuya , Seki Takuya , Weder Christoph , Watanabe Go , Sagara Yoshimitsu
Published: February 2023

The efficiency of force-induced dethreading of rotaxane mechanophores is controlled by the stopper size.