bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractTranscriptional 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

AbstractRibosome 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

AbstractCognition 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

AbstractAlthough 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

AbstractEntanglement, 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

AbstractIn 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

AbstractElectrically 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

AbstractTranscranial 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

AbstractHardwood 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

AbstractProgrammed 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

AbstractA 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

AbstractTo 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

AbstractIn 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

AbstractExtreme 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

AbstractMogrosides 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.