bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selective cell death in HIV-1-infected cells by DDX3 inhibitors leads to depletion of the inducible reservoir
Authors: Rao Shringar , Lungu Cynthia , Crespo Raquel , Steijaert Thijs H. , Gorska Alicja , Palstra Robert-Jan , Prins Henrieke A. B. , van Ijcken Wilfred , Mueller Yvonne M. , van Kampen Jeroen J. A. , Verbon Annelies , Katsikis Peter D. , Boucher Charles A. B. , Rokx Casper , Gruters Rob A. , Mahmoudi Tokameh 
Published: April 2021

AbstractAn innovative approach to eliminate HIV-1-infected cells emerging out of latency, the major hurdle to HIV-1 cure, is to pharmacologically reactivate viral expression and concomitantly trigger intracellular pro-apoptotic pathways in order to selectively induce cell death (ICD) of infected cells, without reliance on the extracellular immune system. In this work, we demonstrate the effect of DDX3 inhibitors on selectively inducing cell death in latent HIV-1-infected cell lines, primary CD4+ T cells and in CD4+ T cells from cART-suppressed people living with HIV-1 (PLWHIV). We used single-cell FISH-Flow technology to characterise the contribution of viral RNA to inducing cell death. The pharmacological targeting of DDX3 induced HIV-1 RNA expression, resulting in phosphorylation of IRF3 and upregulation of IFNβ. DDX3 inhibition also resulted in the downregulation of BIRC5, critical to cell survival during HIV-1 infection, and selectively induced apoptosis in viral RNA-expressing CD4+ T cells but not bystander cells. DDX3 inhibitor treatment of CD4+ T cells from PLWHIV resulted in an approximately 50% reduction of the inducible latent HIV-1 reservoir by quantitation of HIV-1 RNA, by FISH-Flow, RT-qPCR and TILDA. This study provides proof of concept for pharmacological reversal of latency coupled to induction of apoptosis towards the elimination of the inducible reservoir.
Mimicking associative learning using an ion-trapping non-volatile synaptic organic electrochemical transistor
Authors: Ji Xudong , Paulsen Bryan D. , Chik Gary K. K. , Wu Ruiheng , Yin Yuyang , Chan Paddy K. L. , Rivnay Jonathan 
Published: April 2021

AbstractAssociative learning, a critical learning principle to improve an individual’s adaptability, has been emulated by few organic electrochemical devices. However, complicated bias schemes, high write voltages, as well as process irreversibility hinder the further development of associative learning circuits. Here, by adopting a poly(3,4-ethylenedioxythiophene):tosylate/Polytetrahydrofuran composite as the active channel, we present a non-volatile organic electrochemical transistor that shows a write bias less than 0.8 V and retention time longer than 200 min without decoupling the write and read operations. By incorporating a pressure sensor and a photoresistor, a neuromorphic circuit is demonstrated with the ability to associate two physical inputs (light and pressure) instead of normally demonstrated electrical inputs in other associative learning circuits. To unravel the non-volatility of this material, ultraviolet-visible-near-infrared spectroscopy, X-ray photoelectron spectroscopy and grazing-incidence wide-angle X-ray scattering are used to characterize the oxidation level variation, compositional change, and the structural modulation of the poly(3,4-ethylenedioxythiophene):tosylate/Polytetrahydrofuran films in various conductance states. The implementation of the associative learning circuit as well as the understanding of the non-volatile material represent critical advances for organic electrochemical devices in neuromorphic applications.
Percolation on feature-enriched interconnected systems
Authors: Artime Oriol , De Domenico Manlio 
Published: April 2021

AbstractPercolation is an emblematic model to assess the robustness of interconnected systems when some of their components are corrupted. It is usually investigated in simple scenarios, such as the removal of the system’s units in random order, or sequentially ordered by specific topological descriptors. However, in the vast majority of empirical applications, it is required to dismantle the network following more sophisticated protocols, for instance, by combining topological properties and non-topological node metadata. We propose a novel mathematical framework to fill this gap: networks are enriched with features and their nodes are removed according to the importance in the feature space. We consider features of different nature, from ones related to the network construction to ones related to dynamical processes such as epidemic spreading. Our framework not only provides a natural generalization of percolation but, more importantly, offers an accurate way to test the robustness of networks in realistic scenarios.
Magnetic Janssen effect
Authors: Thorens L. , Måløy K. J. , Bourgoin M. , Santucci S. 
Published: April 2021

AbstractA pile of grains, even when at rest in a silo, can display fascinating properties. One of the most celebrated is the Janssen effect, named after the pioneering engineer who explained the pressure saturation at the bottom of a container filled with corn. This surprising behavior arises because of frictional interactions between the grains through a disordered network of contacts, and the vessel lateral walls, which partially support the weight of the column, decreasing its apparent mass. Here, we demonstrate control over frictional interactions using ferromagnetic grains and an external magnetic field. We show that the anisotropic pairwise interactions between magnetized grains result in a radial force along the walls, whose amplitude and direction is fully determined by the applied magnetic field. Such magnetic Janssen effect allows for the fine tuning of the granular column apparent mass. Our findings pave the way towards the design of functional jammed materials in confined geometries, via a further control of both their static and dynamic properties.
Fluid pressurisation and earthquake propagation in the Hikurangi subduction zone
Authors: Aretusini S. , Meneghini F. , Spagnuolo E. , Harbord C. W. , Di Toro G. 
Published: April 2021

AbstractIn subduction zones, seismic slip at shallow crustal depths can lead to the generation of tsunamis. Large slip displacements during tsunamogenic earthquakes are attributed to the low coseismic shear strength of the fluid-saturated and non-lithified clay-rich fault rocks. However, because of experimental challenges in confining these materials, the physical processes responsible for the coseismic reduction in fault shear strength are poorly understood. Using a novel experimental setup, we measured pore fluid pressure during simulated seismic slip in clay-rich materials sampled from the deep oceanic drilling of the Pāpaku thrust (Hikurangi subduction zone, New Zealand). Here, we show that at seismic velocity, shear-induced dilatancy is followed by pressurisation of fluids. The thermal and mechanical pressurisation of fluids, enhanced by the low permeability of the fault, reduces the energy required to propagate earthquake rupture. We suggest that fluid-saturated clay-rich sediments, occurring at shallow depth in subduction zones, can promote earthquake rupture propagation and slip because of their low permeability and tendency to pressurise when sheared at seismic slip velocities.
Three body photodissociation of the water molecule and its implications for prebiotic oxygen production
Authors: Chang Yao , Yu Yong , An Feng , Luo Zijie , Quan Donghui , Zhang Xia , Hu Xixi , Li Qinming , Yang Jiayue , Chen Zhichao , Che Li , Zhang Weiqing , Wu Guorong , Xie Daiqian , Ashfold Michael N. R. , Yuan Kaijun , Yang Xueming 
Published: April 2021

AbstractThe provenance of oxygen on the Earth and other planets in the Solar System is a fundamental issue. It has been widely accepted that the only prebiotic pathway to produce oxygen in the Earth’s primitive atmosphere was via vacuum ultraviolet (VUV) photodissociation of CO2 and subsequent two O atom recombination. Here, we provide experimental evidence of three-body dissociation (TBD) of H2O to produce O atoms in both 1D and 3P states upon VUV excitation using a tunable VUV free electron laser. Experimental results show that the TBD is the dominant pathway in the VUV H2O photochemistry at wavelengths between 90 and 107.4 nm. The relative abundance of water in the interstellar space with its exposure to the intense VUV radiation suggests that the TBD of H2O and subsequent O atom recombination should be an important prebiotic O2-production, which may need to be incorporated into interstellar photochemical models.
Vacuum brazing of Al2O3 and 3D printed Ti6Al4V lap-joints using high entropy driven AlZnCuFeSi filler
Authors: Sharma Ashutosh , Ahn Byungmin 
Published: April 2021

AbstractIn this work, we studied the brazing characteristics of Al2O3 and 3D printed Ti–6Al–4V alloys using a novel equiatomic AlZnCuFeSi high entropy alloy filler (HEAF). The HEAF was prepared by mechanical alloying of the constituent powder and spark plasma sintering (SPS) approach. The filler microstructure, wettability and melting point were investigated. The mechanical and joint strength properties were also evaluated. The results showed that the developed AlZnCuFeSi HEAF consists of a dual phase (Cu–Zn, face-centered cubic (FCC)) and Al–Fe–Si rich (base centered cubic, BCC) phases. The phase structure of the (Cu–Al + Ti–Fe–Si)/solid solution promises a robust joint between Al2O3 and Ti–6Al–4V. In addition, the joint interfacial reaction was found to be modulated by the brazing temperature and time because of the altered activity of Ti and Zn. The optimum shear strength reached 84 MPa when the joint was brazed at 1050 °C for 60 s. The results can be promising for the integration of completely different materials using the entropy driven fillers developed in this study.
Effect of RGO-Y2O3 and RGO-Y2O3:Cr3+ nanocomposite sensor for dopamine
Authors: Shashikumara J. K. , Kalaburgi Bhimanagouda , Swamy B. E. Kumara , Nagabhushana H. , Sharma S. C. , Lalitha P. 
Published: April 2021

AbstractThe RGO-Y2O3 and RGO-Y2O3: Cr3+ (5 mol %) nanocomposite (NC) synthesized by hydrothermal technique. The structure and morphology of the synthesized NCs were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). Y2O3:Cr3+ displays spherical-shaped particles. Conversely, the surface of the RGO displays a wrinkly texture connecting with the existence of flexible and ultrathin graphene sheets. The photoluminescence (PL) emission spectra showed series of sharp peaks at 490, 591, and 687 nm which corresponding to 4F9/2 → 6H15/2, 4F9/2 → 6H13/2, and 4F9/2 → 6H11/2 transitions and lies in the blue, orange, and red region. The prepared NCs were used for the preparation of modified carbon paste electrodes (MCPE) in the electrochemical detection of dopamine (DA) at pH 7.4. Both modified electrodes provide a good current response towards voltammetric detection of DA. Doping is an effective method to improve the conductivity of Y2O3:Cr3+ and developed a method for the sensor used in analytical applications.
Nanopore sequencing reveals TACC2 locus complexity and diversity of isoforms transcribed from an intronic promoter
Authors: Ito Yosuke , Terao Yasuhisa , Noma Shohei , Tagami Michihira , Yoshida Emiko , Hayashizaki Yoshihide , Itoh Masayoshi , Kawaji Hideya 
Published: April 2021

AbstractGene expression is controlled at the transcriptional and post-transcriptional levels. The TACC2 gene was known to be associated with tumors but the control of its expression is unclear. We have reported that activity of the intronic promoter p10 of TACC2 in primary lesion of endometrial cancer is indicative of lymph node metastasis among a low-risk patient group. Here, we analyze the intronic promoter derived isoforms in JHUEM-1 endometrial cancer cells, and primary tissues of endometrial cancers and normal endometrium. Full-length cDNA amplicons are produced by long-range PCR and subjected to nanopore sequencing followed by computational error correction. We identify 16 stable, 4 variable, and 9 rare exons including 3 novel exons validated independently. All variable and rare exons reside N-terminally of the TACC domain and contribute to isoform variety. We found 240 isoforms as high-confidence, supported by more than 20 reads. The large number of isoforms produced from one minor promoter indicates the post-transcriptional complexity coupled with transcription at the TACC2 locus in cancer and normal cells.
Simulation of a flash-flood event over the Adriatic Sea with a high-resolution atmosphere–ocean–wave coupled system
Authors: Ricchi Antonio , Bonaldo Davide , Cioni Guido , Carniel Sandro , Miglietta Mario Marcello 
Published: April 2021

AbstractOn the morning of September 26, 2007, a heavy precipitation event (HPE) affected the Venice lagoon and the neighbouring coastal zone of the Adriatic Sea, with 6-h accumulated rainfall summing up to about 360 mm in the area between the Venetian mainland, Padua and Chioggia. The event was triggered and maintained by the uplift over a convergence line between northeasterly flow from the Alps and southeasterly winds from the Adriatic Sea. Hindcast modelling experiments, using standalone atmospheric models, failed to capture the spatial distribution, maximum intensity and timing of the HPE. Here we analyze the event by means of an atmosphere-wave-ocean coupled numerical approach. The combined use of convection permitting models with grid spacing of 1 km, high-resolution sea surface temperature (SST) fields, and the consistent treatment of marine boundary layer fluxes in all the numerical model components are crucial to provide a realistic simulation of the event. Inaccurate representations of the SST affect the wind magnitude and, through this, the intensity, location and time evolution of the convergence zone, thus affecting the HPE prediction.
Interfacing aptamers, nanoparticles and graphene in a hierarchical structure for highly selective detection of biomolecules in OECT devices
Authors: Peruzzi Carlotta , Battistoni Silvia , Montesarchio Daniela , Cocuzza Matteo , Marasso Simone Luigi , Verna Alessio , Pasquardini Laura , Verucchi Roberto , Aversa Lucrezia , Erokhin Victor , D’Angelo Pasquale , Iannotta Salvatore 
Published: April 2021

AbstractIn several biomedical applications, the detection of biomarkers demands high sensitivity, selectivity and easy-to-use devices. Organic electrochemical transistors (OECTs) represent a promising class of devices combining a minimal invasiveness and good signal transduction. However, OECTs lack of intrinsic selectivity that should be implemented by specific approaches to make them well suitable for biomedical applications. Here, we report on a biosensor in which selectivity and a high sensitivity are achieved by interfacing, in an OECT architecture, a novel gate electrode based on aptamers, Au nanoparticles and graphene hierarchically organized to optimize the final response. The fabricated biosensor performs state of the art limit of detection monitoring biomolecules, such as thrombin-with a limit of detection in the picomolar range (≤ 5 pM) and a very good selectivity even in presence of supraphysiological concentrations of Bovine Serum Albumin (BSA-1mM). These accomplishments are the final result of the gate hierarchic structure that reduces sterich indrance that could contrast the recognition events and minimizes false positive, because of the low affinity of graphene towards the physiological environment. Since our approach can be easily applied to a large variety of different biomarkers, we envisage a relevant potential for a large series of different biomedical applications.
Semi-automated classification of colonial Microcystis by FlowCAM imaging flow cytometry in mesocosm experiment reveals high heterogeneity during seasonal bloom
Authors: Mirasbekov Yersultan , Zhumakhanova Adina , Zhantuyakova Almira , Sarkytbayev Kuanysh , Malashenkov Dmitry V. , Baishulakova Assel , Dashkova Veronika , Davidson Thomas A. , Vorobjev Ivan A. , Jeppesen Erik , Barteneva Natasha S. 
Published: April 2021

AbstractA machine learning approach was employed to detect and quantifyMicrocystiscolonial morphospecies using FlowCAM-based imaging flow cytometry. The system was trained and tested using samples from a long-term mesocosm experiment (LMWE, Central Jutland, Denmark). The statistical validation of the classification approaches was performed using Hellinger distances, Bray–Curtis dissimilarity, and Kullback–Leibler divergence. The semi-automatic classification based on well-balanced training sets fromMicrocystisseasonal bloom provided a high level of intergeneric accuracy (96–100%) but relatively low intrageneric accuracy (67–78%). Our results provide a proof-of-concept of how machine learning approaches can be applied to analyze the colonial microalgae. This approach allowed to evaluateMicrocystisseasonal bloom in individual mesocosms with high level of temporal and spatial resolution. The observation that someMicrocystismorphotypes completely disappeared and re-appeared along the mesocosm experiment timeline supports the hypothesis of the main transition pathways of colonialMicrocystismorphoforms. We demonstrated that significant changes in the training sets with colonial images required for accurate classification ofMicrocystisspp. from time points differed by only two weeks due toMicrocystishigh phenotypic heterogeneity during the bloom. We conclude that automatic methods not only allow a performance level of human taxonomist, and thus be a valuable time-saving tool in the routine-like identification of colonial phytoplankton taxa, but also can be applied to increase temporal and spatial resolution of the study.
Cooperation across multiple game theoretical paradigms is increased by fear more than anger in selfish individuals
Authors: Chierchia G. , Parianen Lesemann F. H. , Snower D. , Singer T. 
Published: April 2021

AbstractCooperative decisions are well predicted by stable individual differences in social values but it remains unclear how they may be modulated by emotions such as fear and anger. Moving beyond specific decision paradigms, we used a suite of economic games and investigated how experimental inductions of fear or anger affect latent factors of decision making in individuals with selfish or prosocial value orientations. We found that, relative to experimentally induced anger, induced fear elicited higher scores on a cooperation factor, and that this effect was entirely driven by selfish participants. In fact, induced fear brought selfish individuals to cooperate similarly to prosocial individuals, possibly as a (selfish) mean to seek protection in others. These results suggest that two basic threat-related emotions, fear and anger, differentially affect a generalized form of cooperation and that this effect is buffered by prosocial value orientation.
The COVID-19 lab score: an accurate dynamic tool to predict in-hospital outcomes in COVID-19 patients
Authors: Antunez Muiños Pablo Jose , López Otero Diego , Amat-Santos Ignacio J. , López País Javier , Aparisi Alvaro , Cacho Antonio Carla E. , Catalá Pablo , González Ferrero Teba , Cabezón Gonzalo , Otero García Oscar , Gil José Francisco , Pérez Poza Marta , Candela Jordi , Rojas Gino , Jiménez Ramos Víctor , Veras Carlos , San Román J. Alberto , González-Juanatey José R. 
Published: April 2021

AbstractDeterioration is sometimes unexpected in SARS-CoV2 infection. The aim of our study is to establish laboratory predictors of mortality in COVID-19 disease which can help to identify high risk patients. All patients admitted to hospital due to Covid-19 disease were included. Laboratory biomarkers that contributed with significant predictive value for predicting mortality to the clinical model were included. Cut-off points were established, and finally a risk score was built. 893 patients were included. Median age was 68.2 ± 15.2 years. 87(9.7%) were admitted to Intensive Care Unit (ICU) and 72(8.1%) needed mechanical ventilation support. 171(19.1%) patients died. A Covid-19 Lab score ranging from 0 to 30 points was calculated on the basis of a multivariate logistic regression model in order to predict mortality with a weighted score that included haemoglobin, erythrocytes, leukocytes, neutrophils, lymphocytes, creatinine, C-reactive protein, interleukin-6, procalcitonin, lactate dehydrogenase (LDH), and D-dimer. Three groups were established. Low mortality risk group under 12 points, 12 to 18 were included as moderate risk, and high risk group were those with 19 or more points. Low risk group as reference, moderate and high patients showed mortality OR 4.75(CI95% 2.60–8.68) and 23.86(CI 95% 13.61–41.84), respectively. C-statistic was 0–85(0.82–0.88) and Hosmer–Lemeshow p-value 0.63. Covid-19 Lab score can very easily predict mortality in patients at any moment during admission secondary to SARS-CoV2 infection. It is a simple and dynamic score, and it can be very easily replicated. It could help physicians to identify high risk patients to foresee clinical deterioration.
Variation in the concentration and regional distribution of magnetic nanoparticles in human brains, with and without Alzheimer’s disease, from the UK
Authors: Hammond Jessica , Maher Barbara A. , Ahmed Imad A. M. , Allsop David 
Published: April 2021

AbstractThe presence of magnetic nanoparticles (MNPs) in the human brain was attributed until recently to endogenous formation; associated with a putative navigational sense, or with pathological mishandling of brain iron within senile plaques. Conversely, an exogenous, high-temperature source of brain MNPs has been newly identified, based on their variable sizes/concentrations, rounded shapes/surface crystallites, and co-association with non-physiological metals (e.g., platinum, cobalt). Here, we examined the concentration and regional distribution of brain magnetite/maghemite, by magnetic remanence measurements of 147 samples of fresh/frozen tissues, from Alzheimer’s disease (AD) and pathologically-unremarkable brains (80–98 years at death) from the Manchester Brain Bank (MBB), UK. The magnetite/maghemite concentrations varied between individual cases, and different brain regions, with no significant difference between the AD and non-AD cases. Similarly, all the elderly MBB brains contain varying concentrations of non-physiological metals (e.g. lead, cerium), suggesting universal incursion of environmentally-sourced particles, likely across the geriatric blood–brain barrier (BBB). Cerebellar Manchester samples contained significantly lower (~ 9×) ferrimagnetic content compared with those from a young (29 years ave.), neurologically-damaged Mexico City cohort. Investigation of younger, variably-exposed cohorts, prior to loss of BBB integrity, seems essential to understand early brain impacts of exposure to exogenous magnetite/maghemite and other metal-rich pollution particles.