bluuebunny/crossref_metadata_2025_split huggingface dataset:
Continuous Polony Gels for Tissue Mapping with High Resolution and RNA Capture Efficiency
Authors: Fu Xiaonan , Sun Li , Chen Jane Y. , Dong Runze , Lin Yiing , Palmiter Richard D. , Lin Shin , Gu Liangcai 
Published: March 2021

AbstractCurrent technologies for acquiring spatial transcript information from tissue sections rely on either RNA probes or spatial barcodes. The former methods require a priori knowledge for probeset formulation; the latter have yet to achieve single cell resolution and/or transcript capture efficiencies approaching dissociative, single-cell methods. Here, we describe a novel spatial transcriptome assay calledpolony (or DNA cluster)-indexedlibrary-sequencing (PIXEL-seq). It improves upon other spatial barcoding methods by employing “continuous” polony oligos arrayed across a customized gel surface. In terms of assay performance, PIXEL-seq attains ≤ 1 µm resolution and captures >1,000 unique molecular identifiers/10×10 µm2. In other words, this global, naive platform achieves subcellular spatial transcriptome mapping while maintaining high transcript capture efficiencies.
A novel SARS-CoV-2 related virus with complex recombination isolated from bats in Yunnan province, China
Authors: Li Li-li , Wang Jing-lin , Ma Xiao-hua , Li Jin-song , Yang Xiao-fei , Shi Wei-feng , Duan Zhao-jun 
Published: March 2021

AbstractA novel beta-coronavirus, SARS-CoV-2, emerged in late 2019 and rapidly spread throughout the world, causing the COVID-19 pandemic. However, the origin and direct viral ancestors of SARS-CoV-2 remain elusive. Here, we discovered a new SARS-CoV-2-related virus in Yunnan province, in 2018, provisionally named PrC31, which shares 90.7% and 92.0% nucleotide identities with SARS-CoV-2 and the bat SARSr-CoV ZC45, respectively. Sequence alignment revealed that several genomic regions shared strong identity with SARS-CoV-2, phylogenetic analysis supported that PrC31 shares a common ancestor with SARS-CoV-2. The receptor binding domain of PrC31 showed only 64.2% amino acid identity with SARS-CoV-2. Recombination analysis revealed that PrC31 underwent multiple complex recombination events within the SARS-CoV and SARS-CoV-2 sub-lineages, indicating the evolution of PrC31 from yet-to-be-identified intermediate recombination strains. Combination with previous studies revealed that the beta-CoVs may possess more complicated recombination mechanism. The discovery of PrC31 supports that bats are the natural hosts of SARS-CoV-2.
Context dependent isoform specific PI3K inhibition confers drug resistance in Hepatocellular carcinoma cells
Authors: Narci Kubra , Kahraman Deniz Cansen , Koyas Altay , Ersahin Tulin , Tuncbag Nurcan , Atalay Rengul Cetin 
Published: March 2021

AbstractBackgroundTargeted therapies for Primary liver cancer (HCC) is limited to the multi-kinase inhibitors, and not fully effective due to the resistance to these agents because of the heterogeneous molecular nature of HCC developed during chronic liver disease stages and cirrhosis. Although combinatorial therapy can increase the efficiency of targeted therapies through synergistic activities, isoform specific effects of the inhibitors are usually ignored. This study concentrated on PI3K/Akt/mTOR pathway and the differential combinatory bioactivities of isoform specific PI3K-αinhibitor (PIK-75) or PI3K-βinhibitor (TGX-221) with Sorafenib dependent on PTEN context.MethodsThe bioactivities of inhibitors on PTEN adequate Huh7 and deficient Mahlavu cells were investigated with real time cell growth, cell cycle and cell migration assays. Differentially expressed genes from RNA-Seq were identified by edgeR tool. Systems level network analysis of treatment specific pathways were performed with Prize Collecting Steiner Tree (PCST) on human interactome and enriched networks were visualized with Cytoscape platform.ResultsOur data from combinatory treatment of Sorafenib and PIK-75 and TGX-221 showed opposite effects; while PIK-75 displays synergistic effects on Huh7 cells leading to apoptotic cell death, Sorafenib with TGX-221 display antagonistic effects and significantly promotes cell growth in PTEN deficient Mahlavu cells. Transcriptomic states of combinatory treatments with PIK-75 and TGX-221 inhibitors were identified in PTEN deficient and adequate cells. Molecular interactions and cell signaling pathways were reconstructed and analyzed in-depth to understand mechanism of differential synergistic or antagonistic effects of PI3K-α(PIK-75) and PI3K-β(TGX-221) inhibitors with Sorafenib.ConclusionsSimultaneously constructed and analyzed differentially expressed cellular networks presented in this study, revealed distinct consequences of isoform specific PI3K inhibition in PTEN adequate and deficient liver cancer cells. We demonstrated the importance of context dependent and isoform specific PI3K/Akt/mTOR signaling inhibition in drug resistance during combination therapies. (https://github.com/cansyl/Isoform-spesific-PI3K-inhibitor-analysis).
Comparative Analysis of T Cell Spatial Proteomics and the Influence of HIV Expression
Authors: Oom Aaron L. , Stoneham Charlotte A. , Lewinski Mary K. , Richards Alicia , Wozniak Jacob M. , Shams-Ud-Doha Km , Gonzalez David J. , Krogan Nevan J. , Guatelli John 
Published: March 2021

AbstractAs systems biology approaches to virology have become more tractable, highly studied viruses such as HIV can now be analyzed in new, unbiased ways, including spatial proteomics. We employed here a differential centrifugation protocol to fractionate Jurkat T cells for proteomic analysis by mass spectrometry; these cells contain inducible HIV-1 genomes, enabling us to look for changes in the spatial proteome induced by viral gene expression. Using these proteomics data, we evaluated the merits of several reported machine learning pipelines for classification of the spatial proteome and identification of protein translocations. From these analyses we found that classifier performance in this system was organelle-dependent, with Bayesian t-augmented Gaussian mixture modeling outperforming support vector machine (SVM) learning for mitochondrial and ER proteins, but underperforming on cytosolic, nuclear, and plasma membrane proteins by QSep analysis. We also observed a generally higher performance for protein translocation identification using a Bayesian model, BANDLE, on SVM-classified data. Comparative BANDLE analysis of cells induced to express the wild-type viral genome vs. cells induced to express a genome unable to express the accessory protein Nef identified known Nef-dependent interactors such as TCR signaling components and coatomer complex. Lastly, we found that SVM classification showed higher consistency and was less sensitive to HIV-dependent noise. These findings illustrate important considerations for studies of the spatial proteome following viral infection or viral gene expression and provide a reference for future studies of HIV-gene-dropout viruses.
Multi-layered regulation of neuroectoderm differentiation by retinoic acid in a primitive streak-like context
Authors: Russo Luigi , Sladitschek Hanna L. , Neveu Pierre A. 
Published: March 2021

SUMMARYThe formation of the primitive streak (PS) and the subsequent induction of neuroectoderm are hallmarks of gastrulation. Combining anin vitroreconstitution of this process based on mouse embryonic stem cells (mESCs) with a collection of knockouts in reporter mESC lines, we reassessed the contribution of retinoic acid (RA) signaling at early stages of neural commitment and its cross-talk with TGFβand Wnt signaling inhibition. Single-cell RNA sequencing analysis captured the temporal unfolding of cell type diversification from epiblast and primitive streak-like cells up to the emergence of anterior and posterior neural fates. In conditions thought to lack RA synthesis, we discovered a hitherto unidentified residual RA production via a sensitive RA reporter. Genetic perturbations proved that the RA-degrading enzyme Cyp26a1 safeguard the developmental capabilities of the PS-like cells, limiting neural differentiation in wild type and inChrd-/-Nog-/-orDkk1-/-cells. Finally, the knockout of the three RAR receptors highlighted their function as negative regulators of loci critical for neural induction. Overall, we identified two mechanisms whereby components of the RA pathway can control the formation of neural progenitors in our PS-like context: a RA-dependent neural induction gated by RARs, and a receptor-mediated repression in the absence of ligand.
A single BNT162b2 mRNA dose elicits antibodies with Fc-mediated effector functions and boost pre-existing humoral and T cell responses
Authors: Tauzin Alexandra , Nayrac Manon , Benlarbi Mehdi , Gong Shang Yu , Gasser Romain , Beaudoin-Bussières Guillaume , Brassard Nathalie , Laumaea Annemarie , Vézina Dani , Prévost Jérémie , Anand Sai Priya , Bourassa Catherine , Gendron-Lepage Gabrielle , Medjahed Halima , Goyette Guillaume , Niessl Julia , Tastet Olivier , Gokool Laurie , Morrisseau Chantal , Arlotto Pascale , Stamatatos Leonidas , McGuire Andrew T. , Larochelle Catherine , Uchil Pradeep , Lu Maolin , Mothes Walther , Serres Gaston De , Moreira Sandrine , Roger Michel , Richard Jonathan , Martel-Laferrière Valérie , Duerr Ralf , Tremblay Cécile , Kaufmann Daniel E. , Finzi Andrés 
Published: March 2021

AbstractThe standard dosing of the Pfizer/BioNTech BNT162b2 mRNA vaccine validated in clinical trials includes two doses administered three weeks apart. While the decision by some public health authorities to space the doses because of limiting supply has raised concerns about vaccine efficacy, data indicate that a single dose is up to 90% effective starting 14 days after its administration. We analyzed humoral and T cells responses three weeks after a single dose of this mRNA vaccine. Despite the proven efficacy of the vaccine at this time point, no neutralizing activity were elicited in SARS-CoV-2 naïve individuals. However, we detected strong anti-receptor binding domain (RBD) and Spike antibodies with Fc-mediated effector functions and cellular responses dominated by the CD4+ T cell component. A single dose of this mRNA vaccine to individuals previously infected by SARS-CoV-2 boosted all humoral and T cell responses measured, with strong correlations between T helper and antibody immunity. Neutralizing responses were increased in both potency and breadth, with distinctive capacity to neutralize emerging variant strains. Our results highlight the importance of vaccinating uninfected and previously-infected individuals and shed new light into the potential role of Fc-mediated effector functions and T cell responses in vaccine efficacy. They also provide support to spacing the doses of two-vaccine regimens to vaccinate a larger pool of the population in the context of vaccine scarcity against SARS-CoV-2.
Myosin turnover controls actomyosin contractile instability
Authors: Thiyagarajan Sathish , Wang Shuyuan , Chew Ting Gang , Huang Junqi , Balasubramanian Mohan K. , O’Shaughnessy Ben 
Published: March 2021

AbstractActomyosin contractile force is harnessed for diverse functions, from cell division to morphogenesis during development. However, actomyosin contractility is intrinsically unstable to self-reinforcing spatial variations that destroy actomyosin architecture if unopposed. The full instability was rarely observed, and how cells control the instability is not established. Here, we observed the instability run its full course in isolated cytokinetic contractile rings lacking component turnover. Myosin II aggregated hierarchically into aggregates of growing size and separation up to a maximum. Molecularly explicit simulations reproduced hierarchical aggregation that precipitated tension loss and ring fracture, and identified the maximum separation as the length of actin filaments mediating mechanical communication between aggregates. Late stage simulated aggregates had aster-like morphology with polarity sorted actin, similar to late stage actomyosin systemsin vitro. Our results suggest myosin II turnover controls actomyosin contractile instability in normal cells, setting myosin aggregate size and intercepting catastrophic hierarchical aggregation and fracture.
Fast tag identification for mobile RFID robots in manufacturing environments
Authors: Wang Honggang , Yu Ruixue , Pan Ruoyu , Liu Mengyuan , Huang Qiongdan , Yang Jingfeng 
Published: March 2021

Purpose
In manufacturing environments, mobile radio frequency identification (RFID) robots need to quickly identify and collect various types of passive tag and active tag sensor data. The purpose of this paper is to design a robot system compatible with ultra high frequency (UHF) band passive and active RFID applications and to propose a new anti-collision protocol to improve identification efficiency for active tag data collection.

Design/methodology/approach
A new UHF RFID robot system based on a cloud platform is designed and verified. For the active RFID system, a grouping reservation–based anti-collision algorithm is proposed in which an inventory round is divided into reservation period and polling period. The reservation period is divided into multiple sub-slots. Grouped tags complete sub-slot by randomly transmitting a short reservation frame. Then, in the polling period, the reader accesses each tag by polling. When tags’ reply collision occurs, the reader tries to re-query collided tags once, and the pre-reply tags avoid collisions through random back-off and channel activity detection.

Findings
The proposed algorithm achieves a maximum theoretical system throughput of about 0.94, and very few tag data frame transmissions overhead. The capture effect and channel activity detection in physical layer can effectively improve system throughput and reduce tag data transmission.

Originality/value
In this paper, the authors design and verify the UHF band passive and active hybrid RFID robot architecture based on cloud collaboration. And, the proposed anti-collision algorithm would improve active tag data collection speed and reduce tag transmission overhead in complex manufacturing environments.
Optimal fault diagnosis strategy for complex systems considering common cause failure under epistemic uncertainty
Authors: Duan Rongxing , Huang Shujuan , He Jiejun 
Published: March 2021

Purpose
This paper aims to deal with the problems such as epistemic uncertainty, common cause failure (CCF) and dynamic fault behaviours that arise in complex systems and develop an effective fault diagnosis method to rapidly locate the fault when these systems fail.

Design/methodology/approach
First, a dynamic fault tree model is established to capture the dynamic failure behaviours and linguistic term sets are used to obtain the failure rate of components in complex systems to deal with the epistemic uncertainty. Second, a β factor model is used to construct a dynamic evidence network model to handle CCF and some parameters obtained by reliability analysis are used to build the fault diagnosis decision table. Finally, an improved Vlsekriterijumska Optimizacija I Kompromisno Resenje algorithm is developed to obtain the optimal diagnosis sequence, which can locate the fault quickly, reduce the maintenance cost and improve the diagnosis efficiency.

Findings
In this paper, a new optimal fault diagnosis strategy of complex systems considering CCF under epistemic uncertainty is presented based on reliability analysis. Dynamic evidence network is easy to carry out the quantitative analysis of dynamic fault tree. The proposed diagnosis algorithm can determine the optimal fault diagnosis sequence of complex systems and prove that CCF should not be ignored in fault diagnosis.

Originality/value
The proposed method combines the reliability theory with multiple attribute decision-making methods to improve the diagnosis efficiency.
Motion of circular cylinders during natural convection flow in X-shaped cavity filled with a nanofluid using ISPH method
Authors: Aly Abdelraheem M. , Mohamed Ehab Mahmoud 
Published: March 2021

Purpose
This study aims to illustrate the impacts of the motion of circular cylinders on the natural convection flow from variable heated partitions inside the X-shaped cavity filled with Al2O3-water nanofluid. A partial layer of a homogeneous/heterogeneous porous medium is located in the top area of the X-shaped cavity.

Design/methodology/approach
Three different cases of the porous media including homogeneous, horizontal heterogeneous and vertical heterogeneous porous media were considered. Three different thermal conditions of the embedded circular cylinders including hot, cold and adiabatic conditions are investigated. An incompressible scheme of smoothed particle hydrodynamics (ISPH) method is modified to compute the non-linear partial differential equations of the current problem. Two variable lengths of the left and right sides of the X-shaped cavity have a high-temperature Th and a low-temperature Tc, respectively. The other wall parts are adiabatic. The numerical simulations are elucidating the dependence of the heat transfer and fluid flow characteristics on lengths of hot/cold source Lh, porous cases, Darcy parameter, thermal conditions of the embedded circular cylinders and solid volume fraction.

Findings
Overall, an increment in length of hot/cold source leads to augmentation on the temperature distributions and flow intensity inside the X-shaped cavity. The hot thermal condition of the circular cylinder augments the temperature distributions. The homogeneous porous medium slows down the flow speed in the top porous layer of the X-shaped cavity. The average Nusselt number decreases as Lh increases.

Originality/value
ISPH method simulated the motion of circular cylinders in the X-shaped cavity. The X-shaped cavity is saturated with a partial layer porous medium. It is found that an increase in hot source length augments the temperature and fluid flow. ISPH method can easily handle the motion of cylinders in the X-shaped cavity. Different thermal conditions of cylinders can change the temperature distributions in X-cavity.
Data dissemination model using Epidemic and Transmission-Segment-based Geographic Routing protocol: a new perspective in vehicular ad hoc networks
Authors: D.N.S. Ravi Kumar , S. Barani 
Published: March 2021

PurposeThe purpose of this paper is to introduce a new data dissemination model in order to improve the performance of transmission in VANET. It proposes a protocol named Epidemic and Transmission-Segment-based Geographic Routing (ETSGR) and outlining the issues due to high mobility of nodes and uncertain physical topologies in the network. The proposed ETSGR is mainly used to analyze the vehicle state, direction, distance, traffic density and link quality of the network.Design/methodology/approachThis research work based on ETSGR protocol mainly uses epidemic algorithm in order to find the vehicle state based on susceptible, infected and recovered (SIR) model. Furthermore, the vehicle position and finding the head node in the network is utilized using the transmission segment protocol based on geographic routing and analyses each node to form the segments and find the destination to transmit the data in timely manner.FindingsThe paper provides the enhancement of the performance based on some metrics such as end-to-end delay that obtained 0.62%, data throughput as 32.3%, packet delivery ratio as 67% and one-hop communication as 13%. The proposed ETSGR protocol analyzes the state of the vehicle correctly and each node segmented to transmit the data with the timely manner and obtaining reliable performance even with high mobility of nodes in the network.Research limitations/implicationsThe proposed ETSGR protocol may have some limitation when considering the timing which should improve even in increasing many number of vehicles and different road segments.Practical implicationsThis paper includes some suggestions for the practical deployment of the approach in which a real-time traffic analysis can be evaluated for taking prior actions during an emergency situation and proper dissemination of data in timely manner can help utilize the guidance of proper planning of roads.Originality/valueThis research fulfills an enhanced protocol to improve the performance of data dissemination.
At the source of integrated interactions across channels
Authors: Bèzes Christophe 
Published: March 2021

PurposeThis research studies what full channel integration means for customers, how channels should be combined so that this integration is perceived by customers and whether a retailer under study can act on the same channel attributes regardless of the type of customer.Design/methodology/approachThe research design uses an online survey of a full sample of 1,015 multichannel buyers, extracted from the behavioral databases of a French specialized retailer. This full sample is segmented into four sub-samples. The data are treated with backward multiple linear regressions.FindingsBased on research in marketing and psychology, this study conceptually demonstrates that integrated interactions perceived by consumers are the outcome of a judgment of congruence that seek to build relationships between them in order to combine them better. Testing three hypotheses, the empirical study shows that channel integration is a psychological process: cumulative (individuals incorporate the information provided by the different channels rather than comparing them), selective (customers never take into account all the attributes of the channels) and subjective (the channel image attributes taken into account differ in number and quality from one type of customer to another).Originality/valueContrary to what the literature assumes, without ever demonstrating it, full integration does not imply that the retailer in question homogenizes or even matches up all the attributes of its channels. The retailer is thus able to act on attributes that promote this integration, while being relatively free to cultivate the incongruence of other attributes more likely to smoothly guide customers to a particular channel – in other words, a path midway between cross-channel and omnichannel.
Impact of foreign direct investment and international tourism on long-run economic growth of Estonia
Authors: Sokhanvar Amin , Jenkins Glenn P. 
Published: March 2021

PurposeInternational tourism and FDI inflows have generated detectable beneficial impacts on the economy of Estonia in the last decades. However, recently, poor international market conditions mostly caused by the trade war and COVID-19 pandemic have been a potential threat to these two factors. Besides, the poor performance of investments in recent years is behind the stagnation of productivity in Estonia. This study examines the dynamics of the effects of these factors on the rate of economic growth in Estonia and provides policy implications in line with sustained recovery.Design/methodology/approachA nonlinear ARDL technique is employed in this study to investigate the long-run effects of FDI and the degree of tourism specialization on economic growth rate.FindingsOur findings indicate that the economic growth rate of Estonia in the long run has been positively affected by both the rate of FDI inflows and international tourism.Originality/valueThis is the first study that employs a non-linear approach to investigate the dynamics of long-run effects of FDI and tourism specialization on the rate of economic growth in Estonia and provides policy implications in line with optimal growth strategy considering the economic structure, the current level of productivity and available potentials in this economy.