bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of molecular candidates which regulate calcium-dependent CD8+T-cell cytotoxicity
Authors: Zöphel Sylvia , Schwär Gertrud , Nazarieh Maryam , Konetzki Verena , Hoxha Cora , Meese Eckart , Hoth Markus , Helms Volkhard , Hamed Mohamed , Schwarz Eva C. 
Published: December 2020

AbstractCytotoxic CD8+T lymphocytes (CTL) eliminate infected cells or transformed tumour cells by releasing perforin-containing cytotoxic granules at the immunological synapse. The secretion of such granules depends on Ca2+-influx through store operated Ca2+channels, formed by STIM-activated Orai proteins. Whereas molecular mechanisms of the secretion machinery are well understood, much less is known about the molecular machinery that regulates the efficiency of Ca2+-dependent target cell killing. Here, we isolated total RNA from natural killer (NK) cells, non-stimulated CD8+T-cells, and from Staphylococcus aureus enterotoxin A (SEA) stimulated CD8+T-cells (SEA-CTL) and conducted whole genome expression profiling by microarray experiments. Based on differential expression analysis of the transcriptome data and analysis of master regulator genes, we identified 31 candidates which potentially regulate Ca2+-homeostasis in CTL. To investigate a putative function of these candidates in CTL cytotoxicity, we transfected either SEA-stimulated CTL (SEA-CTL) or antigen specific CD8+T-cell clones (CTL-MART-1) with siRNAs specific against the identified candidates and analyzed the killing capacity using a real-time killing assay. In addition, we complemented the analysis by studying the effect of inhibitory substances acting on the candidate proteins if available. Finally, to unmask their involvement in Ca2+dependent cytotoxicity, candidates were also analyzed under Ca2+-limiting conditions. Overall, this strategy led to the identification of KCNN4, RCAN3, CCR5 and BCL2 as potential candidates to regulate the efficiency of Ca2+-dependent target cell killing.
In vitrocharacterisation and neurosteroid treatment of an N-Methyl-D-Aspartate receptor antibody-mediated seizure model
Authors: Wright Sukhvir K , Rosch Richard E , Wilson Max A , Upadhya Manoj A , Dhangar Divya R , Clarke-Bland Charlie , Wahid Tamara T , Barman Sumanta , Goebels Norbert , Kreye Jakob , Prüss Harald , Jacobson Leslie , Bassett Danielle S , Vincent Angela , Greenhill Stuart D , Woodhall Gavin L 
Published: December 2020

AbstractSeizures are a prominent feature in N-Methyl-D-Aspartate receptor antibody (NMDAR-Ab) encephalitis, a distinct neuro-immunological disorder in which specific human autoantibodies bind and crosslink the surface of NMDAR proteins thereby causing internalization and a state of NMDAR hypofunction. To further understand ictogenesis in this disorder, and to test a novel treatment compound, we developed an NMDAR-Ab mediated rat seizure model that displays spontaneous epileptiform activityin vivoandin vitro. Using a combination of electrophysiological and dynamic causal modelling techniques we show that, contrary to expectation, reduction of synaptic excitatory, but not inhibitory, neurotransmission underlies the ictal events through alterations in the dynamical behaviour of microcircuits in brain tissue. Moreover,in vitroapplication of an NMDAR-specific neurosteroid, pregnenolone sulfate, that upregulates NMDARs, reduced established ictal activity. This proof-of-concept study highlights the complexity of circuit disturbances that may lead to seizures and the potential use of receptor-specific treatments in antibody-mediated seizures and epilepsy.
GABA relates to functional connectivity changes and retention in visuomotor adaptation
Authors: Nettekoven Caroline , Brady Sinead , Clarke William T , Emir Uzay , Levenstein Jacob , Petitet Pierre , Panouilleres Muriel T N , Bachtiar Velicia , O’Shea Jacinta , Johansen-Berg Heidi , Jenkinson Ned , Stagg Charlotte 
Published: December 2020

AbstractMotor adaptation is fundamental to maintaining accurate movements under changing conditions, but the neurochemical basis of human motor adaptation is not well understood. Here, we used an ultra-high-field MR multimodal acquisition to address the hypothesis that M1 GABA and M1-Cerebellar functional connectivity would relate to retention of adaptation, but not acquisition of adaptation. As such, we demonstrate higher baseline M1 [GABA] relates to greater retention but does not relate to adaptation-acquisition. This relationship is mediated by change in M1-Cerebellar functional connectivity: higher M1 [GABA] relates to a decreased M1-Cerebellar connectivity, resulting in greater retention. These findings showed anatomical, neurochemical and behavioural specificity: As expected, no relationship was found between retention and a control metabolite, retention and connectivity change between control regions and between M1 [GABA] and behaviour in a control condition. The implication of a mechanistic link from neurochemistry to retention advances our understanding of population variability in retention and provides a step towards therapeutic interventions to restore motor abilities.
Unearthing the genes of plant-beneficial marine yeast -Wickerhamomyces anomalusstrain MSD1
Authors: Krishnan S Radhesh , Prabhakaran N , Ragunath K Sengali , Srinivasan R , Ponni K Keerthana , Balaji G , Gracy M , Brindha C , Narayanan Lakshmi , Latha K 
Published: December 2020

AbstractThede novogenome of unique marine yeast,Wickerhamomyces anomalusisolated from seaweed along Indian coast is presented. The genome assembly was carried out using MaSurCA assembler that generated a data size ∼14.3 mb from short and long reads obtained from Illumina Hiseq 4000 and GridION-X5 respectively. This assembled genome data were used for predicting genes using Augustus gene prediction tool that reported 6720 genes and proteins. The gene sequences were used to unravel the metabolic pathway analysis using KAAS database. The protein sequences were used for secondary analysis to predict the presence of signal peptides using SignalP tool, predicting protein family, domains using Pfam tool and prediction of transmembrane helices in proteins using TMHMM tool. Presence of genes involved in plant growth–promotion and regulation (PGPR) including siderophore and IAA production, iron and sulfur transformation, zinc and phosphate solubilization, nitrogen fixation, synthesis of anti-bacterial and volatile organic compound (VOCs), were assigned. Additionally, acid and alkaline phosphatases, ACC deaminases and lytic enzymes such as β-glucanases, proteases and chitinases involved in pathogen suppression, are also reported. The study elucidates comprehensive understanding of PGP attributes of MSD1 and its potential use in agriculture as bio-fertilizer /bio-stimulant.
scClassifR: Framework to accurately classify cell types in single-cell RNA-sequencing data
Authors: Nguyen Vy , Griss Johannes 
Published: December 2020

AbstractMotivationAutomatic cell type identification in scRNA-seq datasets is an essential method to alleviate a key bottleneck in scRNA-seq data analysis. While most existing tools show good sensitivity and specificity in classifying cell types, they often fail to adequately not-classify cells that are not present in the used reference.ResultsscClassifR is a novel R package that provides a complete framework to automatically classify cells in scRNA-seq datasets. It supports both Seurat and Bioconductor’s SingleCellExperiment and is thereby compatible with the vast majority of R-based analysis workflows. scClassifR uses hierarchically organised SVMs to distinguish a specific cell type versus all others. It shows comparable or even superior sensitivity and specificity compared to existing tools while being robust in not-classifying unknown cell types. As a unique feature, it reports ambiguous cell assignments, including the respective probabilities. Finally, scClassifR provides dedicated functions to train and evaluate classifiers for additional cell types.Availability and ImplementationscClassifR is freely available on GitHub (https://github.com/grisslab/scClassifR).
The evolutionary assembly of forest communities along environmental gradients: recent diversification or sorting of pre-adapted clades?
Authors: Linan Alexander G. , Myers Jonathan A. , Edwards Christine E. , Zanne Amy E. , Smith Stephen A. , Arellano Gabriel , Cayola Leslie , Farfan-Ríos William , Fuentes Alfredo F. , Garcia-Cabrera Karina , Gonzales-Caro Sebastián , Loza M. Isabel , Macía Manuel J. , Malhi Yadvinder , Nieto-Ariza Beatriz , Revilla Norma Salinas , Silman Miles , Tello J. Sebastián 
Published: December 2020

SummaryBiogeographic events occurring in the deep past can contribute to the structure of modern ecological communities. However, little is known about how the emergence of environmental gradients shape the evolution of species that underlie community assembly. In this study, we address how the creation of novel environments lead to community assembly via two non-mutually exclusive processes: 1) the immigration and ecological sorting of pre-adapted clades (ISPC), and 2) recent adaptive diversification (RAD). We study these processes in the context of the elevational gradient created by the uplift of the Central Andes.We develop a novel approach and method based on the decomposition of species turnover into within- and among-clade components, where clades correspond to lineages that originated before mountain uplift. Effects of ISPC and RAD can be inferred from how components of turnover change with elevation. We test our approach using data from over 500 Andean forest plots.We found that species turnover between communities at different elevations is dominated by the replacement of clades that originated before the uplift of the Central Andes.Our results suggest that immigration and sorting of clades pre-adapted to montane habitats is the primary mechanism shaping communities across elevations.
Elucidation of the molecular interactions that enable stable assembly and structural diversity in multicomponent immune receptors
Authors: Fong Lam-Kiu , Chalkley Matthew J. , Tan Sophia K. , Grabe Michael , DeGrado William F. 
Published: December 2020

ABSTRACTMulti-component immune receptors are essential complexes in which distinct ligand-recognition and signaling subunits are held together by interactions between acidic and basic residues of their transmembrane helices. A 2-to-1 acidic to basic motif in the transmembrane domains of the subunits is necessary and sufficient to assemble these receptor complexes. Here, we study a prototype for these receptors, a DAP12-NKG2C 2:1 heterotrimeric complex, in which the two DAP12 subunits each contribute a single transmembrane Asp residue, and the NKG2C subunit contributes a Lys to form the complex. DAP12 can also associate with 20 other subunits using a similar motif. Here we use molecular dynamics simulations to understand the basis for the high affinity and diversity of interactions in this group of receptors. Simulations of the transmembrane helices with differing protonation states of the Asp-Asp-Lys triad identified a structurally stable interaction in which a singly protonated Asp-Asp pair forms a hydrogen-bonded carboxyl-carboxylate clamp that clasps onto a charged Lys sidechain. This polar motif was also supported by density functional theory and a Protein Data Bank-wide search. In contrast, the helices are dynamic at sites distal to the stable carboxyl-carboxylate clamp motif. Such a locally stable but globally dynamic structure is well-suited to accommodate the sequence and structural variations in the transmembrane helices of multi-component receptors, which mix and match subunits to create combinatorial functional diversity from a limited number of subunits. It also supports a signaling mechanism based on multi-subunit clustering rather than propagation of rigid conformational changes through the membrane.SIGNIFICANCEReceptors that separate ligand recognition and intracellular signaling into separate protein subunits are ubiquitous in immunity. These subunits mix and match to create combinatorial functional diversity. The transmembrane domains of these receptors assemble through the interaction between two acidic and one basic residue on different helices. Using computational methods to study the DAP12-NKG2C receptor complex we identified a polar motif in which a singly protonated Asp-Asp pair forms a carboxyl-carboxylate clamp that clasps a charged Lys sidechain in the membrane. This local interaction allows dynamic variations in other regions of the helices that tolerate sequence diversity of the interacting subunits in this class of receptors, which signal through multi-subunit clustering rather than propagation of rigid conformational changes through the membrane.
Fructose 1,6-bisphosphate sensing by pyruvate kinase isozymes M2 (PKM2) controls MyoD stability and myogenic differentiation
Authors: Kim Minchul , Zhang Yao , Birchmeier Carmen 
Published: December 2020

AbstractGlucose exerts beneficial effects on myogenesis and muscle physiology. However, the mechanisms by which glucose regulates myogenesis remain ill-defined or incompletely understood. Here, we show that low glycolysis destabilizes MyoD protein, a master myogenic transcription factor. Intriguingly, MyoD is not controlled by the cellular energy status per se, but by the level of fructose 1,6-bisphosphate, an intermediate metabolite of glycolysis. Fructose 1,6-bisphosphate is sensed by pyruvate kinase M2 (PKM2). In the presence of fructose 1,6-bisphosphate, PKM2 form tetramers that sequester the Huwe1 E3 ubiquitin ligase to the cytoplasm. Reduced fructose 1,6-bisphosphate levels dissociate the tetramer, releasing Huwe1 into the nucleus where it targets MyoD for degradation. Genetic or pharmacological modulation of PKM2-Huwe1 axis restores myogenic differentiation in glucose restricted conditions. Our results show that glucose metabolism directly regulates protein stability of a key myogenic factor and provide a rationale for enhancing myogenesis.
Cytosolic localization andin vitroassembly of humande novothymidylate synthesis complex
Authors: Spizzichino Sharon , Boi Dalila , Boumis Giovanna , Lucchi Roberta , Liberati Francesca Romana , Capelli Davide , Montanari Roberta , Pochetti Giorgio , Paone Alessio , Rinaldo Serena , Contestabile Roberto , Paiardini Alessandro , Tramonti Angela , Giardina Giorgio , Cutruzzolà Francesca 
Published: December 2020

ABSTRACTDe novothymidylate synthesis is a crucial pathway for normal and cancer cells. Deoxythymidine monophosphate (dTMP) is synthesized by the combined action of three enzymes: serine hydroxymethyltransferase (SHMT), dihydrofolate reductase (DHFR) and thymidylate synthase (TYMS), the latter two targets of widely used chemotherapeutics such as antifolates and 5-fluorouracil. These proteins translocate to the nucleus after SUMOylation and are suggested to assemble in this compartment into the thymidylate synthesis complex (dTMP-SC). We report the intracellular dynamics of the complex in lung cancer cells byin situproximity ligation assay, showing that it is also detected in the cytoplasm. This result strongly indicates that the role of the dTMP-SC assembly may go beyond dTMP synthesis. We have successfully assembled the dTMP synthesis complexin vitro, employing tetrameric SHMT1 and a bifunctional chimeric enzyme comprising human TYMS and DHFR. We show that the SHMT1 tetrameric state is required for efficient complex assembly, indicating that this aggregation state is evolutionary selected in eukaryotes to optimize protein-protein interactions. Lastly, our results on the activity of the complete thymidylate cyclein vitro, may provide a useful tool to develop drugs targeting the entire complex instead of the individual components.
Emissions prediction of an aero-piston gasoline engine during surveillance flight of an unmanned aerial vehicle
Authors: Dinc Ali , Otkur Murat 
Published: December 2020

Purpose
The purpose of this study is to perform the preliminary design, flight performance and exhaust emissions calculations of a piston engine powered unmanned aerial vehicle (UAV) during a flight cycle which consists of multiple flight altitudes and airspeeds.

Design/methodology/approach
A genuine computer model in Matlab/Simulink was developed to predict the size and weight of UAV and piston engine (using Avgas 100LL fuel) performance together with exhaust emissions in an iterative process.

Findings
The amount of emitted exhaust gases including carbon dioxide, carbon monoxide, hydrocarbons and nitrogen oxides were calculated in a typical UAV mission profile as a whole and also divided into mission flight segments.

Research limitations/implications
Emissions were calculated based on fuel flow and engine speed inputs based on ground test data for emission indices. Test data for emission indices was very limited.

Practical implications
As UAV utilization has been increasing around the world, this study presents important and noticeable results on the emissions that need to be considered for environmental purposes.

Originality/value
In literature, emission prediction studies for UAVs are very rare. In fact, UAVs typically have quite different flight speeds and altitudes than regular manned aircraft and emissions change with speed and altitude. Additionally, unlike manned aircraft, UAVs can fly more than 24 h with different operation characteristics. The originality of this study presents the emission predictions of a piston engine UAV which flies with a significantly different mission profile than a manned aircraft.
Quality of gluten-free cookies made with rice flour of different levels of amylose and cowpea beans
Authors: Dierings de Souza Estefania Julia , Pereira Aline Machado , Fontana Mauro , Vanier Nathan Levien , Gularte Marcia Arocha 
Published: December 2020

PurposeThe objective of this study was to evaluate the effects of rice flour obtained from rice grains with different levels of amylose on technological, nutritional and sensory properties of cookies made with a blend of rice and cowpea flour.Design/methodology/approachThe cookies preparation was set at a ratio of rice flour and cowpea beans 70:30. The studied formulations were: LA: low amylose rice flour; MA: medium-amylose rice flour; HA: high amylose rice flour. The quality of the obtained cookies was analyzed for proximate composition, in vitro protein digestibility, thickness, diameter, dispersion factor, texture, color, amino acid profile and sensory properties.FindingsProximate composition and in vitro protein digestibility showed no differences between the three studied formulations. The medium and low amylose rice flour cookies showed the lowest hardness values. The combination of rice and beans allowed a good balance of essential amino acids. The cookies formulated with high amylose rice flour presented lighter coloration, low hardness and greater sensory preference.Originality/valueRice and cowpea flours are an alternative source for the preparation of gluten-free bakery products, such as cookies. The high amylose content of rice flour has less negative interference in the texture characteristics of the cookies. The combination of rice and beans flour provides a balance of essential amino acids.
Banking sector earnings management using loan loss provisions in the Fintech era
Authors: Ozili Peterson K. 
Published: December 2020

PurposeThis paper analyzes banking sector earnings management using loan loss provisions (LLPs) in the Fintech era.Design/methodology/approachRegression methodology was used to examine earnings management in the Fintech era.FindingsThe findings show evidence for bank income smoothing using LLPs. There is greater income smoothing in the second-wave Fintech era compared to the first-wave Fintech era, and the presence of strong institutions did not lower income smoothing in the second-wave era. Bank income smoothing is also greater in (1) Bank of International Settlement (BIS) and EU countries than in non-EU countries and G7 countries, (2) well-capitalized banking sectors and (3) during economic booms in the second-wave Fintech era.Practical implicationsThe competition for loans and deposits by banks and Fintech lenders in the second-wave Fintech era created additional incentives for banks to engage in income smoothing to report competitive and stable earnings.Originality/valueThe study uses a unique approach to detect country-level earnings management in the banking sector. Also, this study extends the bank earnings management literature by introducing the Fintech era as a determinant of the extent of bank earnings management.
Effect of internal integration on SMEs’ performance: the role of external integration and ICT
Authors: Amoako Timothy , Huai Sheng Zhang , Dogbe Courage Simon Kofi , Pomegbe Wisdom Wise Kwabla 
Published: December 2020

PurposeThe paper investigates the mediation role of external integration in the relationship between internal integration and small and medium enterprises (SMEs) performance. Information and communication technology (ICT) was used to moderate the relationship between internal and external, and external integration and SMEs performance.Design/methodology/approachCross sectional method was used to distribute questionnaires to owners of SMEs in Abossey Okai business enclave to assess the various dimensions in the study. Structural equation modeling was employed to assess the relationship among the dimensions, based on 163 validated questionnaires. Analysis of Moment Structures (Amos) and Statistical Package for Social Sciences (SPSS) were used in analyzing the data.FindingsThe results indicate that, external integration mediated the relationship between internal integration and SMEs performance. In addition, ICT had positive moderating effect in the relationship between internal and external integration, and external integration and SMEs performance.Practical implicationsPractically, this research informs owners and managers of SMEs to appreciate the importance of developing internal structures of a firm and further linking their operations with external partners. Additionally, findings will aid managers’ and owners’ leverage on ICT capabilities to enhance performance in their operations.Originality/valueEngaging external integration to mediate the relationship between internal integration and SMEs performance and extending the relationship to include moderating role of ICT in both relationship that is internal and external integration on one side, and external and firm performance, the current study contributes to supply chain integration (SCI) and ICT available literature.
Improving internal logistics of a bus manufacturing using the lean techniques
Authors: Mourato José , Pinto Ferreira Luís , Sá José Carlos , Silva Francisco J.G. , Dieguez Teresa , Tjahjono Benny 
Published: December 2020

PurposeThis study aims to improve the reception and positioning of materials in the warehouse, as well as the internal logistics of a bus manufacturing company by acting upon the processes of supply line management.Design/methodology/approachThis study is based on the action research methodology which, through a practical approach, intends to generate transferrable knowledge to other organizations whose situations are similar to that of this study. The practical actions and the knowledge acquired co-create the changes needed for the improvement processes.FindingsThrough these improvements, it is possible to standardize supply and eliminate the retention of picking carts on the line, simplify the management of materials provided in supermarket boxes, improve the control of materials and facilitate the process of picking and materials storage. A kanban card-based supply system was also expanded to the bus assembly line, allowing more control over valuable materials.Originality/valueThis study has demonstrated how the implementation of lean techniques on a bus assembly line can lead to increased consistency of supply to the line and improved working conditions, both in the production and warehouse areas. Furthermore, it has set a new standard of the internal logistics processes and the inclusion of process recording in the working instructions.