bluuebunny/crossref_metadata_2025_split huggingface dataset:
MLQ is responsible for stabilisation of subunit a in the holoenzyme of mammalian ATP synthase
Authors: Tauchmannová K , Ho DH , Nůsková H , Pecinová A , Alán L , Rodinová M , Koňaříková E , Vrbacký M , Puertas G , Kaplanová V , Houštěk J , Pecina P , Mráček T 
Published: February 2020

AbstractThe biogenesis of mammalian ATP synthase is complex process believed to proceed via several modules. It starts with the formation of F1 catalytic part, which is in the later steps connected with the membranous subcomplex. The final phase is represented by incorporation of the two mtDNA-encoded subunits Fo-a and A6L. However, little is known about the position of two newly described Fo accessory subunits DAPIT (also termed Usmg5) and MLQ (also known as c14orf2) in the assembly scheme and about their role in regulation of ATP synthase biogenesis. To resolve this, we have utilised several model systems, namely rho0 cells lacking mtDNA and thus both subunits Fo-a and A6L, cells harbouring 9205delTA microdeletion, which results in the absence of the subunit Fo-a, HEK293 cells with knockdown of DAPIT protein and HEK293 cells with knockout of MLQ protein and followed the assembly state of ATP synthase among them.Contrary to previously reported data, we observed normal levels of assembled ATP synthase in DAPIT knockdown and MLQ knockout cells. Our results indicate that lack of DAPIT protein leads to the assembly of more labile, but complete and functional holoenzyme. Absence of either Fo-a alone or Fo-a and A6L results into the normal levels of structurally altered, labile, and ~60 kDa smaller vestigial enzyme complex, which also lacks DAPIT and MLQ. This complex retains the ATP hydrolytic activity but is unable to synthesize ATP. Cells with the MLQ knockout presented with the phenotype similar to the lack of Fo-a: normal content of smaller and labile complex. In the absence of MLQ, vestigial ATP synthase did not contain also subunits Fo-a and A6L. This complex also retained ATP hydrolytic activity, while its phosphorylating capacity was affected. In all the cell lines tested, the individual subunits seemed to be associated only with assembled ATP synthase complex, indicating that once subunits dissociate from the complex, they are degraded in the cell. This hypothesis is supported by the fact, that in the cells lacking subunit MLQ the biosynthesis of both mtDNA-encoded subunits Fo-a and A6L is normal, but they are degraded at faster pace than the rest of the complex.Based on our data, we conclude that MLQ and Fo-a closely associate and their incorporation into the enzyme complex depends on each another. On the contrary, DAPIT protein seems to be incorporated at the very last step and its presence stabilises the holoenzyme.
Rotational snapping: Illusory rhythmicity induced by global and local motion binding
Authors: Han Hio-Been 
Published: February 2020

SUMMARYThe complexity of human perceptual system has often been investigated through its atypical function; the illusion. Here, I introduce a new visual illusion induced by rotational motion binding, which leads to a gestalt perception of illusory object rhythmically popping out and fading away. In this illusion, observers reported non-existing rhythm out of rotating Gabor patches (e.g., local rotation) that also have orbital trajectory with opposite direction (e.g., global rotation), only under the particular combinations of parameters. This illusory rhythmicity was four times faster than the average of global/local rotational speed. Image reconstruction using the response-triggered average revealed the rhythmicity is explained by the circular alignment of array, demonstrating the effect of repeated contour integration and its perceptual consequences.
MaTAR25LncRNA Regulates theTensin1Gene to Impact Breast Cancer Progression
Authors: Chang Kung-Chi , Diermeier Sarah D. , Yu Allen T. , Brine Lily D. , Russo Suzanne , Bhatia Sonam , Alsudani Habeeb , Kostroff Karen , Bhuiya Tawfiqul , Brogi Edi , Bennett C. Frank , Rigo Frank , Spector David L. 
Published: February 2020

SUMMARYMisregulation of long non-coding RNA genes has been linked to a wide variety of cancer types. Here we report onMammaryTumorAssociatedRNA 25 (MaTAR25), a nuclear enriched and chromatin associated lncRNA that plays a role in mammary tumor cell proliferation, migration, and invasion, bothin vitroandin vivo.MaTAR25functions by interacting with purine rich element binding protein B (PURB), and associating with a major downstream target geneTensin 1(Tns1) to regulate its expression intrans. Knockout ofMaTAR25results in down-regulation ofTns1leading to a reorganization of the actin cytoskeleton, and a reduction of focal adhesions and microvilli. The human ortholog ofMaTAR25,LINC01271, is upregulated with human breast cancer stage and metastasis.SIGNIFICANCELncRNAs have great potential to reveal new regulatory mechanisms of function as well as having exciting therapeutic capacity given their ease of being targeted by nucleic acid drugs. Our study ofMaTAR25,and its human orthologLINC01271,reveal an unexpected function of this lncRNA in breast cancer progression by regulatingTns1gene expression, whose protein product is a critical component of focal adhesions linking signaling between the extracellular matrix and the actin cytoskeleton. We identifiedLINC01271 asthe human ortholog ofMaTAR25, and importantly, increased expression ofLINC01271is associated with poor patient prognosis and cancer metastasis. Our findings demonstrate thatLINC01271represents an exciting therapeutic target to alter breast cancer progression.
JEDI: Circular RNA Prediction based on Junction Encoders and Deep Interaction among Splice Sites
Authors: Jiang Jyun-Yu , Ju Chelsea J.-T. , Hao Junheng , Chen Muhao , Wang Wei 
Published: February 2020

AbstractCircular RNA is a novel class of endogenous non-coding RNAs that have been largely discovered in eukaryotic transcriptome. The circular structure arises from a non-canonical splicing process, where the donor site backsplices to an upstream acceptor site. These circular form of RNAs are conserved across species, and often show tissue or cell-specific expression. Emerging evidences have suggested its vital roles in gene regulation, which are further associated with various types of diseases. As the fundamental effort to elucidate its function and mechanism, numerous efforts have been devoted to predicting circular RNA from its primary sequence. However, statistical learning methods are constrained by the information presented with explicit features, and the existing deep learning approach falls short on fully exploring the positional information of the splice sites and their deep interaction.We present an effective and robust end-to-end framework, JEDI, for circular RNA prediction using only the nucleotide sequence. Our framework first leverages the attention mechanism to encode each junction site based on deep bidirectional recurrent neural networks and then presents the novel cross-attention layer to model deep interaction among these sites for backsplicing. Finally, JEDI is capable of not only addressing the task of circular RNA prediction but also interpreting the relationships among splice sites to discover the hotspots for backsplicing within a gene region. Experimental evaluations demonstrate that JEDI significantly outperforms several state-of-the-art approaches in circular RNA prediction on both isoform-level and gene-level. Moreover, JEDI also shows promising results on zero-shot backsplicing discovery, where none of the existing approaches can achieve.The implementation of our framework is available athttps://github.com/hallogameboy/JEDI.
cDNA library screening to identify interacting proteins of Golgi-localized type II membrane proteins
Authors: Lund Christian Have , Bromley Jennifer R. , López-Marqués Rosa Laura , Sakuragi Yumiko 
Published: February 2020

AbstractIn eukaryotes, biosynthesis of many extracellular matrix glycans occurs in the Golgi apparatus. These proteins include glycosyltransferases, modifying enzymes and nucleotide-sugar conversion enzymes, many of which possess a type II membrane topology. Growing evidence indicates that both the function and Golgi localization of many of these proteins are regulated through protein-protein interactions (PPIs). Given the essential nature and conservation of extracellular matrix polysaccharides, it is likely that PPIs are more prevalent among biosynthetic enzymes. However the identification of PPIs among Golgi proteins has been technically challenging due to the generally low abundance and unique membrane topology of these proteins. The aim of this article is to explore the feasibility of cDNA library screening by a yeast-based modified split ubiquitin system as a mean for unbiased screening for PPIs involving a Golgi-localized type II membrane. As a test case, a galacturonosyltransferase1 (GAUT1), involved in pectin biosynthesis in the higher plant Arabidopsis thaliana, was used as the bait. Construction and screening of Arabidopsis cDNA libraries using GAUT1 as the bait successfully led to identification of GAUT7, a previously reported interaction partner of GAUT1, which validates the method. Furthermore, 25 novel candidate interaction partners were identified. The results contribute to shape a field guide for identifying PPIs involving glycan biosynthetic enzymes in eukaryotic cells.
A Comprehensive Assessment of Human Natural Killer Cell Phenotype and Function in Whole Blood
Authors: Market M , Tennakoon G , Ng J , Scaffidi M , Kennedy M A , de Souza C Tanese , Auer R C 
Published: February 2020

AbstractThe majority of data on human Natural Killer (NK) cell phenotype and function has been generated using cryopreserved peripheral blood mononuclear cells (PBMCs). However, cryopreservation can have adverse effects on PBMCs. In contrast, investigating immune cells in whole blood can reduce the time, volume of blood required, and potential artifacts associated with manipulation of the cells. Whole blood collected from healthy donors and cancer patients was processed by three separate protocols that can be used independently or in parallel to assess extracellular receptors, intracellular signaling protein phosphorylation, and intracellular and extracellular cytokine production in human NK cells. To assess extracellular receptor expression, 200 μL of whole blood was incubated with an extracellular staining (ECS) mix and cells were subsequently fixed and RBCs lysed prior to analysis. The phosphorylation status of signaling proteins was assessed in 500 μL of whole blood following co-incubation with interleukin (IL)−2/12 and the ECS mix for 20 minutes prior to cell fixation and RBC lysis and subsequent permeabilization for staining with an intracellular staining (ICS) mix. Cytokine production (IFNγ) was similarly assessed by incubating 1 mL of whole blood with PMA-ionomycin or IL−2/12 prior to incubation with ECS and subsequent ICS antibodies. In addition, plasma was collected from stimulated samples prior to ECS for quantification of secreted IFNγ by ELISA. Results were consistent, despite inherent interpatient variability. Although we did not investigate an exhaustive list of targets, this approach enabled quantification of representative ECS surface markers including activating (NKG2D and DNAM−1) and inhibitory (NKG2D, PD−1, TIGIT, and TIM−3) receptors, cytokine receptors (CD25, CD122, CD132, and CD212) and ICS markers associated with NK cell activation following stimulation, including signaling protein phosphorylation (p-STAT4, p-STAT5, p-p38 MAPK, p-S6K) and IFNγ in both healthy donors and cancer patients. In addition, we compared extracellular receptor expression using whole blood versus cryopreserved PBMCs and observed a significant difference in the expression of almost all receptors. The methods presented permit a relatively rapid parallel assessment of immune cell receptor expression, signaling protein activity, and cytokine production in a minimal volume of whole blood from both healthy donors and cancer patients.
Analysis of spherical shell structure based on SBFEM
Authors: Lin Gao , Ye Wen-Bin , Li Zhi-Yuan , Liu Jun 
Published: February 2020

Purpose
The purpose of this paper is to present an accurate and efficient element for analysis of spherical shell structures.

Design/methodology/approach
A scaled boundary finite element method is proposed, which offers more advantages than the finite element method and boundary element method. Only the boundary of the computational domain needs to be discretized, but no fundamental solution is required.

Findings
The method applies to thin as well as thick spherical shells, irrespective of the shell geometry, boundary conditions and applied loading. The numerical solution converges to highly accurate result with raising the order of high-order elements.

Originality/value
The modeling strictly follows three-dimensional theory of elasticity. Formulation of the surface finite elements using three translational degree of freedoms per node is required, which results in considerably simplifying the computation. In the thickness directions, it is solved analytically, no problem of high aspect ratio arises and transverse shear locking can be successfully avoided.
An experimental/numerical hydrothermal analysis on natural convection and TiO2-SiO2/W-EG nanofluid’s properties in a hollow/finned cavity
Authors: Zaresharif Mahshid , Zarei Fatemeh , Ranjbar Ali Mohammad , Kok Foong Loke , Ross David 
Published: February 2020

Purpose
This paper aims to provide an experimental/numerical analysis of free convection within a hollow/finned cavity.

Design/methodology/approach
The hollow square cavity is equipped with eight active fins which have a similar configuration and different temperatures. Furthermore, four different thermal arrangements are considered to determine the order of temperature for each fin. The coupled lattice Boltzmann method is used, which not only maintains the considerable advantages of standard lattice Boltzmann method such as accuracy but also enhances the stability of this method.

Findings
The cavity is filled with TiO2-SiO2/Water-Ethylene Glycol nanofluid. The thermal conductivity and dynamic viscosity of nanofluid are experimentally measured using high-precision devices in six concentrations of the nanoparticle. In this study, some main parameters, including a range of Rayleigh number (103 < Ra < 106), the concentration of nanofluid (0.5 to 3 Vol.%) and thermal arrangements of fins, are considered. The effects of these main parameters on the flow, isotherms, heat transfer performance and entropy generation are studied.

Originality/value
The originality of this paper is combining the numerical simulation (lattice Boltzmann method) using a modern approach with experimental observations of nanofluid’s properties.
Natural convection from cross blade inside a nanofluid-filled cavity using ISPH method
Authors: Raizah Zehba A.S. 
Published: February 2020

Purpose
The purpose of this study is to apply the incompressible smoothed particle hydrodynamics method for simulating the natural convection flow inside a cavity including cross blades or circular cylinder cylinder.

Design/methodology/approach
The base fluid is water and copper-water nanofluid is treated as a working fluid. The left and rights walls are maintained at a cool temperature, the horizontal cavity walls are isolated and the inner shape was heated. The physical parameters are the length of the blades L_Blade, the number of cross blades, circular cylinder radius L_R, Rayleigh number Ra and the nanoparticles volume fraction.

Findings
The results reveal that the lengths of the cross blade, number of the blades and radius of the circular cylinder is working as an enhancement factor for heat transfer and fluid flows inside a cavity. Adding nanoparticles augments heat transfer and reduces the fluid flow intensity inside a cavity. The best case for buoyancy-driven flow was obtained when the inner shape is the circular cylinder at a higher Rayleigh number.

Originality/value
This work uses a distinctive numerical method to study the natural convection heat from cross blades inside a cavity filled with nanofluid. It provides a new analysis of this issue and presented good results.
The success of short-term study abroad programs: a social networks perspective
Authors: DeJordy Rich , Milevoj Emil , Schmidtke James M. , Bommer William H. 
Published: February 2020

PurposeThe purpose of this paper is to examine the effects of individual difference variables and social relationships on student learning outcomes of short-term study abroad programs.Design/methodology/approachThis study used a social network analysis (SNA) approach to examine the effects of friendship, advice and communication networks on student learning outcomes.FindingsResults indicated that demographic characteristics (e.g. sex, years of work experience) did not influence learning outcomes nor the enjoyment of the experience. Social networks positively influenced students’ perceived improvement in managerial skills, their ability to reflect on their international experience and their intercultural sensitivity.Research limitations/implicationsSocial relationships may be an important factor to consider in understanding the relationship between short-term study abroad programs and learning outcomes.Practical implicationsProgram directors and faculty members need to consider the design of assignments and activities that may facilitate the development of specific types of social relationships (e.g. friendship, communication and advice). These specific social relationships may have unique influences on specific learning outcomes of short-term study abroad programs.Originality/valueThis study is the first study that examined the effects of different types of social relationships on learning outcomes for short-term study abroad programs. The results have important implications for both future research and the design of international study-abroad programs.
Drivers of brand credibility in consumer evaluation of global brands and domestic brands in an emerging market context
Authors: Srivastava Ankur , Dey Dipanjan Kumar , M.S. Balaji 
Published: February 2020

Purpose
The purpose of this study is to examine the impact of brand credibility on purchase intentions toward global brands and domestic brands in an emerging market context. It further examines three drivers of brand credibility: perceived globalness, perceived local iconness and perceived authenticity.

Design/methodology/approach
A structured questionnaire was used for data collection. Systematic random sampling using the mall intercept technique was used to collect cross-sectional data from 836 customers in India. Hypotheses were tested by using structural equation modeling with AMOS 21.

Findings
The results demonstrate the significance of brand credibility on purchase intentions. Furthermore, brand globalness differentially influence brand credibility for global and domestic brands.

Research limitations/implications
The findings provide key insights for marketers regarding consumer evaluation of global brands and domestic brands in emerging markets.

Originality/value
This study contributes to the literature by proposing and testing the key role of brand credibility in consumer choice of global brands versus domestic brands in an emerging market context.
In-plane stability of shallow concrete arches under fire
Authors: Bouras Yanni , Vrcelj Zora 
Published: February 2020

PurposeConcrete arch structures are commonly constructed for various civil engineering applications. Despite their frequent use, there is a lack of research on the response and performance of concrete arches when subjected to fire loading. Hence, this paper aims to investigate the response and in-plane failure modes of shallow circular concrete arches subjected to mechanical and fire loading.Design/methodology/approachThis study is conducted through the development of a three-dimensional finite element (FE) model in ANSYS. The FE model is verified by comparison to a non-discretisation numerical model derived herein and the reduced modulus buckling theory, both used for the non-linear inelastic analysis of shallow concrete arches subjected to uniformly distributed radial loading and uniform temperature field. Both anti-symmetric and symmetric buckling modes are examined, with analysis of the former requiring geometric imperfection obtained by an eigenvalue buckling analysis.FindingsThe FE results show that anti-symmetric bifurcation buckling is the dominant failure mode in shallow concrete arches under mechanical and fire loading. Additionally, parametric studies are presented which illustrate the influence of various parameters on fire resistance time.Originality/valueFire response of concrete arches has not been reported in the open literature. The authors have previously investigated the stability of shallow concrete arches subjected to mechanical and uniform thermal loading. It was found that temperature greatly reduced the buckling loads of concrete arches. However, this study was limited to the simplifying assumptions made which include elastic material behaviour and uniform temperature loading. The present study provides a realistic insight into the fire response and stability of shallow concrete arches. The findings herein may be adopted in the fire design of shallow concrete arches.
The philosophy of quality in education: a qualitative approach
Authors: Brinia Vasiliki , Poullou Vasiliki , Panagiotopoulou Angeliki-Rafailia 
Published: February 2020

Purpose
This paper aims to explore the perceptions of pre-school educators for the application of total quality philosophy in kindergartens in the prefecture of Corinthia, Greece. Dimensions, such as the adoption of quality philosophy in the pre-school unit by the superiors, the active participation of teachers in decision-making and human resource management parameters, are examined.

Design/methodology/approach
The methodological approach of qualitative research was selected for the collection, processing and analysis of data based on the methodological tools of the interview with a semi-structured questionnaire and deliberate random sampling of kindergarten teachers serving in public units where they have teaching and/or administrative tasks.

Findings
The analysis of the data shows that there is no particular familiarity with the basic parameters of total quality philosophy in pre-school education and is related to empirical planning and lack of long-term vision. However, participatory decision-making and emotional intelligence are found as essential elements for ensuring an efficient and open-ended school culture.

Originality/value
The study is the first of its kind in Greece and abroad and its findings can be used to enrich the thematic scope of application of total quality management dimensions to pre-school education and in particular, those dimensions related to the leadership profile of teachers exercising responsibility tasks.