bluuebunny/crossref_metadata_2025_split huggingface dataset:
A cost-effective and efficient approach for generating and assembling reagents for conducting real-time PCR
Authors: Mote Ridim D , Laxmikant V Shinde , Singh Surya Bansi , Tiwari Mahak , Hemant  , Srivastava Juhi , Tripathi Vidisha , Seshadri Vasudevan , Majumdar Amitabha , Subramanyam Deepa 
Published: July 2021

AbstractReal-time PCR is a widely used technique for quantification of gene expression. However, commercially available kits for real-time PCR are very expensive. The ongoing coronavirus pandemic has severely hampered the economy in a number of developing countries, resulting in a reduction in available research funding. The fallout of this will result in limiting educational institutes and small enterprises from using cutting edge biological techniques such as real-time PCR. Here, we report a cost-effective approach for preparing and assembling cDNA synthesis and real-time PCR mastermixes with similar efficiencies as commercially available kits. Our results thus demonstrate an alternative to commercially available kits.
Bioimage postprocessing based on discrete wavelet transform and Lucy-Richardson deconvolution methods
Authors: Bai Haoxin , Che Bingchen , Zhao Tianyun , Zhao Wei , Wang Kaige , Zhang Ce , Bai Jintao 
Published: July 2021

AbstractAccompanied with the increasing requirements of probing micro/nanoscopic structures of biological samples, a variety of image processing algorithms have been developed for visualization or to facilitate data analysis. However, it remains challenging to enhance both the signal-to-noise ratio and image resolution using a single algorithm. In this investigation, we propose an approach utilizing discrete wavelet transform (DWT) in combination with Lucy-Richardson (LR) deconvolution (DWDC). Our results demonstrate that the signal-to-noise ratio and resolution of live cell’s microtubule network are considerably improved, allowing recognition of features as small as 120 nm. Notably, the approach is independent of imaging system and shows robustness in processing fibrous structures, e.g. the cytoskeleton networks.
A Ca2+ wave generates a force during cell extrusion in zebrafish
Authors: Yamada Sohei , Bessho Yasumasa , Fujita Yasuyuki , Hosokawa Yoichiroh , Matsui Takaaki 
Published: July 2021

AbstractWhen oncogenic transformed or damaged cells appear within an epithelial sheet, they are apically extruded by surrounding cells. Recently, using cultured mammalian epithelial cells and zebrafish embryonic epithelial cells, we found that a calcium (Ca2+) wave propagates from RasV12-transformed cells and laser-irradiated damaged cells to surrounding cells and promotes apical extrusion by inducing polarized movements of the surrounding cells. In mammalian cell cultures, we reported that the inositol trisphosphate (IP3) receptor, gap junctions, and the mechanosensitive Ca2+ channel TRPC1 are involved in Ca2+ wave-mediated polarized movements. However, which molecules regulate Ca2+ wave-mediated polarized movements in zebrafish and whether the Ca2+ wave can generate a force remain unknown. In this study, we aimed to answer these questions. By performing pharmacological and gene knockout experiments, we showed that a Ca2+ wave induced by the IP3 receptor and trpc1 led to formation of cryptic-lamellipodia and polarized movements of surrounding cells toward extruding cells in zebrafish. By using an in vivo force measurement method, we found that the Ca2+ wave generated approximately 1 kPa of force toward extruding cells. Our results reveal a previously unidentified molecular mechanism underlying the Ca2+ wave in zebrafish and demonstrate that the Ca2+ wave generates a force during cell extrusion.
Conversion rate to the secondary conformation state in the binding mode of SARS-CoV-2 spike protein to human ACE2 may predict infectivity efficacy of the underlying virus mutant
Authors: Sevenich Marc M. , van den Heuvel Joop , Gering Ian , Mohrlüder Jeannine , Willbold Dieter 
Published: July 2021

ABSTRACTSince its outbreak in 2019 SARS-CoV-2 has spread with high transmission efficiency across the world, putting health care as well as economic systems under pressure [1, 2]. During the course of the pandemic, the originally identified SARS-CoV-2 variant has been widely replaced by various mutant versions, which showed enhanced fitness due to increased infection and transmission rates [3, 4]. In order to find an explanation, why SARS-CoV-2 and its emerging mutated versions showed enhanced transfection efficiency as compared to SARS-CoV 2002, an improved binding affinity of the spike protein to human ACE has been proposed by crystal structure analysis and was identified in cell culture models [5-7]. Kinetic analysis of the interaction of various spike protein constructs with the human ACE2 was considered to be best described by a Langmuir based 1:1 stoichiometric interaction. However, we demonstrate in this report that the SARS-CoV-2 spike protein interaction with ACE2 is best described by a two-step interaction, which is defined by an initial binding event followed by a slower secondary rate transition that enhances the stability of the complex by a factor of ∼190 with an overall KD of 0.20 nM. In addition, we show that the secondary rate transition is not only present in SARS-CoV-2 wt but is also found in B.1.1.7 where its transition rate is five-fold increased.
Allele-resolved single-cell multi-omics uncovers the dynamics and transcriptional kinetics of X-chromosome upregulation
Authors: Lentini Antonio , Cheng Huaitao , Noble JC , Papanicolaou Natali , Coucoravas Christos , Andrews Nathanael , Deng Qiaolin , Enge Martin , Reinius Björn 
Published: July 2021

AbstractX-chromosome inactivation (XCI) and upregulation (XCU) are the major opposing chromosome-wide modes of gene regulation that collectively achieve dosage compensation in mammals, but the regulatory link between the two remains elusive. Here, we use allele-resolved single-cell RNA-seq combined with chromatin accessibility profiling to finely dissect the separate effects of XCI and XCU on RNA levels during mouse development. We uncover that balanced X dosage is flexibly attained through expression tuning by XCU in a sex- and lineage-specific manner along varying degrees of XCI and across developmental and cellular states. Male blastomeres achieve XCU upon zygotic genome activation while females experience two distinct waves of XCU, upon imprinted- and random XCI, and ablation of Xist impedes female XCU. Contrary to widely established models of mammalian dosage compensation, naïve female embryonic cells carrying two active X chromosomes do not exhibit upregulation but express both alleles at basal level, yet collectively exceeding the RNA output of a single hyperactive allele. We show, in vivo and in vitro, that XCU is kinetically driven by X-specific modulation of transcriptional burst frequency, coinciding with increased compartmentalization of the hyperactive allele. Altogether, our data provide unprecedented insights into the dynamics of mammalian XCU, prompting a revised model of the chain in events of allelic regulation by XCU and XCI in unitedly achieving stable cellular levels of X-chromosome transcripts.
ECM dimensionality tunes actin tension to modulate the endoplasmic reticulum and spheroid phenotype
Authors: Kai FuiBoon , Ou Guanqing , Tourdot Richard W. , Stashko Connor , Gaietta Guido , Swift Mark F. , Volkmann Niels , Long Alexandra F. , Han Yulong , Huang Hector H. , Northey Jason J. , Leidal Andrew M. , Viasnoff Virgile , Bryant David M. , Guo Wei , Wiita Arun P. , Guo Ming , Dumont Sophie , Hanein Dorit , Radhakrishnan Ravi , Weaver Valerie M. 
Published: July 2021

AbstractPrimary tissue organoids and cell spheroids recapitulate tissue physiology with remarkable fidelity. We investigated how engagement with a three dimensional laminin-rich extracellular matrix supports the polarized, stress resilient spheroid phenotype of mammary epithelial cells. Cells within a three dimensional laminin-rich extracellular matrix decreased and redistributed the actin crosslinker filamin to reduce their cortical actin tension. Cells with low cortical actin tension had increased plasma membrane protrusions that promoted negative plasma membrane curvature and fostered protein associations with the plasma membrane, consistent with efficient protein secretion. By contrast, cells engaging a laminin-rich extracellular matrix in two dimensions had high filamin-dependent cortical actin tension, exhibited compromised endoplasmic reticulum function including increased expression of PKR-like Endoplasmic Reticulum Kinase signaling effectors, and had compromised protein secretion. Cells with low filamin-mediated cortical actin tension and reduced endoplasmic reticulum stress response signaling secreted, and assembled, a polarized endogenous basement membrane and survived better, and their spheroids were more resistant to exogenous stress. The findings implicate filamin-dependent cortical actin tension in endoplasmic reticulum function and highlight a role for mechanics in organoid homeostasis.
Autoimmune regulator act in synergism with thymocyte adhesion in the control of lncRNAs in medullary thymic epithelial cells
Authors: Duarte Max Jordan , Mascarenhas Romário S. , Assis Amanda Freire , Tanaka Pedro Paranhos , Speck-Hernandez Cesar A. , Passos Geraldo Aleixo 
Published: July 2021

AbstractThe autoimmune regulator (Aire) gene in medullary thymic epithelial cells (mTECs) encodes the AIRE protein, which interacts with its partners within the nucleus. This “Aire complex” induces stalled RNA Pol II on chromatin to proceed with transcription elongation of a large set of messenger RNAs and microRNAs. Considering that RNA Pol II also transcribes long noncoding RNAs (lncRNAs), we hypothesized that Aire might be implicated in the upstream control of this RNA species. To test this, we employed a loss-of-function approach in which Aire knockout mTECs were compared to Aire wild-type mTECs for lncRNA transcriptional profiling both in vitro and in vivo model systems. RNA sequencing enables the differential expression profiling of lncRNAs when these cells adhere in vitro to thymocytes or do not adhere to them as a way to test the effect of cell adhesion. Sets of lncRNAs that are unique and that are shared in vitro and in vivo were identified. Among these, we found the Aire-dependent lncRNAs as for example, Platr28, Ifi30, Morrbid, Malat1, and Xist. This finding represents the first evidence that Aire mediates the transcription of lncRNAs in mTECs. Microarray hybridizations enabled us to observe that temporal thymocyte adhesion modulates the expression levels of such lncRNAs as Morrbid, Xist, and Fbxl12o after 36h of adhesion. This finding shows the existence of a synergistic mechanism involving a link between thymocyte adhesion, Aire, and lncRNAs in mTECs that might be important for immune self-representation.
A Gradient-based Spectral Explainability Method for EEG Deep Learning Classifiers
Authors: Ellis Charles A. , Sendi Mohammad S.E. , Miller Robyn L. , Calhoun Vince D. 
Published: July 2021

AbstractThe automated feature extraction capabilities of deep learning classifiers have promoted their broader application to EEG analysis. In contrast to earlier machine learning studies that used extracted features and traditional explainability approaches, explainability for classifiers trained on raw data is particularly challenging. As such, studies have begun to present methods that provide insight into the spectral features learned by deep learning classifiers trained on raw EEG. These approaches have two key shortcomings. (1) They involve perturbation, which can create out-of-distribution samples that cause inaccurate explanations. (2) They are global, not local. Local explainability approaches can be used to examine how demographic and clinical variables affected the patterns learned by the classifier. In our study, we present a novel local spectral explainability approach. We apply it to a convolutional neural network trained for automated sleep stage classification. We apply layer-wise relevance propagation to identify the relative importance of the features in the raw EEG and subsequently examine the frequency domain of the explanations to determine the importance of each canonical frequency band locally and globally. We then perform a statistical analysis to determine whether age and sex affected the patterns learned by the classifier for each frequency band and sleep stage. Results showed that δ, β, and γ were the overall most important frequency bands. In addition, age and sex significantly affected the patterns learned by the classifier for most sleep stages and frequency bands. Our study presents a novel spectral explainability approach that could substantially increase the level of insight into classifiers trained on raw EEG.
Modeling microRNA-driven post-transcriptional regulation by using exon-intron split analysis (EISA) in pigs
Authors: Mármol-Sánchez Emilio , Cirera Susanna , Zingaretti Laura M. , Jacobsen Mette Juul , Ramayo-Caldas Yuliaxis , Jørgensen Claus B. , Fredholm Merete , Cardoso Tainã Figueiredo , Quintanilla Raquel , Amills Marcel 
Published: July 2021

AbstractThe contribution of microRNAs (miRNAs) to mRNA regulation has often been explored bypost hocselection of downregulated genes and determining whether they harbor binding sites for miRNAs of interest. This approach, however, does not discriminate whether these mRNAs are also downregulated at the transcriptional level. Here, we have characterized the transcriptional and post-transcriptional changes of mRNA expression in two porcine tissues:gluteus mediusmuscle of fasted and fed Duroc gilts and adipose tissue of lean and obese Duroc-Göttingen minipigs. Exon-intron split analysis (EISA) of RNA-seq data allowed us to identify downregulated mRNAs with high post-transcriptional signals in fed or obese states, and we assessed whether they harbor binding sites for upregulated miRNAs in any of these two physiological states. We found 26 downregulated mRNAs with high post-transcriptional signals in the muscle of fed gilts and 21 of these were predicted targets of upregulated miRNAs also in the fed state. For adipose tissue, 44 downregulated mRNAs in obese minipigs displayed high post-transcriptional signals, and 25 of these were predicted targets of miRNAs upregulated in the obese state. These results suggest that the contribution of miRNAs to mRNA repression is more prominent in the skeletal muscle system. Finally, we identified several genes that may play relevant roles in the energy homeostasis of the pig skeletal muscle (DKK2andPDK4) and adipose (SESN3andESRRG) tissues. By differentiating transcriptional from post-transcriptional changes in mRNA expression, EISA provides a valuable view about the regulation of gene expression, complementary to canonical differential expression analyses.
Emergence of a geometric pattern of cell fates from tissue-scale mechanics in the Drosophila eye
Authors: Gallagher Kevin D. , Mani Madhav , Carthew Richard W. 
Published: July 2021

ABSTRACTPattern formation of biological structures involves the arrangement of different types of cells in an ordered spatial configuration. In this study, we investigate the mechanism of patterning the Drosophila eye into a precise triangular grid of photoreceptor clusters called ommatidia. Previous studies had led to a long-standing biochemical model whereby a reaction-diffusion process is templated by recently formed ommatidia to propagate a molecular prepattern across the eye epithelium. Here, we find that the templating mechanism is instead, mechanical in origin; newly born columns of ommatidia serve as a template to spatially pattern cell flows that move the cells in the epithelium into position to form each new column of ommatidia. Cell flow is generated by a pressure gradient that is caused by a narrow zone of cell dilation precisely positioned behind the growing wavefront of ommatidia. The newly formed lattice grid of ommatidia cells are immobile, deflecting and focusing the flow of other cells. Thus, the self-organization of a regular pattern of cell fates in an epithelium is mechanically driven.
Accounting for (public) value(s): reconsidering publicness in accounting research and practice
Authors: Bracci Enrico , Saliterer Iris , Sicilia Mariafrancesca , Steccolini Ileana 
Published: July 2021

PurposeThis paper aims to highlight the importance of (public) value(s) and publicness in accounting and accountability research. It pinpoints a range of issues that scholars need to contemplate when reconsidering publicness in accounting research and practice.Design/methodology/approachThe paper adopts an interdisciplinary literature review associated with a conceptual discussion of the actual and future challenges of public service accounting and accountability in considering public value(s).FindingsThe paper illustrates the centrality of (public) value(s) at the individual, organizational and societal levels in shaping and being shaped by calculative practices, and shows that looking at the interconnections between values and accounting is a fruitful research avenue. Moreover, it highlights the power of embracing interdisciplinary approaches to illuminate these interconnections and relate them to complex and current phenomena.Originality/valueThe paper’s originality lies in the reconsideration of (public) value(s) for public service accounting scholars, providing a critical reflection and setting new research avenues.
Financial ratios and efficiency in Malaysian listed companies
Authors: Alarussi Ali Saleh Ahmed 
Published: July 2021

PurposeThis paper examines the financial ratios that may have a significant effect on the efficiency in Malaysian listed companies. Nine financial ratios measure seven variables which are firm visibility, tangibility, working capital, leverage, liquidity, productivity and profitability.Design/methodology/approachData are collected from 108 public listed companies in Malaysia. The data extracted from companies' annual reports for three years 2012–2014. STATA software analysis is used to examine these relationships.FindingsThe results show each of tangibility and liquidity have negative relationships with efficiency ratio. In against of that, profitability, working capital and productively positively link to efficiency. Leverage which is measured by two ratios – Debt ratio and Debt equity ratio – shows mix results. Debt ratio shows a positive but not significant relationship with efficiency ratio and Debt equity ratio shows a negative significant relationship with efficiency ratio.Practical implicationsThe results benefit companies, investors, economists and governments regulators in Malaysia-to understand the efficiency determinants, so help to make the right decision to enhance the efficiency level in companies which leads to enhance the amount of investments which in turn, enhance the country's economy in general.Originality/valueThis study differs than previous studies number of aspects: first the study covers a three years' period between 2012 and 2014, this period presents the movement of Malaysian current into depreciation with more than 45 percent of its value. Second, in the Malaysia context, this study examines new variables such as firm visibility, tangibility, and productivity. Third, the results of this study will help managers, shareholders, investors, regulators and other parties to make right decisions that will enhance the level of firm efficiency which enhances the investments and the economy of Malaysia.
A curriculum guide model to the next normal in developing construction supervisory training programmes
Authors: Manoharan Kesavan , Dissanayake Pujitha B.G. , Pathirana Chintha , Deegahawature Dharsana , Silva K.D. Renuka Ruchira 
Published: July 2021

PurposeThis study aims to develop a curriculum guide model to upgrade the construction supervision practices, considering evolving challenges and thereby the next normal of the industry.Design/methodology/approachBoth qualitative and quantitative research designs were adopted to identify productivity-related challenges that can be addressed through effective supervision in construction. Meetings, discussions, workshops and surveys were conducted among construction experts to systematically develop the competencies of construction supervision. The necessary mapping models were used to identify the level of outcomes for each competency element along with the learning domains and programme outcomes.FindingsA curriculum guide model consisting of 64 competency elements has been introduced with corresponding assessment weightages and mapping outcomes. Using this model, a new training programme has been designed and tested with weightage percentages on learning domains.Research limitations/implicationsAlthough the scope of the study is limited to Sri Lanka, the findings can be interpreted for critical learning in other developing countries too.Practical implicationsThe study outcomes are expected to make a high impact on improving the standards of vocational training education in the country, thereby upgrading the current industry practices.Originality/valueThe developed guide model is expected to be a valuable tool for training providers/organisations in upgrading their programmes/practices with the scope of productivity improvement. The obtained mapping outcomes are significant for the evolving next normal situations in teaching, learning and assessment methods with regard to construction supervision practices.
Design and implementation of artificial magnetic conductor surface as decoupling structure in microstrip antenna arrays
Authors: Shaik Khader Zelani , P. Siddaiah , Prasad K. Satya 
Published: July 2021

PurposeMillimeter wave spectrum represents new opportunities to add capacity and faster speeds for next-generation services as fifth generation (5G) applications. In its Spectrum Frontiers proceeding, the Federal Communications Commision decided to focus on spectrum bands where the most spectrums are potentially available. A low profile antenna array with new decoupling structure is proposed and expected to resonate at higher frequency bands, i.e. millimeter wave frequencies, which are suitable for 5G applications.Design/methodology/approachThe presented antenna contains artificial magnetic conductor (AMC) surface as decoupling structure. The proposed antenna array with novel AMC surface is operating at 29.1GHz and proven to be decoupling structure and capable of enhancing the isolation by reducing mutual coupling as 8.7dB between the array elements. It is evident that, and overall gain is improved as 10.1% by incorporating 1x2 Array with AMC Method. Mutual coupling between the elements of 1 × 2 antenna array is decreased by 39.12%.FindingsThe proposed structure is designed and simulated using HFSS software and the results are obtained in terms of return loss, gain, voltage standing wave ratio (VSWR) and mutual coupling. The S-Parameters of each stage of design is tabulated and compared with each other to prove the decoupling capability of AMC surface in antenna arrays.Originality/valueThe proposed structure is designed and simulated using HFSS software, and the results are obtained in terms of return loss, gain, VSWR and mutual coupling. The S-Parameters of each stage of design is tabulated and compared with each other to prove the decoupling capability of AMC surface in antenna arrays.