bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic rearrangements of mobile genetic elements associated with carbapenem resistance of Acinetobacter baumannii
Authors: Vijayakumar Saranya , John Jobin Jacob , Vasudevan Karthick , Mathur Purva , Ray Pallab , Neeravi Ayyanraj , Baskaran Asthawarthani , Kirubananthan Agilandeeswari , Anandan Shalini , Biswas Indranil , Walia Kamini , Veeraraghavan Balaji 
Published: February 2022

AbstractWith the excessive genome plasticity, Acinetobacter baumannii has the capability to acquire and disseminate antimicrobial resistance genes that are often associated with mobile genetic elements (MGE). Analyzing the genetic environment of resistance genes often provides valuable information on the origin, emergence, evolution and spread of resistance. Thus, we characterized the genomic features of some clinical isolates of carbapenem-resistant A. baumannii to understand the role of diverse MGE and their genetic context that are responsible for the dissemination of carbapenem resistance genes. For this, a total of 17 clinical isolates of A. baumannii obtained from multiple hospitals in India between the years 2018 and 2019 were analysed. Antimicrobial resistance determinants, genetic context of resistance genes and molecular epidemiology were studied using whole genome sequencing. A high prevalence of blaOXA-23 was observed followed by the presence of dual carbapenemase, blaOXA-23 and blaNDM. Three novel Oxford sequence types were identified. Majority of the isolates belonged to dominant clone, IC2 followed by less prevalent clones such as IC7 and IC8. Complex diverse AbaR4 like and AbGRI-like islands belonging to IC2 lineage were identified. To the best of our knowledge, this is the first study that provides a comprehensive profiling of resistance islands along with the MGE, acquired antimicrobial resistance genes and the distribution of clonal lineages of carbapenem resistant A. baumannii from India.
Mesenchymal-epithelial transition in lymph node metastases of oral squamous cell carcinoma is accompanied by ZEB1 expression
Authors: Horny Kai , Sproll Christoph , Peiffer Lukas , Furtmann Frauke , Gerhardt Patricia , Gravemeyer Jan , Stoecklein Nikolas H. , Spassova Ivelina , Becker Jürgen C. 
Published: February 2022

AbstractBackgroundOral squamous cell carcinoma (OSCC), an HPV-negative head and neck cancer, frequently metastasizes to the regional lymph nodes but only occasionally beyond. Initial phases of metastasis are associated with an epithelial-mesenchymal transition (EMT), the consolidation phase is associated with mesenchymal-epithelial transition (MET). This dynamic is referred to as epithelial-mesenchymal plasticity (EMP). While it is known that EMP is essential for cancer cell invasion and metastatic spread, less is known about the heterogeneity of EMP states within a tumor and even less about the heterogeneity between the primary and metastatic lesions.MethodsTo capture heterogeneity of EMP states in OSCC, we performed single-cell RNA sequencing (scRNAseq) of 5 primary tumors and 9 matching lymph node metastases and re-analyzed publicly available scRNAseq data of 9 additional primary tumors. To account for possible bias in cell type compositions by scRNAseq, these were also deconvoluted from bulk transcriptome analyses. Protein expression of selected genes were confirmed by immunohistochemistry.ResultsFrom the 23 OSCC lesions the single cell transcriptome of a total of 7,263 carcinoma cells was available for in-depth analyses. We initially focused on one lesion to avoid inter-patient heterogeneity as a confounding factor and identified OSCC cells expressing genes characteristic of different epithelial and partial EMT stages, such as keratins and SPRR1B (cornifin B) or vimentin and matrix metallopeptidases. RNA velocity information together with the increase in inferred copy number variations indicated a progressive trajectory towards epithelial differentiation in this metastatic lesion. Extension to all samples revealed a less stringent but essentially similar pattern. Interestingly, cells undergoing MET show increased activity of the EMT activator ZEB1. Immunohistochemistry confirmed that ZEB1 was co-expressed with the epithelial marker cornifin B in individual tumor cells - more frequently in lymph node metastases. The lack of E-cadherin mRNA expression suggests this is a partial MET.ConclusionsThis study reveals that EMP enables different partial EMT and epithelial phenotypes of OSCC cells, which are endowed with capabilities essential for the different stages of the metastatic process, including maintenance of cellular integrity. During MET, ZEB1 appears to be functionally active, indicating a more complex role of ZEB1 than mere induction of EMT.
Cytocapsulae and cytocapsular tubes are golden targets for precise, effective and efficient cancer diagnosis and therapy in 307 kinds of liquid and solid cancers
Authors: Yi Tingfang , Wagner Gerhard 
Published: February 2022

AbstractCancer is a leading cause of human lethality worldwide. A cancer cell is not only the cytoplasm and nucleus enclosed in the cell membrane. A malignant tumor is not only a mass of cancer cells. Cancer in a patient is not only isolated tumors distributed in tissues and organs. The comprehensive understanding of the complete structural compartments and their biological functions of cancer cells, malignant tumors and tumor systems in patients in vivo is an indispensable prerequisite for effective drug development and efficient clinical cancer pharmacotherapies. However, there remains an open question for a long time: what are the complete structural compartments of cancer cells, malignant tumors and tumor systems in the patient body? Here, we comprehensively and systematically investigated the complete structural compartments of cancer cells, malignant tumors and cytocapsular tube (CCT) network-tumor system (CNTS) of 307 types/subtypes of cancers in 33 kinds of tissues and organs by biochemistry and molecular biology assays with 9,811 clinical cancer tissue specimens from 9,637 cancer patients and >110,000 immunohistochemistry (IHC) fluorescence staining images. We discovered the complete structural compartments of cancer cells, malignant tumors and CNTSs in 307 kinds of cancers, elucidated mechanisms of cytocapsular growth and CCT elongation, and identified the comprehensive procedures of cancer evolution in patients. This study paves avenues for curing all kinds of cancers.
Force sensing on cells and tissues by atomic force microscopy
Authors: Holuigue Hatice , Lorenc Ewelina , Chighizola Matteo , Schulte Carsten , Varinelli Luca , Deraco Marcello , Guaglio Marcello , Gariboldi Manuela , Podestà Alessandro 
Published: February 2022

AbstractBiosensors are aimed to detect tiny physical and chemical stimuli in biological systems. Physical forces are ubiquitous, being implied in all cellular processes, including cell adhesion, migration, and differentiation. Given the strong interplay between cells and their microenvironment, the extracellular matrix (ECM), the structural and mechanical properties of the ECM play an important role in the transmission of external stimuli to single cells within the tissue. Vice versa, also cells themselves use self-generated forces to probe the biophysical properties of the ECM. ECM mechanics influences cell fate, regulates tissue development and show peculiar features in health and disease conditions of living organisms. Force sensing in biological systems is therefore crucial to dissect and understand complex biological processes, such as mechanotransduction.Atomic Force Microscopy (AFM), which can both sense and apply forces at the nanoscale, with sub-nanoNewton sensitivity, represents an enabling technology and a crucial experimental tool in biophysics and mechanobiology.In this work, we report on the application of AFM to study of biomechanical fingerprints of different components of biological systems, such as the ECM, the whole cell, and cellular components, like the nucleus and the glycocalyx. We show that physical observables like the (spatially resolved) Young’s modulus of elasticity of ECMs or cells, and the effective thickness and stiffness of the glycocalyx, can be quantitatively characterised by AFM. Their modification can be correlated to changes of the microenvironment, physio-pathological conditions, or gene regulation.
Beyond G1/S regulation: How cell size homeostasis is tightly controlled throughout the cell cycle?
Authors: Liu Xili , Yan Jiawei , Kirschner Marc W. 
Published: February 2022

AbstractTo achieve a stable mass distribution over multiple generations, proliferating cells require some means of counteracting stochastic noise in the rate of growth, the time spent in the cell cycle, and the imprecision of the equality of cell division. In the most widely accepted model, cell size is thought to be regulated at the G1/S transition, such that cells smaller than a critical size pause at the end of G1 phase until they have accumulated mass to a predetermined size threshold, at which point the cells proceed through the rest of the cell cycle. However, a model, based solely on a specific size checkpoint at G1/S, cannot readily explain why cells with deficient G1/S control mechanisms are still able to maintain a very stable cell mass distribution. Furthermore, such a model would not easily account for how stochastic variation in cell mass during the subsequent phases of the cell cycle can be anticipated at G1/S. To address such questions, we applied computationally enhanced Quantitative Phase Microscopy (ceQPM) to populations of proliferating cells, which enables highly accurate measurement of cell dry mass of individual cells throughout the cell cycle. From these measurements we can evaluate the factors that contribute to cell mass homeostasis at any point in the cell cycle. Our findings reveal that cell mass homeostasis is accurately maintained, despite disruptions to the normal G1/S machinery or perturbations in the rate of cell growth. Control of cell mass accumulation is clearly not confined to the G1/S transition but is instead exerted throughout the cell cycle. Using several mammalian cell types, we find that the coefficient of variation in dry mass of cells in the population begins to decline well before the G1/S transition and continues to decline throughout S and G2 phases. Among the different cell types tested, the detailed response of cell growth rate to cell mass differs. However, in general, when it falls below that for exponential growth, the natural increase in the coefficient of variation of cell mass is effectively constrained. We find that both size-dependent cell cycle regulation and size-dependent growth rate modulation contribute to reducing cell mass variation within the population. Through the interplay and coordination of these two processes, accurate cell mass homeostasis emerges. Such findings reveal previously unappreciated and very general principles of cell size control in proliferating cells. These same regulatory processes might also be operative in terminally differentiated cells. Further quantitative dynamical studies should lead to a better understanding of the underlying molecular mechanisms of cell size control.
GWAShub: A Web-based Resource to Democratize Genome-Wide Association Studies in Crop Plants
Authors: Daware Anurag , Srivastava Rishi , Das Durdam , Malik Naveen , Tyagi Akhilesh K. , Parida Swarup K. 
Published: February 2022

AbstractGenome-wide association study (GWAS) is a popular approach for linking natural genetic variation with phenotype variation and thus is central to crop quantitative genetics. The ever-increasing wealth of publicly available genomic sequence information for crop plants presents an unprecedented opportunity for utilizing GWAS for the identification of genes governing a plethora of agronomic traits. However, the lack of technical expertise and computational infrastructure is still hindering the ability of plant breeders to conduct GWAS in a self-reliant manner. Here, we present a GWAShub web server that provides a user-friendly interface for performing comprehensive GWAS and post-GWAS in crop plants utilizing publicly available genomic sequence variation data, comprehensive annotation data and diverse computational tools. The utility of GWAS-hub was further demonstrated by conducting large-scale GWAS for flowering/maturity time traits in chickpea. This analysis identified three different flowering/maturity time associated genes, all encoding different histone methyltransferases. Thus, epigenetic regulation is identified as vital mechanism regulating flowering time and maturity duration in chickpea. Finally, we hope GWAShub (www.gwashub.com) will enable resource-scarce researchers to join the GWAS revolution fueled by advancements in next-generation sequencing and computational genomics
Affective arousal explains infant gaze following under various social context
Authors: Ishikawa Mitsuhiko , Senju Atsushi , Kato Masaharu , Itakura Shoji 
Published: February 2022

AbstractGaze following is fundamental to human sociocognitive development, such as language and cultural learning. Previous studies have revealed that infant gaze following is not a reflexive orienting to adult’s eye movement. Instead, infants adaptively modulate gaze following behaviour depending on social contexts. However, the neurophysiological mechanisms underlying contextual modulation of gaze following remain unclear. We tested whether contextual modulation of infant gaze following is mediated by the infants’ heart rate, which is hypothesised to indicate the calculation of action value. Forty-one 6- to 9-month-old infants participated in this study. Infants observed either a reliable face, which gazed toward the location of an object, or an unreliable face, which gazed away from the location of an object. Then, the infants watched a video of the same model making eye contact or not showing any ostensive signals, before shifting her gaze toward one of two objects. We revealed that reliability and eye contact independently increased heart rates, which then fully mediate the effect of these social cues on the frequency of infant gaze following. Results suggest that each social cue independently enhances physiological arousal which then accumulatively predicts the likelihood of infant gaze following behaviour.
Low-power and low-energy CNFET-based approximate full adder cell for image processing applications
Authors: Safaei Mehrabani Yavar , Maleknejad Mojtaba , Rostami Danial , Uoosefian HamidReza 
Published: February 2022

Purpose
Full adder cells are building blocks of arithmetic circuits and affect the performance of the entire digital system. The purpose of this study is to provide a low-power and high-performance full adder cell.

Design/methodology/approach
Approximate computing is a novel paradigm that is used to design low-power and high-performance circuits. In this paper, a novel 1-bit approximate full adder cell is presented using the combination of complementary metal-oxide-semiconductor, transmission gate and pass transistor logic styles.

Findings
Simulation results confirm the superiority of the proposed design in terms of power consumption and power–delay product (PDP) criteria compared to state-of-the-art circuits. Also, the proposed full adder cell is applied in an 8-bit ripple carry adder to accomplish image processing applications including image blending, motion detection and edge detection. The results confirm that the proposed cell has premier compromise and outperforms its counterparts.

Originality/value
The proposed cell consists of only 11 transistors and decreases the switching activity remarkably. Therefore, it is a low-power and low-PDP cell.
MHD flow of a nanofluid due to a nonlinear stretching/shrinking sheet with a convective boundary condition: Tiwari–Das nanofluid model
Authors: Khan Umair , Zaib Aurang , Pop Ioan , Waini Iskandar , Ishak Anuar 
Published: February 2022

Purpose
Nanofluid research has piqued the interest of scientists due to its intriguing applications in nanoscience, biomedical and electrical engineering, medication delivery, biotechnology, food processing, chemotherapy and other fields. This paper aims to inspect the behavior of the mixed convection magnetohydrodynamic flow and heat transfer induced by a nonlinear stretching/shrinking sheet in a nanofluid with a convective boundary condition. Tiwari and Das mathematical nanofluid model is incorporated in the analysis.

Design/methodology/approach
The mathematical model is initially transformed to a nondimensional form by using dimensionless variables. Then the nondimensional partial differential equations are further transformed to a set of similarity equations by using the similarity technique. These equations are solved numerically by the bvp4c function in MATLAB software.

Findings
For a certain range of the stretching/shrinking parameter, two solutions are obtained. The friction factor and the heat transfer rate escalate due to suction parameter with adding nanoparticles volume fraction by almost 27.15% and 0.153% for the upper branch solution, while the friction factor declines by almost 30.10% but the heat transfer rate augments by 0.145% for the lower branch solution. Furthermore, the behavior of the nanoparticle volume fractions on the heat transfer rate behaves differently in the presence of the mixed convection effect. The temperature of fluid augments with increasing Biot number for both solutions.

Originality/value
The present work considers the flow and heat transfer induced by a stretching/shrinking sheet in a nanofluid using the Tiwari–Das nanofluid model with a convective boundary condition, where the effect of the buoyancy force is taken into consideration. It is shown that two solutions are found for a certain range of the shrinking strength, while the solution is unique for the stretching case. This study is important for scientists working in the growing field of nanofluids to become familiar with the flow properties and behaviors of such nanofluids.
SME financing through public equity: review of the Indian SME exchanges
Authors: Ghalke Avinash , Kumar Satish , Rao S.V.D. Nageswara 
Published: February 2022

Purpose
Timely access to reasonably priced financing is critical to promote and sustain small and medium sized businesses (SMEs). This study aims to examine the role of the newly constituted SME exchanges in funding the growth of Indian SME firms. The impact of obtaining public equity capital on the firm’s growth prospects, capital structure and credit profile is the focus of this paper. In addition, this study compares the cost and speed of raising capital on specialised SME exchanges to the main board.

Design/methodology/approach
To examine the impact of raising public equity capital, this study uses a difference-in-difference (DID) regression analysis. SMEs that raised financing on the SME exchange between 2013 and 2018 make up the treatment sample. This study uses a propensity score matching technique to find the control group from a sample of unlisted enterprises to reduce the likelihood of selection bias.

Findings
This study finds that SME profitability drops after an initial public offering (IPO), which is consistent with previous research. This study also discovered that after a company is listed, its total debt falls. This study also shows that after the IPO, there is no change in the borrowing costs of SME enterprises. Finally, this study finds an evidence of a decline in sales growth following the IPO, implying that the firms use the IPO money to rebalance their accounts after a period of heavy investment rather than for growth finance.

Originality/value
A thriving and efficient equity financing market for SMEs has the potential to establish itself as a viable alternative to the existing dominant bank financing option. To the best of the authors’ knowledge, this research is the first to examine the role of SME exchanges in the funding of Indian SME firms.
The contribution of case-based learning to adopting a multidimensional view in educational leadership students
Authors: Shaked Haim 
Published: February 2022

PurposeAdopting a multidimensional view is a characteristic of systems thinking in school leadership, which involves recognizing that each component of the school system necessarily has more than one cause, result or solution. This study explores how case-based learning has contributed to the development of adopting a multidimensional view in educational leadership students.Design/methodology/approachThe present study was qualitative in nature. Study participants were 32 graduate students from an Israeli college of education who participated in case-based learning held in a 14-session course. The data collected for this study included journal entries written by these students after each session. Overall, 318 journal entries were analyzed through a four-step process: sorting, coding, categorizing and theorizing.FindingsData analysis indicated three aspects of adopting a multidimensional view developed through case-based learning: acquiring a principal's perspective, recognizing other schools' perspectives and exposure to other individuals' perspectives.Originality/valueThis study joins other recent efforts to find ways to develop influential educational leaders, suggesting that case-based learning contributes to the development of adopting a multidimensional view in educational leadership students.