bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-Wide Detection of Imprinted Differentially Methylated Regions Using Nanopore Sequencing
Authors: Akbari Vahid , Garant Jean-Michel , O’Neill Kieran , Pandoh Pawan , Moore Richard , Marra Marco A. , Hirst Martin , Jones Steven J.M. 
Published: July 2021

AbstractImprinting is a critical part of normal embryonic development in mammals, controlled by defined parent-of-origin (PofO) differentially methylated regions (DMRs) known as imprinting control regions. As we and others have shown, direct nanopore sequencing of DNA provides a mean to detect allelic methylation and to overcome the drawbacks of methylation array and short-read technologies. Here we leverage publicly-available nanopore sequence data for 12 standard B-lymphocyte cell lines to present the first genome-wide mapping of imprinted intervals in humans using this technology. We were able to phase 95% of the human methylome and detect 94% of the well-characterized imprinted DMRs. In addition, we found 28 novel imprinted DMRs (12 germline and 16 somatic), which we confirmed using whole-genome bisulfite sequencing (WGBS) data. Analysis of WGBS data in mus musculus, rhesus macaque, and chimpanzee suggested that 12 of these are conserved. We also detected subtle parental methylation bias spanning several kilobases at seven known imprinted clusters. These results expand the current state of knowledge of imprinting, with potential applications in the clinic. We have also demonstrated that nanopore long reads, can reveal imprinting using only parent-offspring trios, as opposed to the large multi - generational pedigrees that have previously been required.
Machine-learning-based predictions of caloric restriction associations across ageing-related genes
Authors: Vega-Magdaleno Gustavo Daniel , Bespalov Vladislav , Zheng Yalin , Freitas Alex A. , de Magalhaes Joao Pedro 
Published: July 2021

AbstractCaloric restriction (CR) is the most studied pro-longevity intervention; however, a complete understanding of its underlying mechanisms remains elusive, and new research directions may emerge from the identification of novel CR-related genes and CR-related genetic features. This work used a Machine Learning (ML) approach to classify ageing-related genes as CR-related or NotCR-related using 9 different types of predictive features: PathDIP pathways, two types of features based on KEGG pathways, two types of Protein-Protein Interactions (PPI) features, Gene Ontology (GO) terms, Genotype-Tissue Expression (GTEx) expression features, Gene-Friends co-expression features and protein sequence descriptors. Our findings suggested that features biased towards curated knowledge (i.e. GO terms and biological pathways), had the greatest predictive power, while unbiased features (mainly gene expression and co-expression data) have the least predictive power. Moreover, a combination of all the feature types diminished the predictive power compared to predictions based on curated knowledge. Feature importance analysis on the two most predictive classifiers mostly corroborated existing knowledge and supported recent findings linking CR to the Nuclear Factor Erythroid 2-Related Factor 2 (NRF2) signalling pathway and G protein-coupled receptors (GPCR). We then used the two strongest combinations of feature type and ML algorithm to predict CR-relatedness among ageing-related genes currently lacking CR-related annotations in the data, resulting in a set of promising candidate CR-related genes (GOT2, GOT1, TSC1, CTH, GCLM, IRS2 and SESN2) whose predicted CR-relatedness remain to be validated in future wet-lab experiments.
Probing the toxic interactions between the reactive dye Drimaren Red and Human Serum Albumin
Authors: Menezes Thaís Meira , de Assis Caio Rodrigo Dias , da Silva Neto Antônio Marinho , Gubert Priscila , Ghislandi Marcos Gomes , Neves Jorge Luiz 
Published: July 2021

ABSTRACTAzo dyes like Drimaren Red CL-5B (DR, CI Reactive Red 241) represent a class of compounds extensively used in the textile industry and are extremely dangerous to the environment and human health. Therefore, understanding the binding characteristics between such substances and biological macromolecules is essential from a toxic-kinetic perspective. The molecular interaction between DR and Human Serum Albumin (HSA) was investigated through spectroscopic techniques and molecular docking approaches. The results indicate that DR quenches HSA fluorescence following a static mechanism (corroborated by UV-Vis studies) with a moderate interaction (Ka~105 M−1), guided by electrostatic interactions (ΔS°> 0 and ΔH°< 0). DR is 5.52 nm distant from fluorophore residue Trp-214 (according to FRET investigations), and the interaction is mainly related to Tyr residues (as revealed by synchronous fluorescence). The Ellman assay identified a decrease in the content of HSA free thiol. The results of the RLS demonstrate that there are HSA alterations, suggesting damage to the confirmation of the protein. Molecular docking suggests the binding site of DR was located in subdomain IIB HSA, corroborating the experimental properties. Finally, the results suggest a high potential for DR toxicity triggered by contact with key proteins, which affects the biomolecule functionalities.
Amplification-free detection of viral RNA by super resolution imaging-based CRISPR/Cas13a System
Authors: He Qian , Chen Qun , Li Fang , Yuan Xi , Wang Chuhui , Liu Changyue , Xu Lidan , Zhong Xiaoyun , Wei Jiazhang , Pandey Vijay , Yu Dongmei , Dong Yuhan , Zhang Yongbing , Deng Lin , Du Ke , Qin Peiwu 
Published: July 2021

AbstractRNA detection is crucial for biological research and clinical diagnosis. The current methods include both direct and amplification-based RNA detection. These methods require complicated procedures, suffering from low sensitivity, slow turnaround, and amplification bias. The CRISPR/Cas13a system is a direct RNA detection method via target RNA induced collateral cleavage activity. However, to detect low concentration RNA with CRISPR/Cas13a, target amplification is always required. Herein, we optimize the components of the CRISPR/Cas13a assay to enhance the sensitivity of viral RNA detection which improve the detection limit from 1 pM up to 100 fM. In addition, the integration of CRISPR/Cas13a biosensing and single molecule super resolution imaging is a novel strategy for direct and amplification-free RNA detection. After surface modification, fluorescent RNA reporters are immobilized on the glass coverslip surface and fluorescent signals are captured by total internal reflection fluorescence microscopy (TIRFM), shifting the measurement from spectroscopy to imaging. We quantify the fluorescence signal intensity before and after collateral cleavage of the CRISPR system when viral RNA is present and achieve a detection limit of 10 fM. Therefore, we provide a novel TIRFM-based system to visualize the CRISPR trans-cleavage for direct and robust RNA detection.
Open access in silico tools to predict the ADMET profiling and PASS (Prediction of Activity Spectra for Substances of Bioactive compounds of Garlic (Allium sativum L.)
Authors: Ferrari Ivan Vito 
Published: July 2021

AbstractBackgroundGarlic (Allium sativum L.) is a common spice with many health benefits, mainly due to its diverse bioactive compounds, (see below) such as organic sulphides, saponins, phenolic compounds, and polysaccharides. Several studies have demonstrated its functions such as anti-inflammatory, antibacterial, and antiviral, antioxidant, cardiovascular protective and anticancer property. In this work we have investigated the main bioactive components of garlic through a bioinformatics approach. Indeed, we are in an era of bioinformatics where we can predict data in the fields of medicine. Approaches with open access in silico tools have revolutionized disease management due to early prediction of the absorption, distribution, metabolism, excretion, and toxicity (ADMET) profiles of the chemically designed and eco-friendly next-generation drugs.MethodsThis paper encompasses the fundamental functions of open access in silico prediction tools, as PASS database (Prediction of Activity Spectra for Substances) that it estimates the probable biological activity profiles for compounds. This paper also aims to help support new researchers in the field of drug design and to investigate best bioactive compounds in garlic.Resultsscreening through each of pharmacokinetic criteria resulted in identification of Garlic compounds that adhere to all the ADMET properties.ConclusionsIt was established an open-access database (PASS database, available bioinformatics tool SwissADME, PreADMET pkCSM database) servers were employed to determine the ADMET (metabolism, distribution, excretion, absorption, and toxicity) attributes of garlic molecules and to enable identification of promising molecules that follow ADMET properties.Graphical abstract
TAF4b transcription networks regulating early oocyte differentiation
Authors: Gura Megan A. , Relovska Sona , Abt Kimberly M. , Seymour Kimberly A. , Wu Tong , Kaya Haskan , Turner James M. A. , Fazzio Thomas G. , Freiman Richard N. 
Published: July 2021

ABSTRACTEstablishment of a healthy ovarian reserve is contingent upon numerous regulatory pathways during embryogenesis. Previously, mice lacking TBP-associated factor 4b (Taf4b) were shown to exhibit a diminished ovarian reserve. However, potential oocyte-intrinsic functions of TAF4b have not been examined. Here we use a combination of gene expression profiling and chromatin mapping to characterize the TAF4b gene regulatory network in mouse oocytes. We find thatTaf4b-deficient oocytes display inappropriate expression of meiotic, chromatin, and X-linked genes, and unexpectedly we found a connection with Turner Syndrome pathways. Using Cleavage Under Targets and Release Using Nuclease (CUT&RUN), we observed TAF4b enrichment at genes involved in meiosis and DNA repair, some of which are differentially expressed inTaf4b-deficient oocytes. Interestingly, TAF4b target genes were enriched for Sp/KLF family motifs rather than TATA-box, suggesting an alternate mode of promoter interaction. Together, our data connects several gene regulatory nodes that contribute to the ovarian reserve.
Natural immunity against COVID-19 significantly reduces the risk of reinfection: findings from a cohort of sero-survey participants
Authors: Mishra Bijaya Kumar , Bhattacharya Debdutta , Kshatri Jaya Singh , Pati Sanghamitra 
Published: July 2021

AbstractConflicting reports on the persistence of antibody levels in individuals recovered from COVID-19 infection, suggest that the immunity against COVID-19 may not be lasting for long. In India, by 30th June, 2021, not less than 30 million people were infected with COVID-19 and 0.39 million people were reported to have lost their life to the disease in India. I the current study we followed up with a subsample of our previous sero-survey participants to assess whether natural immunity against SARS-CoV-2 was associated with a reduced risk of re-infection. We conducted telephonic interview of a total of 3038 participants, out of which 2238 participants responded and 5 participants were found to be not alive, as conveyed by their close relatives. There was a non-response rate of 26.1%. Out of the 2238 participants, 1170 were sero-positive and 1068 were sero-negative for antibody against COVID-19. Our survey found that only 3 individuals in the sero-positive group got infected with COVID-19 whereas 127 individuals reported contracting the infection the sero-negative group. Interestingly, from the 127 sero-negative individuals who later contracted COVID-19 infection, 30 needed hospitalization, out of which 12 were on oxygen therapy, four in ICU and one was on ventilator. At the other hand, from the 3 sero-positives re-infected with COVID-19, one had hospitalization, but didnnot require oxygen support or critical care. These findings reinforce the strong plausibility that development of antibody following natural infection not only protects against re-infection by the virus to a great extent, but also safeguards against progression to severe COVID-19 disease.
New Zealand study of not-for-profit (NFP) shows high degree of employee involvement doesn't produce results without strong HRM policies
Authors: Smith David 
Published: July 2021

Purpose
There is a growing interest in employee involvement as a means to enhance commitment and wellbeing. Typically, there is a degree of power sharing in decisions at all levels. In large organizations, the strategy has been shown to deliver benefits. The authors wanted to study the themes in a small NFP.

Design/methodology/approach
The authors chose an extreme case of a small NFP organized on democratic lines but with only informal HRM policies. They felt an extreme case would be instructive. The organization, which they gave the pseudonym OA, is a small non-profit agency that offers education around sexual violence and advice and support to survivors. As a collective, it involves everyone in decision-making. The lead author carried out the detailed study over six months based in the office. It involved formal interviews with six existing employees and six ex-employees, or volunteers, as well as a clinical supervisor.

Findings
The study showed that without systematic and strategic HRM policies, strong forms of employee participation won’t deliver higher levels of equity. Although the NFP in the study operated as a collective, it lacked even basic HR policies. The consequences included poor management, high turnover, burnout and inadequate training.

Originality/value
The authors said the results showed that small size and organizational commitment did not always support effective employee participation. Weak HR policies made the problems of poor communication and decision-making worse and caused a lot of stress. As a result, the high turnover impacted performance. The findings add a note of caution to existing findings about employee participation. In fact, perversely, it can even lead to worse outcomes. Arguably, they say, HRM is even more essential in a small NFP environment because of the structural constraints and lack of funding.
Analytical hierarchy processes and Pareto analysis for mitigating cybercrime in the financial sector
Authors: Akinbowale Oluwatoyin Esther , Klingelhöfer Heinz Eckart , Zerihun Mulatu Fekadu 
Published: July 2021

Purpose
The purpose of this study is to use a decision support model based on the Analytical Hierarchy Process (AHP) and Pareto analysis (PA) for ranking the impact of different kinds of cybercrime in organisations in the financial sector to support decisions on cybercrime mitigation.

Design/methodology/approach
From a structured questionnaire to the staff of 17 licensed banks in South Africa in charge of management, administration and operations, the perceived effect of cybercrime on the organisation’s goals, namely, organisation’s profitability, goodwill, customers’ satisfaction and risk management was derived. The pairwise comparison of the organisation’s goals and identified forms of cybercrime was done using the AHP.

Findings
The results obtained indicate that there was a consensus (100% of the answers) that the effect of cybercrime has negatively impacted the organisation’s objectives profitability and goodwill. Also, still 95.23% of the respondents agreed that the effect of cybercrime has negatively impacted the level of customers’ satisfaction, while only 7.15% saw an impact on the organisation’s risk management processes. Using these results in the AHP, analysis delivers a hierarchical order about the relevance of prevalent forms of cybercrime for the organisation´s cybercrime mitigation. The PA further shows the magnitude of the forms of cybercrime relative to each other.

Practical implications
Hence, this study provides a decision support framework for organisational management in the quest to explore the impact of cyber fraud. It can serve as a practical guided approach for the application of AHP analysis for the existing and emerging forms of cybercrime.

Originality/value
The novelty of this study lies in the fact that the combination of the AHP and PA to support solving a multi-criteria decision problem relating to the prevalence of cybercrime has not been sufficiently highlighted by the existing literature.
Completeness of the qualitative characteristics using Foucauldian critical discourse analysis and content analysis paradigms: towards a revised conceptual framework
Authors: Evans Gareth , Lusher Joanne , Day Stephen 
Published: July 2021

Purpose
The qualitative characteristics of decision-useful financial information (as set out in the revised March 2018 Conceptual Framework for financial reporting of the International Accounting Standards Board [IASB]) are fundamental for standard setting relied on by companies when making accounting policy changes and choices. However, there has not been an overarching universally agreed conceptual context of the qualitative characteristics. This paper aims to study the completeness of the qualitative characteristics towards suggesting a revision of the Conceptual Framework.

Design/methodology/approach
The present study evaluated the completeness of these qualitative characteristics using Foucauldian critical discourse analysis and content analysis paradigms to elucidate the inclusion conundrum. Foucauldian analysis allowed focus on power relationships, governmentality and subjectification in accounting society, as expressed through language and practices of the IASB who ultimately decide on the qualitative characteristics. Content analysis was used to analyse data collected via interviews with preparers and users of banks’ accounts, changes in banks’ accounting policies after the conceptual framework was published and comment letters from banks who wrote to the IASB.

Findings
Novel findings from this study revealed the potential significant omissions of the constraints of “materiality”, “transparency” and “regulatory/supervisory framework”. Also, surrounding the qualitative characteristics having been shown to be valid and includable, the adjective “decision-useful” reinstated in the chapter title and the IASB project team technical writers needing to show completeness of attention to all comments.

Originality/value
From these findings, a freshly formulated chapter in the conceptual framework on the qualitative characteristics can now be submitted for consideration by the IASB, with potential for international post-implementation review.
Pracademia: an answer but not the answer to an enduring question
Authors: Eacott Scott 
Published: July 2021

PurposeThe pracademia movement is gaining increasing traction in education, particularly in educational leadership. Offered as a means to bridge practice and academia, questions remain as to whether it resolves or perpetuates the theory–practice divide. This paper systematically approaches this problem.Design/methodology/approachTheoretically informed by the relational approach, this conceptual paper articulates the preliminaries and underlying assumptions of pracademia before exploring the implications for the field of educational leadership.FindingsHaving established the underlying assumptions, this paper offers three standards – description, explanation and alternative – for assessing knowledge claims in the field that does not default to distinct knowledge worlds (e.g. academic, practice) or categories of knowledge generators (e.g. academics, practitioners, pracademics).Originality/valueThrough a relational approach, this work breaks down the boundaries of theory and practice to offer a new way of thinking about knowledge claims. The new approach is consistent with the intent of bridging theory and practice without the need to assume them to be separate in the first place.
A conceptual framework for an agile asset performance management process
Authors: Karar Ahmed Noaman , Labib Ashraf , Jones Dylan Francis 
Published: July 2021

PurposeDisturbances in terms of major crises such as pandemics, fluctuations in demand and oil price, energy consumption and supply chain can significantly impair the maintenance programs effectiveness and efficiency. Hence, there is an urgent need for an agile asset performance management (AAPM) framework.Design/methodology/approachThis paper's main objective is to design a comprehensive framework for an AAPM system that sustains the desired asset performance by reacting efficiently, quickly and intelligently to the changes in the operating context parameters and asset health conditions. Such a framework is adaptive to changes in scenarios and aims to systematise the decision support process, considering different objectives.FindingsThe development of the proposed framework has led to identifying an innovative way of seamless integration between crucial reliability and asset management tools. Also, the methodology implementation is expected to promote the practical use of its reliability tools and enable asset stakeholders to break silo working for clear communication around asset performance.Originality/valueThe implementation of the AAPM framework follows a new approach developed during this research and coined by the authors as the “8S approach.”
Effects of V/III ratio of InGaN quantum well at high growth temperature for near ultraviolet light emitting diodes
Authors: Md Sahar Mohd Ann Amirul Zulffiqal , Hassan Zainuriah , Ng Sha Shiong , Lim Way Foong , Lau Khai Shenn , Alias Ezzah Azimah , Ahmad Mohd Anas , Hamzah Nur Atiqah , Mohd Asri Rahil Izzati 
Published: July 2021

Purpose
The aims of this paper is to study the effects of the V/III ratio of indium gallium nitride (InGaN) quantum wells (QWs) on the structural, optical and electrical properties of near-ultraviolet light-emitting diode (NUV-LED).

Design/methodology/approach
InGaN-based NUV-LED is successfully grown on the c-plane patterned sapphire substrate at atmospheric pressure using metal organic chemical vapor deposition.

Findings
The indium composition and thickness of InGaN QWs increased as the V/III ratio increased from 20871 to 11824, according to high-resolution X-ray diffraction. The V/III ratio was also found to have an important effect on the surface morphology of the InGaN QWs and thus the surface morphology of the subsequent layers. Apart from that, the electroluminescence measurement revealed that the V/III ratio had a major impact on the light output power (LOP) and the emission peak wavelength of the NUV-LED. The LOP increased by up to 53% at 100 mA, and the emission peak wavelength of the NUV-LED changed to a longer wavelength as the V/III ratio decreased from 20871 to 11824.

Originality/value
This study discovered a relation between the V/III ratio and the properties of QWs, which resulted in the LOP enhancement of the NUV-LED. High TMIn flow rates, which produced a low V/III ratio, contribute to the increased LOP of NUV-LED.