bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolic predictors of phenotypic traits can replace and complement measured clinical variables in transcriptome-wide association studies
Authors: Niehues Anna , Bizzarri Daniele , Reinders Marcel J.T. , Slagboom P. Eline , van Gool Alain J. , van den Akker Erik B. , ’t Hoen Peter A.C. ,   the BBMRI-NL BIOS and Metabolomics Consortia
Published: February 2022

AbstractTranscriptome-wide association studies (TWAS) can provide valuable insights into biological and disease-underlying mechanisms. For studying clinical effects, availability of (confounding) phenotypic traits is essential. The (re)use of RNA-seq or other omics data can be limited by missing, incomplete, or inaccurate phenotypic information. A possible solution are molecular predictors inferring clinical or behavioral phenotypic traits. Such predictors have been developed based on different omics data types and are being applied in various studies.In this study, we applied 17 metabolic predictors to infer various traits, including diabetes status or exposure to lipid medication. We evaluated whether these metabolic surrogates can be used as an alternative to reported information for studying the respective phenotypes using TWAS. Our results revealed that in most cases, the use of metabolic surrogates yields similar results compared to using reported information, making them suitable substitutes for such studies.The application of metabolomics-derived surrogate outcomes opens new possibilities for reuse of multi-omics data sets, especially in situations where availability of clinical metadata is limited. Missing or incomplete information can be complemented by these surrogates, thereby increasing the size of available data sets. Studies would likely also benefit from the use of such surrogates to correct for potential biological confounding. This should be further investigated.Author summaryTranscriptome-wide association studies (TWAS) can be used to associate gene expression levels with phenotypic traits. These associations can provide insights into biological mechanisms including those that underlie diseases. Such studies require molecular profiling data from a large number of individuals as well as information on the phenotypic trait of interest. Biobanks that collect samples and corresponding molecular data, also collect information on phenotypic traits or clinical information. However, this information can be heterogeneous and/or incomplete, or a certain piece of information could be missing entirely. In this study, we apply metabolic predictors to infer various traits, including diabetes status or exposure to lipid medication. We evaluate whether these metabolic surrogates can be used as an alternative to reported information for studying the respective phenotypes using TWAS. Our results reveal that in many cases, the use of metabolic surrogates yields similar results compared to using reported information, making them suitable substitutes for such studies. The possibility of using these surrogate outcomes can thus increase the size of data sets for studies where phenotypic information is incomplete or missing.
Aucubin promoted neuron functional recovery by suppressing inflammation and neuronal apoptosis in a spinal cord injury model
Authors: Xiao Shining , Zhong Nanshan , Yang Quanming , Li Anan , Tong Weilai , Zhang Yu , Yao Geliang , Wang Shijiang , Liu Jiaming , Liu Zhili 
Published: February 2022

AbstractSpinal cord injury (SCI) can cause severe motor impairment. Post-SCI treatment has focused primarily on secondary injury, with neuroinflammation and neuronal apoptosis as the primary therapeutic targets. Aucubin (Au), a Chinese herbal medicine, exerts anti-inflammatory and neuroprotective effects. The therapeutic effects of Au in SCI have not been reported. We showed that Au can promote functional recovery after SCI. Recovery may occur through the toll-like receptor 4 (TLR4)/nuclear factor kappa B (NF-κB) pathway to promote M2/M1 polarization in microglia and inhibit mitochondrial dysfunction to reduce neuronal apoptosis. These biochemical changes result in reduced secondary injury and facilitate axon regeneration. Therefore, Au may be a promising post-SCI therapeutic medication.
Assessing functional connectivity differences and work-related fatigue in surviving COVID-negative patients
Authors: Hafiz Rakibul , Gandhi Tapan Kumar , Mishra Sapna , Prasad Alok , Mahajan Vidur , Natelson Benjamin H. , Di Xin , Biswal Bharat B. 
Published: February 2022

AbstractThe Coronavirus Disease 2019 (COVID-19) has affected all aspects of life around the world. Neuroimaging evidence suggests the novel coronavirus can attack the central nervous system (CNS), causing cerebro-vascular abnormalities in the brain. This can lead to focal changes in cerebral blood flow and metabolic oxygen consumption rate in the brain. However, the extent and spatial locations of brain alterations in COVID-19 survivors are largely unknown. In this study, we have assessed brain functional connectivity (FC) using resting-state functional MRI (RS-fMRI) in 38 (25 males) COVID patients two weeks after hospital discharge, when PCR negative and 31 (24 males) healthy subjects. FC was estimated using independent component analysis (ICA) and dual regression. When compared to the healthy group, the COVID group demonstrated significantly enhanced FC in thebasal gangliaandprecuneusnetworks (family wise error (fwe) corrected,pfwe< 0.05), while, on the other hand, reduced FC in thelanguagenetwork (pfwe< 0.05). The COVID group also experienced higher fatigue levels during work, compared to the healthy group (p < 0.001). Moreover, within theprecuneusnetwork, we noticed a significant negative correlation between FC and fatigue scores across groups (Spearman’s ρ = - 0.47, p = 0.001, r2= 0.22). Interestingly, this relationship was found to be significantly stronger among COVID survivors within the leftparietal lobe, which is known to be structurally and functionally associated with fatigue in other neurological disorders.Significance StatementEarly neuroimaging studies have mostly focused on structural MRI imaging to report brain abnormalities in acutely ill COVID-19 patients. It is not clear whether functional abnormalities co-exist with structural alterations in patients who have survived the infection and have been discharged from the hospital. A few recent studies have emerged which attempted to address the structural/functional alterations. However, further investigations across different sites are necessary for more conclusive inference. More importantly, fatigue is a highly prevalent symptom among COVID survivors, therefore, the relations of brain imaging abnormalities to fatigue should be investigated. In this study, we try to address these gaps, by collecting imaging data from COVID survivors, now PCR negative, and healthy subjects from a single site – the Indian Institute of Technology (IIT), Delhi, India. Furthermore, this is a continuation of an ongoing study. We have recently shown structural abnormalities and stronger gray matter volume (GMV) correlates of self-reported fatigue in this group of COVID survivors compared to healthy subjects (Hafiz et al., 2022).
CRISPR-based multi-locus real-time tracking reveals single chromosome dynamics and compaction
Authors: Chung Yu-Chieh , Bisht Madhoolika , Tu Li-Chun 
Published: February 2022

AbstractIn eukaryotic nuclei, individual chromosomes occupy discrete three-dimensional spaces with little overlap. Dynamic chromatin organization instantly influences DNA accessibility through modulating local macromolecular density and interactions, driving changes in transcription activities. Chromatin anchoring to nuclear landmarks often leads to massive reorganization and motion changes. Chromatin dynamics has been reported to be locally confined but contributes to the large-scale coherent chromatin motion across the entire nucleus. However, the dynamics and compaction of chromosomal sub-regions along a single chromosome are not well-understood. In this study, we combined quantitative real-time single-molecule fluorescence microscopy, CRISPR-based genomic labeling, biophysical analysis and polymer models to characterize the dynamics of specific genomic loci and chromatin-nuclear landmark interactions on human chromosome 19 in living cells. Precise genomic labeling allows us to dissect loci motions and chromatin elasticity on a single chromosome basis. We found that the dynamics of genomic loci were all subdiffusive but varied at different regions along the chromosome. The mobility of genomic loci was similar among interior chromosomal loci but deviated for the loci at pericentromeric and near-telomeric regions. Tighter compaction on chromosome 19 long arm, compared to the short arm was observed, which may correlate to more active genes on the short arm than the long arm, shown by our RNA-seq analysis. The strong tethering interaction was found for loci at the pericentromeric region, suggesting a higher degree of local condensation, perhaps through stronger interactions or association between pericentromeric regions and their microenvironments, such as chromatin-nuclear body association through sequence-specific domains on DNA.
Loss of H3K9 tri-methylation alters chromosome compaction and transcription factor retention during mitosis
Authors: Djeghloul Dounia , Dimond Andrew , Kramer Holger , Brown Karen , Patel Bhavik , Wang Yi-Fang , Futschik Matthias E. , Whilding Chad , Montoya Alex , Veland Nicolas , Cheriyamkunnel Sherry , Montavon Thomas , Jenuwein Thomas , Merkenschlager Matthias , Fisher Amanda G. 
Published: February 2022

AbstractRecent studies have shown that repressive chromatin machinery, including DNA methyltransferases (DNMTs) and Polycomb Repressor Complexes (PRCs), bind to chromosomes throughout mitosis and their depletion results in increased chromosome size. Here we show that enzymes that catalyse H3K9 methylation, such as Suv39h1, Suv39h2, G9a and Glp, are also retained on mitotic chromosomes. Surprisingly however, mutants lacking H3K9me3 have unusually small and compact mitotic chromosomes that are associated with increased H3S10ph and H3K27me3 levels. Chromosome size and centromere compaction in these mutants were rescued by providing exogenous Suv39h1, or inhibiting Ezh2 activity. Quantitative proteomic comparisons of native mitotic chromosomes isolated from wildtype versus Suv39h1/Suv39h2 double-null ESCs revealed that H3K9me3 was essential for the efficient retention of bookmarking factors such as Esrrb. These results highlight an unexpected role for repressive heterochromatin domains in preserving transcription factor binding through mitosis, and underscore the importance of H3K9me3 for sustaining chromosome architecture and epigenetic memory during cell division.
Human neural progenitors establish a diffusion barrier in the ER membrane during cell division
Authors: bin Imtiaz Muhammad Khadeesh , Royall Lars N. , Jessberger Sebastian 
Published: February 2022

AbstractAsymmetric segregation of cellular components regulates the fate and behavior of somatic stem cells. Similar to dividing budding yeast and precursor cells in C. elegans, it has been shown that mouse neural progenitors establish a diffusion barrier in the membrane of the endoplasmic reticulum (ER), which has been associated with asymmetric partitioning of damaged proteins and cellular age. However, the existence of an ER-diffusion barrier in human cells remains unknown. Here we used fluorescence loss in photobleaching (FLIP) imaging to show that human embryonic stem cell (hESC)- and induced pluripotent stem cell (iPSC)-derived neural progenitor cells establish an ER-diffusion barrier during cell division. The human ER-diffusion barrier is regulated via Lamin-dependent mechanisms and is associated with asymmetric segregation of mono- and polyubiquitinated, damaged proteins. Further, forebrain regionalized organoids derived from hESCs were used to show the establishment of an ER-membrane diffusion barrier in more naturalistic tissues mimicking early steps of human brain development. Thus, the data provided here show that human neural progenitors establish a diffusion barrier during cell division in the membrane of the ER, which may allow for asymmetric segregation of cellular components, contributing to the fate and behavior of human neural progenitor cells.SummaryHuman neural progenitors (NPCs) establish a diffusion barrier during cell division in the membrane of the endoplasmic reticulum, allowing for asymmetric segregation of cellular components, which may contribute to the fate and behavior of human NPCs.
Upgrading of fire safety requirement for tall buildings in Bulgaria and proposal of implementing fire safety management under facility management
Authors: Ivanov Martin Lyubomirov , Chow Wan Ki , Yue Tsz Kit , Tsang Hing Lung , Peng Wei 
Published: February 2022

Purpose
The purpose of this paper is to check and fill the gap between the existing fire safety regulations for newly built tall buildings in Bulgaria and those in areas with rapid economic growth in the Asia-Oceania regions like the Hong Kong Special Administrative Region and Mainland China, by making comparative analysis and identifying good practices. The main focus is on the development of fire safety designs, facilities and management, which shall be recognized as essential parts of facility management in tall buildings.

Design/methodology/approach
Bulgarian regulations are analyzed and then compared with those in the Hong Kong Special Administrative Region and Mainland China. In addition, the scientific aspect of fire load density in the fire codes is discussed. The possibility of implementing a fire engineering approach to supplement prescriptive codes is outlined. The essential roles of fire safety management and fire safety culture are presented.

Findings
Key points and recommendations that are worthy for discussion about incorporation in the Bulgarian tall buildings fire safety requirements are upgraded requirements for fire load density, detection and sprinkler systems in tall residential buildings, refuge floors, ventilation/air conditioning control systems, full-scale burning tests and fire engineering approach. The importance of fire safety management is emphasized as a main, key component in facility management.

Originality/value
The research is the first study focusing on implementation of additional and specific fire safety regulations for tall buildings in Bulgaria.
Impact of Covid-19 on the built environment
Authors: Mahima M. , Shanthi Priya R. , Rajagopal Prashanthini , Pradeepa C. 
Published: February 2022

PurposeThis literature review paper aims to discuss the impacts and measures taken on Covid-19 with respect to architecture, built form and its allied fields along with observations from around the world with the end results of its implementation.Design/methodology/approachVarious research journals from Science Direct and Taylor and Francis among others were referred and reviewed to learn more on Covid-19 along with its impacts on people and their built environment. Keywords that aligned with the topic of interest like pandemic, Covid-19, coronavirus, urban spaces, built environment and built-up space were identified. Research papers that aligned with the scope of the paper and its keywords were found. An excel sheet with the basic data of these papers was written down. The essence of each of these articles were understood and linked with the topic in hand. A review of all these papers was written coherently to the topic. Future scope in this field of study was also identified.FindingsIt discusses the various measures taken around the world in built-up spaces along with the various measures given by researchers, architects and urban planners to mitigate and reduce the transmission of Covid-19 in the built environment and urban spaces. The discussed measures along with observations from around the world have also been discussed with its end results. Discussions and conclusions on these design strategies and recommendations are made with the anticipation of a paradigm shift due to post-pandemic changes. Current scenarios of public spaces in densely populated countries are discussed. Future scope in this ongoing field of study includes measures that can be taken in specific to some particular built-up typologies like markets, theaters, parks, bazaars, etc.Research limitations/implicationsThe limitation of this study is the restricting of the study of Covid-19 to only architectural, urban and public realm scales. The study does not facilitate the involvement of other fields and their influence with Covid-19.Originality/valueThis paper has been completely written by the author and the co-authors and has not been copied from any other sources.
Challenges in the evaluation process of training and development programmes in public universities in Saudi Arabian higher education
Authors: Othayman Majed Bin , Mulyata John , Meshari Abdulrahim , Debrah Yaw 
Published: February 2022

PurposeThis article aims to investigate the challenges faced during the training and development (T&D) evaluation process from the point of view of faculty members and HR managers in Saudi Arabian public universities, and to examine the influence of these challenges on the effectiveness of T&D programmes in public universities.Design/methodology/approachExploratory research using semi-structured interviews to determine the challenges faced during T&D evaluation was employed. Participants included faculty members (n = 23) and senior managers (n = 05) working in four public universities in Saudi Arabia. The interviews were transcribed and subjected to thematic analysis.FindingsThe outcome highlights the challenges faced during the T&D evaluation process: a lack of performance measurement and role ambiguity H.R.M. practices. Finally, this study aims to investigate how do these challenges influence the higher education sector.Originality/valueTo the best of the researcher's knowledge, this is one of the first attempts to explore challenges within the T&D evaluation process in Saudi Arabian higher education. The results should therefore broaden the scope of the available literature and fill a research gap, particularly regarding the Gulf Cooperation Council (GCC) of Nations.
Wear particles recognition through teachable machine
Authors: More Puja Prakash , Jaybhaye Maheshwar D. 
Published: February 2022

Purpose
The purpose of this paper is to adapt teachable machine as a web-based tool for recognition of wear pattern and type of wear by training a convolutional neural network (CNN) model. This helps to monitor the health of the lubricated system as a part of condition monitoring.

Design/methodology/approach
Ferrography technique is used for analysis of wear particles. It helps monitor the condition of lubricated mechanical system. In present paper, CNN model is developed for identifying the type of wear particles coming out of Gearbox system using teachable machine.

Findings
From the experimentation, it has been observed that the wear severity index has been increased due to increase in wear particle concentration. CNN model has achieved an accuracy of 95.4% to recognize five categories of wear particles.

Originality/value
Teachable machine is generally used for the prediction of images, gestures and sound features. An attempt is made to apply this model for micro and nano wear particles to classify them based on their characteristics.
Tax avoidance in banking institutions: an analysis of the top seven Nigerian banks
Authors: Folorunso Dada , Lokanan Mark Eshwar 
Published: February 2022

Purpose
The purpose of this paper is to review the quantum and magnitude of tax avoidance in Nigeria's top seven banks by using recognized tax avoidance proxies of the Generally Accepted Accounting Principles (GAAP) and the International Financial Reporting Standard (IFRS) effective tax rate (ETR) and book-tax gap analysis for the appraisal.

Design/methodology/approach
Data for the paper came from the annual reports of the banks between 2011 and 2019. The individual bank’s tax data was analyzed for trends and then consolidated to establish the average percentages and the exact amount of the tax the banks evaded each year and cumulatively over the review period. The data were then matched with analytics of the drivers of tax avoidance in the reconciliation statement to highlight essential tax planning items and strategies being exploited by each bank in the pursuit of aggressive tax avoidance behavior.

Findings
F-test comparing the aggregate means (all banks) for tax evasion proxies of ETR and the book-tax gap was conducted at a 95% confidence interval. The results of this paper indicate no significant difference between the means obtained, thus affirming that the same pattern of tax evasion was consistent among the banks for the years reviewed.

Originality/value
The findings of this paper highlight the tax avoidance behavior of the referenced banks, identify weaknesses in the corporate tax planning policy pursued and serve to alert policymakers of the need to strengthen the laws and block loopholes that provide rooms for unrestrained tax avoidance behavior in the banking sector.
Does religious knowledge level affect brand association and purchase intention of luxury cars? Case of the Lexus cars in Indonesia
Authors: Ratnasari Ririn Tri , Prajasari Anniza Citra , Kassim Salina 
Published: February 2022

Purpose
This study aims to analyze the role of religious knowledge level in influencing customers’ brand association and purchase intention of luxury cars by focusing on the Indonesian context and taking the Lexus brand as a case in point.

Design/methodology/approach
A sample of 159 respondents was taken from a population of Muslim consumers who live in Java province, Indonesia, and who have not had Lexus luxury car but have had other cars before. Using a quantitative research approach on primary data collected in several cities in Indonesia, the study adopts the partial least square as a method of analysis.

Findings
The study shows that brand association positively and significantly influences Muslim consumers’ attitudes on luxury cars, in this case, the Lexus brand. More importantly, the level of religious knowledge among Muslim consumers is shown to significantly weaken the influence of consumer attitudes toward purchase intention on luxury cars. The study also shows that brand association has a significant influence on Muslim consumers’ purchase intention on luxury cars.

Research limitations/implications
This study only explores the consumers’ perceptions based on their income levels. Further details of the consumers when making purchases of the luxury cars are not being considered; this includes who the decision-maker is, gender and education level.

Practical implications
There are several important implications that come from this study, especially on the risk of after-sales that will be experienced by luxury car owners, in this case, the Lexus brand. Luxury car manufacturers should show and highlight different characters in representing each variant or each type, to be more reflective of the intention and personalities of consumers who purchase luxury cars and not only to show the impression of owning the luxury cars.

Social implications
There are also social implications of this research where although middle- and high-income consumers do not always intend to buy luxury cars due to the role of religiosity that directs the Muslim consumers to evaluate whether it is really necessary to buy the luxury cars.

Originality/value
There has been a gap in the literature in assessing the role of religious knowledge level in affecting brand association as well as purchase intention, especially from a quantitative research approach and particularly focusing on the Indonesian context. This study including in responsible consumption as a good customer, which is one of Sustainable Development Goals items.