bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Atlas of Inflammation-Resolution (AIR)
Authors: Serhan Charles N. , Gupta Shailendra , Perretti Mauro , Godson Catherine , Brennan Eoin , Li Yongsheng , Soehnlein Oliver , Shimizu Takao , Werz Oliver , Chiurchiù Valerio , Azzi Angelo , Dubourdeau Marc , Gupta Suchi Smita , Schopohl Patrick , Hoch Matti , Gjorgevikj Dragana , Khan Faiz M. , Brauer David , Tripathi Anurag , Cesnulevicius Konstantin , Lescheid David , Schultz Myron , Repsilber Dirk , Kruse Robert , Sala Angelo , Haeggström Jesper Z. , Levy Bruce D. , Filep János G. , Wolkenhauer Olaf 
Published: January 2020

AbstractAcute inflammation is a protective reaction by the immune system in response to invading pathogens or tissue damage. Ideally, the response should be localized, self-limited, and returning to homeostasis. If not resolved, acute inflammation can result in organ pathologies leading to chronic inflammatory phenotypes. Acute inflammation and inflammation resolution are complex coordinated processes, involving a number of cell types, interacting in space and time. The biomolecular complexity and the fact that several biomedical fields are involved, make a multi and interdisciplinary approach necessary.This Atlas of Inflammation Resolution (AIR) is a web-based resource capturing the state-of-the-art in acute inflammation and inflammation resolution research. The AIR provides an interface for users to search thousands of interactions, arranged in inter-connected multi-layers of process diagrams, covering a wide range of clinically relevant phenotypes. The AIR serves as an open access knowledgebase, including a gateway to numerous public databases. It is furthermore possible for the user to map experimental data onto the molecular interaction maps of the AIR, providing the basis for bioinformatics analyses and systems biology approaches. By mapping experimental data onto the Atlas, it can be used to elucidate drug action as well as molecular mechanisms underlying different disease phenotypes. For the visualization and exploration of information, the AIR uses the Minerva platform, which is a well-established tool for the presentation of disease maps. The molecular details of the AIR are encoded using international standards.The Atlas of Inflammation Resolution was created as a freely accessible resource, supporting research and education in the fields of acute inflammation and inflammation resolution. The AIR connects research communities, facilitates clinical decision making, and supports research scientists in the formulation and validation of hypotheses.
Extensive fragmentation and re-organization of gene co-expression patterns underlie the progression of Systemic Lupus Erythematosus
Authors: Ntasis Vasilis F. , Panousis Nikolaos I. , Tektonidou Maria G. , Dermitzakis Emmanouil T. , Boumpas Dimitrios T. , Bertsias George K. , Nikolaou Christoforos 
Published: January 2020

AbstractSystemic Lupus Erythematosus (SLE) is the prototype of autoimmune diseases, characterized by extensive gene expression perturbations in peripheral blood immune cells. Circumstantial evidence suggests that these perturbations may be due to altered epigenetic profiles and chromatin accessibility but the relationship between transcriptional deregulation and genome organization remains largely unstudied. We developed a genomic approach that leverages patterns of gene coexpression from genome-wide transcriptome profiles in order to identify statistically robust Domains of Co-ordinated gene Expression (DCEs). By implementing this method on gene expression data from a large SLE patient cohort, we identify significant disease-associated alterations in gene co-regulation patterns, which also correlate with the SLE activity status. Low disease activity patient genomes are characterized by extensive fragmentation leading to DCEs of smaller size. High disease activity genomes display excessive spatial redistribution of co-expression domains with expanded and newly-appearing (emerged) DCEs. Fragmentation and redistribution of gene coexpression patterns correlate with SLE-implicated biological pathways and clinically relevant endophenotypes such as kidney involvement. Notably, genes lying at the boundaries of split DCEs of low activity genomes are enriched in the interferon and other SLE susceptibility signatures, suggesting the implication of DCE fragmentation at early disease stages. Interrogation of promoter-enhancer interactions from various immune cell subtypes shows that a significant percentage of nested connections are disrupted by a DCE split or depletion in SLE genomes. Collectively, our results underlining an important role for genome organization in shaping gene expression in SLE, could provide valuable insights into disease pathogenesis and the mechanisms underlying disease flares.SignificanceAlthough widespread gene expression changes have been reported in Systemic Lupus Erythematosus (SLE), attempts to link gene deregulation with genome structure have been lacking. Through a computational framework for the segmentation of gene expression data, we reveal extensive fragmentation and reorganization of gene co-regulation domains in SLE, that correlates with disease activity states. Gene co-expression domains pertaining to biological functions implicated in SLE such as the interferon pathway, are being disrupted in patients, while others associated to severe manifestations such as nephritis, emerge in previously uncorrelated regions of the genome. Our results support extensive genome re-organization underlying aberrant gene expression in SLE, which could assist in the early detection of disease flares in patients that are in remission.Graphical Abstract
Structural analysis of Sub16 sedolisin ofTrichophyton rubrumreveals a flexible nature of its pro domain
Authors: Latka Chitra , Bikshapathi Jagga , Aggarwal Priyanka , Bhavesh Neel Sarovar , Chakraborty Rahul , Khan Sabab Hasan , Taneja Bhupesh 
Published: January 2020

AbstractTrichophyton rubrumis one of the leading causes of superficial skin infections worldwide. It is a keratinolytic fungus specialized in colonization of keratinized tissue of skin, hair and nails for long periods of time. The fungus encodes a wide repertoire of secreted proteases in its genome that not only aid in nutrient acquisition but also establishment of infection on the host. The proteases are synthesized in ‘prepro’ form that requires removal of the prosegment for activation. In order to gain insights into the structural association of the pro domain with the catalytic domain, we investigate the structural features of the pro domain of the secreted sedolisin member Sub16 ofT. rubrum. Our results show that the pro domain of Sub16 may have inherent flexibility in the absence of the associated catalytic domain which is stabilized in complex with catalytic domain. This is the first report of structural investigation on a stand-alone pro domain of sedolisin family of subtilases that will help in design of further structural studies of this protein.
Modeling metabolic variation with single-cell expression data
Authors: Zhang Yuanchao , Kim Man S. , Nguyen Elizabeth , Taylor Deanne M. 
Published: January 2020

AbstractCellular metabolism encompasses the biochemical reactions and transportation of various metabolites in cells and their surroundings, which are integrated at all levels of cellular functions. We developed a method to systematically simulate cellular metabolism using single-cell RNA-seq (scRNA-seq) data through constraint-based context specific metabolic modeling. We simulated the NAD+biosynthesis activity in 7 different mouse tissues, and the simulated NAD+biosynthesis flux levels showed significant linear correlation with experimental measurements in previous research. We also show that the simulated NAD+biosynthesis fluxes are reproducible using two additional scRNA-seq datasets.
Phylogenetic signal is associated with the degree of variation in root-to-tip distances
Authors: Vankan Mezzalina , Ho Simon Y.W. , Pardo-Diaz Carolina , Duchêne David A. 
Published: January 2020

AbstractThe phylogenetic information contained in sequence data is partly determined by the overall rate of nucleotide substitution in the genomic region in question. However, phylogenetic signal is affected by various other factors, such as heterogeneity in substitution rates across lineages. These factors might be able to predict the phylogenetic accuracy of any given gene in a data set. We examined the association between the accuracy of phylogenetic inference across genes and several characteristics of branch lengths in phylogenomic data. In a large number of published data sets, we found that the accuracy of phylogenetic inference from genes was consistently associated with their mean statistical branch support and variation in their gene tree root-to-tip distances, but not with tree length and stemminess. Therefore, a signal of constant evolutionary rates across lineages appears to be beneficial for phylogenetic inference. Identifying the causes of variation in root-to-tip lengths in gene trees also offers a potential way forward to increase congruence in the signal across genes and improve estimates of species trees from phylogenomic data sets.
eQTL Catalogue: a compendium of uniformly processed human gene expression and splicing QTLs
Authors: Kerimov Nurlan , Hayhurst James D. , Peikova Kateryna , Manning Jonathan R. , Walter Peter , Kolberg Liis , Samoviča Marija , Sakthivel Manoj Pandian , Kuzmin Ivan , Trevanion Stephen J. , Burdett Tony , Jupp Simon , Parkinson Helen , Papatheodorou Irene , Yates Andrew , Zerbino Daniel R. , Alasoo Kaur 
Published: January 2020

AbstractAn increasing number of gene expression quantitative trait locus (eQTL) studies have made summary statistics publicly available, which can be used to gain insight into complex human traits by downstream analyses, such as fine mapping and colocalisation. However, differences between these datasets, in their variants tested, allele codings, and in the transcriptional features quantified, are a barrier to their widespread use. Consequently, target genes for most GWAS signals have still not been identified. Here, we present the eQTL Catalogue (https://www.ebi.ac.uk/eqtl/), a resource which contains quality controlled, uniformly recomputed QTLs from 21 eQTL studies. We find that for matching cell types and tissues, the eQTL effect sizes are highly reproducible between studies, enabling the integrative analysis of these data. Although mostcis-eQTLs were shared between most bulk tissues, the analysis of purified cell types identified a greater diversity of cell-type-specific eQTLs, a subset of which also manifested as novel disease colocalisations. Our summary statistics can be downloaded by FTP, accessed via a REST API, and visualised on the Ensembl genome browser. New datasets will continuously be added to the eQTL Catalogue, enabling the systematic interpretation of human GWAS associations across many cell types and tissues.
Sex ratio and sexual conflict in a collective action problem
Authors: Lindstedt C. , Gerber N. , Kokko H. 
Published: January 2020

AbstractThe maintenance of cooperation is difficult whenever collective action problems are vulnerable to freeriding (reaping the benefits without contributing to the maintenance of the good). We identify a novel factor that can make a system tolerate an extent of freeriding. If a population consists of discrete types with demographically distinct roles, such that the success of one type does not imply it can spread to replace other types in the population, then collective goods may persist in the presence of free-riders because they are necessarily kept in a minority role. Biased sex ratios (e.g. in haplodiploids) create conditions where individuals of one sex are a minority. We show that this can make the less common sex contribute less to a public good in a setting where the relevant life-history stage — larval group defence against predators — does not feature any current breeding opportunities that might lead to confounding reasons behind sex-specific behaviour. We test our model with haplodiploid pine sawfly larvae, showing that female larvae are the main contributors to building the antipredator defence against predators.Significance statementIndividuals in groups can cooperate to achieve something together, but with an evolutionary difficulty: if benefits of cooperation are shared equally among all, freeriders get the same benefit as others while paying less for it. We propose a novel reason why freeriding does not automatically spread until the collectively beneficial outcome is destroyed: sometimes groups consist of individuals of distinct categories, limiting freerider spread. If, for example, there are always fewer males than females, then even if every male becomes a freerider, the whole group still survives simply because not everyone can be male. Pine sawfly larvae defend against predators by regurgitating sticky fluids, but females contribute more to this common defence, and we show this example fits our model.
Bicc1anddicerregulate left-right patterning through post-transcriptional control of the Nodal-inhibitordand5
Authors: Maerker Markus , Getwan Maike , Dowdle Megan E. , Pelliccia José L. , McSheene Jason C. , Yartseva Valeria , Minegishi Katsura , Vick Philipp , Giraldez Antonio J. , Hamada Hiroshi , Burdine Rebecca D. , Sheets Michael D. , Schweickert Axel , Blum Martin 
Published: January 2020

AbstractRotating cilia at the vertebrate left-right organizer (LRO) generate an asymmetric leftward flow, which is sensed by cells at the left LRO margin. How the flow signal is processed and relayed to the laterality-determining Nodal cascade in the left lateral plate mesoderm (LPM) is largely unknown. We previously showed that flow down-regulates mRNA expression of the Nodal inhibitor Dand5 in left sensory cells. De-repression of the co-expressed Nodal drives LPM Nodal cascade induction. Here, we identify the mechanism ofdand5downregulation, finding that its posttranscriptional repression is a central process in symmetry breaking. Specifically, the RNA binding protein Bicc1 interacts with a proximal element in the 3’-UTR ofdand5to repress translation in adicer1-dependent manner. Thebicc1/dicer1module acts downstream of flow, as LRO ciliation was not affected upon its loss. Loss ofbicc1ordicer1was rescued by parallel knockdown ofdand5, placing both genes in the process of flow sensing.
A simple model for glioma grading based on texture analysis applied to conventional brain MRI
Authors: Suárez-García José Gerardo , Hernández-López Javier Miguel , Moreno-Barbosa Eduardo , de Celis-Alonso Benito 
Published: January 2020

AbstractAccuracy of glioma grading is fundamental for the diagnosis, treatment planning and prognosis of patients. The purpose of this work was to develop a low cost and easy to implement classification model which distinguishes low grade gliomas (LGGs) from high grade gliomas (HGGs), through texture analysis applied to conventional brain MRI. Different combinations between MRI contrasts (T1Gdand T2) and one segmented glioma region (necrotic and non-enhancing tumor core (NCR/NET)) were studied. Texture features obtained from the Gray Level Size Zone Matrix (GLSZM) were calculated. An under-samplig method was proposed to divide the data into different training subsets and subsequently extract complementary information for the creation of distinct classification models. The sensitivity, specificity and accuracy of the models were calculated. The best model was explicitly reported. The best model included only three texture features and reached a sensitivity, specificity and accuracy of 94.12%, 88.24% and 91.18% respectively. According to the features of the model, when the NCR/NET region was studied, HGGs had a more heterogeneous texture than LGGs in the T1Gdimages and LGGs had a more heterogeneous texture than HGGs in the T2images. These novel results partially contrast with results from literature. The best model proved to be useful for the classification of gliomas. Complementary results showed that heterogeneity of gliomas depended on the studied MRI contrast. The model presented stands out as a simple, low cost, easy to implement, reproducible and highly accurate glioma classifier. What is more important, it should be accessible to populations with reduced economic and scientific resources.
Prophylactic and therapeutic HBV vaccination by an HBs-expressing cytomegalovirus vector lacking an interferon antagonist
Authors: Huang Hongming , Rückborn Meike , Le-Trilling Vu Thuy Khanh , Zhu Dan , Yang Shangqing , Zhou Wenqing , Yang Xuecheng , Feng Xuemei , Lu Yinping , Lu Mengji , Dittmer Ulf , Yang Dongliang , Trilling Mirko , Liu Jia 
Published: January 2020

ABSTRACTCytomegalovirus (CMV)-based vaccines show promising effects against chronic infections in non-human primates. Therefore, we examined the potential of HBV vaccines based on mouse CMV (MCMV) vectors expressing the small HBsAg. Immunological consequences of vaccine virus attenuation were addressed by either replacing the dispensable genem157(‘MCMV-HBs’) or the geneM27(‘ΔM27-HBs’), the latter encodes a potent interferon antagonist targeting the transcription factor STAT2.M27was chosen, since human cytomegalovirus (HCMV) encodes an analogous gene product, which also induced proteasomal STAT2 degradation by exploiting Cullin RING ubiquitin ligases. Vaccinated mice were challenged with HBV through hydrodynamic injection. MCMV-HBs and ΔM27-HBs vaccination achieved accelerated HBV clearance in serum and liver as well as robust HBV-specific CD8+ T cell responses. When we explored the therapeutic potential of MCMV-based vaccines, especially the combination of ΔM27-HBs prime and DNA boost vaccination resulted in increased intrahepatic HBs-specific CD8+ T cell responses and HBV clearance in persistently infected mice. Our results demonstrated that vaccines based on a replication competent MCMV attenuated through the deletion of an interferon antagonist targeting STAT2 elicit robust anti-HBV immune responses and mediate HBV clearance in mice in prophylactic and therapeutic immunization regimes.
ATG8-interacting (ATI) 1 and 2 define a plant starvation-induced ER-phagy pathway and serve as MSBP1 (MAPR5) cargo-receptors
Authors: Wu Jian , Michaeli Simon , Galili Gad , Peled-Zehavi Hadas 
Published: January 2020

AbstractER-phagy, the selective autophagy of endoplasmic reticulum (ER) components, is known to operate in eukaryotes from yeast and unicellular algae to animals and plants. Thus far, only ER-stress derived ER-phagy was reported and analyzed in plants. In this study we characterize an ER-phagy pathway inArabidopsis thalianathat is triggered by dark-induced starvation and not by ER-stress. This pathway is defined by the previously reported ATG8-interacting proteins, ATI1 and ATI2 and is regulated by the TOR signaling pathway. We further identified ER-localized Membrane Steroid Binding Protein 1 (MSBP1) as an ATI1 and 2 interacting protein and an autophagy cargo, and show that ATI1 and 2 serve as its cargo receptors. Together, these findings expand our knowledge on plants responses during energy deprivation and highlight the role of this special type of ER-phagy in this process.
Making a case for 3D printing for housing delivery in South Africa
Authors: Aghimien Douglas , Aigbavboa Clinton , Aghimien Lerato , Thwala Wellington D. , Ndlovu Lebu 
Published: January 2020

PurposeConsidering the need for standard and cost-effective housing delivery in South Africa, this study aims to make a case for three-dimensional (3D) printing in housing delivery through an assessment of the inherent benefits and the factors that could acts as barriers to its adoption.Design/methodology/approachThe study used a survey of construction professionals currently actively involved in a construction project in the country. Analysis of data gathered was done using a four-step analysis approach and relevant descriptive and inferential statistics were adopted.FindingsThe study revealed through factor analysis that 3D printing in housing delivery promises better cost delivery, increased productivity and stakeholder satisfaction, socio-economic benefits, improved quality and faster housing delivery. While these benefits exist, factors such as technical and operational issues of the 3D printing itself, organizational and personnel issues as well as lack of awareness of the inherent benefits and understanding of the technology among stakeholders can prove to be barriers to the adoption of the technology.Practical implicationsIn the quest to achieve standard and affordable housing which is part of its National Development Plan 2030, the government can adopt 3D printing which promises significant benefits in terms of cost, time, quality, productivity and stakeholders’ satisfaction. Property developers can also adopt the technology to improve their housing delivery, competitive advantage and the economic value of their properties.Originality/valueThe study contributes significantly to the body of knowledge as it reveals the benefits and barriers of adopting 3D printing in housing delivery in South Africa – an aspect that has not gained significant attention in the fourth industrial revolution and housing delivery discuss in the country.
Corporate real estate and corporate strategy alignment in South Africa
Authors: Ntene Tsoanelo , Azasu Samuel , Owusu-Ansah Anthony 
Published: January 2020

PurposeThis paper aims to discuss whether alignment between corporate real estate strategy and corporate strategy exists for non-property companies listed on the Johannesburg Securities Exchange and what effects alignment has on the firms’ financial performance.Design/methodology/approachThe study was both qualitative and quantitative in nature, with a specific focus on non-property firms listed on the Johannesburg Securities Exchange. The qualitative part of the study involved the analysis of the firms’ annual reports to determine the presence and use of corporate real estate strategies and their alignment to corporate strategy and the extraction of financial indicator data. The quantitative portion of the study involved the use of multivariate analysis, to distinguish and quantify the relationship, if any, between corporate real estate strategy and the identified financial performance indicators. The independent variables were the CRE strategies employed and the dependent variable was the share price. The methods used in this study have been applied before in European and Asian studies; this assisted in ensuring that validity and reliability was achieved.FindingsThe study finds that the most used strategy by firms (47%) is that which facilitates production, operation and service delivery. The Consumer Goods, Healthcare and Telecommunications sectors appear to demonstrate the highest level of alignment. Return on Shareholder Funds has a strong significant positive correlation with share price. Flexibility as a corporate real estate strategy also has a significant positive coefficient, which indicates a positive relationship with share price.Research limitations/implicationsAlthough consistent with results of studies conducted in Europe and Asia, the results of this research may not be applicable to privately held non-listed firms, state-owned enterprises, non-profits and educational institutions. This study also ignores the dynamic external environment in which firms operate and the necessity of firms adjusting their corporate real estate strategy to their changing business strategy.Practical implicationsThese results suggest that the incorporation of corporate real estate strategy in the firms’ corporate strategy formulation has the potential to enhance shareholder value for South African firms. Real estate developers, landlords and owner occupiers would benefit from better understanding the strategic requirements of corporations to ensure that the solutions they provide increase the likelihood of maximizing shareholder return.Originality/valueThe role of corporate real estate strategy in the firms’ corporate strategy formulation has the ability to enhance shareholder value. This research adds to the scant literature on corporate real estate management in South Africa.