bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accurate microRNA annotation of animal genomes using trained covariance models of curated microRNA complements in MirMachine
Authors: Umu Sinan Uğur , Paynter Vanessa M. , Trondsen Håvard , Buschmann Tilo , Rounge Trine B. , Peterson Kevin J. , Fromm Bastian 
Published: November 2022

SummaryThe annotation of microRNAs, an important class of post-transcriptional regulators, depends on the availability of transcriptomics data and expert knowledge. This led to a large gap between novel genomes made available and high-quality microRNA complements. Using >16,000 microRNAs from the manually curated microRNA gene database MirGeneDB, we generated trained covariance models for all conserved microRNA families. These models are available in MirMachine, our new tool for the annotation of conserved microRNA complements from genomes only. We successfully applied MirMachine to a wide range of animal species, including those with very large genomes, additional genome duplications and extinct species, where smallRNA sequencing will be hard to achieve. We further describe a microRNA score of expected microRNAs that can be used to assess the completeness of genome assemblies. MirMachine closes a long-persisting gap in the microRNA field facilitating automated genome annotation pipelines and deeper studies on the evolution of genome regulation, even in extinct organisms.HighlightsAn annotation pipeline using trained covariance models of microRNA familiesEnables massive parallel annotation of microRNA complements of genomesMirMachine creates meaningful annotations for very large and extinct genomesmicroRNA score to assess genome assembly completenessGraphical abstract
Direct observation of the evolution of cell-type specific microRNA expression signatures supports the hematopoietic origin model of endothelial cells
Authors: Jenike Ana E. , Jenike Katharine M. , Peterson Kevin J. , Fromm Bastian , Halushka Marc K. 
Published: November 2022

AbstractThe evolution of specialized cell-types is a long-standing interest of biologists, but given the deep time-scales very difficult to reconstruct or observe. microRNAs have been linked to the evolution of cellular complexity and may inform on specialization. The endothelium is a vertebrate specific specialization of the circulatory system that enabled a critical new level of vasoregulation. The evolutionary origin of these endothelial cells is unclear. We hypothesized that Mir-126, an endothelial cell-specific microRNA may be informative.We here reconstruct the evolutionary history of Mir-126. Mir-126 likely appeared in the last common ancestor of vertebrates and tunicates, a species without an endothelium, within an intron of the evolutionary much older EGF Like Domain Multiple (Egfl) locus. Mir-126 has a complex evolutionary history due to duplications and losses of both the host gene and the microRNA. Taking advantage of the strong evolutionary conservation of the microRNA among Olfactores, and using RNA in situ hybridization (RISH), we localized Mir-126 in the tunicateCiona robusta. We found exclusive expression of the mature Mir-126 in granular amebocytes, supporting a long-proposed scenario that endothelial cells arose from hemoblasts, a type of proto-endothelial amoebocyte found throughout invertebrates.This observed change of expression of Mir-126 from proto-endothelial amoebocytes in the tunicate to endothelial cells in vertebrates is the first direct observation of the evolution of a cell-type in relation to microRNA expression indicating that microRNAs can be a prerequisite of cell-type evolution.Research Highlightsdirect observation of cell-type evolutionhigh conservation of sequence enables for simple RISH experiment of expressionMir-126 follows the evolution of hematopoetic cells to endothelial cells
The sulfated peptide CLEL6 is a negative regulator of anthocyanin biosynthesis inArabidopsis thaliana
Authors: Bühler Eric , Fahrbach Elisa , Schaller Andreas , Stührwohldt Nils 
Published: November 2022

AbstractPost-translationally modified peptides are now recognized as important regulators of plant stress responses. Here we identified the small sulfated CLE-LIKE6 (CLEL6) peptide as a negative regulator of stress-induced anthocyanin biosynthesis. The expression ofCLEL6and its negative effect on anthocyanin biosynthesis were strongly down-regulated by light. The function of CLEL6 depends on proteolytic processing of the CLEL6 precursor by the subtilisin-like serine proteinase 6.1 (SBT6.1), and on tyrosine sulfation by tyrosylprotein sulfotransferase (TPST). Loss of function mutants of eithersbt6.1ortpstshowed significantly higher anthocyanin accumulation upon light stress. The overaccumulation phenotype ofsbt6.1andtpstwas suppressed by application of mature CLEL6. Further confirming the role of CLEL6 as an inhibitor of anthocyanin biosynthesis, overexpression and external application of CLEL6 inhibited the expression of genes involved in anthocyanin biosynthesis in etiolated and light-stressed seedlings. Small post-translationally modified peptides are known to be perceived by leucine-rich-repeat receptor like kinases. Through a genetic approach, using a ROOT MERISTEM GROWTH FACTOR 1 INSENSITIVE (RGI) receptor quintuple mutant, we could show the essential function of the RGI receptor family in CLEL6 signaling. Our data indicate that CLEL6 inhibits anthocyanin biosynthesis through RGI receptors in dark-grown seedlings, and that this inhibition is released when CLEL6 expression is down-regulated upon transition to light.One sentence summaryThe formation of CLEL6 as a negative regulator of anthocyanin biosynthesis depends on proteolytic processing by SBT6.1, post-translational modification by TPST, and perception by RGI receptors.
Analysis of the polar residues located at the head domain of focal adhesion protein vinculin under the presence of theShigellaeffector IpaA and its possible implications duringin vivomechanotransduction
Authors: Cocom-Chan Benjamin , Khakzad Hamed , Valencia-Gallardo Cesar , Van Nhieu Guy Tran 
Published: November 2022

AbstractVinculin is a protein associated to linking adhesion receptors facing the outside of cells and reinforcing them by linking it’s intracellular domain of those receptors or, in the case of Cell-Matrix adhesions, to bind to a first level adaptor protein such as talin. The structural organization of vinculin allows it to bind on one part to specific amphipathic motifs collectively designated as vinculin binding sites (VBS), to a set of different vinculin coactivators or actin regulators, and finally a domain responsible to constantly bind to F-actin in a catch bond manner. However, the ability of vinculin to effectively bind all of those intracellular partners, is highly dependent on its structural organization. Which is critically dependent on its ability to respond to mechanical tension on the molecule itself and not necessarily to its binding capacity to VBSs and complementary activators. This is recognized as the combinatorial model of activation. Nonetheless, Shigella’s IpaA effector protein is able to mimic the conformational changes associated with the ones associated with the mechanical deformation of the molecule. This model of vinculin activation is designated as the non-combinatorial model, as the presence of a single activation-partner is enough to get the same effect. This work is devoted to dig in further to develop the previous work from this lab, as we have been able to characterize thein vitroandin vivoeffects of Shigella’s IpaA-Cterm region as the one responsible for both inducing conformational changes in solution, as well as the formation of super-stable adhesion, associated to maturity markers as VASP and alpha actinin. Additionally the IpaA-Cterm transfection renders those cells with the ability to maintain the adhesion structures stable and even resist the action of actomyosin relaxing molecules. Which renders them as mechanically-independent adhesions. We found that residue substitution at the surface of D1 and D2 interphase, (as well as residues maintaining the D2 domain helical bundles folded), might participate in the maintaining the structural integrity and interdomain interaction during force dependent as revealed by its ability to form protein complexes in vitro and under force-independent settings, as the morphology of cellular adhesions is altered in a way different from the previously reported targeting only the D1-D5 interaction.
Anticodon sequence determines the impact of mistranslating tRNAAlavariants
Authors: Cozma Ecaterina , Rao Megha , Dusick Madison , Genereaux Julie , Rodriguez-Mias Ricard A. , Villén Judit , Brandl Christopher J. , Berg Matthew D. 
Published: November 2022

AbstractTransfer RNAs (tRNAs) maintain translation fidelity through accurate charging by their cognate aminoacyl-tRNA synthetase and codon:anticodon base pairing with the mRNA at the ribosome. Mistranslation occurs when an amino acid not specified by the genetic message is incorporated into proteins and has applications in biotechnology, therapeutics and is relevant to disease. Since the alanyl-tRNA synthetase uniquely recognizes a G3:U70 base pair in tRNAAlaand the anticodon plays no role in charging, tRNAAlavariants with anticodon mutations have the potential to mis-incorporate alanine. Here, we characterize the impact of the 60 non-alanine tRNAAlaanticodon variants on the growth ofSaccharomyces cerevisiae. Overall, 36 tRNAAlaanticodon variants decreased growth in single-or multi-copy. Mass spectrometry analysis of the cellular proteome revealed that 52 of 57 anticodon variants, not decoding alanine or stop codons, induced mistranslation when on single-copy plasmids. Variants with G/C rich anticodons resulted in larger growth deficits than A/U rich variants. In most instances, synonymous anticodon variants impact growth differently, with anticodons containing U at base 34 being the least impactful. For anticodons generating the same amino acid substitution, reduced growth generally correlated with the abundance of detected mistranslation events. Differences in decoding specificity, even between synonymous anticodons, resulted in each tRNAAlavariant mistranslating unique sets of peptides and proteins. We suggest that these differences in decoding specificity are also important in determining the impact of tRNAAlaanticodon variants.
Dynamic Interaction Learning and Multimodal Representation for Drug Response Prediction
Authors: Bi Yanguang , Zhou Mu , Hu Zhiqiang , Zhang Shaoting , Lyu Guofeng 
Published: November 2022

AbstractMining multimodal pharmaceutical data is crucial for in-silico drug candidate screening and discovery. A daunting challenge of integrating multimodal data is to enable dynamic feature modeling generalizable for real-world applications. Unlike conventional approaches using a simple concatenation with fixed parameters, in this paper, we develop a dynamic interaction learning network to adaptively integrate drug and different reactants on multimodal tasks towards robust drug response prediction. The primary objective of dynamic learning falls into two key aspects: at micro-level, we aim to dynamically search specific relational patterns on the whole reactant range for each drug-reactant pair; at macro-level, drug features can be used to adaptively correlate with different reactants. Extensive experiments demonstrate the validity of our approach in both drug protein interaction (DPI) and cancer drug response (CDR) tasks. Our approach achieves superior performance on both DPI (AUC = 0.967) and CDR (AUC = 0.932) tasks, outperforming competitive baselines from four real-world, drug-outcome datasets. In addition, the performance on the challenging blind subsets is remarkably improved, where AUC value increases from 0.843 to 0.937 on blind protein set of DPI task, and Pearson’s correlation value increases from 0.516 to 0.566 on blind drug set of CDR task. A series of case studies highlight the potential generalization and interpretability of dynamic learning in the in-silico drug response assessment.
Inhibition of myeloperoxidase attenuates thoracic aortic aneurysm formation in Marfan disease
Authors: Mehrkens Dennis , Nettersheim Felix Sebastian , Ballmann Felix , Bastigkeit Jil , Brückner Alexander , Dohr Johannes , Geissen Simon , De Vore Lauren , Schelemei Patrik , Picard Felix Ruben , Kochen Malte , Braumann Simon , Kreuzberg Wiebke , Hof Alexander , Guthoff Henning , Brandtner Adrian , Mensah Benedicta Quaye , Groenink Maarten , van Andel Mitzi , Mieremet Arnout , Pfeiler Susanne , Gerdes Norbert , Flögel Ulrich , Zimmermann Laura-Maria , Sengle Gerhard , Eich Marie-Lisa , Schömig-Mariefka Birgid , Adam Matti , Fleischmann Bernd K , Wenzel Daniela , de Waard Vivian , Klinke Anna , Baldus Stephan , Mollenhauer Martin , Winkels Holger 
Published: November 2022

AbstractMarfan syndrome (MFS) is the most prevalent inherited connective tissue disorder, still remains uncurable, and is characterized by high mortality at early age driven by dissection and rupture of thoracic aortic aneurysms. MFS is caused by mutations in the fibrillin-1 gene and aberrant TGFß signaling.Here we addressed whether myeloperoxidase (MPO), a leukocyte derived enzyme with potent matrix modulating properties also influences the aortic phenotype in MFS.MFS patients displayed increased circulating MPO levels compared to controls as well as marked aortic MPO deposition. In an MFS mouse model, MPO induced inflammatory endothelial activation and endothelial to mesenchymal transition which triggered aortic leukocyte recruitment. Moreover, MPO directly contributed to adverse extracellular matrix remodeling by promoting oxidative stress and nitration of proteins within the vascular wall. Genetic MPO deficiency and pharmacological MPO inhibition attenuated MFS-related aneurysm formation. We herein identify MPO as a critical mediator of MFS-related thoracic aortic aneurysm formation and - in the absence of any pharmacological treatment so far in this disease - a first anti-inflammatory target to modulate disease progression.
scCDC: a computational method for gene-specific contamination detection and correction in single-cell and single-nucleus RNA-seq data
Authors: Wang Weijian , Cen Yihui , Lu Zezhen , Xu Yueqing , Sun Tianyi , Xiao Ying , Liu Wanlu , Li Jingyi Jessica , Wang Chaochen 
Published: November 2022

AbstractIn droplet-based single-cell RNA-seq (scRNA-seq) and single-nucleus RNA-seq (snRNA-seq) assays, systematic contamination of ambient RNA molecules biases the estimation of genuine transcriptional levels. To correct the contamination, several computational methods have been developed. However, these methods do not distinguish the contamination-causing genes and thus either under- or over-corrected the contamination in our in-house snRNA-seq data of virgin and lactating mammary glands. Hence, we developed scCDC as the first method that specifically detects the contamination-causing genes and only corrects the expression counts of these genes. Benchmarked against existing methods on synthetic and real scRNA-seq and snRNA-seq datasets, scCDC achieved the best contamination correction accuracy with minimal data alteration. Moreover, scCDC applies to processed scRNA-seq and snRNA-seq data with empty droplets removed. In conclusion, scCDC is a flexible, accurate decontamination method that detects the contamination-causing genes, corrects the contamination, and avoids the over-correction of other genes.
PRESGENE: A web server for PRediction of ESsential GENE using integrative machine learning strategies
Authors: Nandi Sutanu , Panditrao Gauri , Ganguli Piyali , Sarkar Ram Rup 
Published: November 2022

AbstractStudy of essential genes in disease-causing organisms has wide application in the prediction of therapeutic targets and exploring different clinical strategies. Predicting gene essentiality for large set of genes in non-model, less explored organisms is challenging. Computational methods that use machine learning (ML)-based strategies are popularly adopted for essential gene prediction as they provide key advantage of considering diverse biological features. Previous works from our group have demonstrated two ML-based pipelines for predicting essential genes with high accuracy that mitigates the problems of sufficient labeled imbalanced dataset and limited labeled datasets of essential genes. Here we present PRESGENE athttps://presgene.ncl.res.in, a ML-based web server for prediction of essential genes in unexplored eukaryotic and prokaryotic organisms. Our algorithms mitigate the problems of training dataset imbalance and limited availability of experimentally labeled data for essential genes. PRESGENE with its user-friendly web interface and high accuracy will prove to be a seamless experience for biologists looking for an accurate essential gene prediction server with limited labeled data for novel organisms.
The Sino-African higher education exchange: toward building a literature
Authors: Bouchaib Chkaif 
Published: November 2022

PurposeThis paper intends to provide a thematic literature review of the scholarly research articles orbiting the Sino–African education cooperation and exchange, published between 2005 and 2022.Design/methodology/approachThe methodology used in this paper is qualitative in nature with a thematic approach. The author used content analysis techniques to spotlight the major themes of the topic studied. The author selected the papers and theses, based on their heuristic capacity, from two major databases for the English and Chinese literature: Web of Science and CNKI. The selection process resulted in 60 high-quality peer-reviewed articles and theses. Another 30 research articles and theses were used as supplementary resources.FindingsThe literature concentrates on six points: the historical development, the nature of the exchange, the frameworks of the cooperation, vocational training and knowledge transfer, African students in China and their experiences, and education cooperation and soft power. However, research tends to be somewhat polemical rather than an academic debate between Chinese researchers and their western peers. Therefore, empirical studies beyond the geopolitical preoccupations and the “YEA” or “NAY” to the Sino–African education exchange are critically needed.Practical implicationsThe implications of this study go beyond the east/west or developed/developing world rhetoric and focus more on sustainable educational development on a global scale. Understanding how the literature on the Sino–African education engagement is shaping, provides valuable insights into international education in the global south. It can also be implied to approach educational engagement with other destinations such as India, Türkiye and Brazil.Originality/valueThis thematic literature review concentrates on the educational aspect of Sino–African relations. It compares English and Chinese peer-reviewed scholarly articles and theses on China–Africa educational engagement and has heuristic implications for sustainable educational development globally.
An investigation of visual comprehension in memory for 360-degree video advertisements amongst adolescents
Authors: Jayawardena Nirma Sadamali , Ross Mitchell , Quach Sara , Grace Debra 
Published: November 2022

PurposeThe purpose of this study is to investigate visual comprehension in memory for 360-degree video advertisements amongst adolescents under single and repeated viewing conditions.Design/methodology/approachThis study explored visual comprehension in memory for 360-degree video advertisements using the theoretical assumptions of the social psychology theory of social information processing by Wyer (2003). The authors conducted two experiments over a timeline of three months. In the first experiment, participants watched the 360-degree video advertisement once, and after one week, the same set of participants watched the same advertisement again. The theoretical assumptions in the comprehension unit were used to design the experiments and to explore visual comprehension in memory for 360-degree video advertisements. The data were collected using surveys and interviews through an experimental research design approach. NVivo software was used to analyse the data.FindingsThis study found that while female participants were able to comprehend colours in the visuals better, male participants were better able to comprehend facial expressions presented in the visuals. Further, both female and male participants were able to comprehend locations within the advertisement visuals. It was found that participants understood the plot or the story of the advertisement better after the second viewing than after the first viewing.Practical implicationsThe two main contributions from this study are as follows: from a theoretical perspective, the application of a social psychology theory for the advertising sector enables us to gather more insights about the social cognition stages of a human mindset such as information retrieval, judgement, decision making, goal stimulation and short- and long-term memory. In doing so, this study not only explored adolescents' visual comprehension memory of 360-degree video advertisements, but it also contributed to the theory of social information processing by Wyer (2003) by exploring consumer visual comprehension memory. From a practical perspective, the findings of this study provide a solid foundation for future advertising firms or agencies, marketers, and salespeople on how to design effective advertisements using 360-degree video versions in a way that appeals to consumer visual memory.Originality/valueThis paper can be considered as amongst the first studies which combine social psychology with advertising to investigate visual comprehension memory for 360-degree video advertisements amongst adolescents.
Resource Overall Equipment Cost Loss indicator to assess equipment performance and product cost
Authors: Stefana Elena , Cocca Paola , Fantori Federico , Marciano Filippo , Marini Alessandro 
Published: November 2022

PurposeThis paper aims to overcome the inability of both comparing loss costs and accounting for production resource losses of Overall Equipment Effectiveness (OEE)-related approaches.Design/methodology/approachThe authors conducted a literature review about the studies focusing on approaches combining OEE with monetary units and/or resource issues. The authors developed an approach based on Overall Equipment Cost Loss (OECL), introducing a component for the production resource consumption of a machine. A real case study about a smart multicenter three-spindle machine is used to test the applicability of the approach.FindingsThe paper proposes Resource Overall Equipment Cost Loss (ROECL), i.e. a new KPI expressed in monetary units that represents the total cost of losses (including production resource ones) caused by inefficiencies and deviations of the machine or equipment from its optimal operating status occurring over a specific time period. ROECL enables to quantify the variation of the product cost occurring when a machine or equipment changes its health status and to determine the actual product cost for a given production order. In the analysed case study, the most critical production orders showed an actual production cost about 60% higher than the minimal cost possible under the most efficient operating conditions.Originality/valueThe proposed approach may support both production and cost accounting managers during the identification of areas requiring attention and representing opportunities for improvement in terms of availability, performance, quality, and resource losses.