bluuebunny/crossref_metadata_2025 huggingface dataset:
Cell lineage as a predictor of immune response in neuroblastoma
Authors: Sengupta Satyaki , Das Sanjukta , Crespo Angela , Miller Brian , Sharma Bandana , Zhang Shupei , Dries Ruben , Huang Hao , Krajewska Malgorzata , Debruyne David N. , Soriano Luigi , Cohen Malkiel A. , Versteeg Rogier , Jaenisch Rudolf , Spranger Stefani , Lieberman Judy , George Rani E.
Published: January 2021

Immunotherapy for patients with neuroblastoma has met with limited success, partly due to an incomplete understanding of the mechanisms underlying immune responsiveness in this clinically and genetically heterogenic tumor. Here, we undertook an unbiased analysis using dimension reduction and UMAP visualization of transcriptional signatures derived from 498 primary neuroblastoma tumors. Four distinct clusters based on differentially expressed genes emerged, of which one, representing about 30% and comprising mainly ofMYCN-nonamplified tumors, was notable for the high expression of genes associated with both immune response activation and suppression. This capacity to elicit a productive immune response resided exclusively in tumors with dominant populations of undifferentiated, neural crest-like or mesenchymal cells; by contrast, tumors comprising primarily of committed, adrenergic neuron-like cells were less immunogenic. Mesenchymal neuroblastoma cells were enriched for innate and adaptive immune gene signatures, demonstrated engagement with cytotoxic T and natural killer cells, and induced immune cell infiltration in an immunocompetent mouse model. Transcriptional or targeted therapy-induced reprogramming of adrenergic cells to the mesenchymal state led to reactivation of tumor cell-intrinsic immune genes. Key immune response genes in adrenergic tumor cells were found to be epigenetically silenced by the PRC2 complex, and such repression could be relieved by either mesenchymal cell state reprogramming or EZH2 inhibition, leading to increased activation of natural killer cells by the tumor cells. These data identify cell lineage as a major determinant of the immunogenic potential in neuroblastoma that could be used to stratify patients who are most likely to benefit from immunotherapy.
Multi-omic Characterization of Human Tubular Epithelial Cell Response to Serum
Authors: Lidberg Kevin A. , Muthusamy Selvaraj , Adil Mohamed , Patel Ranita S. , Wang Lu , Bammler Theo K. , Reichel Jonathan , Yeung Catherine K. , Himmelfarb Jonathan , Kelly Edward J. , Akilesh Shreeram
Published: January 2021

Proteinuria, the spillage of serum proteins into the urine, is a feature of glomerulonephritides, podocyte disorders and diabetic nephropathy. However, the response of tubular epithelial cells to serum protein exposure has not been systematically characterized. Using transcriptomic profiling we studied serum-induced changes in primary human tubular epithelial cells cultured in 3D microphysiological devices. Serum proteins induced cellular proliferation, cytokine secretion and activated a coordinated stress response. We orthogonally confirmed our findings by comparing the transcriptomic and epigenomic landscapes of intact human kidney cortex and isolated tubular epithelial cells cultured in fetal bovine serum. Importantly, key transcriptomic programs in response to either type of serum exposure remained consistent, including comparisons to an established mouse model of kidney injury. This serum-induced transcriptional response was dominated by switching off of nuclear receptor-driven programs and activation of AP-1 and NF-κB signatures in the tubular epigenomic landscape. These features of active regulation were seen at canonical kidney injury genes (HAVCR1) and genes associated with COVID-19 (ACE2,IL6). Our data provide a reference map for dissecting the regulatory and transcriptional response of kidney tubular epithelial cells injury induced by serum.
Recombination and low-diversity confound homoplasy-based methods to detect the effect of SARS-CoV-2 mutations on viral transmissibility
Authors: Giorgi Elena E. , Bhattacharya Tanmoy , Fischer Will , Yoon Hyejin , Abfalterer Werner , Korber Bette
Published: January 2021

The SARS-CoV-2 variant carrying the Spike protein mutation G614 was first detected in late January 2020 and within a few months became the dominant form globally. In the months that followed, many studies, both in vitro and in animal models, showed that variants carrying this mutation were more infectious and more readily transmitted than the ancestral Wuhan form. Here we investigate why a recently published study by van Dorp et al. failed to detect such higher transmissibility of the G614 variant using homoplasy-based methods. We show that both low diversity and recombination confound the methods utilized by van Dorp et al. and significantly decrease their sensitivity. Furthermore, though they claim no evidence of recombination in their dataset, we and several other studies identify a subset of the sequences as recombinants, possibly enough to affect their statistic adversely.
Long-read assembly and comparative evidence-based reanalysis ofCryptosporidiumgenome sequences reveal new biological insights
Authors: Baptista Rodrigo P. , Li Yiran , Sateriale Adam , Sanders Mandy J. , Brooks Karen L. , Tracey Alan , Ansell Brendan R. E. , Jex Aaron R. , Cooper Garrett W. , Smith Ethan D. , Xiao Rui , Dumaine Jennifer E. , Berriman Matthew , Striepen Boris , Cotton James A. , Kissinger Jessica C.
Published: January 2021

Cryptosporidiosis is a leading cause of waterborne diarrheal disease globally and an important contributor to mortality in infants and the immunosuppressed. Despite its importance, theCryptosporidiumcommunity still relies on a fragmented reference genome sequence from 2004. Incomplete reference sequences hamper experimental design and interpretation. We have generated a newC. parvumIOWA genome assembly supported by PacBio and Oxford Nanopore long-read technologies and a new comparative and consistent genome annotation for three closely related speciesC. parvum,C. hominisandC. tyzzeri. The newC. parvumIOWA reference genome assembly is larger, gap free and lacks ambiguous bases. This chromosomal assembly recovers 13 of 16 possible telomeres and raises a new hypothesis for the remaining telomeres and associated subtelomeric regions. Comparative annotation revealed that most “missing” orthologs are found suggesting that species differences result primarily from structural rearrangements, gene copy number variation and SNVs inC. parvum, C. hominisandC. tyzzeri. We made >1,500C. parvum annotation updates based on experimental evidence. They included new transporters, ncRNAs, introns and altered gene structures. The new assembly and annotation revealed a complete DNA methylaseDnmt2ortholog. 190 genes under positive selection including many new candidates were identified using the new assembly and annotation as reference. Finally, possible subtelomeric amplification and variation events inC. parvumare detected that reveal a new level of genome plasticity that will both inform and impact future research.
Acidovoraxpan-genome reveals specific functional traits for plant beneficial and pathogenic plant-associations
Authors: Siani Roberto , Stabl Georg , Gutjahr Caroline , Schloter Michael , Radl Viviane
Published: January 2021

Beta-proteobacteria belonging to the genusAcidovoraxhave been described from various environments. Many strains can interact with a range of hosts, including humans and plants, forming neutral, beneficial or detrimental associations. In the frame of this study we investigated genomic properties of 52 bacterial strains of the genusAcidovorax, isolated from healthy roots ofLotus japonicus, with the intent of identifying traits important for effective plant-growth promotion. Based on single-strain inoculation bioassays withL. japonicus, performed in a gnotobiotic system, we could distinguish 7 robust plant-growth promoting strains from strains with no significant effects on plant-growth. We could show that the genomes of the two groups differed prominently in protein families linked to sensing and transport of organic acids, production of phytohormones, as well as resistance and production of compounds with antimicrobial properties. In a second step, we compared the genomes of the tested isolates with those of plant pathogens and free-living strains of the genusAcidovoraxsourced from public repositories. Our pan-genomics comparison revealed features correlated with commensal and pathogenic lifestyle. We could show that commensals and pathogens differ mostly in their ability to use plant-derived lipids and in the type of secretion-systems being present. Most free-livingAcidovoraxstrains did not harbour any secretion-systems. Overall, our data indicated thatAcidovoraxstrains undergo extensive adaptations to their particular lifestyle by horizontal uptake of novel genetic information and loss of unnecessary genes.
The recycling endosome protein Rab25 coordinates collective cell movements in the zebrafish surface epithelium
Authors: Willoughby Patrick Morley , Allen Molly , Yu Jessica , Korytnikov Roman , Chen Tianhui , Liu Yupeng , So Isis , Macpherson Neil , Mitchell Jennifer , Fernandez-Gonzalez Rodrigo , Bruce Ashley E. E.
Published: January 2021

In emerging epithelial tissues, cells undergo dramatic rearrangements to promote tissue shape changes. Dividing cells remain interconnected via transient cytokinetic bridges. Bridges are cleaved during abscission and currently, the consequences of disrupting abscission in developing epithelia are not well understood. We show that the Rab GTPase, Rab25, localizes near cytokinetic midbodies and likely coordinates abscission through endomembrane trafficking in the epithelium of the zebrafish gastrula during epiboly. In maternal-zygotic Rab25a and Rab25b mutant embryos, morphogenic activity tears open persistent apical cytokinetic bridges that failed to undergo timely abscission. Cytokinesis defects result in anisotropic cell morphologies that are associated with a reduction of contractile actomyosin networks. This slows cell rearrangements and alters the viscoelastic responses of the tissue, all of which likely contribute to delayed epiboly. We present a model in which Rab25 trafficking coordinates cytokinetic bridge abscission and cortical actin density, impacting local cell shape changes and tissue-scale forces.
EEG in game user analysis: A framework for expertise classification during gameplay
Authors: Hafeez Tehmina , Saeed Sanay Muhammad Umar , Arsalan Aamir , Anwar Syed Muhammad , Ashraf Muhammad Usman , Alsubhi Khalid
Published: January 2021

Video games have become a ubiquitous part of demographically diverse cultures. Numerous studies have focused on analyzing the cognitive aspects involved in game playing that could help provide an optimal gaming experience level by improving video game design. To this end, we present a framework for classifying the game player’s expertise level using wearable electroencephalography (EEG) headset. We hypothesize that expert/novice players’ brain activity is different, which can be classified using the frequency domain features extracted from EEG signals of the game player. A systematic channel reduction approach is presented using a correlation-based attribute evaluation method. This approach identifies two significant EEG channels, i.e., AF3 and P7, from the Emotiv EPOC headset’s fourteen channels. The features extracted from these EEG channels contribute the most to the video game player’s expertise level classification. This finding is validated by performing statistical analysis (t-test) over the extracted features. Moreover, among multiple classifiers used, K-nearest neighbor is the best classifier in classifying the game player’s expertise level with up to 98.04% classification accuracy.

Author summary

Tehmina Hafeez ROLES Investigation, Writing – original draft * E-mail:tehminamalik.52@gmail.comAFFILIATION Department of Computer Engineering, University of Engineering and Technology, Taxila, 47050, Pakistan.

Sanay Muhammad Umar Saeed (Corresponding author) ROLES Conceptualization, Writing – review editing * E-mail:sanay.muhammad@uettaxila.edu.pkAFFILIATION Department of Computer Engineering, University of Engineering and Technology, Taxila, 47050, Pakistan.

Aamir Arsalan ROLES Methodology, Writing – review editing * E-mail:aamir.arsalan@uettaxila.edu.pkAFFILIATION Department of Computer Engineering, University of Engineering and Technology, Taxila, 47050, Pakistan.

Syed Muhammad Anwar ROLES Validation, Writing – review editing * E-mail:s.anwar@uettaxila.edu.pkAFFILIATION Department of Software Engineering, University of Engineering and Technology, Taxila, 47050, Pakistan.

Muhammad Usman Ashraf (Corresponding author) ROLES Validation, Writing – review editing * E-mail:usman.ashraf@skt.umt.edu.pkAFFILIATION Department of Computer Science, University of management and Technology, Lahore (Sialkot), 51040, Pakistan.

Khalid Alsubhi ROLES Conceptualization, Writing – review editing AFFILIATION Department of Computer Science, King Abdul Aziz University, Jeddah, Saudi Arabia.
Linear regression of sampling distributions of the mean
Authors: Torres David J , Vasilic Ana , Pacheco Jose
Published: January 2021

We show that the simple and multiple linear regression coefficients and the coefficient of determinationR2computed from sampling distributions of the mean (with or without replacement) are equal to the regression coefficients and coefficient of determination computed with individual data. Moreover, the standard error of estimate is reduced by the square root of the group size for sampling distributions of the mean. The result has applications when formulating a distance measure between two genes in a hierarchical clustering algorithm. We show that the Pearson R coefficient can measure how differential expression in one gene correlates with differential expression in a second gene.
Experimental and Molecular Predictions of the Adjuvanticity of Snail Mucin on Hepatitis B Vaccine in Albino Mice
Authors: Joshua Parker E. , Nwauzor Cynthia O. , Odimegwu Damian C. , Ukachukwu Uzochukwu G. , Asomadu Rita O. , Ezeorba Timothy P. C.
Published: January 2021

Although aluminum-containing adjuvants are widely used in human vaccination due to their excellent safety profile, they exhibit low effectiveness with many recombinant antigens. This study investigated the adjuvanticity of snail mucin with recombinant Hepatitis B Vaccine (rHBsAg). Twenty-five (25) female mice distributed unbiasedly into 5 groups were used in the study and were administered different rHBsAg/Mucin formulation at 7 days intervals. Blood samples were collected a day following the administration for analysis. The results of liver function and body weight analysis were indications that snail mucin had no adverse effect on the mice. The treatment group (administer mucin and rHBsAg) showed significantly (P<0.05) higher mean titres of anti-HBsAg antibodies when compared with the negative controls and the positive control administered with two doses of rHBsAg. Furthermore, a comparable immune response to positive control administered with three doses rHBaAG was recorded.In silicoprediction, studies of the protein-protein interaction of a homology modelled snail mucus protein and HBsAg gave an indication of enhanced HBV antigen-antibody interaction. Therefore, this study has shown that snail mucin possesses some adjuvant properties and enhances immune response towards rHBsAg vaccine. However, there is a need for further molecular dynamics studies to understand its mechanism of action.
Characterization of Critical Determinants of ACE2-RBD Interaction
Authors: Brown Emily E. F. , Rezaei Reza , Jamieson Taylor , Dave Jaahnavi , Martin Nikolas T. , Singaravelu Ragunath , Crupi Mathieu J.F. , Boulton Stephen , Tucker Sarah , Duong Jessie , Poutou Joanna , Pelin Adrian , Yasavoli-Sharahi Hamed , Taha Zaid , Arulanandam Rozanne , Surendran Abera , Ghahremani Mina , Austin Bradley , Matar Chantal , Diallo Jean-Simon , Bell John C. , Ilkow Carolina S. , Azad Taha
Published: January 2021

Despite sequence similarity to SARS-CoV-1, SARS-CoV-2 has demonstrated greater widespread virulence and unique challenges to researchers aiming to study its pathogenicity in humans. The interaction of the viral receptor binding domain (RBD) with its main host cell receptor, angiotensin-converting enzyme 2 (ACE2), has emerged as a critical focal point for the development of anti-viral therapeutics and vaccines. Utilizing our recently developed NanoBiT technology-based biosensor, we selectively identify and characterize the impact of mutating certain amino acid residues in the RBD of SARS-CoV-2 and in ACE2. Specifically, we examine the mutational effects on RBD-ACE2 binding ability, before and after the addition of competitive inhibitors, as well as neutralizing antibody activity. These critical determinants of virus-host interactions may provide more effective targets for ongoing vaccines, drug development, and potentially pave the way for determining the genetic variation underlying disease severity.
Comparative genomics reveals factors associated with phenotypic expression ofWolbachia
Authors: Baião Guilherme Costa , Janice Jessin , Galinou Maria , Klasson Lisa
Published: January 2021

Wolbachiais a widespread, vertically transmitted bacterial endosymbiont known for manipulating arthropod reproduction. Its most common form of reproductive manipulation is Cytoplasmic incompatibility (CI), observed when a modification in the male sperm leads to embryonic lethality unless a compatible rescue factor is present in the female egg. CI attracts scientific attention due to its implications for host speciation and in the use ofWolbachiafor controlling vector-borne diseases. However, our understanding of CI is complicated by the complexity of the phenotype, whose expression depends on both symbiont and host factors. In the present study, we perform a comparative analysis of nine completeWolbachiagenomes with known CI properties in the same genetic host background,Drosophila simulansSTC. We describe genetic differences between closely related strains and uncover evidence that phages and other mobile elements contribute to rapid evolution of both genomes and phenotypes ofWolbachia. Additionally, we identify both known and novel genes associated with the modification and rescue functions of CI. We combine our observations with published phenotypic information and discuss how variability incifgenes, novel CI-associated genes andWolbachiatiter might contribute to poorly understood aspects of CI such as strength and bidirectional incompatibility. We speculate that high titer CI strains could be better at invading new hosts already infected with a CIWolbachia, due to a higher rescue potential, and suggest that titer might thus be a relevant parameter to consider for future strategies using CIWolbachiain biological control.
The SON RNA splicing factor is required for intracellular trafficking that promotes centriole assembly
Authors: Stemm-Wolf Alexander J. , O’Toole Eileen T. , Sheridan Ryan M. , Morgan Jacob T. , Pearson Chad G.
Published: January 2021

Control of centrosome assembly is critical for cell division, intracellular trafficking and cilia. Regulation of centrosome number occurs through the precise duplication of centrioles that reside in centrosomes. Here we explored transcriptional control of centriole assembly and find that the RNA splicing factor SON is specifically required for completing procentriole assembly. Whole genome mRNA sequencing identified genes whose splicing and expression are affected by the reduction of SON, with an enrichment in genes involved in the microtubule cytoskeleton, centrosome and centriolar satellites. SON is required for the proper splicing and expression ofCEP131which encodes a major centriolar satellite protein and is required to organize the trafficking and microtubule network around the centrosomes. This study highlights the importance of the distinct microtubule trafficking network that is intimately associated with nascent centrioles and is responsible for procentriole development.
A thermodynamic model for water activity and redox potential in evolution and development
Authors: Dick Jeffrey M.
Published: January 2021

Reactions involving water and oxygen are basic features of geological and biological processes. To understand how life interacts with its environment requires monitoring interactions with H2O and O2 at timescales relevant to not only organismal growth but also billions of years of geobiological evolution. Here, chemical transformations intrinsic to evolution and development were characterized by analyzing data from recent phylostratigraphic and proteomic studies. This two-stage analysis involves obtaining chemical metrics (carbon oxidation state and stoichiometric hydration state) from the elemental compositions of proteins followed by modeling the relative stabilities of target proteins against a proteomic background to infer thermodynamic parameters (oxygen fugacity, water activity, and virtual redox potential (Eh)). The main results of this study are a rise in carbon oxidation state of proteins spanning the time of the Great Oxidation Event, a rise in virtual redox potential that coincides with the likely emergence of aerobic metabolism, a rise in carbon oxidation state of proteins inferred from the transcriptome in late stages of Bacillus subtilis biofilm growth, and a drop in stoichiometric hydration state of the fruit fly developmental proteome at the same time as a drop in organismal water content. Stoichiometric hydration state also decreases for proteins with more recent gene ages and through stages of biofilm development, leading to predictions of higher hydration potentials at earlier time points. By building chemical representations of protein evolution and developmental proteomes, exciting new types of geobiochemical proxies can be developed.
RGI-GOLVEN signalling promotes FLS2 abundance to regulate plant immunity
Authors: Stegmann Martin , Zecua-Ramirez Patricia , Ludwig Christina , Lee Ho-Seok , Peterson Brenda , Nimchuk Zachary L. , Belkhadir Youssef , Hückelhoven Ralph
Published: January 2021

Endogenous plant signalling peptides regulate developmental and growth-related processes. Recent research indicates that some of these peptides are classified as phytocytokines as they have regulatory functions during plant immune responses. However, the mechanistic basis for phytocytokine-mediated immune modulation remains largely elusive. Here, we identify GOLVEN2 (GLV2) peptides as novel phytocytokines inArabidopsis thaliana. By peptide application, precursor overexpression and loss-of-function studies we show that GLV2 enhances sensitivity of plants to elicitation with the bacterial flagellin epitope flg22. GLV2 is perceived by ROOT MERISTEM GROWTH FACTOR 1 INSENSITIVE (RGI) receptors and RGI3 forms an flg22-induced complex with the flg22-receptor FLAGELLIN SENSITIVE 2, suggesting that RGIs are part of activated pattern recognition receptor signalling platforms. GLV2 perception increases posttranscriptional FLS2 abundance and RGIs promote FLS2 protein accumulation. Thus, GLV-RGI signalling controls above ground plant immunity via a novel mechanism of phytocytokine activity.
Genomic evolution of epitopes and Low Complexity Regions in Plasmodium
Authors: Medley Sarah N. , Beaudet Alyssa , Piontkivska Helen , Battistuzzi Fabia U.
Published: January 2021

Despite decades-long efforts to eradicate malaria, pathogens genomic complexity and variability continue to pose major challenges for the vaccine and drug development. Here we examined the evolutionary history of epitopes and epitope-like regions to determine whether they share underlying evolutionary mechanisms and potential functions that are relevant to pathogens interactions with the host immune response. Our comparative sequence analyses contrasted patterns of sequence conservation, amino acid composition, and protein structure of epitopes and low complexity regions (LCRs) in 21 Plasmodium species. Our results revealed many similarities in amino acid composition and preferred secondary structures between epitopes and LCRs; however, we also identified differences in evolutionary trends where LCRs exhibit overall lower sequence conservation and higher disorder. We also found that both epitopes and LCRs have a wide array of configurations, with various levels of sequence conservation and structural order. We propose that such combination of different levels of conservation and structural order between epitopes and LCRs in the same gene play a role in maintaining the functional integrity required by the pathogen along with the variability necessary to evade the host immune response, with LCRs playing a role in the evasion particularly in the vicinity of conserved epitopes. Overall, our results suggest that there are at least two categories of LCRs, where some LCRs play a potential protective role for conserved (ordered) epitopes because of their variable (or disordered) sequence, while others are less disordered and are as conserved as epitopes. The former ones may be an evolutionary necessity for Plasmodium to maintain the diversity of epitopes, while the latter category may serve currently unknown function(s) and deserve to be examined in greater detail. Our findings show that there may be many more candidate targets for future anti-malarial treatments than initially thought and that some of these targets may work across strains and species.
Mitophagy antagonism by Zika virus reveals Ajuba as a regulator of PINK1-Parkin signaling, PKR-dependent inflammation, and viral invasion of tissues
Authors: Ponia Sanket S. , Robertson Shelly J. , McNally Kristin L. , Sturdevant Gail L. , Lewis Matthew , Jessop Forrest , Bosio Catherine M. , Kendall Catherine , Gallegos Dylan , Hay Arielle , Schwartz Cindi , Rosenke Rebecca , Saturday Greg , Martens Craig , Best Sonja M.
Published: January 2021

Dysregulated inflammation dominated by chemokine expression is a key feature of disease following infection with the globally important human pathogens, Zika virus (ZIKV) and dengue virus, but a mechanistic understanding of how pro-inflammatory responses are initiated is lacking. Mitophagy is a quality control mechanism that regulates innate immune signaling and cytokine production through selective degradation of damaged mitochondria. Here, we demonstrate that ZIKV NS5 antagonizes mitophagy by binding to the host protein Ajuba and preventing its translocation to depolarized mitochondria where it is required for PINK1 activation and downstream signaling. Consequent mitophagy suppression amplified the production of pro-inflammatory chemokines through PKR sensing of mitochondrial RNA. In Ajuba−/−mice, ZIKV induced early expression of pro-inflammatory chemokines associated with significantly enhanced dissemination to tissues. This work identifies Ajuba as a critical regulator of mitophagy, and demonstrates a role for mitophagy in limiting systemic inflammation following infection by globally important human viruses.
ZCCHC8 is required for the degradation of pervasive transcripts originating from multiple genomic regulatory features
Authors: Collins Joshua W. , Martin Daniel ,   Genomics and Computational Biology Core, Wang Shaohe , Yamada Kenneth M.
Published: January 2021

The vast majority of mammalian genomes are transcribed as non-coding RNA in what is referred to as “pervasive transcription.” Recent studies have uncovered various families of non-coding RNA transcribed upstream of transcription start sites. In particular, highly unstable promoter upstream transcripts known as PROMPTs have been shown to be targeted for exosomal degradation by the nuclear exosome targeting complex (NEXT) consisting of the RNA helicase MTR4, the zinc-knuckle scaffold ZCCHC8, and the RNA binding protein RBM7. Here, we report that in addition to its known RNA substrates, ZCCHC8 is required for the targeted degradation of pervasive transcripts produced at CTCF binding sites, open chromatin regions, promoters, promoter flanking regions, and transcription factor binding sites. Additionally, we report that a significant number of RIKEN cDNAs and predicted genes display the hallmarks of PROMPTs and are also substrates for ZCCHC8 and/or NEXT complex regulation suggesting these are unlikely to be functional genes. Our results suggest that ZCCHC8 and/or the NEXT complex may play a larger role in the global regulation of pervasive transcription than previously reported.
Styles of mesoscale brittle deformations associated with the Miocene folding of the Taishu Group, Tsushima, between the Japan Sea and East China Sea backarc basins
Authors: Yamaji Atsushi , Yanagisawa Tatsuhiko , Sato Katsushi
Published: February 2021

The Taishu Group is a folded, Eocene–Lower Miocene, thick sedimentary package exposed widely on Tsushima Island between the Japan Sea and East China Sea. This location makes the strata important to understand tectonics and paleo‐environments in the Far East, but the timing of the folding is controversial. We studied the styles of brittle deformations of the strata. It was found that flextural‐slip folds were dominant. Mesoscale faults were classified into two groups: NE–SW trending reverse faults and NW–SE trending strike‐slip faults. Members of both the groups showed movements largely perpendicular to the fold axes. The latter group consisted of sinistral and dextral faults. Accordingly, we interpreted that they were transfer faults activated during the folding. Consequently, mesoscale faults and flexural‐slip faults evidence the map‐scale plane strain of the Taishu Group in the plane perpendicular to the NE‐trending fold axes. There were few transpressional deformations in the group. This is inconsistent with the transpression hypothesis for explaining the simultaneous folding and Japan Sea opening. Another hypothesis in which the folds in Tsushima are regarded as an onshore part of the Taiwan‐Shinji fold belt is inconsistent with the timing of folding suggested by mining geologists to be consistent with and contemporaneous with this deformation. On the other hand, we found that dolerite dikes and sills were involved in the folding. Therefore, we conclude that the folding began during the late Early Miocene time and climaxed during the ore mineralization at around 15 Ma. We suggest that the folding in Tsushima was the easternmost manifestation of the compressional regime around the Yellow Sea and East China Sea in the Early to early Middle Miocene, and that the compression was brought about by the arrival of the Philippine Sea plate to initiate buoyant subduction under Kyushu.
Adapting to supply‐and‐demand emerging trends for antigen‐negative red blood cell units
Authors: Trépanier Patrick , Chevrier Marie‐Claire , Constanzo Yanez Jessica , Baillargeon Nadia , St‐Pierre Christine , Perreault Josée
Published: January 2021

Background

A global downtrend in blood usage has been observed by many countries, while the demand for antigen‐negative red blood cell (RBC) units used in antigen‐matched transfusions keeps increasing. The declining number of units collected exposes blood providers to a rapidly evolving supply challenge.

Methods

This study was conducted retrospectively with use of internal data analysis to weigh Québec's situation regarding global and antigen‐negative RBC demand, to measure the effects of community‐directed recruitment and blood drives, and to evaluate the benefits of mass‐scale RBC genotyping.

Results

Our findings confirm a global RBC usage downtrend of over 20% total in the past 10 years with a steady antigen‐negative usage and highlight the most requested negative antigen combinations. Our data also show our +39.5% progress regarding the number of Black donors recruited for antigen matching of patients with sickle cell disease in the past 3 years, as well as a constantly growing number of just‐in‐time blood collection for complex orders. Finally, our data summarize the efficiency of our mass‐scale RBC genotyping efforts.

Conclusion

Altogether, this study confirms the demand trends for regular and antigen‐negative RBC units in Québec and the efficient effects of our recruitment and typing strategies.
A High Resolution Simulation of a Single Shock-Accelerated Particle
Authors: Maxon W. Curtis , Nielsen Tanner , Denissen Nicholas , Regele Jonathan D. , McFarland Jacob
Published: January 2021

Particle drag models, which capture macroviscous and pressure effects, have been developed over the years for various flow regimes to enable cost effective simulations of particle-laden flows. The relatively recent derivation by Maxey and Riley has provided an exact equation of motion for spherical particles in a flow field based on the continuum assumption. Many models that have been simplified from these equations have provided reasonable approximations; however, the sensitivity of particle-laden flows to particle drag requires a very accurate model to simulate. To develop such a model, a two-dimensional axisymmetric Navier–Stokes direct numerical simulation of a single particle in a transient, shock-driven flow field was conducted using the hydrocode FLAG. FLAGs capability to run arbitrary Lagrangian-Eulerian hydrodynamics coupled with solid mechanic models makes it an ideal code to capture the physics of the flow field around and in the particle as it is shock-accelerated—a challenging regime to study. The goal of this work is twofold: to provide a validation for FLAGs Navier–Stokes and heat diffusion solutions and to provide a rationale for recent experimental particle drag measurements.
Supplemental Material: Autogenic translation and counter point bar deposition in meandering rivers
Authors: Sylvester Z. , al. et
Published: January 2021

Animations illustrating the evolution of counter point bars in the study area and in forward models.
Alamandine via MrgD receptor attenuates pulmonary fibrosis via NOX4 and autophagy pathway
Authors: Liu Qingxia , Zheng Bojun , Zhang Yue , Huang Wenhui , Hong Qiaohui , Meng Ying
Published: January 2021

Alamandine (ALA) and its receptor MrgD were recently identified as components of the renin-angiotensin system, which confer protection against cardio-fibrosis and renal-fibrosis; however, the effects of ALA on pulmonary fibrosis are unknown. This study was designed to serve two goals: (i) to evaluate the ALA/MrgD axis ability in the prevention of angiotensin II (Ang II) – induced pulmonary fibrosis in fibroblasts, and (ii) to determine the effect of ALA in bleomycin (BLM) – treated C57B/6 mice. In vivo experiments revealed that the treatment of C57B/6 mice with ALA prevented BLM-induced fibrosis, and these findings were similar to those reported for pirfenidone. The antifibrosis actions of ALA were mediated via alleviation of oxidative injury and autophagy induction. In addition, in vitro studies revealed that ALA treatment attenuated Ang II–induced α-collagen I, CTGF, and α-SMA production in fibroblast which was blocked by D-Pro7-Ang-(1-7), a MrgD antagonist. This led to alleviation of oxidative injury and induction of autophagy similar to that reported for rapamycin. This study demonstrated that ALA via MrgD receptor reduced pulmonary fibrosis through attenuation of oxidative injury and induction of autophagy.
Universality-breaking effects in $$e^+e^-$$ hadronic production processes
Authors: Boglione M. , Simonelli A.
Published: January 2021

Recent BELLE measurements provide the cross section for single hadron production in $$e^+e^-$$

e
+

e
-

annihilations, differential in thrust and in the hadron transverse momentum with respect to the thrust axis. Universality breaking effects due to process-dependent soft factors make it very difficult to relate this cross sections to those corresponding to hadron-pair production in $$e^+e^-$$

e
+

e
-

annihilations, where transverse momentum dependent (TMD) factorization can be applied. The correspondence between these two cross sections is examined in the framework of the Collins-Soper-Sterman factorization, in the collinear as well as in the TMD approach. We propose a scheme that allows to relate the TMD parton densities defined in 1-hadron and in 2-hadron processes, neatly separating, within the soft and collinear parts, the non-perturbative terms from the contributions that can be calculated perturbatively. The regularization of rapidity divergences introduces cut-offs, the arbitrariness of which will be properly reabsorbed by means of a mechanism closely reminiscent of a gauge transformation. In this way, we restore the possibility to perform global phenomenological studies of TMD physics, simultaneously analyzing data belonging to different hadron classes.
Scalar electrodynamics and the decays of the neutral pion
Authors: Bruce Stanley A.
Published: January 2021

We propose an effective model of scalar electrodynamics (SED) in which a (nonscalar) Dirac electron field is included in the general Lagrangian density. This approach is intended to predict possible electrodynamics processes with a discussion of the role of pions that might be significant in QED.
Strong CP and solitonic axions resonant from Higgs’ cusp-kinks radiative corrections
Authors: Maalouf Hani W.
Published: January 2021

A limiting algebraic resonance seems to recuperate the pseudo-scalar Higgs from the simultaneous breaking process. On an energy kernel consideration, an imposed nonharmonic boundary exclusion provides a basis for the scaling (proved derived from the conformal classes) of its extending as radiative correction diagrams, plus whose anomalies eliminate upon reaching geometrically a type of steep power as linked to, completely from the curvature.

A CP violating form, then shows after the appearance of both a parity, plus a polarization defiance, together with the Higgs decoupled to the favor of the equivalence class for a scalar coupling, leading to the types of allowed UV fixed points, with the possible fading of some of its parametric resonances (tachyon) by quantum corrections, into then the estimation of consecutive QCD and fuzzy axion masses by taking into account that their interaction (dimensional) operators such which have the completeness, both of metric and/or gauge types, being so then, first with KSVZ (showing as being resonant along with sterile neutrinos) and DFS types or second with creation of an axion soliton. The fit into the phenomenological constraints is also checked.
Symmetries of theq-NKdV hierarchy
Authors: Liu Wenna , Li Chuanzhong
Published: January 2021

In this paper, the additional symmetries and the string equation of the [Formula: see text]-NKdV hierarchy are established basing on the Orlov–Shulman’s [Formula: see text] operator, and then some properties are also given. Next, we construct the quantum torus symmetry of the [Formula: see text]-NKdV hierarchy and further derive the quantum torus constraints on the tau function of the [Formula: see text]-NKdV hierarchy. Comparing to the [Formula: see text] infinite-dimensional Lie symmetry, this quantum torus symmetry has a nice algebraic structure with double indices. Finally, we study the ghost symmetry of the multicomponent [Formula: see text]-NKdV hierarchy.
Lump solutions to a (2+1)-dimensional fourth-order nonlinear PDE possessing a Hirota bilinear form
Authors: Ma Wen-Xiu , Manukure Solomon , Wang Hui , Batwa Sumayah
Published: January 2021

Through the Hirota bilinear formulation, a (2+1)-dimensional combined fourth-order nonlinear equation is proposed, which possesses lump solutions. Two classes of lump solutions are presented explicitly in terms of the coefficients in the combined nonlinear equation. A set of examples of equations is provided to show the diversity of the considered combined nonlinear equation, together with three-dimensional plots, [Formula: see text]-curves and [Formula: see text]-curves of two specific lump solutions in two cases of the combined equation.
Self-adjointness and conservation laws of Burgers-type equations
Authors: Wang Haifeng , Zhang Yufeng
Published: January 2021

This paper focuses on the self-adjointness of some Burgers-type equations based on the existing definitions. It follows that the corresponding Frobenius Burgers-type equations are constructed by taking values in a commutative subalgebra [Formula: see text]. In order to investigate the self-adjointness of these Frobenius-type equations, we introduce a few additional notations and definitions. Additionally, the conservation laws are obtained of several equations studied by using symmetries.
A novel algorithm for community detection based on resistance distance and similarity
Authors: Lu Pengli , Yu Zhou , Guo Yuhong
Published: January 2021

Community detection is important for understanding the structure and function of networks. Resistance distance is a kind of distance function inherent in the network itself, which has important applications in many fields. In this paper, we propose a novel community detection algorithm based on resistance distance and similarity. First, we propose the node similarity, which is based on the common nodes and resistance distance. Then, we define the distance function between nodes by similarity. Furthermore, we calculate the distance between communities by using the distance between nodes. Finally, we detect the community structure in the network according to the nearest-neighbor nodes being in the same community. Experimental results on artificial networks and real-world networks show that the proposed algorithm can effectively detect the community structures in complex networks.
Generating new nonclassical state by repeatedly operating number operator on coherent state
Authors: Ren Gang , Du Jian-Ming , Zhang Wen-Hai
Published: January 2021

In this paper, using the principle of quantum state superposition, we report a nonclassical quantum state which is constructed by repeatedly operating the number operator on the coherent state. Nonclassical effects of this state are discussed by photon-number distribution, sub-Poissonian statistics, anti-bunching and negativity of Wigner function and squeezing effect. Our work provides an important nonclassical resource, which may be used in quantum communication and quantum optics.
Assessment of bioconvection in magnetized Sutterby nanofluid configured by a rotating disk: A numerical approach
Authors: Khan M. Ijaz , Waqas Hassan , Farooq Umar , Khan Sami Ullah , Chu Yu-Ming , Kadry S.
Published: January 2021

Owing to the growing interest of bioconvection flow of nanomaterials, many investigations on this topic have been performed, especially in this decade. The bioconvection flow of nanofluid includes some novel significance in era of biotechnology and bio-engineering like bio-fuels, microbial enhanced oil recovery, enzymes, pharmaceutical applications, petroleum engineering, etc. The current analysis aims to explore the various thermal properties of Sutterby nanofluid over rotating and stretchable disks with external consequences of variable thermal conductivity, heat absorption/generation consequences, activation energy and thermal radiation. The considered flow problem is changed into dimensionless form with convenient variables. The numerical structure for the obtained non-dimensional equations is numerically accessed with built-in shooting technique. The consequences of various physical parameters are observed for enhancement of velocity, temperature, concentration and motile microorganism. It is noted that both axial and tangential velocity components decrease with Reynolds number and buoyancy ratio parameter. The nanofluid concentration improves with activation energy and concentration Biot number. Moreover, an improved microorganisms profile is noticed with microorganism Biot number and bioconvection Rayleigh number.
THE ELECTRONIC STRUCTURE AT ORGANIC–2D MATERIAL HETEROINTERFACES
Authors: HUANG YU LI , WEE ANDREW THYE SHEN
Published: January 2021

Organic–2D material heterostructures have attracted intensive research interest due to their intriguing properties, with a wide range of potential applications in multifunctional flexible electronic and optoelectronic devices. Central to the realization of such devices is a fundamental understanding of the electronic structures at organic–2D material heterointerfaces. The energy level alignment (ELA) at the interface is of paramount importance because it determines the charge transfer barriers between the two materials in contact. In this paper, we discuss the physical mechanisms determining the ELAs, with special attention on interfacial charge transfer at the heterostructures. We review the current understanding of electronic properties at the heterointerfaces formed by the integration of organics with graphene and 2D transition metal dichalcogenides (TMDs), and conclude with a perspective on the future development of organic–2D material heterostructure.
On m-quasi-Einstein spacetimes
Authors: Ali Shaikh Absos , Kumar Hui Shyamal , Patra Akshoy
Published: January 2021

In this paper, we have studied [Formula: see text]-quasi-Einstein spacetimes. Some basic results of such spacetimes are derived. Perfect and viscous fluid [Formula: see text]-quasi-Einstein spacetimes are also studied and the expressions of pressure, cosmological constant and energy density are obtained. We have proved that if the generator [Formula: see text] of an [Formula: see text]-quasi-Einstein spacetime is a Killing vector field, then the spacetime is either conformally flat or of Petrov-type [Formula: see text]. It is also shown that if the function [Formula: see text] of an [Formula: see text]-quasi-Einstein spacetime satisfying Einstein’s equation is harmonic and the matter distribution is perfect fluid, then Segre’ characteristics of the Ricci tensor is [(1,1), 1]. Finally, an example is constructed for the proper existence of such a spacetime.
Hom-Lie group and hom-Lie algebra from Lie group and Lie algebra perspective
Authors: Merati S. , Farhangdoost M. R.
Published: January 2021

A hom-Lie group structure is a smooth group-like multiplication on a manifold, where the structure is twisted by a isomorphism. The notion of hom-Lie group was introduced by Jiang et al. as integration of hom-Lie algebra. In this paper we want to study hom-Lie group and hom-Lie algebra from the Lie group’s point of view. We show that some of important hom-Lie group issues are equal to similar types in Lie groups and then many of these issues can be studied by Lie group theory.
Bianchi type I Universe: An extension of ΛCDM model
Authors: Prasad Rajendra , Gupta Lalit Kumar , Beesham A. , Goswami G. K. , Yadav Anil Kumar
Published: January 2021

In this paper, we investigate a Bianchi type I exact Universe by taking into account the cosmological constant as the source of energy at the present epoch. We have performed a [Formula: see text] test to obtain the best fit values of the model parameters of the Universe in the derived model. We have used two types of data sets, viz., (i) 31 values of the Hubble parameter and (ii) the 1048 Pantheon data set of various supernovae distance moduli and apparent magnitudes. From both the data sets, we have estimated the current values of the Hubble constant, density parameters [Formula: see text] and [Formula: see text]. The dynamics of the deceleration parameter shows that the Universe was in a decelerating phase for redshift [Formula: see text]. At a transition redshift [Formula: see text], the present Universe entered an accelerating phase of expansion. The current age of the Universe is obtained as [Formula: see text] Gyrs. This is in good agreement with the value of [Formula: see text] calculated from the Plank collaboration results and WMAP observations.
海外传统音乐的生存逻辑探赜
Authors: 臧 卓敏
Published: January 2021

早期华人出国谋生时，常带上家乡的音乐，以寄托思乡之情。随着当代华人身份认同的转变，传统音乐的海外生存状况今非昔比。然而，在新加坡这个多元文化大融合的国度，一个具有鲜明地域特征的传统音乐社团—湘灵音乐社，却顺应环境的变革，突破地域文化的局限，以传统与创新相结合的思路将新加坡南音发扬光大，并成功登上世界音乐的舞台。本文通过追溯新加坡南音社团锐意创新与坚守传统并进的传承轨迹，探索新加坡南音“以变应变”、“以传播促传承”的生存策略的可行性，思考传统音乐的海外生存之道。