bluuebunny/crossref_metadata_2025_split huggingface dataset:
IFN-τ mediated miR-26a targeting PTEN to activate PI3K/AKT signalling to alleviate the inflammatory damage of bEECs
Authors: Liu Junfeng , Liang Qin , Wang Tianyang , Ma Bei , Wang Xin , Li Ping , Shaukat Aftab , Guo Xuefeng , Deng Ganzhen 
Published: June 2022

AbstractEndometritis is the failure of embryo implantation and an important cause of infertility in dairy cows. IFN-τ is a type I interferon unique to ruminants. In regulating the process of inflammatory response, IFN-τ can be expressed through MicroRNAs (miRNAs) to regulate the process of inflammation. However, IFN-τ regulates lipopolysaccharide (LPS)-induced inflammatory injury of bEECs through the highly conserved miR-26a in mammals, and the mechanism remains unclear. Bovine endometrial epithelial cells (bEECs)were isolated and cultured to establish an inflammatory injury model. RT–qPCR and ELISA were used to detect the secretion of inflammatory factors. Dual-luciferase assays and target gene silencing assays determine the regulatory role of miRNAs. The target protein was detected by immunofluorescence and western blotting. This study showed that the expression of miR-26a was significantly down-regulated in mouse endometrium inflammatory injury tissue and LPS stimulated bEECs; and IFN-τ reversed the expression of miR-26a. The study also showed that the overexpression of miR-26a significantly inhibited the secretion of pro-inflammatory cytokines IL-1β, IL-6 and TNF-α. In addition, studies have shown that miR-26a inhibits its translation by targeting PTEN 3′-UTR, which in turn activates the Phosphatidylinositide 3-kinases/protein kinase B (PI3K/AKT) pathway, so that nuclear factor kappa-B (NF-κB) signaling is inhibited. In summary, the results of this study further confirm that IFN-τ as an anti-inflammatory agent can up-regulate the expression of miR-26a and target the PTEN gene to inhibit the inflammatory damage of bEECs.
Metagenomic pipeline for identifying co-infections among distinct SARS-CoV-2 variants of concern: study cases from Alpha to Omicron
Authors: Molina-Mora Jose Arturo , Cordero-Laurent Estela , Calderón-Osorno Melany , Chacón-Ramírez Edgar , Duarte-Martínez Francisco 
Published: June 2022

AbstractConcomitant infection or co-infection with distinct SARS-CoV-2 genotypes has been reported as part of the epidemiological surveillance of the COVID-19 pandemic. In the context of the spread of more transmissible variants during 2021, co-infections are not only important due to the possible changes in the clinical outcome, but also the chance to generate new genotypes by recombination. However, a few approaches have developed bioinformatic pipelines to identify co-infections. Here we present a metagenomic pipeline based on the inference of multiple fragments similar to amplicon sequence variant (ASV-like) from sequencing data and a custom SARS-CoV-2 database to identify the concomitant presence of divergent SARS-CoV-2 genomes, i.e., variants of concern (VOCs). This approach was compared to another strategy based on whole-genome (metagenome) assembly. Using single or pairs of sequencing data of COVID-19 cases with distinct SARS-CoV-2 VOCs, each approach was used to predict the VOC classes (Alpha, Beta, Gamma, Delta, Omicron or non-VOC and their combinations). The performance of each pipeline was assessed using the ground-truth or expected VOC classes. Subsequently, the ASV-like pipeline was used to analyze 1021 cases of COVID-19 from Costa Rica to investigate the possible occurrence of co-infections. After the implementation of the two approaches, an accuracy of 96.2% was revealed for the ASV-like inference approach, which contrasts with the misclassification found (accuracy 46.2%) for the whole-genome assembly strategy. The custom SARS-CoV-2 database used for the ASV-like analysis can be updated according to the appearance of new VOCs to track co-infections with eventual new genotypes. In addition, the application of the ASV-like approach to all the 1021 sequenced samples from Costa Rica in the period October 12th–December 21th 2021 found that none corresponded to co-infections with VOCs. In conclusion, we developed a metagenomic pipeline based on ASV-like inference for the identification of co-infection with distinct SARS-CoV-2 VOCs, in which an outstanding accuracy was achieved. Due to the epidemiological, clinical, and molecular relevance of the concomitant infection with distinct genotypes, this work represents another piece in the process of the surveillance of the COVID-19 pandemic in Costa Rica and worldwide.
Deep learning-based lesion subtyping and prediction of clinical outcomes in COVID-19 pneumonia using chest CT
Authors: Bermejo-Peláez David , San José Estépar Raúl , Fernández-Velilla María , Palacios Miras Carmelo , Gallardo Madueño Guillermo , Benegas Mariana , Gotera Rivera Carolina , Cuerpo Sandra , Luengo-Oroz Miguel , Sellarés Jacobo , Sánchez Marcelo , Bastarrika Gorka , Peces Barba German , Seijo Luis M. , Ledesma-Carbayo María J. 
Published: June 2022

AbstractThe main objective of this work is to develop and evaluate an artificial intelligence system based on deep learning capable of automatically identifying, quantifying, and characterizing COVID-19 pneumonia patterns in order to assess disease severity and predict clinical outcomes, and to compare the prediction performance with respect to human reader severity assessment and whole lung radiomics. We propose a deep learning based scheme to automatically segment the different lesion subtypes in nonenhanced CT scans. The automatic lesion quantification was used to predict clinical outcomes. The proposed technique has been independently tested in a multicentric cohort of 103 patients, retrospectively collected between March and July of 2020. Segmentation of lesion subtypes was evaluated using both overlapping (Dice) and distance-based (Hausdorff and average surface) metrics, while the proposed system to predict clinically relevant outcomes was assessed using the area under the curve (AUC). Additionally, other metrics including sensitivity, specificity, positive predictive value and negative predictive value were estimated. 95% confidence intervals were properly calculated. The agreement between the automatic estimate of parenchymal damage (%) and the radiologists’ severity scoring was strong, with a Spearman correlation coefficient (R) of 0.83. The automatic quantification of lesion subtypes was able to predict patient mortality, admission to the Intensive Care Units (ICU) and need for mechanical ventilation with an AUC of 0.87, 0.73 and 0.68 respectively. The proposed artificial intelligence system enabled a better prediction of those clinically relevant outcomes when compared to the radiologists’ interpretation and to whole lung radiomics. In conclusion, deep learning lesion subtyping in COVID-19 pneumonia from noncontrast chest CT enables quantitative assessment of disease severity and better prediction of clinical outcomes with respect to whole lung radiomics or radiologists’ severity score.
Rotor strength and critical speed analysis of a vertical long shaft fire pump connected with different shaft lengths
Authors: Song Haiqin , Zhang Jinfeng , Zhang Fan 
Published: June 2022

AbstractThe vertical long shaft fire pump (VLSFP) is mainly used in fire-fighting places far away from land and lacking large amounts of water supply. The paper selected the XBC18-178-240LC3 model of VLSFP as the research object. First, the experimental–numerical hydraulic performance of the single-VLSFP was carried out, and then the hydraulic performance of the multi-VLSFP was analyzed by the same numerical simulation method as single-VLSFP. After that, three rotor models (Z4 model, Z5 model-original model and Z6 model) were designed by modeling software, connected by different length and number of the shaft section under the same total length of the intermediate shafts. Finally, the rotor’s strength and critical speed of three models were analyzed and checked via the CFD simulation and the Workbench software. The study mainly found: (1) Through the strength check of the impeller, maximum equivalent stress of the three models was less than the allowable stress of the rotor material, which indicated the structural design of them met the safety requirement; (2) Through the critical speed check of the shafting rotor, the working speed of the VLSFP was lower than 0.8 times the first-order critical speed of the three models, which indicated the rotor could avoid the resonance and the structure of the three models met the dynamic design requirement. According to the stress check of the impeller and the critical speed check of the shafting rotor, combining the time and labor cost when the VLSFP was installed and disassembled many times before and after the test or operation, the paper selected the Z4 model to be the optimal model, which could provide a theoretical support for the subsequent structure design optimization of the vertical long shaft fire pump.
Dimorphic life cycle through transverse division in burrowing hard coral Deltocyathoides orientalis
Authors: Sentoku Asuka , Shimizu Keisuke , Naka Tsubasa , Tokuda Yuki 
Published: June 2022

AbstractThe azooxanthellate solitary scleractinian Deltocyathoides orientalis (family Turbinoliidae), which has bowl-shaped costate corallites, exhibits burrowing behavior on soft substrates and can adapt to an infaunal mode of life. Here, we describe previously unknown aspects of their life history and asexual mode of reproduction based on morphological and molecular phylogenetic analyses. The findings reveal that (1) D. orientalis exhibits asexual reproduction by transverse division; (2) smaller bowl-shaped costate anthocyathus derived from cylindrical to tympanoid anthocaulus were attached to hard substrates, including shell fragments and gravels on soft substrates; and (3) anthocyathus only reproduce sexually after division, and anthocaulus was found to regrow and repeatedly produce anthocyathi through transverse division. The bowl-shaped corallum morphology of the anthocyathus just after division might reduce the time required for skeletal formation to enable infaunal adaption after transverse division. Immediately after division, D. orientalis can smoothly shift to a burrowing lifestyle that efficiently utilizes soft-substrate environments, thus increasing its survival rate. The morphological formation of prospective anthocyathus in the anthocaulus stage is consequently thought to involve an increase in clonal individuals as well as adaptations for a burrowing free-living mode of life in the anthocyathus stage.
Triplet–triplet annihilation-based photon-upconversion to broaden the wavelength spectrum for photobiocatalysis
Authors: Hwang Se-Yeun , Song Dayoon , Seo Eun-Ji , Hollmann Frank , You Youngmin , Park Jin-Byung 
Published: June 2022

AbstractPhotobiocatalysis is a growing field of biocatalysis. Especially light-driven enzyme catalysis has contributed significantly to expanding the scope of synthetic organic chemistry. However, photoenzymes usually utilise a rather narrow wavelength range of visible (sun)light. Triplet–triplet annihilation-based upconversion (TTA-UC) of long wavelength light to shorter wavelength light may broaden the wavelength range. To demonstrate the feasibility of light upconversion we prepared TTA-UC poly(styrene) (PS) nanoparticles doped with platinum(II) octaethylporphyrin (PtOEP) photosensitizer and 9,10-diphenylanthracene (DPA) annihilator (PtOEP:DPA@PS) for application in aqueous solutions. Photoexcitation of PtOEP:DPA@PS nanoparticles with 550 nm light led to upconverted emission of DPA 418 nm. The TTA-UC emission could photoactivate flavin-dependent photodecarboxylases with a high energy transfer efficiency. This allowed the photodecarboxylase from Chlorella variabilis NC64A to catalyse the decarboxylation of fatty acids into long chain secondary alcohols under green light (λ = 550 nm).
Gene expression of the endocannabinoid system in endometrium through menstrual cycle
Authors: Tanaka Keisuke , Amoako Akwasi A. , Mortlock Sally , Rogers Peter A. W. , Holdsworth-Carson Sarah J. , Donoghue Jacqueline F. , Teh Wan Tinn , Montgomery Grant W. , McKinnon Brett 
Published: June 2022

AbstractEndocannabinoids mediate cellular functions and their activity is controlled by a complex system of enzymes, membrane receptors and transport molecules. Endocannabinoids are present in endometrium, a cyclical regenerative tissue requiring tightly regulated cellular mechanisms for maturation. The objective of this study was to investigate the gene expression of key elements involved in the endocannabinoid system across the menstrual cycle. RNA was isolated from endometrial tissue and genome-wide gene expression datasets were generated using RNA-sequencing. An a priori set of 70 genes associated with endocannabinoid system were selected from published literature. Gene expression across the menstrual cycle was analyzed using a moderated t test, corrected for multiple testing with Bonferroni’s method. A total of 40 of the 70 genes were present in > 90% of the samples, and significant differential gene expression identified for 29 genes. We identified 4 distinct regulation patterns for synthesizing enzymes, as well as a distinct regulation pattern for degradations and transporting enzymes. This study charts the expression of endometrial endocannabinoid system genes across the menstrual cycle. Altered expression of genes that control endocannabinoid may allow fine control over endocannabinoid concentrations and their influence on cellular function, maturation and differentiation as the endometrium matures through the menstrual cycle.
Method of calculating shear strength of rock mass joint surface considering cyclic shear degradation
Authors: Dong Shan , Zhang Heng , Peng Yulin , Lu Zhichun , Hou Weihua 
Published: June 2022

AbstractWhen a rock mass shears along a joint surface, the shear resistance is affected by joint surface undulations and friction between the contact regions. During an earthquake, the seismic load causes dynamic deterioration of the joint surface mechanical properties, mostly reflected as follows. (1) The peak shear strength of the joint surface decreases with an increase in the shear rate. (2) Under a seismic load cyclic shear, the undulant angle αk decreases. (3) Under a dynamic load, the friction coefficient of the joint surface is reduced. By studying the cyclic shear test of the joint surface, the strength deterioration effect of the joint surface under cyclic shearing is first analysed, and the equations of the dilatation angle and the basic friction angle of the joint surface under the cyclic shearing load are proposed. Then, starting with the effect of cyclic shear deterioration on the joint surface in the rock mass and the reduction in the dynamic friction coefficient between sliding rock blocks caused by relative velocity, an equation for calculating the shear strength of a rock mass joint surface under cyclic shear loading is recommended. Through two case calculations, the shear strength obtained using the proposed method is compared with the experimental results. The results show that the model proposed in this study is in good agreement with the experimental results and can also be used to calculate the structural surface shear strength of the asperity-rich sample. However, when the calculation equation is used to estimate the cyclic shear strength of the joint surface where the sum of the initial undulation angle and the basic friction angle is greater than 70°, there may be some errors in the calculation results.
Taxoid profile in endophytic fungi isolated from Corylus avellana, introduces potential source for the production of Taxol in semi-synthetic approaches
Authors: Mohammadi Ballakuti Narjes , Ghanati Faezeh , Zare-Maivan Hassan , Alipour Mozhgan , Moghaddam Mahtab , Abdolmaleki Parviz 
Published: June 2022

AbstractTaxol (Paclitaxel) and its derivative taxanes are widely used in chemotherapy and treatment of different types of cancer. Although the extracted taxanes from Taxus sp. are currently used in semi-synthetic production of Taxol, providing alternative always available sources is still a main concern. Due to availability and fast growth rate, microorganisms are much potent alternative sources for taxanes. In the present study, 249 endophytic fungi were isolated from Corylus avellana at six different locations of Iran, among which 18 species were capable to produce taxanes. Genotyping analysis indicated that 17 genera were ascomycetes but only one basidiomycete. Seven taxanes were detected and quantified in solid and suspension cultures by HPLC and their structures were confirmed by LC-Mass analysis. Among endophytes, CA7 had all 7 taxoids and CA1 had the highest Taxol yield. In 78% of endophytes transferring to liquid media was accompanied by increase of taxanes yield and increased taxan production and its release to media up to 90%. Evaluation of cytotoxicity indicated that extracts of all isolated fungi were lethal to MCF7 cells. Since endophytes produced remarkable amounts of taxanes, they can be suggested as alternative inexpensive and easily available resources for Taxol production in semi-synthesis plans.
Asynchronous division at 4–8-cell stage of preimplantation embryos affects live birth through ICM/TE differentiation
Authors: Mashiko Daisuke , Ikeda Zenki , Tokoro Mikiko , Hatano Yu , Yao Tatsuma , Kobayashi Tetsuya J. , Fukunaga Noritaka , Asada Yoshimasa , Yamagata Kazuo 
Published: June 2022

AbstractTo improve the performance of assisted reproductive technology, it is necessary to find an indicator that can identify and select embryos that will be born or be aborted. We searched for indicators of embryo selection by comparing born/abort mouse embryos. We found that asynchronous embryos during the 4–8-cell stage were predisposed to be aborted. In asynchronous mouse embryos, the nuclear translocation of YAP1 in some blastomeres and compaction were delayed, and the number of ICMs was reduced. Hence, it is possible that asynchronous embryos have abnormal differentiation. When the synchrony of human embryos was observed, it was confirmed that embryos that did not reach clinical pregnancy had asynchrony as in mice. This could make synchrony a universal indicator common to all animal species.
Patient-level proteomic network prediction by explainable artificial intelligence
Authors: Keyl Philipp , Bockmayr Michael , Heim Daniel , Dernbach Gabriel , Montavon Grégoire , Müller Klaus-Robert , Klauschen Frederick 
Published: June 2022

AbstractUnderstanding the pathological properties of dysregulated protein networks in individual patients’ tumors is the basis for precision therapy. Functional experiments are commonly used, but cover only parts of the oncogenic signaling networks, whereas methods that reconstruct networks from omics data usually only predict average network features across tumors. Here, we show that the explainable AI method layer-wise relevance propagation (LRP) can infer protein interaction networks for individual patients from proteomic profiling data. LRP reconstructs average and individual interaction networks with an AUC of 0.99 and 0.93, respectively, and outperforms state-of-the-art network prediction methods for individual tumors. Using data from The Cancer Proteome Atlas, we identify known and potentially novel oncogenic network features, among which some are cancer-type specific and show only minor variation among patients, while others are present across certain tumor types but differ among individual patients. Our approach may therefore support predictive diagnostics in precision oncology by inferring “patient-level” oncogenic mechanisms.
Quantitative proteomics and in-cell cross-linking reveal cellular reorganisation during early neuronal differentiation of SH-SY5Y cells
Authors: Barth Marie , Toto Nienguesso Alicia , Navarrete Santos Anne , Schmidt Carla 
Published: June 2022

AbstractThe neuroblastoma cell line SH-SY5Y is commonly employed to study neuronal function and disease. This includes cells grown under standard conditions or differentiated to neuron-like cells by administration of chemical reagents such as retinoic acid (RA) or phorbol-12-myristate-13-acetate (PMA). Even though SH-SY5Y cells are widely explored, a complete description of the resulting proteomes and cellular reorganisation during differentiation is still missing. Here, we relatively quantify the proteomes of cells grown under standard conditions and obtained from two differentiation protocols employing RA or a combination of RA and PMA. Relative quantification and KEGG pathway analysis of the proteins reveals the presence of early differentiating cells and provides a list of marker proteins for undifferentiated and differentiated cells. For characterisation of neuronal sub-types, we analyse expression of marker genes and find that RA-differentiated cells are acetylcholinergic and cholinergic, while RA/PMA-differentiated cells show high expression of acetylcholinergic and dopaminergic marker genes. In-cell cross-linking further allows capturing protein interactions in different cellular organelles. Specifically, we observe structural reorganisation upon differentiation involving regulating protein factors of the actin cytoskeleton.
Bioarchaeological evidence of one of the earliest Islamic burials in the Levant
Authors: Srigyan Megha , Bolívar Héctor , Ureña Irene , Santana Jonathan , Petersen Andrew , Iriarte Eneko , Kırdök Emrah , Bergfeldt Nora , Mora Alice , Jakobsson Mattias , Abdo Khaled , Braemer Frank , Smith Colin , Ibañez Juan José , Götherström Anders , Günther Torsten , Valdiosera Cristina 
Published: June 2022

AbstractThe Middle East plays a central role in human history harbouring a vast diversity of ethnic, cultural and religious groups. However, much remains to be understood about past and present genomic diversity in this region. Here we present a multidisciplinary bioarchaeological analysis of two individuals dated to the late 7th and early 8th centuries, the Umayyad Era, from Tell Qarassa, an open-air site in modern-day Syria. Radiocarbon dates and burial type are consistent with one of the earliest Islamic Arab burials in the Levant. Interestingly, we found genomic similarity to a genotyped group of modern-day Bedouins and Saudi rather than to most neighbouring Levantine groups. This study represents the genomic analysis of a secondary use site with characteristics consistent with an early Islamic burial in the Levant. We discuss our findings and possible historic scenarios in the light of forces such as genetic drift and their possible interaction with religious and cultural processes (including diet and subsistence practices).
The impact of audio effects processing on the perception of hardness of Bass Drum
Authors: Wang Yu , Wu Jie , He Hanfu , Wang Shuaishuai 
Published: June 2022

AbstractIn the music mixing, mixers and music producers often use hardness to describe the feeling of percussion instruments, such as the drum instruments. When dealing with the hardness of drums, the mixer often mixes the sound in terms of frequency and dynamics. One important issue is that it is difficult to define the contribution of adjusting the frequency or dynamics of the drum to the perception of drum tone hardness, and this perception is difficult to be quantified. A subjective user study on the hardness of drum sound is proposed. Taking the audio of the Bass Drum as an example, different audio effects are applied to process the Bass Drum. Twenty‐three participants were recruited to participate the auditory perception test. The result indicates that compression, equalisation, high‐frequency excitation and low‐frequency excitation all have varying degrees of impact on the hardness of the Bass Drum. The high‐frequency excitation and low‐frequency excitation have a statistically significant substantial influence on the sound hardness of the Bass Drum. Taking together, for the first time, the authors’ study comprehensively investigate the impact of audio effect processing on the perception of the hardness of Bass Drum, providing useful guidance for the application of various audio effects on percussion instruments.