bluuebunny/crossref_metadata_2025_split huggingface dataset:
COVID-19 in Egyptian Children: A Multicenter Study
Authors: Abdel Baki Amin , Zaky Samy , Hosny Hossam , Elassal Gehan , Abdelbary Akram , Said Ahmad , Kamal Ehab , Asem Noha , Ibrahim Hamdy , Eid Alaa , Amin Wagdy , El Badry Mohamed , Mossa Abdelmajeed , El-Raey Fathiya , Baghdady Shazly , Tahoon Marwa , Hassany Mohamed , Zaid Hala 
Published: February 2021

Abstract
Objective The novel coronavirus disease 2019 (COVID-19) has made its worldwide spread since its outbreak in December 2019. Limited information is available about the epidemiology and clinical characteristics of COVID-19, especially in Africa and Egypt.
Methods We aimed to study the clinical and epidemiological characteristics of COVID-19 in Egyptian children. This is an observational retrospective cohort study performed at two specialized COVID-19 isolation hospitals in Egypt. All admitted COVID-19 pediatric patients between March 20, 2020, and May 1, 2020, were included in the study.
Discussion This study included 40 COVID-19 confirmed cases (mean age, 9.4 years), 67.5% were male, 85% were asymptomatic, and 15% had mild symptoms. There were no confirmed severe or critically ill cases among the patients.
Conclusion COVID-19 runs in a benign course in Egyptian children with no mortality and no significant morbidity.
Tribological properties of Al2O3/WS2 oil-based composite lubricant utilized on steel-brass frictional couples
Authors: Sujan Kafle , Wang Bingxu , Hu Ming , Meng Shaohua , Zhang Lijian , Hu Ruiqin , Barber Gary C 
Published: February 2021

Abstract
The tribological properties of Al2O3/WS2 composite lubricant were examined by using a ball-on-plate reciprocating sliding wear test configuration utilizing PAO6 base fluid and oleic acid as surfactant. The morphology and chemical composition of the wear tracks were examined by using a scanning electron microscope and a x-ray energy dispersive spectrometer. It was found that the coefficient of friction was reduced by 46.6% after adding 0.5 wt% Al2O3/WS2 composite particles. The wear width and wear depth were reduced by 37% and 59.6% after adding 3 wt% Al2O3/WS2 composite particles. In orthogonal tests, it was proposed that the best tribological performance of Al2O3/WS2 composite lubricant could be achieved while using the normal load of 50 N, frequency of 2 Hz and temperature of 65 °C. Frequency could be considered as the primary factor affecting the tribological properties of compsite lubricant. The excellent lubricating performance could be attributed to the formation of WS2 tribo-film with low shearing resistance, and a portion of the Al2O3 particles were embedded by external force to prevent surface contact between the steel ball and brass plate.
Synergic fabrication of titanium dioxide incorporation into heparin-polyvinyl alcohol nanocomposite: enhanced in vitro antibacterial activity and care of in vivo burn injury
Authors: Li Shougen , Zeng Jia , Yin Dongfang , Liao Peiqiang , Ding Siqing , Mao Ping , Liu Ying 
Published: February 2021

Abstract
In this study, a highly porous heparin-polyvinylalcohol@TiO2 nanocomposite (H-PVA@TiO2) bandage was fabricated by incorporating TiO2 into H-PVA hydrogel for burn injury. The effects of the H-PVA hydrogel and TiO2 nanoparticle composition on the functional group and surface properties of the as-prepared bandages were characterized by Fourier transform infrared spectroscopy (FT-IR) and x-ray diffractometry (XRD). The morphology of the H-PVA hydrogel and H-PVA@TiO2 were evaluated using a scanning electron microscope (SEM) and transmission electron microscope (TEM). A study of the material properties of H-PVA hydrogel has shown that the presence of TiO2 nanoparticles improves its toughness. Prepared H-PVA@TiO2 nanoporous dressing has indicated good antimicrobial activity against types of bacteria (Staphylococcus aureus and Escherichia coli) and excellent biocompatibility with human dermal fibroblast cells (HFFF2) suitable for biological applications. Additionally, in vivo experiments using Kunming mice showed it as-prepared H-PVA@TiO2 nanocomposite dressings improved wound healing and triggered skin cell development alongside collagen growth. Synergistic effects of the H-PVA@TiO2 nanocomposite hydrogel dressing material through in vivo experiments, such as its excellent hydrophilic design, strong bactericidal activity, biocompatibility and wound healing ability, make it a promising candidate for the treatment of burn injuries.
Microstructure and mechanical properties of Mg-2Zn-0.3Ca-0.5La magnesium alloy extruded with different temperatures
Authors: Hong Shu , Yungui Chen , Jianxun Wu , Maochao Zhang , Tang Yongbai 
Published: February 2021

Abstract
The extrusion tests of the Mg-2Zn-0.3Ca-0.5La (ZXLa200) alloy were carried out at different extrusion temperatures (260 °C–320 °C), and the mechanical properties and microstructure were studied and analyzed by means of optical microscope, scanning electron microscope, x-ray diffraction, transmission electron microscope, and tensile testing. The research have demonstrated significant influence of Extrusion temperature towards grain size, recrystallization grains and texture. With the extrusion temperature increases, the recrystallization grain of the extruded ZXLa200 alloy increases, but the texture intensity decreases. During the extrusion process, a large amount of Ca2Mg6Zn3 (50–200 nm) precipitates are precipitated, which inhibited the growth of dynamic recrystallization grains and improved the yield strength of the alloys. The tensile yield strength and elongation of extruded ZXLa200 alloy were acquired to be 375 MPa, 5.9% at 260 °C and 310 MPa, 19.2% at 320 °C.
Genome Size Reduction and Transposon Activity Impact tRNA Gene Diversity While Ensuring Translational Stability in Birds
Authors: Ottenburghs Jente , Geng Keyi , Suh Alexander , Kutter Claudia 
Published: February 2021

Abstract
As a highly diverse vertebrate class, bird species have adapted to various ecological systems. How this phenotypic diversity can be explained genetically is intensively debated and is likely grounded in differences in the genome content. Larger and more complex genomes could allow for greater genetic regulation that results in more phenotypic variety. Surprisingly, avian genomes are much smaller compared to other vertebrates but contain as many protein-coding genes as other vertebrates. This supports the notion that the phenotypic diversity is largely determined by selection on non-coding gene sequences. Transfer RNAs (tRNAs) represent a group of non-coding genes. However, the characteristics of tRNA genes across bird genomes have remained largely unexplored. Here, we exhaustively investigated the evolution and functional consequences of these crucial translational regulators within bird species and across vertebrates. Our dense sampling of 55 avian genomes representing each bird order revealed an average of 169 tRNA genes with at least 31% being actively used. Unlike other vertebrates, avian tRNA genes are reduced in number and complexity but are still in line with vertebrate wobble pairing strategies and mutation-driven codon usage. Our detailed phylogenetic analyses further uncovered that new tRNA genes can emerge through multiplication by transposable elements. Together, this study provides the first comprehensive avian and cross-vertebrate tRNA gene analyses and demonstrates that tRNA gene evolution is flexible albeit constrained within functional boundaries of general mechanisms in protein translation.
Systematic identification of non-coding somatic single nucleotide variants associated with altered transcription and DNA methylation in adult and pediatric cancers
Authors: Chen Fengju , Zhang Yiqun , Creighton Chad J 
Published: February 2021

Abstract
Whole-genome sequencing combined with transcriptomics can reveal impactful non-coding single nucleotide variants (SNVs) in cancer. Here, we developed an integrative analytical approach that, as a first step, identifies genes altered in expression or DNA methylation in association with nearby somatic SNVs, in contrast to alternative approaches that first identify mutational hotspots. Using genomic datasets from the Pan-Cancer Analysis of Whole Genomes (PCAWG) consortium and the Children's Brain Tumor Tissue Consortium (CBTTC), we identified hundreds of genes and associated CpG islands for which the nearby presence of a non-coding somatic SNV recurrently associated with altered expression or DNA methylation, respectively. Genomic regions upstream or downstream of genes, gene introns and gene untranslated regions were all involved. The PCAWG adult cancer cohort yielded different significant SNV-expression associations from the CBTTC pediatric brain tumor cohort. The SNV-expression associations involved a wide range of cancer types and histologies, as well as potential gain or loss of transcription factor binding sites. Notable genes with SNV-associated increased expression include TERT, COPS3, POLE2 and HDAC2—involving multiple cancer types—MYC, BCL2, PIM1 and IGLL5—involving lymphomas—and CYHR1—involving pediatric low-grade gliomas. Non-coding somatic SNVs show a major role in shaping the cancer transcriptome, not limited to mutational hotspots.
The DNA damage inducible lncRNA SCAT7 regulates genomic integrity and topoisomerase 1 turnover in lung adenocarcinoma
Authors: Statello Luisa , Ali Mohamad M , Reischl Silke , Mahale Sagar , Kosalai Subazini Thankaswamy , Huarte Maite , Kanduri Chandrasekhar 
Published: February 2021

Abstract
Despite the rapid improvements in unveiling the importance of lncRNAs in all aspects of cancer biology, there is still a void in mechanistic understanding of their role in the DNA damage response. Here we explored the potential role of the oncogenic lncRNA SCAT7 (ELF3-AS1) in the maintenance of genome integrity. We show that SCAT7 is upregulated in response to DNA-damaging drugs like cisplatin and camptothecin, where SCAT7 expression is required to promote cell survival. SCAT7 silencing leads to decreased proliferation of cisplatin-resistant cells in vitro and in vivo through interfering with cell cycle checkpoints and DNA repair molecular pathways. SCAT7 regulates ATR signaling, promoting homologous recombination. Importantly, SCAT7 also takes part in proteasome-mediated topoisomerase I (TOP1) degradation, and its depletion causes an accumulation of TOP1–cc structures responsible for the high levels of intrinsic DNA damage. Thus, our data demonstrate that SCAT7 is an important constituent of the DNA damage response pathway and serves as a potential therapeutic target for hard-to-treat drug resistant cancers.
Identity: rapid alignment-free prediction of sequence alignment identity scores using self-supervised general linear models
Authors: Girgis Hani Z , James Benjamin T , Luczak Brian B 
Published: February 2021

AbstractPairwise global alignment is a fundamental step in sequence analysis. Optimal alignment algorithms are quadratic—slow especially on long sequences. In many applications that involve large sequence datasets, all what is needed is calculating the identity scores (percentage of identical nucleotides in an optimal alignment—including gaps—of two sequences); there is no need for visualizing how every two sequences are aligned. For these applications, we propose Identity, which produces global identity scores for a large number of pairs of DNA sequences using alignment-free methods and self-supervised general linear models. For the first time, the new tool can predict pairwise identity scores in linear time and space. On two large-scale sequence databases, Identity provided the best compromise between sensitivity and precision while being faster than BLAST, Mash, MUMmer4 and USEARCH by 2–80 times. Identity was the best performing tool when searching for low-identity matches. While constructing phylogenetic trees from about 6000 transcripts, the tree due to the scores reported by Identity was the closest to the reference tree (in contrast to andi, FSWM and Mash). Identity is capable of producing pairwise identity scores of millions-of-nucleotides-long bacterial genomes; this task cannot be accomplished by any global-alignment-based tool. Availability: https://github.com/BioinformaticsToolsmith/Identity.
Les directives pour le traitement par surfactant exogène chez le nouveau-né
Authors: Ng Eugene H , Shah Vibhuti 
Published: February 2021

RésuméLe traitement par surfactant exogène joue un rôle essentiel dans la prise en charge des nouveau-nés atteints du syndrome de détresse respiratoire (maladie des membranes hyalines) parce qu’il améliore la survie et limite les troubles respiratoires. Puisque la ventilation non invasive est de plus en plus utilisée comme principal mode d’assistance respiratoire chez le nouveau-né prématuré à la naissance, l’administration prophylactique de surfactant n’est plus bénéfique. L’administration précoce de surfactant sous forme de traitement de rattrapage est préconisée chez les nouveau-nés dont le syndrome de détresse respiratoire s’aggrave. La stratégie qui consiste à intuber, administrer du surfactant, puis extuber (INSURE) est largement acceptée en pratique clinique, mais des méthodes non invasives plus récentes à l’aide d’un cathéter fin, d’un masque laryngé ou d’un nébuliseur sont en cours d’adoption ou d’exploration. Selon des données limitées, un traitement d’appoint par surfactant exogène pourrait être efficace pour traiter d’autres affections que le syndrome de détresse respiratoire, telles que le syndrome d’aspiration méconiale.
Using time use diaries to track changing behavior across successive stages of COVID-19 social restrictions
Authors: Sullivan Oriel , Gershuny Jonathan , Sevilla Almudena , Foliano Francesca , Vega-Rapun Margarita , de Grignon Juana Lamote , Harms Teresa , Walthery Pierre 
Published: February 2021

AbstractHow did people change their behavior over the different phases of the UK COVID-19 restrictions, and how did these changes affect their risk of being exposed to infection? Time use diary surveys are unique in providing a complete chronicle of daily behavior; 24-hour continuous records of the populations’ activities, their social context and their location. We present results from four such surveys, collected in real time from representative UK samples, both before, and at three points over the course of the current pandemic. Comparing across the four waves, we find evidence of substantial changes in the UK population’s behavior relating to activities, locations and social context. We assign different levels of risk to combinations of activities, locations and copresence, to compare risk-related behavior across successive ‘lockdowns’. We find evidence that during the second lockdown (November 2020) there was an increase in high-risk behaviors relative to the first (starting March 2020). This increase is shown to be associated with more paid work time in the workplace. At a time when capacity is still limited both in respect of immunization and track-trace technology, governments must continue to rely on changes in people’s daily behaviors to contain the spread of COVID-19 and similar viruses. Time use diary information of this type, collected in real time across the course of the COVID-19 pandemic, can provide policy-makers with information to assess and quantify changes in daily behaviors, and the impact they are likely to have on overall behavioral-associated risks.
Novel EGFRvIII-CAR transgenic mice for rigorous preclinical studies in syngeneic mice
Authors: Chuntova Pavlina , Hou Yafei , Naka Ryosuke , Goretsky Yitzhar , Nejo Takahide , Kohanbash Gary , Chen Tiffany , Mende Abigail L. , Montoya Megan , Yamamichi Akane , Downey Kira M. , Diebold David , Skinner Jayne , Liang Hong-Erh , Schwer Bjoern , Okada Hideho 
Published: February 2021

ABSTRACTBackgroundRigorous preclinical studies of chimeric antigen receptor (CAR) immunotherapy will require large quantities of consistent and high-quality CAR-transduced T (CART)-cells that can be used in syngeneic mouse glioblastoma (GBM) models. To this end, we developed a novel transgenic (Tg) mouse strain with a fully murinized CAR targeting epidermal growth factor receptor variant III (EGFRvIII).MethodsWe first established the murinized version of EGFRvIII-CAR and validated its function using a retroviral vector (RV) in C57BL/6J mice bearing syngeneic SB28 GBM expressing EGFRvIII. Next, we created C57BL/6J-background Tg mice carrying the anti-EGFRvIII-CAR downstream of a Lox-Stop-Lox cassette in theRosa26locus. We bred these mice with CD4-Cre Tg mice to allow CAR expression on T-cells and evaluated the function of the CART-cells bothin vitroandin vivo. In order to inhibit immunosuppressive myeloid cells within SB28 GBM, we also evaluated a combination approach of CART and an anti-EP4 compound (ONO-AE3-208).ResultsBoth RV- and Tg-CART-cells demonstrated specific cytotoxic activities against SB28-EGFRvIII cells. A single intravenous infusion of EGFRvIII-CART-cells prolonged the survival of glioma-bearing mice when preceded by a lymphodepletion regimen with recurrent tumors displaying profound EGFRvIII loss. The addition of ONO-AE3-208 resulted in long-term survival in a fraction of CART-treated mice and those survivors demonstrated delayed growth of subcutaneously re-challenged both EGFRvIII+and parental EGFRvIII−SB28.ConclusionOur new syngeneic CAR Tg mouse model can serve as a useful tool to address clinically relevant questions and develop future immunotherapeutic strategies.Importance of studyThe majority of preclinical studies evaluating CART therapy for GBM have utilized xenografts implanted into immunocompromised mice. Because the successful development of these strategies will depend on the understanding of critical interactions between therapeutic cells and the endogenous immune environment, it is essential to develop a novel immunocompetent system which allows us to study these interactions in a robust and reproducible manner. To this end, we created a Tg mouse strain in which all T-cells express a murinized EGFRvIII-CAR. T-cells derived from these mice demonstrated consistent CAR expression and EGFRvIII-specific cytotoxicity while traditional transduction with a CAR vector showed batch-to-batch variability. The syngeneic system also gave us the opportunity to evaluate a combination regimen with blockade of myeloid-derived suppressor cells. The Tg-CART mice represent a novel system for robust, and reproducible preclinical investigations.
Mitochondrial energy dysfunction induces remodeling of the cardiac mitochondrial protein acylome
Authors: Peoples Jessica N. , Ghazal Nasab , Duong Duc M. , Hardin Katherine R. , Seyfried Nicholas T. , Faundez Victor , Kwong Jennifer Q. 
Published: February 2021

ABSTRACTMitochondria are increasingly recognized as signaling organelles because, under conditions of stress, mitochondria can trigger various signaling pathways to coordinate the cell’s response. The specific pathway(s) engaged by mitochondria in response to defects in mitochondrial energy production in vivo and in high-energy tissues like the heart are not fully understood. Here, we investigated cardiac pathways activated in response to mitochondrial energy dysfunction by studying mice with cardiomyocyte-specific loss of the mitochondrial phosphate carrier (SLC25A3), an established model that develops cardiomyopathy as a result of defective mitochondrial ATP synthesis. In heart tissue from these mice, mitochondrial energy dysfunction induced a striking pattern of acylome remodeling, with significantly increased post-translational acetylation and malonylation. Mass spectrometry-based proteomics further revealed that energy dysfunction-induced remodeling of the acetylome and malonylome preferentially impacts mitochondrial proteins. Acetylation and malonylation modified a highly interconnected interactome of mitochondrial proteins, and both modifications were present on the enzyme isocitrate dehydrogenase 2 (IDH2). Intriguingly, IDH2 activity was enhanced in SLC25A3-deleted mitochondria, and further study of IDH2 sites targeted by both acetylation and malonylation revealed that these modifications can have site-specific and distinct functional effects. Finally, we uncovered a novel crosstalk between the two modifications, whereby mitochondrial energy dysfunction-induced acetylation of sirtuin 5 (SIRT5), inhibited its function. Because SIRT5 is a mitochondrial deacylase with demalonylase activity, this finding suggests that acetylation can modulate the malonylome. Together, our results position acylations as an arm of the mitochondrial response to energy dysfunction and suggest a mechanism by which focal disruption to the mitochondrial energy production machinery can have an expanded impact on global mitochondrial function.
Kinesin-3 and kinesin-1 motors direct basement membrane protein secretion to a basal sub-region of the basolateral plasma membrane in epithelial cells
Authors: Zajac Allison L. , Horne-Badovinac Sally 
Published: February 2021

SUMMARYBasement membranes (BMs) are sheet-like extracellular matrices that line the basal surfaces of all epithelia. Since BM proteins form networks, they likely need to be secreted near the basal surface. However, the location of their secretion site and how it is selected are unknown. Working in theDrosophilafollicular epithelium, we identified two kinesins essential for normal BM formation. Our data suggest the two kinesins work together to transport Rab10+ BM protein-filled secretory vesicles towards the basal surface along the polarized microtubule array common to epithelia. This kinesin transport biases BM protein secretion basally. When kinesins are depleted, BM proteins are mis-secreted to more apical regions of the lateral membrane, creating ectopic BM protein networks between cells that disrupt cell movements and tissue architecture. These results introduce a new transport step in the BM protein secretion pathway and highlight the importance of controlling the sub-cellular exocytic site of network-forming proteins.HighlightsA kinesin-3 and a kinesin-1 are required for normal basement membrane (BM) assemblyKinesins move Rab10+ BM secretory vesicles basally on polarized microtubule arraysTransport biases BM exocytosis to basal subregions of the basolateral membraneLoss of kinesins creates ectopic BM networks that disrupt tissue architecture
Meta-Analysis of Oxidative Transcriptomes in Insects
Authors: Bono Hidemasa 
Published: February 2021

AbstractData accumulation in public databases has resulted in extensive use of meta-analysis, a statistical analysis that combines the results of multiple studies. Oxidative stress occurs when there is an imbalance between free radical activity and antioxidant activity, which can be studied in insects by transcriptome analysis. This study aimed to apply a meta-analysis approach to evaluate insect oxidative transcriptomes using publicly available data. We collected oxidative stress response-related RNA sequencing (RNA-seq) data for a wide variety of insect species, mainly from public gene expression databases, by manual curation. Only RNA-seq data ofDrosophila melanogasterwere found and were systematically analyzed using a newly developed RNA-seq analysis workflow for species without a reference genome sequence. The results were evaluated by two metric methods to construct a reference dataset for oxidative stress response studies. Many genes were found to be downregulated under oxidative stress and related to organ system process (GO:0003008) and adherens junction organization (GO:0034332) by gene enrichment analysis. A cross-species analysis was also performed. RNA-seq data ofCaenorhabditis eleganswere curated, since no RNA-seq data of insect species are currently available in public databases. This method, including the workflow developed, represents a powerful tool for deciphering conserved networks in oxidative stress response.