bluuebunny/crossref_metadata_2025_split huggingface dataset:
Full-length transcript sequencing accelerates the transcriptome research of Gymnocypris namensis, an iconic fish of the Tibetan Plateau
Authors: Luo Hui , Liu Haiping , Zhang Jie , Hu Bingjie , Zhou Chaowei , Xiang Mengbin , Yang Yuejing , Zhou Mingrui , Jing Tingsen , Li Zhe , Zhou Xinghua , Lv Guangjun , He Wenping , Zeng Benhe , Xiao Shijun , Li Qinglu , Ye Hua 
Published: June 2020

AbstractGymnocypris namensis, the only commercial fish in Namtso Lake of Tibet in China, is rated as nearly threatened species in theRed List of China’s Vertebrates. As one of the highest-altitude schizothorax fish in China,G. namensishas strong adaptability to the plateau harsh environment. Although being an indigenous economic fish with high value in research, the biological characterization, genetic diversity, and plateau adaptability ofG. namensisare still unclear. Here, we used Pacific Biosciences single molecular real time long read sequencing technology to generate full-length transcripts ofG. namensis. Sequences clustering analysis and error correction with Illumina-produced short reads to obtain 319,044 polished isoforms. After removing redundant reads, 125,396 non-redundant isoforms were obtained. Among all transcripts, 103,286 were annotated to public databases. Natural selection has acted on 42 genes forG. namensis, which were enriched on the functions of mismatch repair and Glutathione metabolism. Total 89,736 open reading frames, 95,947 microsatellites, and 21,360 long non-coding RNAs were identified across all transcripts. This is the first study of transcriptome inG. namensisby using PacBio Iso-seq. The acquisition of full-length transcript isoforms might accelerate the transcriptome research ofG. namensisand provide basis for further research.
Physiological response of mammary glands to Escherichia coli infection: A conflict between glucose need for milk production and immune response
Authors: Blum Shlomo E. , Heller Dan E. , Jacoby Shamay , Krifuks Oleg , Merin Uzi , Silanikove Nissim , Lavon Yaniv , Edery Nir , Leitner Gabriel 
Published: June 2020

AbstractThe mammary immune and physiological responses to distinct mammary-pathogenic E. coli (MPEC) strains were studied. One gland in each of ten cows were challenged intra-mammary and milk composition (lactose, fat, total protein, casein), biochemical (glucose, glucose-6-phosphate (Glu6P), oxalate, malate, lactate, pyruvate and citrate, malate and lactate dehydrogenases, lactate dehydrogenase (LDH), nitrite, lactic peroxidase, catalase, albumin, lactoferrin, immunoglobulin) and clotting parameters were followed for 35 days post-challenge. Challenge lead to clinical acute mastitis, with peak bacterial counts in milk at 16–24 h post-challenge. Biochemical and clotting parameters in milk reported were partially in accord with lipopolysaccharide-induced mastitis, but increased Glu6P and LDH activity and prolonged lactate dehydrogenase and Glu6P/Glu alterations were found. Some alterations measured in milk resolved within days after challenge, while others endured for above one month, regardless of bacterial clearance, and some reflected physiological responses to mastitis such as the balance between aerobic and anaerobic metabolism (citrate to lactate ratios). The results suggest that E. coli mastitis can be divided into two stages: an acute, clinical phase, as an immediate response to bacterial infection in the mammary gland, and a chronic phase, independent of bacteria clearance, in response to tissue damage caused during the acute phase.
A longitudinal study of the development of the saliva microbiome in infants 2 days to 5 years compared to the microbiome in adolescents
Authors: Lif Holgerson Pernilla , Esberg Anders , Sjödin Andreas , West Christina E. , Johansson Ingegerd 
Published: June 2020

AbstractUnderstanding oral microbiota programming attracts increasing interest due to its importance for oral health and potential associations with systemic diseases. Here the oral microbiota was longitudinally characterized in children from 2 days (n = 206) to 5 years of age and in young adults (n = 175) by sequencing of the v3-v4 region of the 16S rRNA gene from saliva extracted DNA. Alpha diversity increased by age, with 2-day- and 3-month-old infants in one sub-group, and 18-month- and 3-year-old children in another. Firmicutes decreased up to 3 years of age, whereas Proteobacteria, Actinobacteria, Bacteroidetes and Fusobacteria abundances increased. Abiotrophia, Actinomyces, Capnocytophaga, Corynebacterium, Fusobacterium, Kingella, Leptotrichia, Neisseria and Porphyromonas appeared from 18-months of age. This was paralleled by expansions in the core microbiome that continued up to adulthood. The age-related microbiota transformation was paralleled by functional alterations, e.g., changed metabolic pathways that reflected e.g., breastfeeding and increasing proportions of anaerobic species. Oral microbiotas differed by feeding mode and weakly by mode of delivery, but not gender, pacifier use or cleaning method or probiotic intake. The study shows that the saliva microbiota is diverse 2 days after birth and under transformation up to 5 years of age and beyond, with fluctuations possibly reflecting age-related environmental influences.
Expression patterns of NbrgsCaM family genes in Nicotiana benthamiana and their potential roles in development and stress responses
Authors: Liu Dandan , Yang Qiuying 
Published: June 2020

AbstractrgsCaMhas been reported as acalmodulin-like(CML) factor induced by viral infection inNicotiana. There are threeCMLsthat belong to thergsCaMfamily inArabidopsis thaliana. In this study, we found a total of 5NbrgsCaMcoding sequences inN. benthamianagenome. We analyzed transcription patterns ofNbrgsCaMsin transgenic plants expressing a β-glucuronidase (GUS) under the promoter ofNbrgsCaMsby histochemistry staining and RT-qPCR. Similar to theirArabidopsishomologs, mostNbrgsCaMshave an overlapping but distinct expression pattern in response to developmental and environmental changes. Specifically, theNbrgsCaM4promoter exhibited robust activity and showed distinct regulatory response to viral infection, developmental stages and other abiotic stimuli. Overall, these findings provide clues for further understanding of theNbrgsCaMfamily genes in regulating plant growth and development under biotic stress and environmental stimulation.
A novel graphene oxide-based ceramic composite as an efficient electrode for capacitive deionization
Authors: Khalil Khalil Abdelrazek , Barakat Nasser A. M. , Motlak Moaeed , Al-Mubaddel Fahad S. 
Published: June 2020

AbstractIn this study, N-doped and TiO2-decorated graphene oxides were developed as efficient nonprecious electrodes for capacitive deionization. The activity of this new material was evaluated in situ and in vivo. The performance of the synthesized material was measured in different saline solutions (0.1, 0.5 and 1.0 M NaCl) as an electrolyte. The results showed that the new material exhibits very good performance (157 F/g at 5 mV/s and 1.0 M NaCl compared to 19.5 F/g for pure graphene oxide). In the desalination test, which was performed in batch mode, the salt adsorption capacity and the efficiency of salt removal were 9.2 mg/g and 98%, respectively. To check the stability, the desalination test was repeated several times, and no change in the performance was observed. The results provide evidence that the newly synthesized material is a potential electrode material for CDI water desalination with satisfactory salt removal ability.
Thermal behavior of spin-current generation in PtxCu1-x devices characterized through spin-torque ferromagnetic resonance
Authors: Wong G. D. H. , Law W. C. , Tan F. N. , Gan W. L. , Ang C. C. I. , Xu Z. , Seet C. S. , Lew W. S. 
Published: June 2020

AbstractHigh temperature studies of spin Hall effect have often been neglected despite its profound significance in real-world devices. In this work, high temperature spin torque ferromagnetic resonance measurement was performed to evaluate the effects of temperature on the Gilbert damping and spin Hall efficiency of PtxCu1−x. When the temperature was varied from 300 K to 407 K, the Gilbert damping was relatively stable with a change of 4% at composition x = 66%. Alloying Pt and Cu improved the spin Hall efficiency of Pt75Cu25/Co/Ta by 29% to a value of 0.31 ± 0.03 at 407 K. However, the critical switching current density is dependent on the ratio between the Gilbert damping and spin Hall efficiency and the smallest value was observed when x = 47%. It was found that at this concentration, the spin transparency was at its highest at 0.85 ± 0.09 hence indicating the importance of interfacial transparency for energy efficient devices at elevated temperature.
Extra Territorial Excursions by European badgers are not limited by age, sex or season
Authors: Kelly David J. , Gaughran Aoibheann , Mullen Enda , MacWhite Teresa , Maher Peter , Good Margaret , Marples Nicola M. 
Published: June 2020

AbstractEuropean badgers (Meles meles) in medium and high density populations show strong territorial behaviour. Territories in these populations are contiguous, well-marked and often unchanging over many years. However, badgers do not always stay within their territorial boundaries. In our medium-density population, most individual badgers made extra-territorial excursions (ETEs) throughout the year. ETEs were most frequent between April and September and least frequent in December and January (the period of winter lethargy). Male badgers made longer and more frequent ETEs than females (especially between January and March, and in autumn). Breeding females made longer and more frequent ETEs than non-breeding females in November. While these peaks correspond with the main mating seasons, mating activity does not explain ETEs throughout the year. The shorter, but more frequent, ETEs in summer months may serve a monitoring purpose, rather than simply providing additional mating opportunities with badgers from outside the ‘home’ social group. We found that young badgers did not make regular ETEs until the summer of their second year. If badgers could be vaccinated as cubs, this would reduce any potential risk of TB spread during ETEs.
A Metabolomics Approach for Early Prediction of Vincristine-Induced Peripheral Neuropathy
Authors: Verma Parul , Devaraj Jayachandran , Skiles Jodi L. , Sajdyk Tammy , Ho Richard H. , Hutchinson Raymond , Wells Elizabeth , Li Lang , Renbarger Jamie , Cooper Bruce , Ramkrishna Doraiswami 
Published: June 2020

AbstractVincristine is a core chemotherapeutic drug administered to pediatric acute lymphoblastic leukemia patients. Despite its efficacy in treating leukemia, it can lead to severe peripheral neuropathy in a subgroup of the patients. Peripheral neuropathy is a debilitating and painful side-effect that can severely impact an individual’s quality of life. Currently, there are no established predictors of peripheral neuropathy incidence during the early stage of chemotherapeutic treatment. As a result, patients who are not susceptible to peripheral neuropathy may receive sub-therapeutic treatment due to an empirical upper cap on the dose, while others may experience severe neuropathy at the same dose. Contrary to previous genomics based approaches, we employed a metabolomics approach to identify small sets of metabolites that can be used to predict a patient’s susceptibility to peripheral neuropathy at different time points during the treatment. Using those identified metabolites, we developed a novel strategy to predict peripheral neuropathy and subsequently adjust the vincristine dose accordingly. In accordance with this novel strategy, we created a free user-friendly tool, VIPNp, for physicians to easily implement our prediction strategy. Our results showed that focusing on metabolites, which encompasses both genotypic and phenotypic variations, can enable early prediction of peripheral neuropathy in pediatric leukemia patients.
Hsa_circ_0003732 promotes osteosarcoma cells proliferation via miR-545/CCNA2 axis
Authors: Li Li , Kong Xiang-an , Zang Mousheng , Dong Jisheng , Feng Yingqi , Gui Binjie , Hu Yong 
Published: June 2020

Abstract
Osteosarcoma (OS) is a primary malignant bone tumor with a high fatality rate. Circular RNAs (circRNAs) are a type of endogenous noncoding RNA that have been verified to participate in cancer pathophysiological processes. We aim to investigate the roles of circRNAs in osteosarcoma tumorigenesis. In the present study, we showed that hsa_circ_0003732 was up-regulated in OS tissues and elevated level of hsa_circ_0003732 was linked to poor prognosis of OS patients. Functional investigation indicated that hsa_circ_0003732 promoted proliferation of OS cells. Furthermore, we identified miR-545 as the hsa_circ_0003732-associated microRNA and CCNA2 was a direct target of miR-545. In addition, hsa_circ_0003732 could elevate CCNA2 expression via miR-545, resulting in the promotion of OS cells proliferation. Altogether, our findings demonstrate that hsa_circ_0003732 promotes OS cells proliferation via miR-545/CCNA2 axis and imply hsa_circ_0003732 may be a potential prognosis biomarker and therapeutic target for OS.
Regulation of Actg1 and Gsta2 is possible mechanism by which capsaicin alleviates apoptosis in cell model of 6-OHDA-induced Parkinson's disease
Authors: Liu Jiahui , Liu Hong , Zhao Zhenxiang , Wang Jianfeng , Guo Dandan , Liu Yiming 
Published: June 2020

Abstract
The present study aimed to identify the gene expression changes conferred by capsaicin in the cell model of 6-OHDA-induced Parkinson's disease, to disclose the molecular mechanism of action of capsaicin. We used capsaicin-treated and paraffin-embedded wax blocks containing substantia nigra tissue from 6-OHDA-induced Parkinson's disease rats to analyze transcriptional changes using Affymetrix GeneChip Whole Transcript Expression Arrays. A total of 108 genes were differentially expressed in response to capsaicin treatment, and seven of these genes were selected for further analysis: Olr724, COX1, Gsta2, Rab5a, Potef, Actg1, and Acadsb, of which Actg1 (actin gamma 1) was down-regulated and Gsta2 (Glutathione S-transferase alpha 2) was up-regulated. We successfully overexpressed Actg1 and Gsta2 in vitro. CCK-8 detection and flow cytometry demonstrated that overexpression of Actg1 and Gsta2 increased apoptosis in the 6-OHDA-induced Parkinson's disease cell model. The imbalance between Actg1 and Gsta2 may be one of the mechanisms of cell damage in Parkinson's disease (PD). Capsaicin can protect the cells and reduce the apoptosis rate by regulating Actg1 and Gsta2.
Potential targets and molecular mechanism of miR-331-3p in hepatocellular carcinoma identified by weighted gene coexpression network analysis
Authors: Chi Qingjia , Geng Xinge , Xu Kang , Wang Chunli , Zhao Han 
Published: June 2020

AbstractHepatocellular carcinoma (HCC) is one of the most common malignant tumor. miR-331-3p has been reported relevant to the progression of HCC, but the molecular mechanism of its regulation is still unclear. In the study, we comprehensively studied the role of miR-331-3p in HCC through weighted gene coexpression network analysis (WGCNA) based on The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO) and Oncomine. WGCNA was applied to build gene co-expression networks to examine the correlation between gene sets and clinical characteristics, and to identify potential biomarkers. Five hundred one target genes of miR-331-3p were obtained by overlapping differentially expressed genes (DEGs) from the TCGA database and target genes predicted by miRWalk. The critical turquoise module and its eight key genes were screened by WGCNA. Enrichment analysis was implemented based on the genes in the turquoise module. Moreover, 48 genes with a high degree of connectivity were obtained by protein–protein interaction (PPI) analysis of the genes in the turquoise module. From overlapping genes analyzed by WGCNA and PPI, two hub genes were obtained, namely coatomer protein complex subunit zeta 1 (COPZ1) and elongation factor Tu GTP binding domain containing 2 (EFTUD2). In addition, the expression of both hub genes was also significantly higher in tumor tissues compared with normal tissues, as confirmed by analysis based on TCGA and Oncomine. Both hub genes were correlated with poor prognosis based on TCGA data. Receiver operating characteristic (ROC) curve validated that both hub genes exhibited excellent diagnostic efficiency for normal and tumor tissues.
Dexmedetomidine exerts neuroprotective effects during high glucose-induced neural injury by inhibiting miR-125b
Authors: Hou Xiaolai , Xu Fenlan , Zhang Cheng , Shuai Jianzhong , Huang Zhenhua , Liang Yu , Xu Xiaoyan 
Published: June 2020

Abstract
Diabetic neuropathy (DNP) is the most common complication of diabetes mellitus affecting approximately 50% of diabetes patients. Studying the effect of potential drugs with antioxidant properties and minimal toxicities on neural cells may lead to the development of new and safe pharmacotherapy. Dexmedetomidine (DEX), a highly selective α2-adrenoceptor agonist, is a clinically used sedative also known to have neural protection effect. In the present study, we aimed to investigate the protective role of DEX in high glucose (HG)-induced neural injury and its potential miRNA-related mechanisms. Our results showed that DEX exerted neuroprotective effects during high glucose-induced damage to PC12 cells in a dose-dependent manner. DEX restored cell viability and repressed LDH, Caspase-3 activity, ROS production, and cell apoptosis in HG-treated PC12 cells. MiR-125b-5p was significantly up-regulated in PC12 cells upon HG treatment and it was demonstrated as an target for DEX. The neuroprotective effects of DEX on HG-induced cellular injury were reversed through miR-125b-5p overexpression, and vitamin D receptor (VDR) is a direct targeted of the miR-125b-5p. Together, our results indicate that DEX displays neuroprotective effects on PC-12 cells under high glucose through regulating miR-125b-5p/VDR axis. Our findings might raise the possibility of potential therapeutic application of DEX for managing diabetic neuropathy neural injuries.
Circular RNA FUNDC1 improves prediction of stroke associated infection in acute ischemic stroke patients with high risk
Authors: Zuo Lei , Li Cai , Zu Juan , Yao Honghong , Yan Fuling 
Published: June 2020

Abstract
Identifying those patients who were at high risk of stroke associated infection (SAI) for preventive antibiotic therapy was imperative for patients’ benefits, thus improving prediction of SAI was critical for all acute ischemic stroke (AIS) patients. Circular RNA FUNDC1 (circFUNDC1) has been reported to be the diagnosis and prognosis biomarker of AIS. Therefore, the present study aimed to figure out whether circFUNDC1 could be the potential predictor of SAI that could help to guide preventive treatment. In total, 68 patients were included in the study, 26 of which had infection and 42 without. Copy number of circFUNDC1 in plasma were quantified by quantitative real-time polymerase chain reaction (qPCR). Platelet spike-in experiment and correlation analysis were conducted to explore possible origins of circFUNDC1 in plasma. A significantly elevated level of circFUNDC1 was found in SAI patients compared with not infected AIS patients (P=0.0258). Receiver operating characteristic (ROC) curves demonstrated the prediction significance of circFUNDC1, with the area under the curve (AUC) at 0.6612 and sensitivity, specificity at 69.23%, 61.90% respectively in predicting SAI. Then, when adding circFUNDC1 in the risk model, the AUC increased from 0.7971 in model A to 0.8038 in model B. Additionally, positive correlation was observed between circFUNDC1 level and neutrophils counts. WBC and neutrophil ratios were significantly elevated in SAI patients compared with non-SAI patients. Therefore, circFUNDC1 could be used to construct a risk model for the prediction of SAI that is beneficial for AIS patients’ preventive treatment.
UPR modulation of host immunity by Pseudomonas aeruginosa in cystic fibrosis
Authors: Bedi Brahmchetna , Lin Kuo-Chuan. , Maurice Nicholas M. , Yuan Zhihong , Bijli Kaiser , Koval Michael , Hart C. Michael , Goldberg Joanna B. , Stecenko Arlene , Sadikot Ruxana T. 
Published: June 2020

Abstract
Cystic fibrosis (CF) is a progressive multiorgan autosomal recessive disease with devastating impact on the lungs caused by derangements of the CF transmembrane conductance regulator (CFTR) gene. Morbidity and mortality are caused by the triad of impaired mucociliary clearance, microbial infections and chronic inflammation. Pseudomonas aeruginosa is the main respiratory pathogen in individuals with CF infecting most patients in later stages. Despite its recognized clinical impact, molecular mechanisms that underlie P. aeruginosa pathogenesis and the host response to P. aeruginosa infection remain incompletely understood. The nuclear hormone receptor peroxisome proliferator-activated receptor (PPAR) γ (PPARγ), has shown to be reduced in CF airways. In the present study, we sought to investigate the upstream mechanisms repressing PPARγ expression and its impact on airway epithelial host defense. Endoplasmic reticulum-stress (ER-stress) triggered unfolded protein response (UPR) activated by misfolded CFTR and P. aeruginosa infection contributed to attenuated expression of PPARγ. Specifically, the protein kinase RNA (PKR)-like ER kinase (PERK) signaling pathway led to the enhanced expression of the CCAAT-enhancer-binding-protein homologous protein (CHOP). CHOP induction led to the repression of PPARγ expression. Mechanistically, we showed that CHOP induction mediated PPARγ attenuation, impacted the innate immune function of normal and ∆F508 primary airway epithelial cells by reducing expression of antimicrobial peptide (AMP) and paraoxanse-2 (PON-2), as well as enhancing IL-8 expression. Furthermore, mitochondrial reactive oxygen species production (mt-ROS) and ER-stress positive feedforward loop also dysregulated mitochondrial bioenergetics. Additionally, our findings implicate that PPARγ agonist pioglitazone (PIO) has beneficial effect on the host at the multicellular level ranging from host defense to mitochondrial re-energization.
Advances and surprises in a decade of oocyte meiosis research
Authors: Mogessie Binyam 
Published: June 2020

Abstract
Eggs are produced from progenitor oocytes through meiotic cell division. Fidelity of meiosis is critical for healthy embryogenesis – fertilisation of aneuploid eggs that contain the wrong number of chromosomes is a leading cause of genetic disorders including Down’s syndrome, human embryo deaths and infertility. Incidence of meiosis-related oocyte and egg aneuploidies increases dramatically with advancing maternal age, which further complicates the ‘meiosis problem’. We have just emerged from a decade of meiosis research that was packed with exciting and transformative research. This minireview will focus primarily on studies of mechanisms that directly influence chromosome segregation.